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 <mamar...@lbl.gov
<mailto:mamar...@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 <patri...@buffalo.edu
<mailto:patri...@buffalo.edu> <mailto:patri...@buffalo.edu
<mailto:patri...@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:_patri...@dyc.edu <mailto:email%3a_patri...@dyc.edu>
<mailto:patri...@dyc.edu <mailto:patri...@dyc.edu>>_
On Nov 13, 2013, at 12:19 PM, Julius Campecino <jcampec...@gmail.com
<mailto:jcampec...@gmail.com> <mailto:jcampec...@gmail.com
<mailto:jcampec...@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 <jcampec...@gmail.com
<mailto:jcampec...@gmail.com> <mailto:jcampec...@gmail.com
<mailto:jcampec...@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 <patri...@buffalo.edu
<mailto:patri...@buffalo.edu> <mailto:patri...@buffalo.edu
<mailto:patri...@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:_patri...@dyc.edu <mailto:email%3a_patri...@dyc.edu>
<mailto:patri...@dyc.edu <mailto:patri...@dyc.edu>>_
On Nov 10, 2013, at 1:26 PM, Julius Campecino <jcampec...@gmail.com
<mailto:jcampec...@gmail.com> <mailto:jcampec...@gmail.com
<mailto:jcampec...@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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