[phenixbb] refining different enantiomers
joel.tyndall at otago.ac.nz
Sun Sep 13 14:13:42 PDT 2015
Just an update on the solution (which was to use the altloc). I needed to use a different residue numbers as well as different names all with an altloc flag
e.g. AABA B 1
BABB B 2
CABC B 3 etc
This way they were all recognised and were all maintained as different molecules with differing stereochemistry
Thanks to all who gave help
From: Phan, Jason [mailto:jason.phan at Vanderbilt.Edu]
Sent: Friday, 11 September 2015 8:05 a.m.
To: Joel Tyndall <joel.tyndall at otago.ac.nz>
Subject: Re: [phenixbb] refining different enantiomers
J, I’d give it the same res num and chain id so the program won’t treat them as different residues. Don’t for get the altloc (AS3L and BS3L in my case).
HETATM 1467 S19AS3L A 204 -5.833 10.423 7.671 0.62 23.15 S
HETATM 1468 N20AS3L A 204 -3.414 9.416 7.552 0.62 24.27 N
HETATM 1469 C21AS3L A 204 -3.040 10.374 10.388 0.62 29.37 C
HETATM 1470 N22AS3L A 204 -2.138 10.275 11.024 0.62 30.28 N
HETATM 1471 N01BS3L A 204 -4.128 11.351 13.823 0.38 32.89 N
HETATM 1472 C02BS3L A 204 -4.731 10.188 13.418 0.38 32.83 C
HETATM 1473 O03BS3L A 204 -4.635 9.141 14.001 0.38 34.60 O
HETATM 1474 O04BS3L A 204 -5.450 10.323 12.316 0.38 28.92 O
On Sep 10, 2015, at 12:02 AM, Joel Tyndall <joel.tyndall at otago.ac.nz<mailto:joel.tyndall at otago.ac.nz>> wrote:
I have a case where we have crystallised a ligand in our protein and the ligand purchased is a mixture of 4 structural isomers (enantiomers and diastereomers). There is no way of telling if one over the other is bound in the active site so we have assumed all 4 are binding. I have generated 4 separate ligands with 4 separate cifs and the all fit the density. I am refining the complex with all 4 ligands at 0.25 occupancy (occupancy refinement is switched off, I have changed the clash guard non-bonded distance threshold is set to 0.0 (as an initial error message came up with nonbonded interactions < 0.5).
My refinement ran to completion, but something is definitely not right. The pdb file won’t load in Coot and in pymol the ligands have imploded/exploded. I am just wondering if this is the best way to refine this structure (or I have missed something) and probably more to the point what have I missed with the ligands. To me it is almost identical to alternate conformations, but I have obviously missed something
I have just install phenix 1.10 on a windows machine.
Joel Tyndall, PhD
Associate Professor in Medicinal Chemistry
National School of Pharmacy
University of Otago
PO Box 56 Dunedin 9054
Ph: +64 3 479 7293
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