Hi Guys, I'm dealing with the same issue with a couple of structures at the moment. Matt you said that you like to leave the side chains in a plausible conformation and let refinement deal with the problem. Generally when I try this their backbone geometry gets all bent out of shape in refinement. What's the best 'kind' of refinement to do in order to deal with this problem?
Cheers, Rhys ________________________________________ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Matthew Franklin [mfrank...@nysbc.org] Sent: 09 November 2012 22:22 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] side chain density Dear Remy and Faisal - Just a geeky bioinformatics note: searching my local copy of the PDB (somewhat out of date), shows that 22,165 out of 72,000 structures contain a 'REMARK 470' line, which is how the PDB notes that atoms are missing from a residue. Some of these are no doubt mistakes by the depositors, but most probably reflect the decision to remove invisible side chain atoms from the coordinates (e.g. trimming back to Cbeta) while keeping the correct residue name. I think we can all agree that virtually every structure in the PDB will have a few residues where some of the atoms are not visible in the density. So the "trim the side chains" crowd is a well-represented minority at 30%, but 70% of depositors chose another option. I personally like to leave all atoms on the side chains; they look wrong to me when beheaded. I just try to put the invisible atoms in a stereochemically plausible conformation, leave the occupancy set to 1, and let the refinement program deal with them. - Matt On 11/9/12 3:47 PM, Remy Loris wrote: > Dear Faisal, > > You definitely do not mutate to alanine as that would imply for the > future "user" of your pdb file that it is a mutant. > Some people feel they have to keep the side chain but put the > occupancies at zero. I think this is a bad practice and strongly > oppose to it as for the future "user" of your deposited pdb file, who > often is not a crystallographer, you suggest a specific conformation > for your side chain that may be interpreted in terms of biology, while > in reality it addopts a huge, disordered ensemble of conformations. > Personally I am of the opinion that you should simply remove the side > chain atoms (but keep the residue name). And that is the same as what > you do with a whole loop that is disordered. I think it is lso the > most common practice in deposited structures. > > Remy Loris > Vrije Universiteit Brussel > > On 09/11/12 20:22, Faisal Tarique wrote: >> Dear all >> >> i have solved a structure ( at 2A resolution) whose Rwork and Rfree >> is 22 and 25 respectively..the Ramachandran plot shows 90% of the >> residues in the most favorable region and with 6 residues in >> generously allowed and no residues in disallowed region. But in some >> areas i can see density missing for side chains ( in loop regions >> )..i have question do i need to mutate them to alanine or leave them >> as such..The density fit analysis in COOT ( traffic light) showing >> those regions with side chain as red.. >> >> thanx in advance >> >> Regards >> >> Faisal >> School of Life Sciences >> JNU >> > > -- Matthew Franklin, Ph. D. Senior Scientist New York Structural Biology Center 89 Convent Avenue, New York, NY 10027 (212) 939-0660 ext. 9374
