I vote for the electron density irrespective of side chains, main chains, ligands, dark matter. The PDB is a collection of experimentally determined structures per its own definition. If density supports it high B is fine - B-factor simply is a parameter of a probability distribution. If you extend that to no density - it becomes problematic. After all, coordinates imply that an atom is actually at some specified place with a certain probability. We may know that the atom necessarily has to be someplace lest it got chewed off for some reason. The experiment just tells you that you do not know where the atom is.
Or in Rumsfeldic: Better a known unknown than a unknown known. Cheers, BR -----Original Message----- From: Boaz Shaanan [mailto:bshaa...@exchange.bgu.ac.il] Sent: Sunday, April 03, 2011 11:02 AM To: hofkristall...@gmail.com; CCP4BB@JISCMAIL.AC.UK Subject: RE: [ccp4bb] what to do with disordered side chains The original posting that started this thread referred to side-chains, as the subject still suggests. Do you propose to omit only side-chain atoms, in which case you end up with different residues, as pointed out by quite a few people,or do you suggest also to omit the main-chain atoms of the problematic residues ? Besides, as mentioned by Phoebe and others, many users (non-crystallographers) of PDB's know already the meaning of the B-factor and will know how to interpret a very high B. It is our task (the crystallographers) to enllighten those who don't know what the B column in a PDB entry stands for. I certainly do and I'm sure many of us do so too. I voted for high B and would vote for it again, if asked. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 ________________________________________ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Bernhard Rupp (Hofkristallrat a.D.) [hofkristall...@gmail.com] Sent: Sunday, April 03, 2011 7:42 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] what to do with disordered side chains Thus my feeling is that if one does NOT see the coords in the electron density, they should NOT be included, and let someone else try to model them in, but they should be aware that they are modeling them. Joel L. Sussman Concur. BMC p 680 'How to handle missing parts' Best wishes, BR On 3 Apr 2011, at 06:15, Frances C. Bernstein wrote: Doing something sensible in the major software packages, both for graphics and for other analysis of the structure, could solve the problem for most users. But nobody knows what other software is out there being used by individuals or small groups. And the more remote the authors of that software are from protein structure solution the more likely it is that they have not/will not properly handle atoms with zero occupancy or high B values, for example. I am absolutely positive that there is software that does its voodoo on ATOM/HETATM records and pays absolutely no attention to anything beyond the x, y, z coordinates (i.e. beyond column 54). Frances Bernstein ===================================================== **** Bernstein + Sons * * Information Systems Consultants **** 5 Brewster Lane, Bellport, NY 11713-2803 * * *** **** * Frances C. Bernstein * *** f...@bernstein-plus-sons.com<mailto:f...@bernstein-plus-sons.com> *** * * *** 1-631-286-1339 FAX: 1-631-286-1999 ===================================================== On Sat, 2 Apr 2011, Jacob Keller wrote: I guess I missed it in the flurry of replies to this thread over the last few days, but what exactly is so terrible about keeping the atoms (since you have chemical evidence from protein sequence that they are there, and even if there is X-ray damage they were originally there and are likely still there in a subset of the molecules), but changing occupancy to zero as an acknowledgment that your data does not provide evidence to support a specific atomic position for these atoms? Some users might pull up the structure, see those atoms, and think their positions were based on data, which they were not, and then draw conclusions based on them. I agree that occ=0 is tantamount to the suggestion you queried, however. A somewhat key question might be: across the various molecular visualization programs, what is the default way to handle atoms with occ=0? Perhaps those programs might be the best place to fix the problem... JPK ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: j-kell...@northwestern.edu<mailto:j-kell...@northwestern.edu> *******************************************
