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If these users exist (I don't doubt that they do), then they would also might think that lysine residues sometimes look identical to alanine - if the atoms after beta carbon of the lysine are deleted in the PDB due to lack of density. So, I guess, if one's objectives in solving structures are to provide these users with coordinates that they could us, then it would make more sense to me to find out what one's "customers" want, rather than speculating about it. Or at least, train one's "customers" how to use one's products - I believe that's what people in business do. However, I think that many people solve structures for their own consumption - they are their own customers - therefore, it's really up to them to cook it anyway they find most tasteful. Others can agree or disagree, but we know that not everybody has the same taste. Cheers, Quyen On Apr 3, 2011, at 12:54 AM, Prof. Joel L. Sussman wrote: > I think Frances is right, i.e. most non crystallographers ignore > "anything beyond the x, y, z coordinates (i.e. beyond column 54)" > [as Frances wrote]. > Thus if a crystallographer put in coords that he/she does NOT see, > even with OCC=0, or an enormously large Bfactor, these coords are usually > treated in just the same way that experimentally observed coords are treated. > 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 > > > > 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 >> * *** [log in to unmask] >> *** * >> * *** 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: [log in to unmask] >>> ******************************************* >>> >