[phenixbb] Autobuild for very elongated models

Wed Oct 14 07:35:59 PDT 2009

Thanks Tom!

Gino
******************************************************************************
Gino Cingolani, Ph.D.
Associate Professor
Thomas Jefferson University
Dept. of Biochemistry & Molecular Biology
233 South 10th Street - Room 826
Philadelphia PA 19107
Office (215) 503 4573
Lab    (215) 503 4595
Fax    (215) 923 2117
E-mail:   gino.cingolani at jefferson.edu
******************************************************************************
"Nati non foste per viver come bruti, ma per seguir virtute e conoscenza"
("You were not born to live like brutes, but to follow virtue and knowledge")
Dante, The Divine Comedy (Inferno,  XXVI, vv. 119-120) 

---- Original message ----
>Date: Wed, 14 Oct 2009 08:28:09 -0600
>From: Tom Terwilliger <terwilliger at lanl.gov>  
>Subject: Re: [phenixbb] Autobuild for very elongated models  
>To: Gino.Cingolani at jefferson.edu,PHENIX user mailing list <phenixbb at phenix-online.org>
>
>Hi Gino,
>
>Here is how to specify a mask in phenix.autobuild (see https://www.phenix-online.org/documentation/faqs.htm 
>#anch68):
>
>-----------------
>How can I specify a mask for density modification in AutoSol/AutoBuild?
>If you want to specify a mask, add this command:
>
>resolve_command_list=" 'model ../../coords.pdb' 'use_model_mask' "
>where there are " and ' quotes and coords.pdb is the model to use for  
>a mask. Note the "../../" because coords.pdb is in your working  
>directory but when resolve runs the run directory is 2 directories  
>lower, so relative to that directory your coords.pdb is at "../../ 
>coords.pdb". You will know it is working if your resolve_xx.log says:
>"Using model mask calculated from coordinates"
>-----------------
>I am not so sure this is the problem, however. I would suggest that  
>you do a quick composite omit map before refinement on your mr model:
>phenix.autobuild data=data.mtz model=MR.1.pdb  
>composite_omit_type=simple_omit
>It is important that this start with you MR unrefined model so that  
>you have no worries about model bias. This procedure will omit a  
>region, refine, calculate a 2Fo-Fc map for the omitted region, then  
>repeat for all other parts of your model and paste them all together  
>and put it in
>AutoBuild_run_1_/OMIT/resolve_composite_map.mtz
>which you can use to calculate a map with LABIN="FP=FP PHIB=PHIM  
>FOM=FOMM" (you need to include the FOM).
>If this map shows density for your whole model...you are in great  
>shape and the problem may indeed be the mask. If it does not...then  
>the model may not be very close and it may be difficult to proceed.
>All the best,
>Tom T
>
>On Oct 14, 2009, at 7:57 AM, Gino Cingolani wrote:
>
>> Hi Everyone,
>>
>> I am trying to solve a very elongated structure (~180A-long) formed  
>> by two long a-helices. I have a good MR solution (Log-Likelihood  
>> Gain ~168.537 to 3.0A resolution), which refines OK immediately  
>> after MR (Rfactor/Rfree 46/50%). The electron density has clear side  
>> chain features and high res data is available to ~2.1A resolution.
>>
>> Logically, I should be able to plug everything into Autobuild and  
>> get a good final model (or at least something better than my input  
>> MR solution). I have tried a million time using different parameters  
>> and datasets, but Autobuild always breaks up my long helical model  
>> into short helical bundles, that refine to random Rfree. In other  
>> words, if my starting MR model is a continuous
>> 80aa-long helix, Autobuild fragments it into three helices of ~30aa  
>> each packed laterally (I see back my initial model if I visualize  
>> symmetry-related atoms in Coot).
>>
>> In parallel, I have made the following observation.
>> If I use DM to improve my phases, prior to Autobuild, I noticed that  
>> something similar happens. DM gives great density for less than half  
>> of my long helix while the rest is flattened.
>> If I look at the solvent mask generated by DM, it basically flattens  
>> half of my elongated model. It seems that at least DM fails to  
>> generate a solvent mask that makes sense with such an elongated  
>> structure (by the way, the unit cell is a=25, b=37, c=220 in  
>> P212121). This problem can be circumvented in DM where
>> an outside solvent mask can be inputted, but what about in phenix?
>>
>> Is it possible that Autobuild is failing because Resolve also makes  
>> a poor solvent mask? Is there a way to see and/or edit the solvent  
>> mask generated by Resolve? Or even better, can I input a new solvent  
>> mask in Autobuild?
>>
>> Thanks in advance for the feedback!
>>
>> Gino
>>
>>
>> ******************************************************************************
>> Gino Cingolani, Ph.D.
>> Associate Professor
>> Thomas Jefferson University
>> Dept. of Biochemistry & Molecular Biology
>> 233 South 10th Street - Room 826
>> Philadelphia PA 19107
>> Office (215) 503 4573
>> Lab    (215) 503 4595
>> Fax    (215) 923 2117
>> E-mail:   gino.cingolani at jefferson.edu
>> ******************************************************************************
>> "Nati non foste per viver come bruti, ma per seguir virtute e  
>> conoscenza"
>> ("You were not born to live like brutes, but to follow virtue and  
>> knowledge")
>> Dante, The Divine Comedy (Inferno,  XXVI, vv. 119-120)
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> 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: 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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