Re: [ccp4bb] SC program in CCP4 - No radius found for residue G atom P

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Subject: Re: SC program in CCP4 - No radius found for residue G atom P
From: "Stein, ND (Norman)" n {- dot -} d {- dot -} stein {- at -} DL {- dot -} AC {- dot -} UK
Date: 2008-02-27

Hi Rosemary

SC has stopped because P is not in its list of atomic radii. This list
is located at

$CCP4/lib/data/sc_radii.lib

You will need to edit this file to add a value for P ( and possibly some
of the other atoms in your RNA fragment). The format is fairly
self-explanatory, with asterisks being used for wildcards. Alternatively
you can use your own dictionary of atomic radii, and specify its
location using the SCRADII command

e.g. SC XYZIN xxxx.pdb SCRADII mydictionary.lib

Norman Stein
CCP4
Daresbury Laboratory

________________________________

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Rosemary Harrison
Sent: 27 February 2008 06:11
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] SC program in CCP4 - No radius found for residue G
atom P

Hi,

I have been trying to run SC on a pdb file with an RNA fragment.
I get the answer below. There appears to be a problem with the P in the
RNA backbone.

Has anyone else had this problem and/or suggestions to fix it

Thanks in advance,
Rose Harrison

Parameter values
----------------
Dot density : 15.00 per square Angstrom
Interface separation : 8.00 Angstroms
Trim width : 1.50 Angstroms
Probe radius : 1.70 Angstroms
Weight factor : 0.50 per square Angstrom
No radius found for
Residue G Atom P

SC: S/r assign_r: no radius for residue/atom
SC: S/r assign_r: no radius for residue/atom

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CCP4bb <-- 2008 <-- February 2008 <-- 27 February 2008

Previous message:
Subject: Structural Biologist - permanent position in Central London
From: Andrew Turnbull aturnbull {- at -} CANCERTECHNOLOGY {- dot -} COM
Date: 2008-02-27 Next message:
Subject: torsion restraints COOT
From: Brenda Patterson ucbccka {- at -} UCL {- dot -} AC {- dot -} UK
Date: 2008-02-27