[Chimera-users] Water Ice Structures

[Elaine Meng]

Could you clarify what "did not work for me" means?    Also, as mentioned you would need to get Chimera version 1.6 (a recent daily build) for the CIF symmetry information to be read and applied by Unit Cell.  "Help... About UCSF Chimera" in the menu will show you which version you have.

I opened it and Unit Cell did make copies.  However, I suspect something may be amiss because several copies seem to be overlapping,  but I really don't know much about how it is supposed to look -- so it would be useful for you to be more descriptive.  Are you comparing what you see with a picture in some book or article that shows what it is supposed to look like, or how it looks in some other program?  Finally, if it is wrong I don't know if it is an error in the file or an error by Chimera.
Thanks
Elaine

On Jun 23, 2011, at 11:35 AM, Matthew Thompson wrote:

> Hi Elaine,
> 
> Thanks for helping me.  I've attached the file I used.  It is the cif
> file for Ice (VI).  The higher-order analysis did not work for me.
> 
> Matt
> 
> 
> On Thu, Jun 23, 2011 at 1:28 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
>> Hi Matt,
>> Actually, that AMS website might have the forms you need, except I don't see ice VII.  After I opened the ice VI cif file, I used Unit Cell (under Tools... Higher-Order Structure in the Chimera menu) to "make copies" and "show outline" which gives the appearance below.  I had also showed atom-name labels (Chimera menu "Actions... Labels... name").
>> 
>> Reading symmetry information from CIF files is a new feature available only in Chimera 1.6 (daily build download),
>> <http://www.cgl.ucsf.edu/chimera/docs/relnotes/snapshot.html>
>> so if you see any problems with that let us know.  At least for this ice VI structure, the relationship of the 3 atoms in the original structure (white) to the unit cell outline box looks the same as in the Jmol view at that website.
>> 
>> I hope this helps,
>> Elaine
>> 
>> 
>> 
>> 
>> 
>> On Jun 23, 2011, at 10:06 AM, Elaine Meng wrote:
>> 
>>> Then again, that CIF file really only has three atoms in it, named Wat1 Wat2 Wat3, so perhaps Chimera has done all it can to show it!   Besides which file is used, it is unclear what you meant by not loading properly.
>>> Elaine
>>> 
>>> On Jun 23, 2011, at 9:43 AM, Elaine Meng wrote:
>>> 
>>>> Hi Matt,
>>>> We can't really tell what is going on without that file.  Is it proprietary?  You could send it to just me and I would keep it amongst the developers here.  However, by googling I see there is an ice(VI) CIF available from this page,
>>>> <http://rruff.geo.arizona.edu/AMS/result.php?mineral=Ice>
>>>> 
>>>> and I was able to open it in Chimera, but only three dots appear and I get the following errors in the Reply Log.  If that is the same file you used and the same result, let us know.
>>>> 
>>>> MMLIB:WARNING] GetSpaceGroup('P 42/n m c') not found
>>>> [MMLIB:WARNING] monomer description not found in zipfile for 'GLOBAL'
>>>> [MMLIB:WARNING] monomer description not found for 'global'
>>>> [MMLIB:WARNING] monomer description not found in zipfile for 'GLOBAL'
>>>> [MMLIB:WARNING] monomer description not found for 'global'
>>>> [MMLIB:WARNING] read_atoms: no geom_bond section found
>>>> [MMLIB:WARNING] read_atoms: no geom_angle section found
>>>> [MMLIB:WARNING] monomer description not found in zipfile for 'GLOBAL'
>>>> [MMLIB:WARNING] monomer description not found for 'global'
>>>> AMS_DATA.cif opened
>>>> 
>>>> The CIF reader was developed mainly for mmCIF from the PDB and does not cover the universe of CIF possibilities.  It may be a current limitation as opposed to a bug, but we would need to know which file you used.
>>>> 
>>>> Besides sending email to chimera-users, another approach is to use "Help... Report a Bug" in the Chimera menu and include a description of steps needed to reproduce the problem, attach any file needed to reproduce the problem, and include your email address if you wish feedback.
>>>> Best,
>>>> Elaine
>>>> ----------
>>>> Elaine C. Meng, Ph.D.
>>>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
>>>> Department of Pharmaceutical Chemistry
>>>> University of California, San Francisco
>>>> 
>>>> On Jun 22, 2011, at 8:44 PM, Matthew Thompson wrote:
>>>> 
>>>>> I am looking for the crystal structures of "normal" ice (Ih), ice(VI),
>>>>> and ice(VII).  I have found the .cif file for ice(VI), but I can't
>>>>> seem to get it to load properly into Chimera.  I am really only
>>>>> familiar with using pdb's in Chimera.  These would be used in a
>>>>> presentation given this coming weekend at the National School for
>>>>> Neutron and X-ray Scattering.  Any help in this would be greatly
>>>>> appreciated
>>>>> 
>>>>> Thanks
>>>>> Matt
>>>>> _
>>>>> Matthew K. Thompson, PhD
>>>>> North Carolina State University
>>>>> Raleigh, NC 27695
>>>>> Office: 919-515-2105
>>>>> Cell: 919-455-1775
>>>> 
>> 
>> 
>> 
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