[phenixbb] PHENIX refine: detached sidechain atoms
Oliver King
oliver.king at chem.ox.ac.uk
Thu Jun 24 04:58:12 PDT 2010
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
On 24/06/2010 10:41, Vellieux Frederic wrote:
> Hi,
>
> Can't you go to Coot before refining, and in the Model/Fit/Refine menu
> use either "Real Space Refine Zone" or "Regularize Zone" (I suspect the
> former preferred) on the residues that cause problems, before trying
> Phenix refinement again? I'd try to do that first...
>
> Fred.
>
> Oliver King wrote:
>
>> Hi All,
>>
>> I've noticed that when refining a model in phenix.refine using a PDB
>> file from Refmac, the sidechain atoms of certain residues become
>> detached from the rest of the molecule and appear to float on their
>> own, at least when viewing in Coot. I think this is down to the format
>> of the PDB file. For example the atoms of a Leu residue from a
>> phenix.refine file which displays well is of the form:
>>
>> ATOM 1 N LEU A 8 50.022 -34.247 -5.817 1.00
>> 58.12 N
>> ATOM 2 CA LEU A 8 49.788 -34.905 -4.539 1.00
>> 55.84 C
>> ATOM 3 C LEU A 8 48.339 -35.358 -4.348 1.00
>> 60.39 C
>> ATOM 4 O LEU A 8 48.008 -36.016 -3.360 1.00
>> 68.40 O
>> ATOM 5 CB LEU A 8 50.219 -34.011 -3.373 1.00
>> 57.98 C
>> ATOM 6 CG LEU A 8 51.690 -34.126 -2.975 1.00
>> 65.66 C
>> ATOM 7 CD1 LEU A 8 52.014 -33.170 -1.836 1.00
>> 59.99 C
>> ATOM 8 CD2 LEU A 8 52.020 -35.566 -2.594 1.00
>> 68.57 C
>>
>> where as from a Refmac PDB which also behaves well, it is of the form:
>>
>> ATOM 1 N LEU A 8 50.453 -35.722 -5.617 1.00
>> 20.00 N
>> ATOM 2 CA LEU A 8 49.649 -35.131 -4.482 1.00
>> 20.00 C
>> ATOM 3 CB LEU A 8 50.190 -33.735 -4.147 1.00
>> 20.00 C
>> ATOM 4 CG LEU A 8 51.461 -33.755 -3.275 1.00
>> 20.00 C
>> ATOM 5 CD1 LEU A 8 52.556 -32.768 -3.741 1.00
>> 20.00 C
>> ATOM 6 CD2 LEU A 8 51.082 -33.546 -1.799 1.00
>> 20.00 C
>> ATOM 7 C LEU A 8 48.166 -35.063 -4.824 1.00
>> 20.00 C
>> ATOM 8 O LEU A 8 47.822 -34.257 -5.568 1.00
>> 20.00 O
>>
>> but after refinement in phenix it becomes
>>
>> ATOM 1 N LEU A 8 50.734 -35.936 -5.935 1.00
>> 54.45 N
>> ATOM 2 CA LEU A 8 49.846 -35.185 -4.892 1.00
>> 51.89 C
>> ATOM 3 CB LEU A 8 50.377 -33.761 -4.516 1.00
>> 51.22 C
>> ATOM 4 CG LEU A 8 51.550 -33.730 -3.431 1.00
>> 59.27 C
>> ATOM 5 CD1 LEU A 8 52.457 -32.407 -3.635 1.00
>> 60.88 C
>> ATOM 6 CD2 LEU A 8 51.120 -34.090 -1.879 1.00
>> 55.50 C
>> ATOM 7 C LEU A 8 48.268 -35.042 -5.221 1.00
>> 47.92 C
>> ATOM 8 O LEU A 8 47.989 -34.282 -6.195 1.00
>> 47.32 O
>>
>> and the CD2 atom is now too far away to be part of the residue in Coot
>>
>> Is there an easy way to convert a PDB from Refmac into one which will
>> behave itself when put through phenix.refine? I've tried using
>> phenix.pdb_tools and also putting the model through Molprobity and
>> hoping that that the output would be corrected.
>>
>> Thanks,
>>
>> Olly King
>>
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>>
>>
>
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