Hi Kelly, I think if you compute a map using "Create maps" option in PHENIX GUI then twinning should be taken care of automatically (although you cannot specify your own twin operator - it is determined internally). Also you can always compute the omit map by omitting your ligand from the PDB file and using this model as input for "Create maps" ? You can "omit" the ligand by setting its occupancies to zero: phenix.pdbtools model.pdb occupancies.set=0 selection="chain A and resseq 123" Finally, if you are using 1.5, you can use phenix.refine to compute maps: phenix.refine model.pdb data.mtz strategy=none main.number_of_macro_cycles=1 twin_law="h,-k,l" output.prefix=maps_only Pavel. PS> You don't need to have a system administrator rights to to install PHENIX: you can always install it locally under your account. On 2/17/10 1:46 PM, Kelly Daughtry wrote:
Hello all, The omit_map in the new gui (version 1.5) is great, but I can not include a twin law when calculating the omit map, thus the result is very messy unclear maps. I do not know if 1.6 has the solution or not, I am still lobbying our computer guy to upgrade to it...
Is there a way from the command line i can include the twin law in autobuild so I can calculate the omit map, or can I just add it into the eff file?
My other solution has been to use the create maps function with my data and pdb with ligand removed. This works, giving me a nice Fo-DFc map, but it would be nice to be able to show a true omit map for the ligand, as is customary in most structure papers I have run across.
Thanks in advance for any help you can provide!
Kelly
******************************************************* Kelly Daughtry PhD Candidate Department of Physiology and Biophysics Boston University School of Medicine 590 Commonwealth Ave R 390 Boston MA, 02215 (P) 617-358-5548 ******************************************************* _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb