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.
Xiangpeng Kong Lab
NYU Langone Medical Center
New York, NY 10016
This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
More information about the phenixbb