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Hmm, I'd like to stay as close as possible to the biological "truth"... In this case, you know that the lysine side chain atoms are there but you just can't see them! I always leave these atoms in, in a preferred rotamer (with 1.0 occupancy!) and let the B-values refine to >100. These high B-values clearly indicate the issue at hand, and you can colour the model accordingly. Obviously, for missing loops or ends the situation is a bit different, as you might have lossed them due to proteolysis, and it is impossible to model them in without data. I think putting atoms in with 0 occupancy only confuses users, and you artificiallly lower the R values of the structure. Flip -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Eleanor Dodson Sent: Wednesday, January 10, 2007 12:21 To: [EMAIL PROTECTED] Cc: ccp4bb@dl.ac.uk Subject: Re: [ccp4bb]: Modelling disordered side-chains I really have no view providing that if you include the whole side chain you must set the atom occupancy to 0.00 forthe invisible atoms.. Eleanor Nicholas Noinaj wrote: >*** For details on how to be removed from this list visit the *** >*** CCP4 home page http://www.ccp4.ac.uk *** > > >Hi, > >i would like to get opinions on whether or not one removes side-chain atoms where there is no density. for example, if one can only observe density up to the beta-carbon for lysine (say at > 0.5 sigma), does one leave the lysine side chain intact, knowing it must be disordered, or does one terminate at the beta-carbon, making the coordinates reflect what is actually observed in the density. > >It seems both approaches are published and people seem to have conflicting opinions on the topic. It would be nice to come to some concensus, possibly clear up the issue for us newbies. > >Thanks in advance for all feedback! > > > >Cheers, >NIck > > > > >________________________________________ > >Nicholas Noinaj >University of Kentucky College of Medicine >Department of Molecular and Cellular Biochemistry >The Center for Structural Biology >Biomedical Biological Sciences Research Building, Rm 236 >741 S. Limestone >Lexington, Ky 40536 >Lab: 859-323-8183 >Cell: 859-893-4789 >Home: 859-228-0978 >[EMAIL PROTECTED] >noinaj.com > > > > > > > > > >
