Hello all, I'm refining a structure with 4 molecules in the AU. The molecules have substantial differences in certain regions, so I want to exclude those regions from the NCS restraints calculation and usage. How do i do this? As far as I can see, by selecting residues via for example "chain A and (resseq 20:50 or resseq 88:299), etc" the NCS restraints are calculated from the specified part of the molecules but still applied to the entire molecules, which I don't want.
Thanks for any hints! Bert van den Berg University of Massachusetts Medical School Program in Molecular Medicine Biotech II, 373 Plantation Street, Suite 115 Worcester MA 01605 Phone: 508 856 1201 (office); 508 856 1211 (lab) e-mail: [email protected] http://www.umassmed.edu/pmm/faculty/vandenberg.cfm -----Original Message----- From: CCP4 bulletin board on behalf of Artem Evdokimov Sent: Fri 2/27/2009 7:00 PM To: [email protected] Subject: Re: [ccp4bb] Off topic: Mammalian gene expression in E. coli Hello, The short answer is 'yes'. If you can use both methods :) The issue with limited proteolysis lies in the questionable state of the full-length protein - if the stuff is nasty and misfolded, then fagments generated by proteolytic digest aren't going to be meaningful. On the other hand if you have a small amount of decent quality full-length protein, digest can be extremely useful. Deuterium exchange is a nice technique if one of your friends is an altruistic mass-spectroscopist :) Purely theoretical methods are limited as well, especially if you're working with a bunch of unknown domains in a sequence that has low identity with anything that has associated structures. And in the end, even for known structures (or very similar ones) truncation can generate surprises - both positive and negative ones. Artem >Hi: >I am following this with interest. Nice and useful info. >My question is: how do you "chop the protein into useful hunks"? >Using some domain identifying software or using limited proteolysis? >Thanks >Subbu
