[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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