Dear Profs. Eleanor and Isaac,
Thank you for your quick and kind replies.
I have already changed occupancies as Eleanor mentioned, and got
approximate values. But my hope is to try to get much precise ones if
possible.
I have heard from my colleague SHELX can refine occupancies, and
got its license. I'll next try SHELX.
Thank you very much again.
Best wishes,
Nobuo Kamiya
Begin forwarded message:
Hi there,
I'm not 100% sure, but I don't think REFMAC can do occupancy refinement.
I've had success with phenix.refine, however, and can recommend this for
what you mentioned.
Isaac
----------
Dr Isaac Westwood
Department of Pharmacology
University of Oxford
Mansfield Road
Oxford
OX1 3QT
tel: 01865 271595
email: [EMAIL PROTECTED]
From: Eleanor Dodson <[EMAIL PROTECTED]>
Date: 2007年 12月 17日 19:02:28:JST
To: [email protected]
Subject: Re: [ccp4bb] Occupancy refinement of substrate using refmac5
Reply-To: [EMAIL PROTECTED]
I dont think REFMAC can refine occupancy, but the way I would
tackle it is to first refine B factors, then if those for the
ligand are much higher than for the protein maybe test changing
those occupancies to 0.7 , 0,5 and so on..
But in fact B factors and occupancies are highly correlated, and
you would probably expect a ligand soaking in after crystallisation
to have higher B factors, so it is very difficult to get a
definitive answer.
Eleanor
nkamiya wrote:
Dear all,
This is my first mail to CCP4BB.
I'm now refining crystal structures of an enzyme at a resolution of
1.5A using refmac5 through CCP4i. Before X-ray data collections,
the substrate and co-factor ions were soaked into the crystals. Their
occupancies seem to be less than the unity because negative peaks
can be found around the substrate and co-factors in the difference
Fourier maps.
I found "Developers Options" in the CCP4i window of refmac5 to
specify an external keyword script file. If refmac5 can refine
occupancies of substrate and co-facotrs independently, by using the
script file, under the condition of fixed temperature factors, please
let me know examples of the script files and how to use them.
Best wishes,
Nobuo Kamiya
*********
Prof. Nobuo Kamiya
email: [EMAIL PROTECTED]
fax: +81-6-6605-2557
tel: +81-6-6605-3131
Osaka City University
3-3-138, Sugimoto, Sumiyoshi, Osaka
Osaka 558-8585, Japan
*********
*********
Prof. Nobuo Kamiya
email: [EMAIL PROTECTED]
fax: +81-6-6605-2557
tel: +81-6-6605-3131
Osaka City University
3-3-138, Sugimoto, Sumiyoshi, Osaka
Osaka 558-8585, Japan
*********
