[phenixbb] Autobuild for very elongated models

Wed Oct 14 07:41:32 PDT 2009

Hi Gino,

I should have added that the use of a model mask in autobuild is most  
appropriate for calculating maps (maps_only=true) .  If you use it in  
a full cycle of autobuild you may get into trouble because autobuild  
also uses the keyword "model=..." and so the model building may not  
work correctly.

So the best thing to do is try it in a single cycle, with  
maps_only=true, and have a look at the map.

All the best,
Tom T

On Oct 14, 2009, at 8:35 AM, Gino Cingolani wrote:

> 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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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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