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Re: [ccp4bb] model corrections in coot |
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CCP4bb navigationCCP4bb <-- 2008 <-- May 2008 <-- 03 May 2008Subject: Re: model corrections in coot From: Paul Emsley paul {- dot -} emsley {- at -} BIOCH {- dot -} OX {- dot -} AC {- dot -} UK 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. "Stereochemisty" meaning... what, in this case? Perhaps you mean the Ramachandran plot? The traffic lights in newer versions are there to address this sort of issue. > 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! [snip] Presumably you have a ligand that does not have a full description in the refmac library. Whatever cif library you use to refine your ligand in Refmac should be imported into Coot, and this problem will go away. > Should I use planar peptide restraints as well to sort this problem? Planar peptide restraints are unrelated to finding restraints for a ligand. However, there is a good chance that they will reduce the damage to a Ramachandran plot. That being said, all Coots less than 0.5 do a poor job at maintaining good Ramachandran geometry. > I have tried Wincoot 0.3.3 and Coot for linux 0.1.1. Those are old Coots - particularly the "linux" version. Consider updating to 0.4.1 or (if adventurous) 0.5-pre. Paul. CCP4bb navigationCCP4bb <-- 2008 <-- May 2008 <-- 03 May 2008 |
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