-----BEGIN PGP SIGNED MESSAGE----- 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 suggestion! 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, Miguel 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@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) -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) iD8DBQFFr0pYF6oOrDvhbQIRAihzAJ4nyNYsU+rvHMXv3MxUqhazw16/HQCeNk7+ qWgtrurtkVMKQHDo6rWrpJ4= =oxrA -----END PGP SIGNATURE-----