Hi - I have a problem regarding occupancies of hydrogens in residues with alternate conformations. Specifically, when a residue exists in alternate conformations, the H hydrogen of the following residue (the one attached to the N) also exists in the same number of alternate locations. The occupancies of these hydrogens do not add up to 1.00 like the occupancies of the hydrogens for the preceding residue do. In fact, these occupancies are all 1.00. Is that a bug, a feature, or did I commit a user error somehow? Example: ... ATOM 956 H AHIS A 293 6.967 -36.722 8.227 1.00 15.31 H ATOM 957 H BHIS A 293 6.913 -36.667 8.216 1.00 15.31 H ATOM 958 H CHIS A 293 6.888 -36.648 8.202 1.00 15.31 H ... The preceding Ser A 292 exists in three alternate conformations with occupancies A=0.53, B=0.18, C=0.29; sum = 1.00 The corresponding hydrogens have occupancies A=0.52, B=0.19, C=0.29; sum = 1.00 (I can accept that they have somewhat different occupancies than the attached heavy atoms, based on a previous thread about this issue, although the discrepancies are now much smaller in the 1.3- final version compared to 1.3-rc2) The H hydrogens of the following residue (His A 293) have occupancies A=1.00, B=1.00, C=1.00; sum = 3.00, and the RCSB starts yelling. Should I just manually edit the values and set them to the occupancies of the hydrogens in the preceding residue? Any help appreciated. Thanks so much. Best - MM -------------------------------------------------------------------------------- Mischa Machius, PhD Associate Professor Department of Biochemistry UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd.; ND10.214A Dallas, TX 75390-8816; U.S.A. Tel: +1 214 645 6381 Fax: +1 214 645 6353
Hi Mischa, I just made up an example with fake data and model: http://cci.lbl.gov/~afonine/for_mischa/ and it seems to work fine using my current development source code. So, even if it doesn't work with the most recent version (8-11-2008) (although I didn't try, may be it works), it will definitely work in the next version. Cheers, Pavel. On 10/17/2008 7:55 AM, Mischa Machius wrote:
Hi - I have a problem regarding occupancies of hydrogens in residues with alternate conformations. Specifically, when a residue exists in alternate conformations, the H hydrogen of the following residue (the one attached to the N) also exists in the same number of alternate locations. The occupancies of these hydrogens do not add up to 1.00 like the occupancies of the hydrogens for the preceding residue do. In fact, these occupancies are all 1.00.
Is that a bug, a feature, or did I commit a user error somehow?
Example: ... ATOM 956 H AHIS A 293 6.967 -36.722 8.227 1.00 15.31 H ATOM 957 H BHIS A 293 6.913 -36.667 8.216 1.00 15.31 H ATOM 958 H CHIS A 293 6.888 -36.648 8.202 1.00 15.31 H ...
The preceding Ser A 292 exists in three alternate conformations with occupancies A=0.53, B=0.18, C=0.29; sum = 1.00 The corresponding hydrogens have occupancies A=0.52, B=0.19, C=0.29; sum = 1.00 (I can accept that they have somewhat different occupancies than the attached heavy atoms, based on a previous thread about this issue, although the discrepancies are now much smaller in the 1.3- final version compared to 1.3-rc2) The H hydrogens of the following residue (His A 293) have occupancies A=1.00, B=1.00, C=1.00; sum = 3.00, and the RCSB starts yelling.
Should I just manually edit the values and set them to the occupancies of the hydrogens in the preceding residue?
Any help appreciated. Thanks so much. Best - MM
-------------------------------------------------------------------------------- Mischa Machius, PhD Associate Professor Department of Biochemistry UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd.; ND10.214A Dallas, TX 75390-8816; U.S.A. Tel: +1 214 645 6381 Fax: +1 214 645 6353
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participants (2)
-
Mischa Machius -
Pavel Afonine