To the delete-the-atom-nik's: do you propose deleting the whole residue or just the side chain? I can understand deleting the whole residue, but deleting only the side chain seems to me to be placing a stumbling block also, and even possibly confusing for an experienced crystallographer: the .pdb says "lys" but it looks like an ala? Which is it? I could imagine a lot of frustration-hours arising from this practice, with people cross-checking sequences, looking in the methods sections for mutations...
JPK On Sun, Apr 3, 2011 at 11:42 AM, Bernhard Rupp (Hofkristallrat a.D.) <[email protected]> wrote: > 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 > * *** [email protected] > *** * > * *** 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: [email protected] > > ******************************************* > > > > -- ******************************************* Jacob Pearson Keller Northwestern University Medical Scientist Training Program cel: 773.608.9185 email: [email protected] *******************************************
