[Ifeffit] error in ATOMS
Matthew Marcus
mamarcus at lbl.gov
Wed Nov 13 14:35:43 CST 2013
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
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