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[ccp4bb] model corrections in coot
 

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CCP4bb <-- 2008 <-- May 2008 <-- 03 May 2008
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Subject: Re: problem with coot/cns
From: Sabuj Pattanayek sabuj {- dot -} pattanayek {- at -} VANDERBILT {- dot -} EDU
Date: 2008-05-02 		Next message:
Subject: Raw Image Workshop BNL 22 May 08
From: "Herbert J {- dot -} Bernstein" yaya {- at -} BERNSTEIN-PLUS-SONS {- dot -} COM
Date: 2008-05-03


Subject: model corrections in coot
From: Usha Nair miahu73 {- at -} YAHOO {- dot -} COM
Date: 2008-05-03
Dear all,

I have been trying to manually build a loop into low resolution maps (data between 18 and 2.85A) in coot. However, I find that coot messes up the stereochemistry of my model. This despite the fact that the program appears to be reading the refmac library for standard amino acids just fine. The only untoward message I get is when I try to do geometry analysis (under the validate menu). While I get the required plot, I get a message saying no restraints were found. The whole message is given below.

No restraints found!
Non-existent or minimal description of restrained residues.
Are you sure that you read a non-minimal mmCIF dictionary for this monomer? Are you sure the PDB residue name matches the dictionary residue name?
If not, try File--> Import CIF Dictionary.
Alternatively, did you check that the atom names of the PDB file match those of the restraints?

Should I use planar peptide restraints as well to sort this problem? I have tried Wincoot 0.3.3 and Coot for linux 0.1.1.

Thanks in advance,
Mia


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CCP4bb navigation

CCP4bb <-- 2008 <-- May 2008 <-- 03 May 2008
Previous message:
Subject: Re: problem with coot/cns
From: Sabuj Pattanayek sabuj {- dot -} pattanayek {- at -} VANDERBILT {- dot -} EDU
Date: 2008-05-02 		Next message:
Subject: Raw Image Workshop BNL 22 May 08
From: "Herbert J {- dot -} Bernstein" yaya {- at -} BERNSTEIN-PLUS-SONS {- dot -} COM
Date: 2008-05-03


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