Hi, I am refining a low resolution data. According to sigma vs. resolution, my resolution is 4.7A. Because there are four identical molecular per asymetric unit, I can use positional refinement. There are about 65% alpha-helices in the structure, so I want to use secondary structure restrain. Does phenix has this restrain in the refinement? I am using Phenix-1.4 version.
Hello,
I am refining a low resolution data. According to sigma vs. resolution, my resolution is 4.7A.
not sure what is "sigma vs. resolution" but hope you made the right decision.
Because there are four identical molecular per asymetric unit, I can use positional refinement. There are about 65% alpha-helices in the structure, so I want to use secondary structure restrain. Does phenix has this restrain in the refinement?
Sorry for missing documentation on this subject. First of all, get the latest version of PHENIX (the one you have is very old): http://www.phenix-online.org/download/nightly_builds.cgi Then (once you have the latest), yes, you can use secondary structure restraints. phenix.refine model.pdb data.hkl main.secondary_structure_restraints=true so phenix.refine automatically determines secondary structure and applies the restrains. Note, GIGO principle applies, that is if your input model is distorted then it's unlikely that the procedure will figure out the secondary structure correctly. To make it a less black-box, you can run phenix.secondary_structure_restraints model.pdb > ss_restraints.params and then check (and edit if necessary) the ss_restraints.params file, and then run phenix.refine as following: phenix.refine model.pdb data.hkl main.secondary_structure_restraints=true ss_restraints.params I hope Nat comments more if I missed something. Let me know if you have any other questions. Good luck! Pavel.
On Sun, Oct 10, 2010 at 4:48 PM, Pavel Afonine
Sorry for missing documentation on this subject.
First of all, get the latest version of PHENIX (the one you have is very old):
http://www.phenix-online.org/download/nightly_builds.cgi
Then (once you have the latest), yes, you can use secondary structure restraints.
There is documentation on this in the last few builds: http://www.phenix-online.org/version_docs/dev-551/refinement.htm#anch26 -Nat
Hi, I have the similar problem when I am working on refining my low resolution model (3.5 Ang). One component of my protein complex represents a beta-sandwish structure, and the conecting loops between beta-strands are disordered. After refinement, the beta-sheets were disrupted. What do you suggest about this problem. PC Date: Sun, 10 Oct 2010 16:48:57 -0700 From: [email protected] To: [email protected]; [email protected] Subject: Re: [phenixbb] about low resolution refinement Hello, I am refining a low resolution data. According to sigma vs. resolution, my resolution is 4.7A. not sure what is "sigma vs. resolution" but hope you made the right decision. Because there are four identical molecular per asymetric unit, I can use positional refinement. There are about 65% alpha-helices in the structure, so I want to use secondary structure restrain. Does phenix has this restrain in the refinement? Sorry for missing documentation on this subject. First of all, get the latest version of PHENIX (the one you have is very old): http://www.phenix-online.org/download/nightly_builds.cgi Then (once you have the latest), yes, you can use secondary structure restraints. phenix.refine model.pdb data.hkl main.secondary_structure_restraints=true so phenix.refine automatically determines secondary structure and applies the restrains. Note, GIGO principle applies, that is if your input model is distorted then it's unlikely that the procedure will figure out the secondary structure correctly. To make it a less black-box, you can run phenix.secondary_structure_restraints model.pdb > ss_restraints.params and then check (and edit if necessary) the ss_restraints.params file, and then run phenix.refine as following: phenix.refine model.pdb data.hkl main.secondary_structure_restraints=true ss_restraints.params I hope Nat comments more if I missed something. Let me know if you have any other questions. Good luck! Pavel. _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
2010/10/16 Pei-Chun Lin
I have the similar problem when I am working on refining my low resolution model (3.5 Ang).
One component of my protein complex represents a beta-sandwish structure, and the conecting loops between beta-strands are disordered. After refinement, the beta-sheets were disrupted. What do you suggest about this problem.
The same advice as before applies: use secondary structure restraints. I recommend that you try to make your model as good as possible before running the annotation (either independently or as part of phenix.refine), because sheets are much harder to define manually and it's better if the automatic method identifies them. -Nat
participants (4)
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crystallogrphy -
Nathaniel Echols -
Pavel Afonine -
Pei-Chun Lin