Well they aren't conserved so I guess I'll have to do some manual remodelling. The new version of HHPred is nice about building you a quick homology model to start with though (using Modeller). Thanks Tom! On 22 March 2012 00:56, Terwilliger, Thomas C wrote:

Hi Morten,

I asked about this...and if your input model has Cys-Cys disulfides and the sequence file also has these cysteine residues, then the disulfides should be maintained by Rosetta. If that isn't happening, let me know!

I hope that helps! All the best, Tom T

------------------------------ *From:* [email protected] [ [email protected]] on behalf of Morten Groftehauge [ [email protected]] *Sent:* Wednesday, March 21, 2012 8:25 AM *To:* PHENIX user mailing list *Subject:* [phenixbb] Rosetta and disulphides

Hi phenix-bb'ers,

Is there anyway to make phenix.mr_rosetta take disulphide bridges into account? It's a rather enormous restraint on conformational space after all (wait is that a constraint or restraint? I get confused).

Cheers, Morten

-- Morten K Grøftehauge, PhD Pohl Group Durham University

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-- Morten K Grøftehauge, PhD Pohl Group Durham University

On Thu, Mar 22, 2012 at 6:23 AM, Maike Bublitz wrote:

1) I have trouble getting a molecular replacement job to run (Phenix Version 1.7.3-928), where I want to keep one ensemble fixed in its known orientation, only looking for a second ensemble. I keep on getting the following error message, both from the GUI and from command line (using a 'mymr.eff' parameter file):

**************************************** AutoMR Input failed Python argument types in SOLU.addSOLU_6DIM_ENSE(InputMR_AUTO, str, list, bool, list, float, bool, bool, bool) did not match C++ signature: addSOLU_6DIM_ENSE(phaser::SOLU {lvalue}, std::string, scitbx::vec3<double>, bool, scitbx::vec3<double>, double, bool, bool, bool, bool, scitbx::vec3<double>, double) **************************************** *************ERROR ENDING *******************

I can't figure out what I'm doing wrong. Any suggestions?

2) Which parameters would I need to specify to let phenix.autobuild build a model for one protein of a 2-component complex from scratch, while keeping the other component unchanged (and using it to calculate the

This is definitely a bug. Two suggestions: a) try the Phaser-MR GUI instead, it may not have this problem, or b) update to the latest nightly build and see if it's fixed there. I will see if we can add a regression test for specifying a fixed ensemble. phases)? Is that possible? I think you need to define the existing component as ligands, as described here: https://www.phenix-online.org/version_docs/dev-1012/autobuild.htm#anch103 I suspect this means that you'll need to supply an initial map for phases, rather than having it calculate them from the "ligands", but I've never actually tried this myself. -Nat

Hi Maike, What you are doing looks like it should work, however you might want to use this value for keep_pdb_atoms: keep_pdb_atoms=False #keep the ligand atoms if model (pdb) and ligand overlap because as it is you will take the atoms from the model that autobuild builds if they overlap with the ones from your input model. Note that autobuild will try to build everything...and then in places where your input model is present, it should be used. If that isn't happening, please let me know and I'll try to figure out why. All the best, Tom T ________________________________ From: [email protected] [[email protected]] on behalf of Maike Bublitz [[email protected]] Sent: Friday, March 23, 2012 7:35 AM To: [email protected] Subject: Re: [phenixbb] phenix_automr error and autobuild question Thank you Nat, Phaser-MR (from the GUI) worked fine with the fixed ensemble. But for the autobuild problem - it does run if I provide an mtz file with phases derived from the known part of the model for the initial map, but it seems to ignore the pdb file which I define as ligand and obviously tries to build the whole thing - which fails. Here are some of the parameters I have defined in the .eff file. Am I missing something? autobuild { data = mydata_phased_with_partial_model_in_sigmaa.mtz model = None seq_file = component_to_build.fasta map_file = mydata_phased_with_partial_model_in_sigmaa.mtz refinement_file =mydata_phased_with_partial_model_in_sigmaa.mtz hires_file = Auto input_files { input_labels = FP SIGFP PHIC WCMB None None None None FreeRflag input_map_labels = FP PHIC WCMB input_refinement_labels =FP SIGFP FreeRflag input_lig_file_list = refined_known_component.pdb keep_input_ligands = True keep_input_waters = False keep_pdb_atoms = True refine_eff_file_list = None map_file_is_density_modified = False map_file_fom = None use_map_file_as_hklstart = False use_map_in_resolve_with_model = False } model_building { build_type = *RESOLVE RESOLVE_AND_BUCCANEER include_input_model = False refine = True two_fofc_in_rebuild = False refine_map_coeff_labels = "2FOFCWT PH2FOFCWT" filled_2fofc_maps = True map_phasing = False } rebuild_in_place { rebuild_in_place = Auto True *False } Best regards, Maike On 22.03.2012 14:33, Nathaniel Echols wrote: On Thu, Mar 22, 2012 at 6:23 AM, Maike Bublitz mailto:[email protected]> wrote: 1) I have trouble getting a molecular replacement job to run (Phenix Version 1.7.3-928), where I want to keep one ensemble fixed in its known orientation, only looking for a second ensemble. I keep on getting the following error message, both from the GUI and from command line (using a 'mymr.eff' parameter file): **************************************** AutoMR Input failed Python argument types in SOLU.addSOLU_6DIM_ENSE(InputMR_AUTO, str, list, bool, list, float, bool, bool, bool) did not match C++ signature: addSOLU_6DIM_ENSE(phaser::SOLU {lvalue}, std::string, scitbx::vec3<double>, bool, scitbx::vec3<double>, double, bool, bool, bool, bool, scitbx::vec3<double>, double) **************************************** *************ERROR ENDING ******************* I can't figure out what I'm doing wrong. Any suggestions? This is definitely a bug. Two suggestions: a) try the Phaser-MR GUI instead, it may not have this problem, or b) update to the latest nightly build and see if it's fixed there. I will see if we can add a regression test for specifying a fixed ensemble.

2) Which parameters would I need to specify to let phenix.autobuild build a model for one protein of a 2-component complex from scratch, while keeping the other component unchanged (and using it to calculate the phases)? Is that possible?

I think you need to define the existing component as ligands, as described here: https://www.phenix-online.org/version_docs/dev-1012/autobuild.htm#anch103 I suspect this means that you'll need to supply an initial map for phases, rather than having it calculate them from the "ligands", but I've never actually tried this myself. -Nat _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb