Hi, I think this is a good option-candidate for phenix.maps. Currently phenix.maps can create a variety of maps and can output them in X-plor or MTZ format. Yes, generating an omit map is missing in phenix.maps as an explicit option. But you can just manually omit the region in question and compute a Kick Map. It is a simple alternative to "SA omit map" or "Iterative Build omit map". Or alternatively: a) omit the region in question, b) do some refinement, c) after refinement phenix.refine will give your the omit maps or you can just use phenix.maps to compute the map. I this this is the complete solution for what you want. For more information about phenix.maps just type this command in the command line and hit Enter - the quick manual will be printed to the screen. Pavel. On 5/29/10 5:05 PM, Nathaniel Echols wrote:

On Sat, May 29, 2010 at 2:27 PM, Susan Tsutakawa mailto:[email protected]> wrote:

Continuing the conversation on looking at Phenix maps in pymol, what is the best way to generate .xplor maps in Autobuild. I would like to generate a figure in pymol with an omit map. I wasn't able to find documentation explicitly stating how this can be done.

The GUI generates XPLOR maps automatically; otherwise, I don't think there's a simple mechanism in Phenix for this right now. I started working on a script for this but got sidetracked - I'll see if I can dust off the code and get something working for the next release.

For now, I'd recommend using the FFT program in CCP4.

-Nat ------------------------------------------------------------------------

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Dear Chris, this did it for me. Create a file which you can call whatever you want even the extension doesn't matter. E.g.: cif_link.params Put in this file your links: (Which Atom of residue1 will be connected to which Atom in residue2 is already defined in mon_lib_list.cif) refinement.pdb_interpretation.apply_cif_link { data_link = NAG-ASN residue_selection_1 = chain A and resname NAG and resid 500 residue_selection_2 = chain A and resname ASN and resid 297 } refinement.pdb_interpretation.apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain A and resname NAG and resid 500 residue_selection_2 = chain A and resname NAG and resid 501 } refinement.pdb_interpretation.apply_cif_link { data_link = BETA1-4 residue_selection_1 = chain A and resname NAG and resid 501 residue_selection_2 = chain A and resname BMA and resid 502 } refinement.pdb_interpretation.apply_cif_link { data_link = ALPHA1-3. residue_selection_1 = chain A and resname BMA and resid 502 residue_selection_2 = chain A and resname MAN and resid 503 } 4) add this file in the GUI Or run % phenix.refine model.pdb data.hkl cif_link.params 5)Trouble shooting a)run iotbx.phil cif_link.params (this checks if the syntax is right) b) check .eff file the links should be added there. You can also check the . geo file if you see anything strange. c)Having unknown to phenix.refine item in PDB file (novel ligand, etc... (BMA is also not there) ). phenix.refine uses the CCP4 Monomer Library as the source of stereochemical information for building geometry restraints and reporting statistics. If phenix.refine is unable to match an item in input PDB file against the Monomer Library it will stop with "Sorry" message explaining what to do and listing the problem atoms. If this happened, it is necessary to obtain a cif file (parameter file, describing unknown molecule) by either making it manually or having eLBOW program to generate it: phenix.elbow model.pdb --do-all --output=all_ligands this will ask eLBOW to inspect the model_new.pdb file, find all unknown items in it and create one cif file for them all_ligands.cif. Alternatively, one can specify a three-letters name for the unknown residue: phenix.elbow model.pdb --residue=MAN --output=man !Check the file if everything is ok! Please correct if this is not ok, or there is an easier way now. Kind regards George. -----Ursprüngliche Nachricht----- Von: [email protected] [mailto:[email protected]] Im Auftrag von Chris Ulens Gesendet: Monday, May 31, 2010 9:14 PM An: PHENIX user mailing list Betreff: Re: [phenixbb] NAG-NAG description Dear glycobiologists and phenixfriends. I am trying to refine a NAG-NAG chain attached to an Asn122 in my (pentameric) structure. What is the proper description in the cif_link.params that is the equivalent of the pdb description pasted below that phenix so kindly ignores? Also, what is the proper way to define the cif_link.params file in the GUI? Thank you. -Chris LINK ND2 ASN A 122 C1 NAG A 834 1555 1555 1.37 LINK O4 NAG A 834 C1 NAG A 835 1555 1555 1.43 LINK ND2 ASN B 122 C1 NAG B 834 1555 1555 1.37 LINK O4 NAG B 834 C1 NAG B 835 1555 1555 1.43 LINK ND2 ASN C 122 C1 NAG C 834 1555 1555 1.37 LINK O4 NAG C 834 C1 NAG C 835 1555 1555 1.43 LINK ND2 ASN D 122 C1 NAG D 834 1555 1555 1.37 LINK O4 NAG D 834 C1 NAG D 835 1555 1555 1.43 LINK ND2 ASN E 122 C1 NAG E 834 1555 1555 1.37 LINK O4 NAG E 834 C1 NAG E 835 1555 1555 1.43 --------------------------------------------------- Chris Ulens, Ph.D. Lab of Structural Neurobiology Department of Molecular Cell Biology Campus Gasthuisberg, ON1 Herestraat 49, PB 601 B-3000 Leuven Belgium e [email protected] t +32 16 345812 f +32 16 345699 w http://www.xtal.be _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Great. Thank you for implementing it. Sent from phone. Please excuse if email is too terse. On Jun 1, 2010, at 11:45 AM, Nathaniel Echols wrote:

On Sat, May 29, 2010 at 2:27 PM, Susan Tsutakawa wrote: Continuing the conversation on looking at Phenix maps in pymol, what is the best way to generate .xplor maps in Autobuild. I would like to generate a figure in pymol with an omit map. I wasn't able to find documentation explicitly stating how this can be done.

Okay, starting tomorrow (or whenever the next installer is ready):

phenix.mtz2map resolve_composite_map.mtz

You can specify a PDB file if you want it to create the map around your molecule (or a selection thereof) instead of the unit cell. It is tailored for RESOLVE and phenix.refine map coefficients, which have fairly well-defined column labels; others should work too, but it may be clumsier.

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