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:
[email protected]******************************************************************************
"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 <[email protected]>
Subject: Re: [phenixbb] Autobuild for very elongated models
To: [email protected],PHENIX user mailing list <[email protected]>
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: [email protected]
******************************************************************************
"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: [email protected]
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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