[Ifeffit] error in ATOMS
Julius Campecino
jcampecino at gmail.com
Wed Nov 13 16:04:06 CST 2013
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 <mamarcus at lbl.gov> 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 <mamarcus at lbl.gov<mailto:
>> mamarcus at 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 <
>> patridge at buffalo.edu <mailto:patridge at buffalo.edu> <mailto:
>> patridge at buffalo.edu <mailto:patridge at 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<tel:
>> 716-829-8096>>
>> Email:_patridgc at dyc.edu <mailto:Email%3A_patridgc at dyc.edu>
>> <mailto:patridgc at dyc.edu <mailto:patridgc at dyc.edu>>_
>>
>>
>>
>>
>>
>> On Nov 13, 2013, at 12:19 PM, Julius Campecino <
>> jcampecino at gmail.com <mailto:jcampecino at gmail.com> <mailto:
>> jcampecino at gmail.com <mailto:jcampecino at 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 at gmail.com <mailto:jcampecino at gmail.com> <mailto:
>> jcampecino at gmail.com <mailto:jcampecino at 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 at buffalo.edu <mailto:patridge at buffalo.edu> <mailto:
>> patridge at buffalo.edu <mailto:patridge at 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 <tel:716-829-8096>>
>> Email:_patridgc at dyc.edu <mailto:Email%3A_patridgc at dyc.edu>
>> <mailto:patridgc at dyc.edu <mailto:patridgc at dyc.edu>>_
>>
>>
>>
>>
>>
>> On Nov 10, 2013, at 1:26 PM, Julius Campecino <
>> jcampecino at gmail.com <mailto:jcampecino at gmail.com> <mailto:
>> jcampecino at gmail.com <mailto:jcampecino at 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
>> <Atoms.png>___________________
>> ______________________________
>> Ifeffit mailing list
>> Ifeffit at millenia.cars.aps.anl.__gov <mailto:
>> Ifeffit at millenia.cars.aps.anl.gov> <mailto:Ifeffit at millenia.cars.__
>> aps.anl.gov <mailto:Ifeffit at 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 at millenia.cars.aps.anl.__gov <mailto:
>> Ifeffit at millenia.cars.aps.anl.gov> <mailto:Ifeffit at millenia.cars.__
>> aps.anl.gov <mailto:Ifeffit at 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 at millenia.cars.aps.anl.__gov <mailto:
>> Ifeffit at millenia.cars.aps.anl.gov> <mailto:Ifeffit at millenia.cars.__
>> aps.anl.gov <mailto:Ifeffit at 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 at millenia.cars.aps.anl.__gov <mailto:
>> Ifeffit at millenia.cars.aps.anl.gov> <mailto:Ifeffit at millenia.cars.__
>> aps.anl.gov <mailto:Ifeffit at 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 at millenia.cars.aps.anl.__gov <mailto:
>> Ifeffit at 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 at millenia.cars.aps.anl.__gov <mailto:Ifeffit at 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 at millenia.cars.aps.anl.gov
>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>>
>> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20131113/52c462fa/attachment.html>
More information about the Ifeffit
mailing list