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 1.00000Thanks for your help. Julius
On Wed, Nov 13, 2013 at 10:09 AM, Matthew Marcus <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 <patridge@buffalo.edu <mailto:patridge@buffalo.edu>> wrote:Phone: 716-829-8096 <tel:716-829-8096>
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
Email:_patridgc@dyc.edu <mailto:patridgc@dyc.edu>_
On Nov 13, 2013, at 12:19 PM, Julius Campecino <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>> 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:Phone: 716-829-8096 <tel:716-829-8096>
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
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,Ifeffit@millenia.cars.aps.anl.gov <mailto:Ifeffit@millenia.cars.aps.anl.gov>
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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