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.
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> 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.
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