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: [log in to unmask]
> From: Eleanor Dodson <[log in to unmask]>
> Date: 2007年 12月 17日 19:02:28:JST
> To: [log in to unmask]
> Subject: Re: [ccp4bb] Occupancy refinement of substrate using refmac5
> Reply-To: [log in to unmask]
>
> 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: [log in to unmask]
>> 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: [log in to unmask]
fax: +81-6-6605-2557
tel: +81-6-6605-3131
Osaka City University
3-3-138, Sugimoto, Sumiyoshi, Osaka
Osaka 558-8585, Japan
*********
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