[phenixbb] Autobuild for very elongated models

Tom Terwilliger terwilliger at lanl.gov
Wed Oct 14 07:28:09 PDT 2009

Hi Gino,

Here is how to specify a mask in phenix.autobuild (see https://www.phenix-online.org/documentation/faqs.htm 

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  
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
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)
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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
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