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

...

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) _______________________________________________ phenixbb mailing list [email protected] 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: [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

_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb

---

phenixbb mailing list [email protected] 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: [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