[Chimera-users] chimera to rebuild crystal

Miguel Ortiz Lombardia molatwork at yahoo.es
Thu Jan 18 02:22:16 PST 2007

Hash: SHA1

Hi Tom,

Thanks to you! This is an awesome tool!!

Let me just add a comment from someone working in protein/nucleic acids
(not virus) crystallography:

Although your use of the term "NCS" though very correct, it may be
confusing for some people in our field. The reason is that 90% (?) of
the time we deposit a full asymmetric unit, regardless of whether there
is or not non-crystallographic symmetry. Therefore, coordinates for a
full AU still can represent a crystal where _there_is_ NCS. This is
because we normally refine all atoms in the AU except for the 10% (?) of
the time when they are constrained (NCS-related molecules in the AU are
forced to be in perfectly equivalent positions). We normally use
restraints more or less relaxed or even no restraints at all if
resolution is high enough. Only for very low resolution crystals with
constrained NCS, people deposit the "independent" part of the AU and
give MATRIX records for the rest of the positions. So, my suggestion is
that you might substitute "strict NCS" (or "explicit NCS", etc) for
"NCS" and make clear that NCS may be present even if the coordinates
contain the full AU. But perhaps your users are mainly virus
crystallographers or EM people, who wouldn't care much... So, just a

Would it be very difficult to change the code so each chain in the AU is
represented by a green sphere and the distance calculations are made
relative to each of them? Also, in the other AU's, each sphere would
represent a chain... As you see, this relates to my suggestion in a way,
though the different chains in the AU need not to be related by NCS.

I've been looking in the code but haven't failed to find where the lists
are generated...

Thank you again! Even as it is, this tool is really helpful to analyse
molecular contacts!

Best regards,


Thomas Goddard escribió:
> Hi Miguel,
>   Thanks for the clarification.  I agree that it is important to get
> just the contacting chains, not the whole asymmetric units, and that
> both crystal symmetries and unit cell translations need to be considered.
>   The basic code to achieve this is already in Chimera so it should not
> be difficult to add.  The needed routines are used by the "crystal
> contacts" experimental plugin
> http://www.cgl.ucsf.edu/chimera/experimental/crystal_contacts/clashes.html
> although that tool works at the level of whole asymmetric units.  Some
> adaptations of that code would allow it to instead consider individual
> chains and display all atoms of each chains instead of a single sphere
> for each chain.  I'll let you know when I have written code you can try.
>     Tom

- --
Miguel Ortiz Lombardía
Centro de Investigaciones Oncológicas
C/ Melchor Fernández Almagro, 3
28029 Madrid, Spain
Tel. +34 912 246 900
Fax. +34 912 246 976
email: molatwork at yahoo.es
www: http://www.ysbl.york.ac.uk/~mol/
Le travail est ce que l'homme a trouvé de mieux
pour ne rien faire de sa vie.                          (Raoul Vaneigem)
Version: GnuPG v1.4.2.2 (GNU/Linux)


More information about the Chimera-users mailing list