Re: [ccp4bb] CNS to PDB format conversion

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

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From: Kevin Cowtan cowtan {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-09-02

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Subject: Re: CNS to PDB format conversion
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-09-02

That could be due to anything - a really useless message..
You arent trying to rerun an older refmac script are you - the rerun job
button was broken at some point.

If you "reset defalt parameters" and then set up the job again it might
work..
Eleanor

Manoj Saxena wrote:
> Hi
>
> Thanks for your quick response.
> a) I have used CNS script cns_to_o.inp and then used the CCP4 COORDCONV utility with
> convert file in PDB to PDB option and input the unit cell information.
> (have tried Xplor to PDB option earlier, it failed with input error).
> b) Then I run refmac with the input PDB file(from COORDCONV) and mtz file.
>
> and got the following error message.
>
> ***************************************************************************
> * Information from CCP4Interface script
> ***************************************************************************
> The program run with command: /usr/local/ccp4-6.1.1/bin/refmac5 XYZIN
> "/Network/Servers/genuinerisk.bmb.psu.edu/Users/manoj/Documents/crystallography/dRc
> c1t2/CCP4/cns_opdb.pdb" XYZOUT "/tmp/manoj/Project1_131_2_pdb_1.tmp" HKLIN
> "/Network/Servers/genuinerisk.bmb.psu.edu/Users/manoj/Documents/crystallography/dRc
> c1t2/dRcc1t2_ct488a1/rdmct488a1_p212121_b.mtz" HKLOUT
> "/tmp/manoj/Project1_131_3_mtz_1.tmp" LIBOUT
> "/Network/Servers/genuinerisk.bmb.psu.edu/Users/manoj/Documents/crystallography/dRc
> c1t2/CCP4/Project1_131_lib.cif"
> has failed with error message
> Refmac_5.5.0072: Fatal error. Cannot continue
> ***************************************************************************
>
>
> #CCP4I TERMINATION STATUS 0 Refmac_5.5.0072: Fatal error. Cannot continue
> #CCP4I TERMINATION TIME 01 Sep 2009 11:17:49
> #CCP4I MESSAGE Task failed
>
>
> My guess is that the file conversion to PDB have not worked. I will appreciate any help to
> understand what going on and how do I resolve this .
> Thanks
>
> Penn State university
> Biochemistry
> State College
> PA
> Manoj
>
>
> On Tue, 01 Sep 2009 20:29:44 +0530 wrote
>
> The CNS script cns_to_o.inp will convert CNS .mtf
> files to .pdb files. You can edit the CNS form using the CNS web
> interface and then run the script from the command line. Alternatively,
> I think the CCP4 program COORDCONV will convert XPLOR/CNS files to PDB
> format (I haven't done this, however.)
>
> Manoj Saxena wrote:
> Hi all,
>
> How to convert CNS coordinate file to PDB file format that can be used
> for refinement in
> refmac. Is there any utility in CCP4 or other GUI based interface that
> can convert CNS output
> file to PDB .
>
> Thanks .
>
> Manoj
>
> Penn Sate University
> Biochemistry
> State College
> PA
>
>
>
>
>
>
>
>
>
>

CCP4bb navigation

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

Previous message:
Subject: Re: MAMA-mask
From: Kevin Cowtan cowtan {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-09-02

Next message:
Subject: Re: Weird expression behavior
From: Ezra Peisach epeisach {- at -} GMAIL {- dot -} COM
Date: 2009-09-02