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I agree, refmac does not sort it out. Making a macroligand will help but
this is not at all an ideal situation as you will still observe
repulsion despite the fact that the sum of occupancies = 1.0.
In HIV proteinase you will often find that the inhibitor binds in two
directions. Years ago I tried 3 different programs - Xplor, Refmac and
SHELXH - and found that SHELXH clearly did the best job without any
patching. You can even easily appoint certain water molecules belonging
to just one orientation.
- Jeroen -
[EMAIL PROTECTED] wrote:
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I am not 100% sure that REFMAC is sorting that out correctly, though.
I had a case recently where I tried to refine two very similar ligands binding to the same binding site. I tried the way Eleanor suggested and I also tried defining them as Alig and Blig. REFMAC doesn't complain and refines the two ligands, but in the part where the two ligands are identical they don't superimpose exactly anymore. If I refine them separately and superimpose them afterwards they are superimposing exactly in the parts that are identical!
To me it looks as if the two ligands in the same site still repel each other
but that they are kept together by the x-ray term. Is there a well documented
example, where somebody successfully managed to refine two ligands in the same
binding site and how (s)he defined the two ligands and created the dictionaries
exactly?
If I try the same refinement in CNX with some patching, the two ligands
superimpose exactly in the identical parts.
Regards
Christian
Dr. Christian Engel
Research Scientist
Structural Biology
Sanofi-Aventis
Tel.: +49 (0)69 305 12946
Fax: +49 (0)69 305 80169
Sanofi-Aventis
Industriepark Höchst
Building G865A
65926 Frankfurt am Main
Germany
-----Ursprüngliche Nachricht-----
Von: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] Auftrag von
Eleanor Dodson
Gesendet: Donnerstag, 1. Juni 2006 10:50
An: Elena Kovaleva
Cc: [email protected]
Betreff: Re: [ccp4bb]: multiple occupancy/different ligands
Just put them both in, each with partial occupancy, and 2 dictionary
entries. REFMAC should sort it out..
Eleanor
Elena Kovaleva wrote:
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Hi,
I wonder if there is someone out there who knows a way to trick Refmac
into doing simultaneous refinement of somewhat superimposable but
structurally different ligands (both of which partially occupy the
same site). For example if a substrate and an intermediate are present
or an intermediate and a product. Would making a library file for a
"macro"-ligand consisting of 2 separate parts (separate connectivity,
partial occupancy, etc) be a reasonable approach or is there an
easier/proper way to refine partially present ligands?
Will be grateful for any suggestions.
Thanks,
Lena
Elena G. Kovaleva, Ph.D.
Department of Biochemistry, University of Minnesota
5-202 BS&BE, 312 Church St, Minneapolis, MN 55455
Ph (612) 625-3688, Fax (612) 625-2163
