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Hi, all<br><br>I have a similar question.<br><br>I have spent several months working on a MAD data (3.5 Ang) and already build 70% of the model (R/Rfree=30/40).<br>Recently, I collected two dataset (pk and infl, both 3.1 Ang) from single point mutation, and native data(3.3 Ang).<br>I first tried to use phenix autosol to generate a new map by using point mutation dataset, <br>but failed to generate a reasonable map for unknown reason (phenix complained different cell dimensions) <br><br>Now I am thinking to combine all data I have (although I don't know if this make sense to you) like this:<br><br>phenix.autobuild data=resolve_3.5Ang.mtz<br>hires_file=3.1Ang_pk.sca<br>hires_file=3.1Ang_inf.sca<br>hires_file=3.3Ang_native.sca<br>model=partial_model.pdb<br>seq_file=seq.dat<br><br><br>Can I use three hires command? Does this make sense to you all?<br><br>Any suggestion will be helpful to me since this my first structure and it is 3.5 Ang!<br><br><br>PC<br><br><br><br><br>> Fr!
om: terwilliger@lanl.gov<br>> To: phenixbb@phenix-online.org<br>> Date: Tue, 8 Sep 2009 08:58:44 -0600<br>> Subject: Re: [phenixbb] low resolution map<br>> <br>> Hi Venkat,<br>> <br>> You can combine your low-res phased data with your high-res native <br>> data in phenix.autobuild using the keyword<br>> <br>> hires_file=my_native_data.mtz<br>> <br>> This will substitute your native FP and SIGFP, extend the resolution <br>> to that of your native, and keep your experimental phases.<br>> <br>> You should probably add a step to keep and extend your freeR flags:<br>> <br>> iotbx.r_free_flags_completion_simple exptl_fobs_freeR_flags.mtz 2.8<br>> <br>> where exptl_fobs_freeR_flags.mtz is your refinement data file from <br>> your previous runs of autobuild (which contains your current set of <br>> freeR flags). This will produce a file with JUST the extended freeR <br>> flags. You can then combine this extende!
d set of freeR flags with your <br>> hires file most easily with t
he reflection tools in the current PHENIX <br>> GUI. Then use that hires_file in autobuild.<br>> <br>> Let me know if that doesn't help!<br>> All the best,<br>> Tom T<br>> <br>> <br>> On Sep 7, 2009, at 9:55 PM, r n wrote:<br>> <br>> > Hi all<br>> ><br>> > I am working on low resolution structure sad data and build 70% of <br>> > the molecule and R/Rfree is 25/32%, there are some weak density for <br>> > remaining 20% of the molecule,.<br>> ><br>> > I was trying to improve the map using the both experimental (3.5 <br>> > Ang) and native data (2.8 Ang) using phenix.Gui<br>> > using two dataset for autobuild, but not successful, Phenix not <br>> > able to find extra residues other than what I have given as input <br>> > after5 cycle of autobuild.<br>> ><br>> > How can I combine the two data set with low and high resolution <br>> > extend the phase with phen!
ix?<br>> > Any possibility of identifying the missing parts just even as poly <br>> > ala trace?<br>> ><br>> > Is it possible to achieve phase combination and extension to improve <br>> > the map ?<br>> > Possible a fragment or domain using known phases and map by Phenix?<br>> ><br>> > Any suggestions will be appreciated<br>> > Thanks<br>> > Venkat<br>> ><br>> > From: r n <ramme29@yahoo.com><br>> > To: PHENIX user mailing list <phenixbb@phenix-online.org><br>> > Sent: Wednesday, September 2, 2009 6:11:01 PM<br>> > Subject: Re: [phenixbb] low resolution map<br>> ><br>> > Dear Tom<br>> ><br>> > thanks.<br>> ><br>> > From: Tom Terwilliger <terwilliger@lanl.gov><br>> > To: PHENIX user mailing list <phenixbb@phenix-online.org><br>> > Sent: Wednesday, September 2, 2009 9:20:55 AM<br>> > Subject: Re: [phenixbb] lo!
w resolution map<br>> ><br>> > Hi Venkat,<br>> > Yes
, you can use autobuild to create a map including model and <br>> > experimental phase information:<br>> ><br>> > phenix.autobuild data=sad_phase_info.mtz <br>> > model=partial_mr_solution.pdb \<br>> > seq_file=seq.dat maps_only=true<br>> ><br>> > This will refine the partial model, use it along with the sad phases <br>> > in density modification, and produce coefficients for a new map for <br>> > you:<br>> ><br>> > --- Density-modified map coefficients FP PHIM FOM ---<br>> > hklout_denmod: AutoBuild_run_3_/cycle_best_2.mtz<br>> ><br>> ><br>> > All the best,<br>> > Tom T<br>> ><br>> ><br>> > On Sep 2, 2009, at 8:12 AM, r n wrote:<br>> ><br>> >> Hi<br>> >><br>> >> I would like to know for low resolution data with poor phase <br>> >> information (SAD and partial MR), Is there possibility to<br>> >> in Phenix !
to improve the phase and map using the partial model at <br>> >> low resolution (3.5 Ang), similar to TNT/BUSTER.<br>> >><br>> >> Thanks<br>> >> venkat<br>> >><br>> >><br>> >><br>> >> _______________________________________________<br>> >> phenixbb mailing list<br>> >> phenixbb@phenix-online.org<br>> >> http://www.phenix-online.org/mailman/listinfo/phenixbb<br>> ><br>> ><br>> > Thomas C. Terwilliger<br>> > Mail Stop M888<br>> > Los Alamos National Laboratory<br>> > Los Alamos, NM 87545<br>> ><br>> > Tel: 505-667-0072 email: terwilliger@LANL.gov<br>> > Fax: 505-665-3024 SOLVE web site: http:// <br>> > solve.lanl.gov<br>> > PHENIX web site: http:www.phenix-online.org<br>> > ISFI Integrated Center for Structure and Function Innovation web <br>> > site: http://techcente!
r.mbi.ucla.edu<br>> > TB Structural Genomics Consortium web site
: http://www.doe-mbi.ucla.edu/TB<br>> > CBSS Center for Bio-Security Science web site: http://www.lanl.gov/ <br>> > cbss<br>> ><br>> ><br>> ><br>> ><br>> ><br>> ><br>> > _______________________________________________<br>> > phenixbb mailing list<br>> > phenixbb@phenix-online.org<br>> > http://www.phenix-online.org/mailman/listinfo/phenixbb<br>> <br>> <br>> Thomas C. Terwilliger<br>> Mail Stop M888<br>> Los Alamos National Laboratory<br>> Los Alamos, NM 87545<br>> <br>> Tel: 505-667-0072 email: terwilliger@LANL.gov<br>> Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov<br>> PHENIX web site: http:www.phenix-online.org<br>> ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu<br>> TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB<br>> CBSS Center for Bio-Se!
curity Science web site: http://www.lanl.gov/cbss<br>> <br>> <br>> <br>> <br>> _______________________________________________<br>> phenixbb mailing list<br>> phenixbb@phenix-online.org<br>> http://www.phenix-online.org/mailman/listinfo/phenixbb<br><br /><hr />With Windows Live, you can organize, edit, and <a href='http://www.microsoft.com/middleeast/windows/windowslive/products/photo-gallery-edit.aspx' target='_new'>share your photos.</a></body>
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