Re: [ccp4bb] generating a cif file using refmac

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: Processing data as P1.
From: Phil Evans pre {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2009-06-26

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From: "Dr {- dot -} F Long" fei {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-06-28

Subject: Re: generating a cif file using refmac
From: Matthew Chu linghonmatthew {- at -} GMAIL {- dot -} COM
Date: 2009-06-27

Hi Madhavi,

try the prodrg server:

http://davapc1.bioch.dundee.ac.uk/prodrg/index.html

2009/6/26 Nalam, Madhavi

> Hello:
> I am using CCP4 version 6.1.1 now.
>
> I refine protein-small molecule complexes (the small molecules are new
> and hence I have to input the cif file).
> In the previous versions of CCP4, refmac used to fail and generate a cif
> file in the first run when I introduce the inhibitor into the pdb file.
> Now, in the new version, refmac doesn't run at all and asks me to input
> the cif file.
>
> I tried Sketcher but the problem is Sketcher is opening a proline
> molecule although I am trying to open my inhibitor molecule as a pdb
> file (again this problem is not there before)
>
> In my experience the cif files generated by refmac and sketcher are
> slightly different, at least for the molecules I am working with, and
> the ones generated by refmac are correct.
>
> Although there are other programs that generate cif files, I would like
> to generate them using refmac if possible.
>
> Any help would be greatly appreciated.
> Thanks,
> Madhavi
>

--
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Matthew LH Chu PhD
School of Pharmacy and Pharmaceutical Sciences
University of Manchester
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CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: Processing data as P1.
From: Phil Evans pre {- at -} MRC-LMB {- dot -} CAM {- dot -} AC {- dot -} UK
Date: 2009-06-26

Next message:
Subject: BALBES jobs in queue
From: "Dr {- dot -} F Long" fei {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-06-28