Hi there. I have always been taught that, "if you can't see it you can't model it" - so if I can't see density beyond the C-beta of a lys, I remove the atoms in coot. As long as the amino acid name is correct in the pdb file, then everything *should* take care of itself down the line (in refmac, certainly)
Putting the whole side chain in with an occupancy of 0 may prompt an inexperienced user of atomic models to infer that the side chain is in the position you arbitrarily decided is correct. 99 times out of 100 this may make no difference, but with more and more in silico analysis available to lay-users, we have to be careful our models don't mislead people. Just my tuppence worth. Dave
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 > > > > > > > > > >
-- --------------------------------------- David Briggs, PhD. Father & Crystallographer www.dbriggs.talktalk.net iChat AIM ID: DBassophile
