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Hi Paul, How can I add Hs (hydrogens) stereochemically to protein or peptide using COOT without altering the coordinates of non-hydrogen atoms. Thanks. Sam. ---------------------------------------- > Date: Thu, 19 Jun 2008 15:57:46 +0100 > From: [log in to unmask] > Subject: Re: [ccp4bb] Coot and Hs > To: [log in to unmask] > > Dear Roberto, > > Roberto Steiner wrote: >> Dear all, >> >> a problem possibly at the coot/mmdb interface... > > Indeed. > >> If one uploads a pdb file (from phenix.refine in the example below) >> that contains Hs into Coot and then writes it out (with or without any >> modification done on it) Coot shifts the HG2n of THR on the right by >> one column space. Because column 17 is kept empty the result is three >> identical HG2 THR protons. > > Technical answer: > > The current PDB parser in Coot is from mmdb and is for PDB format > version 2.3. Phenix.refine and other modern programs use PDB format > version 3.0 [1] - released over a year ago. PDB version 3.0 > "Remediated" does not wrap the hydrogen (or other) names and so the > hydrogen name "unmangler" - which is what is tripping you up - need not > be executed. I'd like to make Coot compatible with the current PDB > standard. If CCP4 were to release a version of mmdb compatible with > Coot, I could do that right away [2]. I'm hoping that they will do so > today^H^H^H^H^H soon. > >> The only solution right now (that I know of) is to remove all Hs and >> generate them again (molprobity for example) prior to refinement. > > Bleugh. Non-optimal (no matter how fine Molprobity is). > > Paul. > > [1] or version 3.1? > [2] I imagine. _________________________________________________________________ Introducing Live Search cashback . It's search that pays you back! http://search.live.com/cashback/?&pkw=form=MIJAAF/publ=HMTGL/crea=introsrchcashback