Hi Oliver, this is not expected to happen, and you don't need to do anything with your PDB file to run it with phenix.refine. Can you send me the inputs for your refinement run (model, data and the command including parameter file(s) is any) so I can reproduce this behavior myself and explain what happens? At this point I have too little information about your refinement run, version of PHENIX and so on to say something. All files will be used confidentially and for addressing this issue only. Pavel. On 6/24/10 3:42 AM, 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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