PHENIX refine: detached sidechain atoms
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
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
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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
Hi Olly,
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. ... but after refinement in phenix it becomes
All the bonds are systematically too long. I'm having trouble understanding how this can happen. Could you send me (not the list!) the input pdb file and the phenix.refine log file? Ralf
The CG-CD2 bond is too long after phenix refinement and coot treats it as broken. Unless you have ultrahigh resolution, covalent bonds must be restrained, and expected value for GG-CD2 is 1.521A. It's 1.53A and 1.54A in your "good" examples, so coot shows the covalent bond. Then something happens during refinement and phenix.refine fails to maintain the correct bond length, it goes up to 1.65A, which is ~4 times more than standard deviation expected for this bond in monomer libraries. Accordingly, coot shows this as a broken bond. You may want to tighten up the restraints - make sure that your RMSDbonds stays below 0.02A. No PDB conversion program will fix it as there are no format errors. Cheers, Ed. On Thu, 2010-06-24 at 11:42 +0100, 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
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
-- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs
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
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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. 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
_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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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participants (6)
-
Ed Pozharski -
Oliver King -
Pavel Afonine -
Ralf W. Grosse-Kunstleve -
Schubert, Carsten [PRDUS] -
Vellieux Frederic