[phenixbb] PHENIX refine: detached sidechain atoms

Vellieux Frederic Frederic.Vellieux at ibs.fr
Thu Jun 24 04:01:47 PDT 2010


There is a CCP4 program that deals with PDB files, I can't remember the 
name though (there are so many programs within CCP4...). It will 
"standardize" your PDB file. The program might be called pdbcur or 
pdbset , I am not certain...

So I would either try pdbcur and pdbset, or send an email to ccp4bb to 
inquire there.

Fred.

Oliver King wrote:
> Hi Fred,
>
> Thanks for the helpful suggestion, however it isn't just Leu residues 
> it's Val, Ile, Ala, Pro and others that suffer this problem. I just 
> tried to regularise the Leu and then refine again in Phenix and now 
> both the CD1 and CD2 atoms have detached!
> ATOM      1  N   LEU A   8      50.623 -35.571  -6.058  1.00 
> 52.51           N
> ATOM      2  CA  LEU A   8      49.795 -35.076  -4.891  1.00 
> 52.71           C
> ATOM      3  CB  LEU A   8      50.211 -33.647  -4.508  1.00 
> 49.42           C
> ATOM      4  CG  LEU A   8      51.469 -33.402  -3.616  1.00 
> 57.61           C
> ATOM      5  CD1 LEU A   8      51.910 -31.789  -3.631  1.00 
> 55.67           C
> ATOM      6  CD2 LEU A   8      51.323 -34.077  -2.105  1.00 
> 53.78           C
> ATOM      7  C   LEU A   8      48.247 -35.000  -5.245  1.00 
> 48.34           C
> ATOM      8  O   LEU A   8      47.949 -34.270  -6.261  1.00 
> 47.33           O
>
> Initially I thought that my monomer library was corrupt, however the 
> same happens both after reinstalling Phenix and when refining on a 
> different installation on another computer. I was just hoping to find 
> a way to standardise the PDB file format between the two programs but 
> realise that this may open a whole can of worms!
>
> Thanks,
>
> Olly




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