Dear Friend, I am using command line prompt to refine protein-dna complex using phenix.refine. I used the following command: phenix.refine YCd1p3_output.mtz sep71_001.pdb_modified.pdb simulated_annealing=true main.ncs=true refinement.ncs.excessive_distance_limit=6 ncs_groups_3.params ncs.find_automatically=False ordered_solvent=true strategy=rigid_body+individual_sites+group_adp+tls individual_sites="((chain A and not "(resid 176 or resid 179 or resid 238 or resid 242)") or (chain B and not "(resid 176 or resid 179 or resid 238 or resid 242)") or (chain C and not "(resid 176 or resid 179 or resid 238 or resid 242)") or (chain D and not "(resid 176 or resid 179 or resid 238 or resid 242)")) output.write_maps=true output.prefix=sep72 --overwrite If I omit the portion [individual_sites="((chain A and not "(resid 176 or resid 179 or resid 238 or resid 242)") or .........], it is running fine. I want to exclude some residues say resid 176, 179, 238 and 242 from all four chains in the refinement. how can I incorporate that in command line promt or using a .params file? I know my msitake is in the command individual_sites="((chain A and not "(resid 176 or resid 179 or resid 238 or resid 242)") or ......... Thanking you in advance... Raja

Since in this case the same residues were omitted from each and every chain refined, could the selection have been: ((chain A or chain B or chain C or chain D) and not (resid 176 or resid 179 or resid 238 or resid 242))"? Ralf W. Grosse-Kunstleve wrote:

Could you try this?

phenix.refine YCd1p3_output.mtz sep71_001.pdb_modified.pdb simulated_annealing=true main.ncs=true refinement.ncs.excessive_distance_limit=6 ncs_groups_3.params ncs.find_automatically=False ordered_solvent=true strategy=rigid_body+individual_sites+group_adp+tls sites.individual="((chain A and not (resid 176 or resid 179 or resid 238 or resid 242)) or (chain B and not (resid 176 or resid 179 or resid 238 or resid 242)) or (chain C and not (resid 176 or resid 179 or resid 238 or resid 242)) or (chain D and not (resid 176 or resid 179 or resid 238 or resid 242)))" output.write_maps=true output.prefix=sep72 --overwrite

Changes are: - sites.individual=... - double-quotes in the selection removed - added one at the end of the selection

Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

Hi Raja, phenix.refine uses the following criteria for water picking/refinement: 1) peak at mFo-DFc map is higher than ~3sigma, and 2) peak center is within a hydrogen bond to another atom (water or macromolecule), and 3) peak has approximately the same shape as a water molecule would have at this resolution and local environment, and 4) peak at 2mFo-DFc is higher than ~1.0 sigma, after a round of coordinate and B-factor refinement, the criteria (2-3-4) are still ok, and 5) refined B-factor of newly placed water is meaningful (didn't jump to large value), otherwise a water is deleted. All the relevant parameters are specified under refinement.ordered_solvent scope of parameters. To see them just type from the command line: phenix.refine --show-defaults=all You can find some information about this in phenix.refine manual: http://www.phenix-online.org/documentation/nightlies/1.4-159/refinement.htm#... but I have to update it to reflect recent changes. Normally you don't change these parameters, simply run something like this to add and refined water: phenix.refine model.pdb data.hkl ordered_solvent=true Pavel. On 9/8/09 3:43 PM, Raja Dey wrote:

Hi Ralf, Thanks for the right command. It is now working. One more question. Which map is using by the command ordered_solvent=true ? Is it 2fo-fc and at 1 sigma level? How can I specify a map and sigma level(say fo-fc at 3 sigma level) to pick up the waters?

Thanks for your help.

Raja

----- Original Message ----- From: "Ralf W. Grosse-Kunstleve" Date: Monday, September 7, 2009 4:36 pm Subject: Re: [phenixbb] how to exclude a residue in the refinement in command line To: [email protected]

...

Could you try this?

phenix.refine YCd1p3_output.mtz sep71_001.pdb_modified.pdb simulated_annealing=true main.ncs=true refinement.ncs.excessive_distance_limit=6 ncs_groups_3.params ncs.find_automatically=False ordered_solvent=true strategy=rigid_body+individual_sites+group_adp+tls sites.individual="((chain A and not (resid 176 or resid 179 or resid 238 or resid 242)) or (chain B and not (resid 176 or resid 179 or resid 238 or resid 242)) or (chain C and not (resid 176 or resid 179 or resid 238 or resid 242)) or (chain D and not (resid 176 or resid 179 or resid 238 or resid 242)))" output.write_maps=true output.prefix=sep72 --overwrite

Changes are: - sites.individual=... - double-quotes in the selection removed - added one at the end of the selection

Ralf _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb