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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