[Ifeffit] error in ATOMS
Julius Campecino
jcampecino at gmail.com
Wed Nov 13 13:09:16 CST 2013
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> 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>> 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 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>> 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>> 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>> 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 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>> 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>_______________________________________________
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>>>
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>>
>>
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