I need to specify a group of residues/atoms that must exist on the same plane for refinement. I think the keyword is refinement.geometry_restraints.planarities may be the right keyword, but I'm unsure as to the syntax for defining the selection? Thanks FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D
Hi Francis, Currently we don't support what you are looking for; sorry. geometry_restraints.edits would be the place to look, but you'll find only bond and angle. I didn't get to the other restraint types. However, in theory you could work with .cif files, although it may be a bit cumbersome. Could you explain in some detail which atoms you want to restrain? I'll put the geometry_restraints.edits.planarity support up higher on my todo list. Ralf
Hi Ralf This is in relation to refining RNA/DNA structures. I'm basically trying to duplicate the restraints specified in http:// cns.csb.yale.edu/cgi-bin/cns_solve_1.2/cns_view.cgi?&file=inputs/ auxiliary/dna-rna_restraints.def. Basically, in RNA A-form helicies the sugar pucker is restrained around 3 angles, and the atoms of the bases must be planar. FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D On Oct 9, 2007, at 10:27 AM, Ralf W. Grosse-Kunstleve wrote:
Hi Francis, Currently we don't support what you are looking for; sorry. geometry_restraints.edits would be the place to look, but you'll find only bond and angle. I didn't get to the other restraint types. However, in theory you could work with .cif files, although it may be a bit cumbersome. Could you explain in some detail which atoms you want to restrain? I'll put the geometry_restraints.edits.planarity support up higher on my todo list. Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
P.S. Can I specify dihedral bond angles? I see only three atom_selections under geometry_restraints.edits.angle FR --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D On Oct 9, 2007, at 10:27 AM, Ralf W. Grosse-Kunstleve wrote:
Hi Francis, Currently we don't support what you are looking for; sorry. geometry_restraints.edits would be the place to look, but you'll find only bond and angle. I didn't get to the other restraint types. However, in theory you could work with .cif files, although it may be a bit cumbersome. Could you explain in some detail which atoms you want to restrain? I'll put the geometry_restraints.edits.planarity support up higher on my todo list. Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Funny enough, yesterday I asked Pavel a very similar question:
1. If resolution is high enough, lets say 1.5A or so, how can I specifically
release the restrains in the active site? To define atom A, the first
sphere, and second sphere.. example would be a phosphate, oxygens of that
and the side chain of amino acid residues which come within a distance.. can
you give me a syntax example for that?
Don't make programs which are too good, users start to ask for a lot :))
Cheers, Partha
On 10/9/07, Ralf W. Grosse-Kunstleve
Can I specify dihedral bond angles?
No, that's missing, too. The underlying library supports bond, angle, dihedral, chirality, and planarity. Only the first two are currently supported under geometry_restraints.edits. Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- MRC National Institute for Medical Research Division of Molecular Structure The Ridgeway, NW7 1AA, UK Email: [email protected] Phone: + 44 208 816 2515
Hi Partha, Do you want to completely remove the restraints around the active site? You can do that with this block in the parameter file: geometry_restraints.remove { angles = None dihedrals = None chiralities = None planarities = None } Where you see None, enter atom selections. The restraints of the given type (angles, dihedrals, etc.) involving the corresponding selected atoms will be removed. You can have multiple lines for each restaint type. You can check the result by inspecting the .geo file. It is a bit big, but the atom labels are formatted exactly the same way as you see them in your pdb file, e.g. angle: (2, 1, 4) " C LEU A 325 " " CA LEU A 325 " " CB LEU A 325 " angle_model: 110.834 angle_ideal: 110.1 weight: 0.277008 you can search for " C LEU A 325 " in your pdb file or vice versa. You could also try diff orig.geo mod.geo to check the effect of your selections. Ralf
participants (3)
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Francis E Reyes -
Partha Chakrabarti -
Ralf W. Grosse-Kunstleve