error in ATOMS

Julius Campecino

10 Nov 2013 10 Nov '13

6:26 p.m.

Hi Bruce, Here's the screen shot of my work in ATOMS. It's supposed to be more than 7 atoms in the core column but that's also one thing I do not know how to add change and add more atoms. When I click "Run Atoms", it gives me this error "Can't call method "tag" on an undefined value at C:/strawberry/perl/site/lib/Demeter/Atoms.pm line 668.'' I am using the recent version 0.9.18.2 of the Demeter installer. Thank you for your help! Julius

Attachments:

attachment.html (text/html — 568 bytes)
Atoms.png (image/png — 100.6 KB)

Show replies by date

Christopher Patridge

11 Nov 11 Nov

2:51 p.m.

Julius, While I am not certain what the error means, there is a button displayed right above the atom list which says "ADD A SITE." I would suggest that having a unit cell as large as you do, along with rather weak scatterers such as N, C, O, and I assume H, it is probably unnecessary to have sites beyond the 3rd shell or so since these contribute negligibly to the EXAFS. Chris ******************************************** Dr. Christopher Patridge Assistant Professor of Chemistry Dept of Math and Natural Science D'youville College 320 Porter Ave., Buffalo, NY 14201 Phone: 716-829-8096 Email: patridgc@dyc.edu On Nov 10, 2013, at 1:26 PM, Julius Campecino wrote:

...

Hi Bruce,

Here's the screen shot of my work in ATOMS. It's supposed to be more than 7 atoms in the core column but that's also one thing I do not know how to add change and add more atoms.

When I click "Run Atoms", it gives me this error "Can't call method "tag" on an undefined value at C:/strawberry/perl/site/lib/Demeter/Atoms.pm line 668.'' I am using the recent version 0.9.18.2 of the Demeter installer.

Thank you for your help!

Julius _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Julius Campecino

4:48 p.m.

Hi Chris, Yeah, I did try "add a site" but it is not responding. Does anyone else experience this problem? Thank you, Chris. Julius On Mon, Nov 11, 2013 at 9:51 AM, Christopher Patridge wrote:

...

Julius,

While I am not certain what the error means, there is a button displayed right above the atom list which says "ADD A SITE." I would suggest that having a unit cell as large as you do, along with rather weak scatterers such as N, C, O, and I assume H, it is probably unnecessary to have sites beyond the 3rd shell or so since these contribute negligibly to the EXAFS.

Chris

******************************************** Dr. Christopher Patridge Assistant Professor of Chemistry Dept of Math and Natural Science D'youville College 320 Porter Ave., Buffalo, NY 14201 Phone: 716-829-8096 Email: *patridgc@dyc.edu *

On Nov 10, 2013, at 1:26 PM, Julius Campecino wrote:

Hi Bruce,

Here's the screen shot of my work in ATOMS. It's supposed to be more than 7 atoms in the core column but that's also one thing I do not know how to add change and add more atoms.

When I click "Run Atoms", it gives me this error "Can't call method "tag" on an undefined value at C:/strawberry/perl/site/lib/Demeter/Atoms.pm line 668.'' I am using the recent version 0.9.18.2 of the Demeter installer.

Thank you for your help!

Julius _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Julius Campecino

13 Nov 13 Nov

5:19 p.m.

Hi everyone, Did anyone figure out how to fix "Can't call method tag" error and adding sites? Really a novice on fitting and I badly need help on this to get going. Sorry to bother everyone. Thanks! Julius On Mon, Nov 11, 2013 at 8:48 AM, Julius Campecino wrote:

...

Hi Chris,

Yeah, I did try "add a site" but it is not responding. Does anyone else experience this problem? Thank you, Chris.

Julius

On Mon, Nov 11, 2013 at 9:51 AM, Christopher Patridge < patridge@buffalo.edu> wrote:

...
Julius,

While I am not certain what the error means, there is a button displayed right above the atom list which says "ADD A SITE." I would suggest that having a unit cell as large as you do, along with rather weak scatterers such as N, C, O, and I assume H, it is probably unnecessary to have sites beyond the 3rd shell or so since these contribute negligibly to the EXAFS.

Chris

******************************************** Dr. Christopher Patridge Assistant Professor of Chemistry Dept of Math and Natural Science D'youville College 320 Porter Ave., Buffalo, NY 14201 Phone: 716-829-8096 Email: *patridgc@dyc.edu *

On Nov 10, 2013, at 1:26 PM, Julius Campecino wrote:

Hi Bruce,

Here's the screen shot of my work in ATOMS. It's supposed to be more than 7 atoms in the core column but that's also one thing I do not know how to add change and add more atoms.

When I click "Run Atoms", it gives me this error "Can't call method "tag" on an undefined value at C:/strawberry/perl/site/lib/Demeter/Atoms.pm line 668.'' I am using the recent version 0.9.18.2 of the Demeter installer.

Thank you for your help!

Julius _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Christopher Patridge

5:23 p.m.

Julius, I again did not find answer to the error but you could also try the following entity of ATOMS on the web which easily allows a huge number of sites http://cars9.uchicago.edu/cgi-bin/atoms/atoms.cgi Chris ******************************************** Dr. Christopher Patridge Assistant Professor of Chemistry Dept of Math and Natural Science D'youville College 320 Porter Ave., Buffalo, NY 14201 Phone: 716-829-8096 Email: patridgc@dyc.edu On Nov 13, 2013, at 12:19 PM, Julius Campecino wrote:

...

Hi everyone,

Did anyone figure out how to fix "Can't call method tag" error and adding sites? Really a novice on fitting and I badly need help on this to get going. Sorry to bother everyone.

Thanks!

Julius

On Mon, Nov 11, 2013 at 8:48 AM, Julius Campecino wrote: Hi Chris,

Yeah, I did try "add a site" but it is not responding. Does anyone else experience this problem? Thank you, Chris.

Julius

On Mon, Nov 11, 2013 at 9:51 AM, Christopher Patridge wrote: Julius,

While I am not certain what the error means, there is a button displayed right above the atom list which says "ADD A SITE." I would suggest that having a unit cell as large as you do, along with rather weak scatterers such as N, C, O, and I assume H, it is probably unnecessary to have sites beyond the 3rd shell or so since these contribute negligibly to the EXAFS.

Chris

******************************************** Dr. Christopher Patridge Assistant Professor of Chemistry Dept of Math and Natural Science D'youville College 320 Porter Ave., Buffalo, NY 14201 Phone: 716-829-8096 Email: patridgc@dyc.edu

On Nov 10, 2013, at 1:26 PM, Julius Campecino wrote:

...
Hi Bruce,

Here's the screen shot of my work in ATOMS. It's supposed to be more than 7 atoms in the core column but that's also one thing I do not know how to add change and add more atoms.

When I click "Run Atoms", it gives me this error "Can't call method "tag" on an undefined value at C:/strawberry/perl/site/lib/Demeter/Atoms.pm line 668.'' I am using the recent version 0.9.18.2 of the Demeter installer.

Thank you for your help!

Julius _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Julius Campecino

5:58 p.m.

Hi Chris, Same problem: Can't call method "attributes" on an undefined value at /usr/local/lib/perl5/site_perl/5.10.0/Xray/ATP.pm line 342. Can you try running this input and see if it works for you or not? Maybe there is something at my end that is causing this error. ! This atoms input file was generated by WebAtoms 1.8 (Atoms 3.0beta10) ! Atoms written by and copyright (c) Bruce Ravel, 1998-2001 title = WT NiSOD space = P212121 a = 112.260 b = 113.810 c = 128.60 alpha = 90.0 beta = 90.0 gamma = 90.0 core = Ni edge = K rmax = 5.0 atoms ! elem x y z tag occ. Ni 3.10300 27.70100 6.07300 Ni 1.00000 S 4.02900 29.69700 6.64700 S 1.00000 S 1.59500 28.53900 4.74300 S 1.00000 N 2.45400 25.74800 5.82600 N 1.00000 N 3.74200 25.63100 2.96500 N 1.00000 N 4.55400 26.84200 7.01300 N 1.00000 Thanks for your help! Julius On Wed, Nov 13, 2013 at 9:23 AM, Christopher Patridge wrote:

...

Julius,

I again did not find answer to the error but you could also try the following entity of ATOMS on the web which easily allows a huge number of sites

http://cars9.uchicago.edu/cgi-bin/atoms/atoms.cgi

Chris

******************************************** Dr. Christopher Patridge Assistant Professor of Chemistry Dept of Math and Natural Science D'youville College 320 Porter Ave., Buffalo, NY 14201 Phone: 716-829-8096 Email: *patridgc@dyc.edu *

On Nov 13, 2013, at 12:19 PM, Julius Campecino wrote:

Hi everyone,

Did anyone figure out how to fix "Can't call method tag" error and adding sites? Really a novice on fitting and I badly need help on this to get going. Sorry to bother everyone.

Thanks!

Julius

On Mon, Nov 11, 2013 at 8:48 AM, Julius Campecino wrote:

...
Hi Chris,

Yeah, I did try "add a site" but it is not responding. Does anyone else experience this problem? Thank you, Chris.

Julius

On Mon, Nov 11, 2013 at 9:51 AM, Christopher Patridge < patridge@buffalo.edu> wrote:

...
Julius,

While I am not certain what the error means, there is a button displayed right above the atom list which says "ADD A SITE." I would suggest that having a unit cell as large as you do, along with rather weak scatterers such as N, C, O, and I assume H, it is probably unnecessary to have sites beyond the 3rd shell or so since these contribute negligibly to the EXAFS.

Chris

******************************************** Dr. Christopher Patridge Assistant Professor of Chemistry Dept of Math and Natural Science D'youville College 320 Porter Ave., Buffalo, NY 14201 Phone: 716-829-8096 Email: *patridgc@dyc.edu *

On Nov 10, 2013, at 1:26 PM, Julius Campecino wrote:

Hi Bruce,

Here's the screen shot of my work in ATOMS. It's supposed to be more than 7 atoms in the core column but that's also one thing I do not know how to add change and add more atoms.

When I click "Run Atoms", it gives me this error "Can't call method "tag" on an undefined value at C:/strawberry/perl/site/lib/Demeter/Atoms.pm line 668.'' I am using the recent version 0.9.18.2 of the Demeter installer.

Thank you for your help!

Julius _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Matthew Marcus

6:09 p.m.

Shouldn't ATOMS input coordinates be fractional values? I wonder if putting the S 3000A from center might have something to do with it. I'm guessing that this is the metal-sulfer core of a protein, right? mam On 11/13/2013 9:58 AM, Julius Campecino wrote:

...

Hi Chris,

Same problem:

Can't call method "attributes" on an undefined value at /usr/local/lib/perl5/site_perl/5.10.0/Xray/ATP.pm line 342.

Can you try running this input and see if it works for you or not? Maybe there is something at my end that is causing this error.

! This atoms input file was generated by WebAtoms 1.8 (Atoms 3.0beta10) ! Atoms written by and copyright (c) Bruce Ravel, 1998-2001 title = WT NiSOD space = P212121 a = 112.260 b = 113.810 c = 128.60 alpha = 90.0 beta = 90.0 gamma = 90.0 core = Ni edge = K rmax = 5.0 atoms ! elem x y z tag occ. Ni 3.10300 27.70100 6.07300 Ni 1.00000 S 4.02900 29.69700 6.64700 S 1.00000 S 1.59500 28.53900 4.74300 S 1.00000 N 2.45400 25.74800 5.82600 N 1.00000 N 3.74200 25.63100 2.96500 N 1.00000 N 4.55400 26.84200 7.01300 N 1.00000

Thanks for your help!

Julius

On Wed, Nov 13, 2013 at 9:23 AM, Christopher Patridge mailto:patridge@buffalo.edu> wrote:

Julius,

I again did not find answer to the error but you could also try the following entity of ATOMS on the web which easily allows a huge number of sites

http://cars9.uchicago.edu/cgi-bin/atoms/atoms.cgi

Chris

******************************************** Dr. Christopher Patridge Assistant Professor of Chemistry Dept of Math and Natural Science D'youville College 320 Porter Ave., Buffalo, NY 14201 Phone: 716-829-8096 tel:716-829-8096 Email:_patridgc@dyc.edu mailto:patridgc@dyc.edu_

On Nov 13, 2013, at 12:19 PM, Julius Campecino mailto:jcampecino@gmail.com> wrote:

...
Hi everyone,

Did anyone figure out how to fix "Can't call method tag" error and adding sites? Really a novice on fitting and I badly need help on this to get going. Sorry to bother everyone.

Thanks!

Julius

On Mon, Nov 11, 2013 at 8:48 AM, Julius Campecino mailto:jcampecino@gmail.com> wrote:

Hi Chris,

Yeah, I did try "add a site" but it is not responding. Does anyone else experience this problem? Thank you, Chris.

Julius

On Mon, Nov 11, 2013 at 9:51 AM, Christopher Patridge mailto:patridge@buffalo.edu> wrote:

Julius,

While I am not certain what the error means, there is a button displayed right above the atom list which says "ADD A SITE." I would suggest that having a unit cell as large as you do, along with rather weak scatterers such as N, C, O, and I assume H, it is probably unnecessary to have sites beyond the 3rd shell or so since these contribute negligibly to the EXAFS.

Chris

******************************************** Dr. Christopher Patridge Assistant Professor of Chemistry Dept of Math and Natural Science D'youville College 320 Porter Ave., Buffalo, NY 14201 Phone: 716-829-8096 tel:716-829-8096 Email:_patridgc@dyc.edu mailto:patridgc@dyc.edu_

On Nov 10, 2013, at 1:26 PM, Julius Campecino mailto:jcampecino@gmail.com> wrote:

...
Hi Bruce,

Here's the screen shot of my work in ATOMS. It's supposed to be more than 7 atoms in the core column but that's also one thing I do not know how to add change and add more atoms.

When I click "Run Atoms", it gives me this error "Can't call method "tag" on an undefined value at C:/strawberry/perl/site/lib/Demeter/Atoms.pm line 668.'' I am using the recent version 0.9.18.2 of the Demeter installer.

Thank you for your help!

Julius _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Julius Campecino

7:09 p.m.

Yes Matt, that is the metal core. I tried translating the coordinates to the origin and it is still giving me the same problem. I think this has something to do with the attributes/tag after the coordinates. I do not know if some code is not working for the Tag. Have you tried running it on your end? These are the new coordinates. ! This atoms input file was generated by WebAtoms 1.8 (Atoms 3.0beta10) ! Atoms written by and copyright (c) Bruce Ravel, 1998-2001 title = WT NiSOD space = P212121 a = 112.260 b = 113.810 c = 128.60 alpha = 90.0 beta = 90.0 gamma = 90.0 core = Ni edge = K rmax = 5.0 atoms ! elem x y z tag occ. Ni 0.00000 0.00000 0.00000 Ni 1.00000 S 0.92600 1.99600 0.57400 S 1.00000 S -1.50800 0.83800 -1.33000 S 1.00000 N -0.64900 -1.95300 -0.24700 N 1.00000 N 0.63900 -2.07000 -3.10800 N 1.00000 N 1.45100 -0.85900 0.94000 N 1.00000 Thanks for your help. Julius On Wed, Nov 13, 2013 at 10:09 AM, Matthew Marcus wrote:

...

Shouldn't ATOMS input coordinates be fractional values? I wonder if putting the S 3000A from center might have something to do with it. I'm guessing that this is the metal-sulfer core of a protein, right? mam

On 11/13/2013 9:58 AM, Julius Campecino wrote:

...
Hi Chris,

Same problem:

Can't call method "attributes" on an undefined value at /usr/local/lib/perl5/site_perl/5.10.0/Xray/ATP.pm line 342.

Can you try running this input and see if it works for you or not? Maybe there is something at my end that is causing this error.

! This atoms input file was generated by WebAtoms 1.8 (Atoms 3.0beta10) ! Atoms written by and copyright (c) Bruce Ravel, 1998-2001 title = WT NiSOD space = P212121 a = 112.260 b = 113.810 c = 128.60 alpha = 90.0 beta = 90.0 gamma = 90.0 core = Ni edge = K rmax = 5.0 atoms ! elem x y z tag occ. Ni 3.10300 27.70100 6.07300 Ni 1.00000 S 4.02900 29.69700 6.64700 S 1.00000 S 1.59500 28.53900 4.74300 S 1.00000 N 2.45400 25.74800 5.82600 N 1.00000 N 3.74200 25.63100 2.96500 N 1.00000 N 4.55400 26.84200 7.01300 N 1.00000

Thanks for your help!

Julius

On Wed, Nov 13, 2013 at 9:23 AM, Christopher Patridge < patridge@buffalo.edu mailto:patridge@buffalo.edu> wrote:

Julius,

I again did not find answer to the error but you could also try the following entity of ATOMS on the web which easily allows a huge number of sites

http://cars9.uchicago.edu/cgi-bin/atoms/atoms.cgi

Chris

******************************************** Dr. Christopher Patridge Assistant Professor of Chemistry Dept of Math and Natural Science D'youville College 320 Porter Ave., Buffalo, NY 14201 Phone: 716-829-8096 tel:716-829-8096 Email:_patridgc@dyc.edu mailto:patridgc@dyc.edu_

On Nov 13, 2013, at 12:19 PM, Julius Campecino > wrote:

Hi everyone,

...
Did anyone figure out how to fix "Can't call method tag" error and adding sites? Really a novice on fitting and I badly need help on this to get going. Sorry to bother everyone.

Thanks!

Julius

On Mon, Nov 11, 2013 at 8:48 AM, Julius Campecino < jcampecino@gmail.com mailto:jcampecino@gmail.com> wrote:

Hi Chris,

Yeah, I did try "add a site" but it is not responding. Does anyone else experience this problem? Thank you, Chris.

Julius

On Mon, Nov 11, 2013 at 9:51 AM, Christopher Patridge < patridge@buffalo.edu mailto:patridge@buffalo.edu> wrote:

Julius,

While I am not certain what the error means, there is a button displayed right above the atom list which says "ADD A SITE." I would suggest that having a unit cell as large as you do, along with rather weak scatterers such as N, C, O, and I assume H, it is probably unnecessary to have sites beyond the 3rd shell or so since these contribute negligibly to the EXAFS.

Chris

******************************************** Dr. Christopher Patridge Assistant Professor of Chemistry Dept of Math and Natural Science D'youville College 320 Porter Ave., Buffalo, NY 14201 Phone: 716-829-8096 tel:716-829-8096 Email:_patridgc@dyc.edu mailto:patridgc@dyc.edu_

On Nov 10, 2013, at 1:26 PM, Julius Campecino < jcampecino@gmail.com mailto:jcampecino@gmail.com> wrote:

Hi Bruce,

...
Here's the screen shot of my work in ATOMS. It's supposed to be more than 7 atoms in the core column but that's also one thing I do not know how to add change and add more atoms.

When I click "Run Atoms", it gives me this error "Can't call method "tag" on an undefined value at C:/strawberry/perl/site/lib/Demeter/Atoms.pm line 668.'' I am using the recent version 0.9.18.2 of the Demeter installer.

Thank you for your help!

Julius _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov

http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov

http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Robert Gordon

7:36 p.m.

Don't translate to the origin. ATOMS uses crystal symmetry and fractional coordinates. If your atom is not at those coordinates, don't use them. I used: title = WT NiSOD space = P 21 21 21 a = 112.260 b = 113.810 c = 128.60 alpha = 90.0 beta = 90.0 gamma = 90.0 core = Ni edge = K rmax = 5.0 atoms ! elem x y z tag occ. Ni 0.02764 0.24340 0.04722 Ni 1.00000 S 0.03589 0.26093 0.05169 S 1.00000 S 0.01421 0.25076 0.03688 S 1.00000 N 0.02186 0.22624 0.04530 N 1.00000 N 0.03333 0.22521 0.02306 N 1.00000 N 0.04057 0.23585 0.05453 N 1.00000 Which is just the fractional coordinate variation from your earlier file. I have run this without issue in 3 versions of ATOMS/Artemis/DArtemis. On 11/13/2013 1:09 PM, Julius Campecino wrote:

...

Yes Matt, that is the metal core. I tried translating the coordinates to the origin and it is still giving me the same problem. I think this has something to do with the attributes/tag after the coordinates. I do not know if some code is not working for the Tag. Have you tried running it on your end? These are the new coordinates.

! This atoms input file was generated by WebAtoms 1.8 (Atoms 3.0beta10) ! Atoms written by and copyright (c) Bruce Ravel, 1998-2001 title = WT NiSOD space = P212121 a = 112.260 b = 113.810 c = 128.60 alpha = 90.0 beta = 90.0 gamma = 90.0 core = Ni edge = K rmax = 5.0 atoms ! elem x y z tag occ. Ni 0.00000 0.00000 0.00000 Ni 1.00000 S 0.92600 1.99600 0.57400 S 1.00000 S -1.50800 0.83800 -1.33000 S 1.00000 N -0.64900 -1.95300 -0.24700 N 1.00000 N 0.63900 -2.07000 -3.10800 N 1.00000 N 1.45100 -0.85900 0.94000 N 1.00000

Thanks for your help.

Julius

On Wed, Nov 13, 2013 at 10:09 AM, Matthew Marcus mailto:mamarcus@lbl.gov> wrote:

Shouldn't ATOMS input coordinates be fractional values? I wonder if putting the S 3000A from center might have something to do with it. I'm guessing that this is the metal-sulfer core of a protein, right? mam

On 11/13/2013 9:58 AM, Julius Campecino wrote:

Hi Chris,

Same problem:

Can't call method "attributes" on an undefined value at /usr/local/lib/perl5/site_perl/5.10.0/Xray/ATP.pm line 342.

Can you try running this input and see if it works for you or not? Maybe there is something at my end that is causing this error.

! This atoms input file was generated by WebAtoms 1.8 (Atoms 3.0beta10) ! Atoms written by and copyright (c) Bruce Ravel, 1998-2001 title = WT NiSOD space = P212121 a = 112.260 b = 113.810 c = 128.60 alpha = 90.0 beta = 90.0 gamma = 90.0 core = Ni edge = K rmax = 5.0 atoms ! elem x y z tag occ. Ni 3.10300 27.70100 6.07300 Ni 1.00000 S 4.02900 29.69700 6.64700 S 1.00000 S 1.59500 28.53900 4.74300 S 1.00000 N 2.45400 25.74800 5.82600 N 1.00000 N 3.74200 25.63100 2.96500 N 1.00000 N 4.55400 26.84200 7.01300 N 1.00000

Thanks for your help!

Julius

On Wed, Nov 13, 2013 at 9:23 AM, Christopher Patridge mailto:patridge@buffalo.edu mailto:patridge@buffalo.edu>> wrote:

Julius,

I again did not find answer to the error but you could also try the following entity of ATOMS on the web which easily allows a huge number of sites

http://cars9.uchicago.edu/cgi-bin/atoms/atoms.cgi

Chris

******************************************** Dr. Christopher Patridge Assistant Professor of Chemistry Dept of Math and Natural Science D'youville College 320 Porter Ave., Buffalo, NY 14201 Phone: 716-829-8096 tel:716-829-8096 tel:716-829-8096> Email:_patridgc@dyc.edu mailto:Email%3A_patridgc@dyc.edu mailto:patridgc@dyc.edu>_

On Nov 13, 2013, at 12:19 PM, Julius Campecino mailto:jcampecino@gmail.com mailto:jcampecino@gmail.com>> wrote:

Hi everyone,

Did anyone figure out how to fix "Can't call method tag" error and adding sites? Really a novice on fitting and I badly need help on this to get going. Sorry to bother everyone.

Thanks!

Julius

On Mon, Nov 11, 2013 at 8:48 AM, Julius Campecino mailto:jcampecino@gmail.com mailto:jcampecino@gmail.com>> wrote:

Hi Chris,

Yeah, I did try "add a site" but it is not responding. Does anyone else experience this problem? Thank you, Chris.

Julius

On Mon, Nov 11, 2013 at 9:51 AM, Christopher Patridge mailto:patridge@buffalo.edu mailto:patridge@buffalo.edu>> wrote:

Julius,

While I am not certain what the error means, there is a button displayed right above the atom list which says "ADD A SITE." I would suggest that having a unit cell as large as you do, along with rather weak scatterers such as N, C, O, and I assume H, it is probably unnecessary to have sites beyond the 3rd shell or so since these contribute negligibly to the EXAFS.

Chris

******************************************** Dr. Christopher Patridge Assistant Professor of Chemistry Dept of Math and Natural Science D'youville College 320 Porter Ave., Buffalo, NY 14201 Phone: 716-829-8096 tel:716-829-8096 tel:716-829-8096> Email:_patridgc@dyc.edu mailto:Email%3A_patridgc@dyc.edu mailto:patridgc@dyc.edu>_

On Nov 10, 2013, at 1:26 PM, Julius Campecino mailto:jcampecino@gmail.com mailto:jcampecino@gmail.com>> wrote:

Hi Bruce,

Here's the screen shot of my work in ATOMS. It's supposed to be more than 7 atoms in the core column but that's also one thing I do not know how to add change and add more atoms.

When I click "Run Atoms", it gives me this error "Can't call method "tag" on an undefined value at C:/strawberry/perl/site/lib/Demeter/Atoms.pm line 668.'' I am using the recent version 0.9.18.2 of the Demeter installer.

Thank you for your help!

Julius

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov>

http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov>

http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

-- Dr. Robert Gordon Staff Scientist, PNCSRF APS Sector 20 (PNC/XSD) 9700 S Cass Ave. 435E Argonne, IL, USA 60439 630-252-0581 630-252-0580 fax

Matthew Marcus

8:35 p.m.

This still puts the core atoms at huge distances from each other. This can't be right. I don't know if these distances cause the problem you're having, but for any reasonable Rmax, no atom will be in range of the Ni. Maybe it's objecting to making a cluster containing the central atom and no scatterers. mam On 11/13/2013 11:09 AM, Julius Campecino wrote:

...

Yes Matt, that is the metal core. I tried translating the coordinates to the origin and it is still giving me the same problem. I think this has something to do with the attributes/tag after the coordinates. I do not know if some code is not working for the Tag. Have you tried running it on your end? These are the new coordinates.

! This atoms input file was generated by WebAtoms 1.8 (Atoms 3.0beta10) ! Atoms written by and copyright (c) Bruce Ravel, 1998-2001 title = WT NiSOD space = P212121 a = 112.260 b = 113.810 c = 128.60 alpha = 90.0 beta = 90.0 gamma = 90.0 core = Ni edge = K rmax = 5.0 atoms ! elem x y z tag occ. Ni 0.00000 0.00000 0.00000 Ni 1.00000 S 0.92600 1.99600 0.57400 S 1.00000 S -1.50800 0.83800 -1.33000 S 1.00000 N -0.64900 -1.95300 -0.24700 N 1.00000 N 0.63900 -2.07000 -3.10800 N 1.00000 N 1.45100 -0.85900 0.94000 N 1.00000

Thanks for your help.

Julius

On Wed, Nov 13, 2013 at 10:09 AM, Matthew Marcus mailto:mamarcus@lbl.gov> wrote:

Shouldn't ATOMS input coordinates be fractional values? I wonder if putting the S 3000A from center might have something to do with it. I'm guessing that this is the metal-sulfer core of a protein, right? mam

On 11/13/2013 9:58 AM, Julius Campecino wrote:

Hi Chris,

Same problem:

Can't call method "attributes" on an undefined value at /usr/local/lib/perl5/site___perl/5.10.0/Xray/ATP.pm line 342.

Can you try running this input and see if it works for you or not? Maybe there is something at my end that is causing this error.

! This atoms input file was generated by WebAtoms 1.8 (Atoms 3.0beta10) ! Atoms written by and copyright (c) Bruce Ravel, 1998-2001 title = WT NiSOD space = P212121 a = 112.260 b = 113.810 c = 128.60 alpha = 90.0 beta = 90.0 gamma = 90.0 core = Ni edge = K rmax = 5.0 atoms ! elem x y z tag occ. Ni 3.10300 27.70100 6.07300 Ni 1.00000 S 4.02900 29.69700 6.64700 S 1.00000 S 1.59500 28.53900 4.74300 S 1.00000 N 2.45400 25.74800 5.82600 N 1.00000 N 3.74200 25.63100 2.96500 N 1.00000 N 4.55400 26.84200 7.01300 N 1.00000

Thanks for your help!

Julius

On Wed, Nov 13, 2013 at 9:23 AM, Christopher Patridge mailto:patridge@buffalo.edu mailto:patridge@buffalo.edu>> wrote:

Julius,

I again did not find answer to the error but you could also try the following entity of ATOMS on the web which easily allows a huge number of sites

http://cars9.uchicago.edu/cgi-__bin/atoms/atoms.cgi http://cars9.uchicago.edu/cgi-bin/atoms/atoms.cgi

Chris

******************************__************** Dr. Christopher Patridge Assistant Professor of Chemistry Dept of Math and Natural Science D'youville College 320 Porter Ave., Buffalo, NY 14201 Phone: 716-829-8096 tel:716-829-8096 tel:716-829-8096> Email:_patridgc@dyc.edu mailto:Email%3A_patridgc@dyc.edu mailto:patridgc@dyc.edu>_

On Nov 13, 2013, at 12:19 PM, Julius Campecino mailto:jcampecino@gmail.com mailto:jcampecino@gmail.com>> wrote:

Hi everyone,

Did anyone figure out how to fix "Can't call method tag" error and adding sites? Really a novice on fitting and I badly need help on this to get going. Sorry to bother everyone.

Thanks!

Julius

On Mon, Nov 11, 2013 at 8:48 AM, Julius Campecino mailto:jcampecino@gmail.com mailto:jcampecino@gmail.com>> wrote:

Hi Chris,

Yeah, I did try "add a site" but it is not responding. Does anyone else experience this problem? Thank you, Chris.

Julius

On Mon, Nov 11, 2013 at 9:51 AM, Christopher Patridge mailto:patridge@buffalo.edu mailto:patridge@buffalo.edu>> wrote:

Julius,

While I am not certain what the error means, there is a button displayed right above the atom list which says "ADD A SITE." I would suggest that having a unit cell as large as you do, along with rather weak scatterers such as N, C, O, and I assume H, it is probably unnecessary to have sites beyond the 3rd shell or so since these contribute negligibly to the EXAFS.

Chris

******************************__************** Dr. Christopher Patridge Assistant Professor of Chemistry Dept of Math and Natural Science D'youville College 320 Porter Ave., Buffalo, NY 14201 Phone: 716-829-8096 tel:716-829-8096 tel:716-829-8096> Email:_patridgc@dyc.edu mailto:Email%3A_patridgc@dyc.edu mailto:patridgc@dyc.edu>_

On Nov 10, 2013, at 1:26 PM, Julius Campecino mailto:jcampecino@gmail.com mailto:jcampecino@gmail.com>> wrote:

Hi Bruce,

Here's the screen shot of my work in ATOMS. It's supposed to be more than 7 atoms in the core column but that's also one thing I do not know how to add change and add more atoms.

When I click "Run Atoms", it gives me this error "Can't call method "tag" on an undefined value at C:/strawberry/perl/site/lib/__Demeter/Atoms.pm line 668.'' I am using the recent version 0.9.18.2 of the Demeter installer.

Thank you for your help!

Julius _________________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.__gov mailto:Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov> http://millenia.cars.aps.anl.__gov/mailman/listinfo/ifeffit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_________________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.__gov mailto:Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov>

http://millenia.cars.aps.anl.__gov/mailman/listinfo/ifeffit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_________________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.__gov mailto:Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov> http://millenia.cars.aps.anl.__gov/mailman/listinfo/ifeffit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_________________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.__gov mailto:Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov>

http://millenia.cars.aps.anl.__gov/mailman/listinfo/ifeffit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_________________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.__gov mailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.__gov/mailman/listinfo/ifeffit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_________________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.__gov mailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.__gov/mailman/listinfo/ifeffit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Julius Campecino

10:04 p.m.

It worked! Thank you Matt, Chris and Robert for extending your help. Sincerely, Julius On Wed, Nov 13, 2013 at 12:35 PM, Matthew Marcus wrote:

...

This still puts the core atoms at huge distances from each other. This can't be right. I don't know if these distances cause the problem you're having, but for any reasonable Rmax, no atom will be in range of the Ni. Maybe it's objecting to making a cluster containing the central atom and no scatterers. mam

On 11/13/2013 11:09 AM, Julius Campecino wrote:

...
Yes Matt, that is the metal core. I tried translating the coordinates to the origin and it is still giving me the same problem. I think this has something to do with the attributes/tag after the coordinates. I do not know if some code is not working for the Tag. Have you tried running it on your end? These are the new coordinates.

! This atoms input file was generated by WebAtoms 1.8 (Atoms 3.0beta10) ! Atoms written by and copyright (c) Bruce Ravel, 1998-2001 title = WT NiSOD space = P212121 a = 112.260 b = 113.810 c = 128.60 alpha = 90.0 beta = 90.0 gamma = 90.0 core = Ni edge = K rmax = 5.0 atoms ! elem x y z tag occ. Ni 0.00000 0.00000 0.00000 Ni 1.00000 S 0.92600 1.99600 0.57400 S 1.00000 S -1.50800 0.83800 -1.33000 S 1.00000 N -0.64900 -1.95300 -0.24700 N 1.00000 N 0.63900 -2.07000 -3.10800 N 1.00000 N 1.45100 -0.85900 0.94000 N 1.00000

Thanks for your help.

Julius

On Wed, Nov 13, 2013 at 10:09 AM, Matthew Marcus > wrote:

Shouldn't ATOMS input coordinates be fractional values? I wonder if putting the S 3000A from center might have something to do with it. I'm guessing that this is the metal-sulfer core of a protein, right? mam

On 11/13/2013 9:58 AM, Julius Campecino wrote:

Hi Chris,

Same problem:

Can't call method "attributes" on an undefined value at /usr/local/lib/perl5/site___perl/5.10.0/Xray/ATP.pm line 342.

Can you try running this input and see if it works for you or not? Maybe there is something at my end that is causing this error.

! This atoms input file was generated by WebAtoms 1.8 (Atoms 3.0beta10) ! Atoms written by and copyright (c) Bruce Ravel, 1998-2001 title = WT NiSOD space = P212121 a = 112.260 b = 113.810 c = 128.60 alpha = 90.0 beta = 90.0 gamma = 90.0 core = Ni edge = K rmax = 5.0 atoms ! elem x y z tag occ. Ni 3.10300 27.70100 6.07300 Ni 1.00000 S 4.02900 29.69700 6.64700 S 1.00000 S 1.59500 28.53900 4.74300 S 1.00000 N 2.45400 25.74800 5.82600 N 1.00000 N 3.74200 25.63100 2.96500 N 1.00000 N 4.55400 26.84200 7.01300 N 1.00000

Thanks for your help!

Julius

On Wed, Nov 13, 2013 at 9:23 AM, Christopher Patridge < patridge@buffalo.edu mailto:patridge@buffalo.edu mailto:patridge@buffalo.edu>> wrote:

Julius,

I again did not find answer to the error but you could also try the following entity of ATOMS on the web which easily allows a huge number of sites

http://cars9.uchicago.edu/cgi-__bin/atoms/atoms.cgi < http://cars9.uchicago.edu/cgi-bin/atoms/atoms.cgi>

Chris

******************************__**************

Dr. Christopher Patridge Assistant Professor of Chemistry Dept of Math and Natural Science D'youville College 320 Porter Ave., Buffalo, NY 14201 Phone: 716-829-8096 tel:716-829-8096 > Email:_patridgc@dyc.edu mailto:Email%3A_patridgc@dyc.edu mailto:patridgc@dyc.edu>_

On Nov 13, 2013, at 12:19 PM, Julius Campecino < jcampecino@gmail.com mailto:jcampecino@gmail.com mailto:jcampecino@gmail.com>> wrote:

Hi everyone,

Did anyone figure out how to fix "Can't call method tag" error and adding sites? Really a novice on fitting and I badly need help on this to get going. Sorry to bother everyone.

Thanks!

Julius

On Mon, Nov 11, 2013 at 8:48 AM, Julius Campecino < jcampecino@gmail.com mailto:jcampecino@gmail.com mailto:jcampecino@gmail.com>> wrote:

Hi Chris,

Yeah, I did try "add a site" but it is not responding. Does anyone else experience this problem? Thank you, Chris.

Julius

On Mon, Nov 11, 2013 at 9:51 AM, Christopher Patridge mailto:patridge@buffalo.edu mailto:patridge@buffalo.edu>> wrote:

Julius,

While I am not certain what the error means, there is a button displayed right above the atom list which says "ADD A SITE." I would suggest that having a unit cell as large as you do, along with rather weak scatterers such as N, C, O, and I assume H, it is probably unnecessary to have sites beyond the 3rd shell or so since these contribute negligibly to the EXAFS.

Chris

******************************__**************

Dr. Christopher Patridge Assistant Professor of Chemistry Dept of Math and Natural Science D'youville College 320 Porter Ave., Buffalo, NY 14201 Phone: 716-829-8096 tel:716-829-8096 tel:716-829-8096> Email:_patridgc@dyc.edu mailto:Email%3A_patridgc@dyc.edu mailto:patridgc@dyc.edu>_

On Nov 10, 2013, at 1:26 PM, Julius Campecino < jcampecino@gmail.com mailto:jcampecino@gmail.com mailto:jcampecino@gmail.com>> wrote:

Hi Bruce,

Here's the screen shot of my work in ATOMS. It's supposed to be more than 7 atoms in the core column but that's also one thing I do not know how to add change and add more atoms.

When I click "Run Atoms", it gives me this error "Can't call method "tag" on an undefined value at C:/strawberry/perl/site/lib/__Demeter/Atoms.pm line 668.'' I am using the recent version 0.9.18.2 of the Demeter installer.

Thank you for your help!

Julius ___________________ ______________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.__gov mailto:Ifeffit@millenia.cars.aps.anl.gov> http://millenia.cars.aps.anl.__gov/mailman/listinfo/ifeffit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

______________________________ ___________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.__gov mailto:Ifeffit@millenia.cars.aps.anl.gov>

http://millenia.cars.aps.anl.__gov/mailman/listinfo/ifeffit < http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit>

_________________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.__gov mailto:Ifeffit@millenia.cars.aps.anl.gov> http://millenia.cars.aps.anl.__gov/mailman/listinfo/ifeffit < http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit>

_________________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.__gov mailto:Ifeffit@millenia.cars.aps.anl.gov>

http://millenia.cars.aps.anl.__gov/mailman/listinfo/ifeffit < http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit>

_________________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.__gov http://millenia.cars.aps.anl.__gov/mailman/listinfo/ifeffit < http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit>

_________________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.__gov http://millenia.cars.aps.anl.__gov/mailman/listinfo/ifeffit < http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit>

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Robert Gordon

6:14 p.m.

X, Y, and Z coordinates Specify the fractional coordinate of a site in one of the cell axis directions. You may use simple fractions such as "1/2". Space group P 21 21 21 Are your axes in Angstroms? On 11/13/2013 11:58 AM, Julius Campecino wrote:

...

Hi Chris,

Same problem: Can't call method "attributes" on an undefined value at /usr/local/lib/perl5/site_perl/5.10.0/Xray/ATP.pm line 342. Can you try running this input and see if it works for you or not? Maybe there is something at my end that is causing this error.

! This atoms input file was generated by WebAtoms 1.8 (Atoms 3.0beta10) ! Atoms written by and copyright (c) Bruce Ravel, 1998-2001 title = WT NiSOD space = P212121 a = 112.260 b = 113.810 c = 128.60 alpha = 90.0 beta = 90.0 gamma = 90.0 core = Ni edge = K rmax = 5.0 atoms ! elem x y z tag occ. Ni 3.10300 27.70100 6.07300 Ni 1.00000 S 4.02900 29.69700 6.64700 S 1.00000 S 1.59500 28.53900 4.74300 S 1.00000 N 2.45400 25.74800 5.82600 N 1.00000 N 3.74200 25.63100 2.96500 N 1.00000 N 4.55400 26.84200 7.01300 N 1.00000 Thanks for your help!

Julius

On Wed, Nov 13, 2013 at 9:23 AM, Christopher Patridge mailto:patridge@buffalo.edu> wrote:

Julius,

I again did not find answer to the error but you could also try the following entity of ATOMS on the web which easily allows a huge number of sites

http://cars9.uchicago.edu/cgi-bin/atoms/atoms.cgi

Chris

******************************************** Dr. Christopher Patridge Assistant Professor of Chemistry Dept of Math and Natural Science D'youville College 320 Porter Ave., Buffalo, NY 14201 Phone: 716-829-8096 tel:716-829-8096 Email:_patridgc@dyc.edu mailto:patridgc@dyc.edu_

On Nov 13, 2013, at 12:19 PM, Julius Campecino mailto:jcampecino@gmail.com> wrote:

...
Hi everyone,

Did anyone figure out how to fix "Can't call method tag" error and adding sites? Really a novice on fitting and I badly need help on this to get going. Sorry to bother everyone.

Thanks!

Julius

On Mon, Nov 11, 2013 at 8:48 AM, Julius Campecino mailto:jcampecino@gmail.com> wrote:

Hi Chris,

Yeah, I did try "add a site" but it is not responding. Does anyone else experience this problem? Thank you, Chris.

Julius

On Mon, Nov 11, 2013 at 9:51 AM, Christopher Patridge mailto:patridge@buffalo.edu> wrote:

Julius,

While I am not certain what the error means, there is a button displayed right above the atom list which says "ADD A SITE." I would suggest that having a unit cell as large as you do, along with rather weak scatterers such as N, C, O, and I assume H, it is probably unnecessary to have sites beyond the 3rd shell or so since these contribute negligibly to the EXAFS.

Chris

******************************************** Dr. Christopher Patridge Assistant Professor of Chemistry Dept of Math and Natural Science D'youville College 320 Porter Ave., Buffalo, NY 14201 Phone: 716-829-8096 tel:716-829-8096 Email:_patridgc@dyc.edu mailto:patridgc@dyc.edu_

On Nov 10, 2013, at 1:26 PM, Julius Campecino mailto:jcampecino@gmail.com> wrote:

...
Hi Bruce,

Here's the screen shot of my work in ATOMS. It's supposed to be more than 7 atoms in the core column but that's also one thing I do not know how to add change and add more atoms.

When I click "Run Atoms", it gives me this error "Can't call method "tag" on an undefined value at C:/strawberry/perl/site/lib/Demeter/Atoms.pm line 668.'' I am using the recent version 0.9.18.2 of the Demeter installer.

Thank you for your help!

Julius _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

-- Dr. Robert Gordon Staff Scientist, PNCSRF APS Sector 20 (PNC/XSD) 9700 S Cass Ave. 435E Argonne, IL, USA 60439 630-252-0581 630-252-0580 fax

Bruce Ravel

12 Dec 12 Dec

3:46 p.m.

Hi Julius, Your original email from last month came while I was on travel. Happily someone else helped you get over the immediate problem, so this issue has been languishing on my back burner. I finally got around to looking at it this morning. The next release of the software will fix both of the problems you observed: 1. The "add a site" button was broken and should work in the next release. 2. The problem you had with your original crystal data will still happen. Robert's solution was the correct one. In the next release, a situation like yours will fail more gracefully and Artemis will issue a (hopefully) useful error message. Thanks for reporting your problems to the mailing list. It really helps make the software better. I should also point out what an excellent advertisement for the mailing list your original email was. I was out of the country and unavailable, so it's a good thing you didn't try to contact me directly. Because you used the mailing list, someone else was able to help you. That's a system t hat works! B On 11/13/2013 12:19 PM, Julius Campecino wrote:

...

Hi everyone,

Did anyone figure out how to fix "Can't call method tag" error and adding sites? Really a novice on fitting and I badly need help on this to get going. Sorry to bother everyone.

Thanks!

Julius

On Mon, Nov 11, 2013 at 8:48 AM, Julius Campecino mailto:jcampecino@gmail.com> wrote:

Hi Chris,

Yeah, I did try "add a site" but it is not responding. Does anyone else experience this problem? Thank you, Chris.

Julius

On Mon, Nov 11, 2013 at 9:51 AM, Christopher Patridge mailto:patridge@buffalo.edu> wrote:

Julius,

While I am not certain what the error means, there is a button displayed right above the atom list which says "ADD A SITE." I would suggest that having a unit cell as large as you do, along with rather weak scatterers such as N, C, O, and I assume H, it is probably unnecessary to have sites beyond the 3rd shell or so since these contribute negligibly to the EXAFS.

Chris

******************************************** Dr. Christopher Patridge Assistant Professor of Chemistry Dept of Math and Natural Science D'youville College 320 Porter Ave., Buffalo, NY 14201 Phone: 716-829-8096 tel:716-829-8096 Email:_patridgc@dyc.edu mailto:patridgc@dyc.edu_

On Nov 10, 2013, at 1:26 PM, Julius Campecino mailto:jcampecino@gmail.com> wrote:

...
Hi Bruce,

Here's the screen shot of my work in ATOMS. It's supposed to be more than 7 atoms in the core column but that's also one thing I do not know how to add change and add more atoms.

When I click "Run Atoms", it gives me this error "Can't call method "tag" on an undefined value at C:/strawberry/perl/site/lib/Demeter/Atoms.pm line 668.'' I am using the recent version 0.9.18.2 of the Demeter installer.

Thank you for your help!

Julius _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

-- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel

Julius Campecino

3:55 p.m.

Yep! I would like to thank everyone who extended their help. And hopefully soon feff8 (if this offers more sophistication than feff6) will be incorporated to ATOMS :) Thank you, Bruce. Julius On Thu, Dec 12, 2013 at 7:46 AM, Bruce Ravel wrote:

...

Hi Julius,

Your original email from last month came while I was on travel. Happily someone else helped you get over the immediate problem, so this issue has been languishing on my back burner. I finally got around to looking at it this morning.

The next release of the software will fix both of the problems you observed:

1. The "add a site" button was broken and should work in the next release.

2. The problem you had with your original crystal data will still happen. Robert's solution was the correct one. In the next release, a situation like yours will fail more gracefully and Artemis will issue a (hopefully) useful error message.

Thanks for reporting your problems to the mailing list. It really helps make the software better.

I should also point out what an excellent advertisement for the mailing list your original email was. I was out of the country and unavailable, so it's a good thing you didn't try to contact me directly. Because you used the mailing list, someone else was able to help you. That's a system t hat works!

B

On 11/13/2013 12:19 PM, Julius Campecino wrote:

...
Hi everyone,

Did anyone figure out how to fix "Can't call method tag" error and adding sites? Really a novice on fitting and I badly need help on this to get going. Sorry to bother everyone.

Thanks!

Julius

On Mon, Nov 11, 2013 at 8:48 AM, Julius Campecino mailto:jcampecino@gmail.com> wrote:

Hi Chris,

Yeah, I did try "add a site" but it is not responding. Does anyone else experience this problem? Thank you, Chris.

Julius

On Mon, Nov 11, 2013 at 9:51 AM, Christopher Patridge mailto:patridge@buffalo.edu> wrote:

Julius,

While I am not certain what the error means, there is a button displayed right above the atom list which says "ADD A SITE." I would suggest that having a unit cell as large as you do, along with rather weak scatterers such as N, C, O, and I assume H, it is probably unnecessary to have sites beyond the 3rd shell or so since these contribute negligibly to the EXAFS.

Chris

******************************************** Dr. Christopher Patridge Assistant Professor of Chemistry Dept of Math and Natural Science D'youville College 320 Porter Ave., Buffalo, NY 14201 Phone: 716-829-8096 tel:716-829-8096 Email:_patridgc@dyc.edu mailto:patridgc@dyc.edu_

On Nov 10, 2013, at 1:26 PM, Julius Campecino mailto:jcampecino@gmail.com> wrote:

Hi Bruce,

...
Here's the screen shot of my work in ATOMS. It's supposed to be more than 7 atoms in the core column but that's also one thing I do not know how to add change and add more atoms.

When I click "Run Atoms", it gives me this error "Can't call method "tag" on an undefined value at C:/strawberry/perl/site/lib/Demeter/Atoms.pm line 668.'' I am using the recent version 0.9.18.2 of the Demeter installer.

Thank you for your help!

Julius _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov mailto:Ifeffit@millenia.cars.aps.anl.gov

http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

-- Bruce Ravel ------------------------------------ bravel@bnl.gov

National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973

Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

4009

Age (days ago)

4041

Last active (days ago)

List overview

Download

13 comments

5 participants

participants (5)

Bruce Ravel
Christopher Patridge
Julius Campecino
Matthew Marcus
Robert Gordon

error in ATOMS

Julius Campecino

Christopher Patridge

Julius Campecino

Julius Campecino

Christopher Patridge

Julius Campecino

Matthew Marcus

Julius Campecino

Robert Gordon

Matthew Marcus

Julius Campecino

Robert Gordon

Bruce Ravel

Julius Campecino

tags

participants (5)