[phenixbb] rotamers

Sampson, Jared Jared.Sampson at nyumc.org
Thu Mar 24 09:53:25 PDT 2011

On Mar 24, 2011, at 5:27 AM, Pavel Afonine wrote:

I agree, making occupancy zero is kind of abusing it in order to say "I
do not see this atom". But so far I have no feeling about what is more
- set occupancy to zero in order to say "I don't see it in the map", or
- call TYR (or whatever else) something that is according to the atom
content is NOT TYR but is ALA.

What about some kind of atom-type card (along the lines of "ANISOU") that specifies the disordered nature of the atom in question?  So if everything past CB is disordered in a lysine, you would get something like:

ATOM    592  N   LYS A  84     -17.487   3.994  61.377  1.00 32.95           N
ATOM    593  CA  LYS A  84     -17.022   4.714  60.192  1.00 32.98           C
ATOM    594  CB  LYS A  84     -17.046   6.221  60.446  1.00 32.90           C
ATOM    595  CG  LYS A  84     -18.435   6.824  60.503  1.00 32.69           C
DISATM  595  CG  LYS A  84
ATOM    596  CD  LYS A  84     -18.405   8.207  61.132  1.00 37.38           C
DISATM  596  CD  LYS A  84
ATOM    597  CE  LYS A  84     -17.881   9.259  60.164  1.00 41.33           C
DISATM  597  CE  LYS A  84
ATOM    598  NZ  LYS A  84     -17.856  10.600  60.803  1.00 42.35           N
DISATM  598  NZ  LYS A  84
ATOM    599  C   LYS A  84     -15.620   4.293  59.759  1.00 32.36           C
ATOM    600  O   LYS A  84     -15.359   4.124  58.568  1.00 35.18           O

The "most probable" conformation could be included in the coordinates as is often the case now, but at the authors' discretion, certain atoms could be flagged as disordered.  These atoms could then be handled in a way similar to those with occ=0 now (or whatever developers decide).  Then we wouldn't be abusing the occupancy (an objection that seems to be fairly common) but there would be clear indication in the PDB file of the disorder. Of course, where to draw the line between ordered and disordered is highly subjective, but that's the case now, anyway.  Also, this solution would perhaps not be as effective with missing residues as with missing side chains.

How to display this kind of difference in visualization programs would be an issue as well, but I could imagine (for example) a PyMOL command to do something like

hide sticks, disordered

being relatively straightforward to implement. And in Coot, perhaps a toolbar button like the exisiting "Delete" that would be instead "Flag atom as disordered" and a different color or transparency used to indicate the disordered atoms.

I realize altering the PDB format may not be the favored approach to this issue, and I'm not very well versed in the intricacies of crystallographic software design, but this all just occurred to me so I'm throwing it out there.


Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
New York, NY 10016

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