[Chimera-users] Water Ice Structures

[Elaine Meng]

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