[phenixbb] low resolution map

[Tom Terwilliger]

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 <ramme29 at yahoo.com>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> Sent: Wednesday, September 2, 2009 6:11:01 PM
> Subject: Re: [phenixbb] low resolution map
>
> Dear Tom
>
> thanks.
>
> From: Tom Terwilliger <terwilliger at lanl.gov>
> To: PHENIX user mailing list <phenixbb at phenix-online.org>
> 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: terwilliger at LANL.gov
> 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: terwilliger at LANL.gov
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