[Chimera-users] Water Ice Structures

Fri Jun 24 13:34:59 PDT 2011

There might be a problem with the particular cif file.

If an atom gets "multiplied" by the crystallographic symmetry (meaning it is
on a "special position"), the occupancy factor in the cif file should be
accordingly low, because only a fraction of the atom lies in the asymmetric
unit, with the "whole" atom generated by the crystallographic symmetry.

So, I think the cif files from that site look strange (occupancy factors not
adjusted to crystallographic symmetry).

Atoms on special positions actually do occur occasionally in protein
structures, most often for water molecules or heteroatoms. When an atom sits
on a symmetry element such as a two-fold axis, the occupancy factor will by
0.5 (for a two-fold axis) to make up for the symmetry generated part.

Ursula

On Thu, Jun 23, 2011 at 5:55 PM, Tom Goddard <goddard at sonic.net> wrote:

> **
> Hi Matthew,
>
>   Thanks for sending your file.  It allowed me to figure out an error in
> Chimera parsing of CIF crystal symmetry.  Chimera was using symmetries
> expressed in fractional unit cell coordinates when it thought they were real
> space coordinates.  I've fixed that and the Unit Cell dialog in tonight's
> daily build will give a more sensible result for CIF files.
>
>   I've attached a picture of your CIF file which I think is ice VII, not
> ice VI as you said.  This shows 2 by 2 by 2 unit cells.  I turned of the
> "pack molecules in unit cell" option and used the fixed code.  It still
> looks weird with 4 hydrogens coming of each oxygen.  I believe this is
> because their are several possible orientations for each water -- the water
> orientations are disordered with half occupancy at each hydrogen position,
> as described in this reference
>
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC300465/pdf/pnas00186-0123.pdf
>
> "One can also assume that the proton positions are disordered, in the same
> sense as they are in ice I or ice Ic ("cubicice").1,8 The structure is
> therefore described statisticaly as follows: spacegroup Pn3m(O_h^4),a=
> 3.30A,O in 2 (a) (000, 1/2 1/2 1/2),1/2 H in8(e) (xxx, etc.), with x ~
> 0.17."
>
>   Reading about CIF and small-molecule crystals I found that the symmetries
> can place atoms exactly on top of each other.  In your file I get 24 oxygens
> at every position and 6 hydrogens at every position.  What I read said these
> duplicates should be eliminated, but Chimera does not do this.  In protein
> crystals the symmetry operators never give the same position.  This will
> need some future fix when I understand it better.
>
>     Tom
>
>
>
>  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> <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> <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> <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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