Re: [ccp4bb] CNS to PDB format conversion

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

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From: Kris Tesh Kris {- dot -} Tesh {- at -} RIGAKU {- dot -} COM
Date: 2009-09-01

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Subject: Re: CNS to PDB format conversion
From: Manoj Saxena mks131 {- at -} REDIFFMAIL {- dot -} COM
Date: 2009-09-01

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

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CCP4bb navigation

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

Previous message:
Subject: Re: cracking crystal
From: Kris Tesh Kris {- dot -} Tesh {- at -} RIGAKU {- dot -} COM
Date: 2009-09-01

Next message:
Subject: Fructose 2,6 Bisphosphate
From: hugh morgan morgan_hugh {- at -} YAHOO {- dot -} CO {- dot -} UK
Date: 2009-09-01