[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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