Good to know, that is a nasty side-effect of a complex procedure. We had a similar case here, which was if I remember correctly was also phenix version dependent, and we could not make sense of it. The ligand in our case was actually generated in elbow, so that would not shield one from problems. It always helps to give the cif files a second look.
-----Original Message----- From: [email protected] [mailto:phenixbb- [email protected]] On Behalf Of Pavel Afonine Sent: Friday, June 25, 2010 1:22 AM To: [email protected]; PHENIX user mailing list Subject: Re: [phenixbb] PHENIX refine: detached sidechain atoms - SOLUTION
Hi Oliver,
thanks for sending the inputs so we could reproduce this issue and figure out what is wrong.
The problem maker is the CIF file for your ligand that specifies unrealistic (too small) esds for some torsional angles that in turn creates huge terms in geometry restraints target that finally resulted in a huge X-ray weight. Using huge X-ray weight obviously means that you are doing nearly unrestrained refinement and therefore no surprises that the geometry was systematically distorted. This is something we will be catching automatically in future, but meanwhile it is a good idea to use correct ligand CIF files.
The solution: create a CIF file using either phenix.elbow or, better, using phenix.ready_set commands. For example,
phenix.ready_set model.pdb
will create a CIF file for all ligands in your model.pdb file. Using this file in refinement eliminates the problem that you have reported this morning. Also, this command adds H atoms to model.pdb file, that you can then use in subsequent refinements.
I went ahead some more and did some refinement using the strategy that I think is the best for your case.
Your starting R-factors (corresponding to the model you sent me): r_work = 0.1853 r_free = 0.2523 bonds = 0.069 angles = 4.460
And after some refinement that I've done: r_work = 0.1779 r_free = 0.2202 bonds = 0.015 angles = 1.600
In refinement I used: - automatic water update; - TLS; - riding hydrogen atoms.
You can further improve your model by: - running automatic rotamer fixing (fix_rotamers=true); - weights optimization (optimize_wxc=true optimize_wxu=true); - more thoughtful selection of TLS groups.
I'm sending to you all the files OFFLIST (in the next email).
Please let me know if you have any questions.
Pavel.
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
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
On 6/24/10 3:42 AM, Oliver King wrote: format 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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