[phenixbb] refining different enantiomers

Joel Tyndall joel.tyndall at otago.ac.nz
Sun Sep 13 14:13:42 PDT 2015

Hi all,

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:

Hi all,

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
New Zealand
Skype: jtyndall

Ph: +64 3 479 7293

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