Or using a recent installer from the nightly builds page, "phenix.omit_map" launches a GUI for this. On Aug 28, 2009, at 7:59 AM, Thomas C. Terwilliger wrote:

Hi Qun, Yes, you can make a SA composite omit map with:

phenix.autobuild data=data.mtz model=coords.pdb composite_omit_type=sa_omit

All the best, Tom T

...

...

Hi, I am using molecular replacement to build a model against a 2.2A resolution data set. However, the template model only has 23% sequence identity. First, I use chainsaw in CCP4i to prune all side chain to be poly-Ala except the identical residues. Then I use AutoMR and rigid body refinement, I got Rfree=50%. The continuous electron density is not bad showing second structures. However, the model has some out-of-registration problem, for example, two proline are in a alpha-helix. In other words, it has model bias. I want to use composite SA-omit to get a less model bias map, not a simple composite omit map or a SA_omit map ommiting a part of the region. Does someone know who to do this?

Thanks!

Qun Wan postdoc fellow Case Western Reserve University _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

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------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 [email protected]

Hi Venkat, Yes, you can use autobuild to create a map including model and experimental phase information: phenix.autobuild data=sad_phase_info.mtz model=partial_mr_solution.pdb \ seq_file=seq.dat maps_only=true This will refine the partial model, use it along with the sad phases in density modification, and produce coefficients for a new map for you: --- Density-modified map coefficients FP PHIM FOM --- hklout_denmod: AutoBuild_run_3_/cycle_best_2.mtz All the best, Tom T On Sep 2, 2009, at 8:12 AM, r n wrote:

Hi

I would like to know for low resolution data with poor phase information (SAD and partial MR), Is there possibility to in Phenix to improve the phase and map using the partial model at low resolution (3.5 Ang), similar to TNT/BUSTER.

Thanks venkat

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Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss

Hi all I am working on low resolution structure sad data and build 70% of the molecule and R/Rfree is 25/32%, there are some weak density for remaining 20% of the molecule,. I was trying to improve the map using the both experimental (3.5 Ang) and native data (2.8 Ang) using phenix.Gui using two dataset for autobuild, but not successful, Phenix not able to find extra residues other than what I have given as input after5 cycle of autobuild. How can I combine the two data set with low and high resolution extend the phase with phenix? Any possibility of identifying the missing parts just even as poly ala trace? Is it possible to achieve phase combination and extension to improve the map ? Possible a fragment or domain using known phases and map by Phenix? Any suggestions will be appreciated Thanks Venkat ________________________________ From: r n To: PHENIX user mailing list Sent: Wednesday, September 2, 2009 6:11:01 PM Subject: Re: [phenixbb] low resolution map Dear Tom thanks. ________________________________ From: Tom Terwilliger To: PHENIX user mailing list Sent: Wednesday, September 2, 2009 9:20:55 AM Subject: Re: [phenixbb] low resolution map Hi Venkat, Yes, you can use autobuild to create a map including model and experimental phase information: phenix.autobuild data=sad_phase_info.mtz model=partial_mr_solution.pdb \ seq_file=seq.dat maps_only=true This will refine the partial model, use it along with the sad phases in density modification, and produce coefficients for a new map for you: --- Density-modified map coefficients FP PHIM FOM --- hklout_denmod: AutoBuild_run_3_/cycle_best_2.mtz All the best, Tom T On Sep 2, 2009, at 8:12 AM, r n wrote: Hi

I would like to know for low resolution data with poor phase information (SAD and partial MR), Is there possibility to in Phenix to improve the phase and map using the partial model at low resolution (3.5 Ang), similar to TNT/BUSTER.

Thanks venkat

________________________________

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Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss

Hi, Does phenix have SA-torsion angle refinement option similar to what is available in CNS? Thanks, Esmael

Hi Ralf, Thanks a lot for the info. I downloaded the latest phenix version for MAC; we I ran it I got this error message. toshow_stack(1): /usr/local/phenix-1.4-159/cctbx_project/cctbx/sgtbx/ __init__.py(79) __init__ show_stack(2): /usr/local/phenix-1.4-159/cctbx_project/iotbx/mtz/ __init__.py(181) space_group_info show_stack(3): /usr/local/phenix-1.4-159/cctbx_project/iotbx/mtz/ __init__.py(677) crystal_symmetry show_stack(4): /usr/local/phenix-1.4-159/cctbx_project/iotbx/mtz/ crystal_symmetry_from_mtz.py(9) extract_from show_stack(5): /usr/local/phenix-1.4-159/cctbx_project/iotbx/ crystal_symmetry_from_any.py(73) extract_from show_stack(6): /usr/local/phenix-1.4-159/cctbx_project/iotbx/ crystal_symmetry_from_any.py(87) extract_and_append show_stack(7): /usr/local/phenix-1.4-159/phenix/phenix/refinement/ command_line.py(462) process_args show_stack(8): /usr/local/phenix-1.4-159/phenix/phenix/refinement/ command_line.py(208) __init__ show_stack(9): /usr/local/phenix-1.4-159/phenix/phenix/refinement/ command_line.py(68) run show_stack(10): /usr/local/phenix-1.4-159/phenix/phenix/command_line/ refine.py(11) <module> Bus error (Python call stack above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical. Defining the variables did not help. Could you please advise. Thanks, Esmael On Sep 8, 2009, at 4:02 PM, Ralf W. Grosse-Kunstleve wrote:

...

Does phenix have SA-torsion angle refinement option similar to what is available in CNS?

Yes, with a recent installer (less than a week or two old) you can try it out by adding

simulated_annealing_torsion=True

in addition to the other settings for turning on simulated annealing.

There are some known problems that I didn't have a chance to fix yet, but if it doesn't crash it should be OK. If you get a crash or weird results, let me know.

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

Hi Esmael, yes, with phenix.refine you can do SA refinement in torsion angle space. Use "simulated_annealing_torsion=true" flag for this. You also need to use a recent PHENIX version from nightly builds: http://www.phenix-online.org/download/nightly_builds.cgi Pavel. On 9/8/09 1:43 PM, esmael wrote:

Hi,

Does phenix have SA-torsion angle refinement option similar to what is available in CNS?

Thanks, Esmael

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Hi, all I have a similar question. I have spent several months working on a MAD data (3.5 Ang) and already build 70% of the model (R/Rfree=30/40). Recently, I collected two dataset (pk and infl, both 3.1 Ang) from single point mutation, and native data(3.3 Ang). I first tried to use phenix autosol to generate a new map by using point mutation dataset, but failed to generate a reasonable map for unknown reason (phenix complained different cell dimensions) Now I am thinking to combine all data I have (although I don't know if this make sense to you) like this: phenix.autobuild data=resolve_3.5Ang.mtz hires_file=3.1Ang_pk.sca hires_file=3.1Ang_inf.sca hires_file=3.3Ang_native.sca model=partial_model.pdb seq_file=seq.dat Can I use three hires command? Does this make sense to you all? Any suggestion will be helpful to me since this my first structure and it is 3.5 Ang! PC

From: [email protected] To: [email protected] Date: Tue, 8 Sep 2009 08:58:44 -0600 Subject: Re: [phenixbb] low resolution map

Hi Venkat,

You can combine your low-res phased data with your high-res native data in phenix.autobuild using the keyword

hires_file=my_native_data.mtz

This will substitute your native FP and SIGFP, extend the resolution to that of your native, and keep your experimental phases.

You should probably add a step to keep and extend your freeR flags:

iotbx.r_free_flags_completion_simple exptl_fobs_freeR_flags.mtz 2.8

where exptl_fobs_freeR_flags.mtz is your refinement data file from your previous runs of autobuild (which contains your current set of freeR flags). This will produce a file with JUST the extended freeR flags. You can then combine this extended set of freeR flags with your hires file most easily with the reflection tools in the current PHENIX GUI. Then use that hires_file in autobuild.

Let me know if that doesn't help! All the best, Tom T

On Sep 7, 2009, at 9:55 PM, r n wrote:

...

Hi all

I am working on low resolution structure sad data and build 70% of the molecule and R/Rfree is 25/32%, there are some weak density for remaining 20% of the molecule,.

I was trying to improve the map using the both experimental (3.5 Ang) and native data (2.8 Ang) using phenix.Gui using two dataset for autobuild, but not successful, Phenix not able to find extra residues other than what I have given as input after5 cycle of autobuild.

How can I combine the two data set with low and high resolution extend the phase with phenix? Any possibility of identifying the missing parts just even as poly ala trace?

Is it possible to achieve phase combination and extension to improve the map ? Possible a fragment or domain using known phases and map by Phenix?

Any suggestions will be appreciated Thanks Venkat

From: r n To: PHENIX user mailing list Sent: Wednesday, September 2, 2009 6:11:01 PM Subject: Re: [phenixbb] low resolution map

Dear Tom

thanks.

From: Tom Terwilliger To: PHENIX user mailing list Sent: Wednesday, September 2, 2009 9:20:55 AM Subject: Re: [phenixbb] low resolution map

Hi Venkat, Yes, you can use autobuild to create a map including model and experimental phase information:

phenix.autobuild data=sad_phase_info.mtz model=partial_mr_solution.pdb \ seq_file=seq.dat maps_only=true

This will refine the partial model, use it along with the sad phases in density modification, and produce coefficients for a new map for you:

--- Density-modified map coefficients FP PHIM FOM --- hklout_denmod: AutoBuild_run_3_/cycle_best_2.mtz

All the best, Tom T

On Sep 2, 2009, at 8:12 AM, r n wrote:

...

Hi

I would like to know for low resolution data with poor phase information (SAD and partial MR), Is there possibility to in Phenix to improve the phase and map using the partial model at low resolution (3.5 Ang), similar to TNT/BUSTER.

Thanks venkat

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

Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545

Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http:// solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/ cbss

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Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545

Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss

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Hi all I did phased small protein using SAD at 3.5 Ang data and able to build around 80 residues  as alanine and missing other half. So I do have a partial model and tried to used that to and combine with experimental phase and resulting map is not better than the experimental map alone. I do have other native data set slightly better resolution with different space group. I know my partial model is not enough to get any phase information in these data set.  Is it any possibility in phenix to improve the phase that I could help to model further? Any suggestions will be appreciated thanks venkat

Pavel, how can I specify the request for averaged Kick Maps on the command line , please? Cheers, Uli ----- Original Message ----- From: Pavel Afonine To: [email protected] ; PHENIX user mailing list Sent: Friday, August 28, 2009 6:31 PM Subject: Re: [phenixbb] question about composite SA_omit map in phenix Hi Qun Wan, Alternatively, you can ask phenix.refine to compute Average Kick Map, which is expected to be less biased or less noisy. For more details about kick map, see recent publication: Acta Cryst. (2009). D65, 921-931. Please let me know if you have questions. Pavel. On 8/28/09 7:52 AM, crystallogrphy wrote: Hi, I am using molecular replacement to build a model against a 2.2A resolution data set. However, the template model only has 23% sequence identity. First, I use chainsaw in CCP4i to prune all side chain to be poly-Ala except the identical residues. Then I use AutoMR and rigid body refinement, I got Rfree=50%. The continuous electron density is not bad showing second structures. However, the model has some out-of-registration problem, for example, two proline are in a alpha-helix. In other words, it has model bias. I want to use composite SA-omit to get a less model bias map, not a simple composite omit map or a SA_omit map ommiting a part of the region. Does someone know who to do this? Thanks! Qun Wan postdoc fellow Case Western Reserve University ---------------------------------------------------------------------------- _______________________________________________ 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