[ccp4bb] Amino acid side chains without density
Dear CCP4bb, Sorry for asking a naive question. I am trying to deposit a structure in PDB. I would like to know whether we have to delete the side chains of amino acids for which we are not finding density or people prefer keeping the side chains occupancy zero? Is there any other way to do this?
Re: [ccp4bb] Amino acid side chains without density
I think you'll find that this is not a naive question.. I doubt there is a consensus for this. Neither option is ideal, mainly because of possible confusion generated for non-crystallographers. My preference is to include the side chain but set the atoms i do not see to zero occupancy. The PDB does not like this however Others will probably chime in here; in any case i think this has been discussed before, so digging in the archives might help as well. Bert From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Sasha Pausch [sashapau...@gmail.com] Sent: Tuesday, November 11, 2014 1:14 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Amino acid side chains without density Dear CCP4bb, Sorry for asking a naive question. I am trying to deposit a structure in PDB. I would like to know whether we have to delete the side chains of amino acids for which we are not finding density or people prefer keeping the side chains occupancy zero? Is there any other way to do this?
Re: [ccp4bb] Amino acid side chains without density
Dear Sasha, There was a survey done by Ed Pozharski back in 2011 The results of the online survey on what to do with disordered side chains (from total of 240 responses): Delete the atoms 43% Let refinement take care of it by inflating B-factors41% Set occupancy to zero12% Other 4% Reference: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1103L=CCP4BBD=0P=321265 So, the other way (appart from what you mention) is to keep the atoms and let the B-factors refine to relatively large values. Best regards, Folmer 2014-11-11 14:14 GMT+01:00 Sasha Pausch sashapau...@gmail.com: Dear CCP4bb, Sorry for asking a naive question. I am trying to deposit a structure in PDB. I would like to know whether we have to delete the side chains of amino acids for which we are not finding density or people prefer keeping the side chains occupancy zero? Is there any other way to do this? -- Folmer Fredslund
Re: [ccp4bb] Amino acid side chains without density
Dear Sasha, you should bear in mind that the major part of users of your deposited structure will not be crystallographers, and they probably don't know what e.g. a B-value is. So also may no use Coot to visualise the structure hence may not be pointed at graphically that occupancies are set to zero. E.g. I have the impression that sometimes people running molecular dynamics simulations take a PDB file for granted and as absolute truth, even irrespective of the resolution and other quality indicators. Therefore you are on the safe side to delete side chains for which you don't see density. When you place them, you decide for a position without experimental evidence. You can run two tests: 1) remove the side chain and refine. Does the difference map indicate where the side chain should be? Put it back, otherwise leave it out The difference density is a little more sensitive than the direct map. 2) place the side chain a little bit, e.g. select a different rotamer in Coot that does not clash. Then refine. Does the side chain go back to where you initially placed it? Then there may be some signal in the data supporting that position. Otherwise, leave it out. Best, Tim On 11/11/2014 02:14 PM, Sasha Pausch wrote: Dear CCP4bb, Sorry for asking a naive question. I am trying to deposit a structure in PDB. I would like to know whether we have to delete the side chains of amino acids for which we are not finding density or people prefer keeping the side chains occupancy zero? Is there any other way to do this? -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: OpenPGP digital signature
