- phenixbb - phenix-online.org

Defining heavy atom sites for AutoSol
by Kyle Dolan 23 Jul '10

23 Jul '10

Hi all, I used AutoSol to generate SAD phases for a protein after completing a partial MR model. My strategy worked, but I noticed there were more heavy atom sites in the solution than I was expecting. Having continued to build and refine the structure, I am fairly certain that I know which sites are the real sites and which ones are noise. I would like to use the real sites to reproduce the experimental phases in AutoSol or another Phenix module to perhaps improve the map quality (essentially running just SOLVE or Phaser without HYSS or model-building). What is the right approach? I am guessing something like this: phenix.autosol data.sca sequence.dat sites_file=sites.pdb build=False Cheers, Kyle Kyle T. Dolan Department of Biochemistry and Molecular Biology The University of Chicago ktd(a)uchicago.edu

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Re: [phenixbb] phenix.automr ensemble/component question
by Thomas C. Terwilliger 23 Jul '10

23 Jul '10

Hi Scott, Your first command looks good to me. It is saying that the composition of the crystal is 2 copies of each chain: component_1.component_copies=2 component_2.component_copies=2 and you want to search for 2 copies of each of your search models: ensemble_1.copies_to_find=2 ensemble_2.copies_to_find=2 All the best, Tom T > Hi Phenixers, > > I'm a bit confused about the proper syntax for my phenix.automr job. > This is probably a simple concept, but I'm running on 3 hours of sleep > as my kid was up all night, and my synapses aren't working so good. > > I expect 2 copies of my protein per AU > > My protein is composed of two domains > > I have a single PDB search model for each domain > > is either of these commands correct? > > phenix.automr data=mydata.sca \ > ensemble_1.coords=domain1.pdb \ > ensemble_1.identity=95 \ > ensemble_1.copies_to_find=2 \ > component_1.mass=40579 \ > component_1.component_copies=2 \ > ensemble_2.coords=domain2.pdb \ > ensemble_2.identity=95 \ > ensemble_2.copies_to_find=2 \ > component_2.mass=13410 \ > component_2.component_copies=2 > > > or > > > phenix.automr data=mydata.sca \ > ensemble_1.coords=domain1.pdb \ > ensemble_1.identity=95 \ > ensemble_1.copies_to_find=1 \ > component_1.mass=40579 \ > component_1.component_copies=2 \ > ensemble_2.coords=domain2.pdb \ > ensemble_2.identity=95 \ > ensemble_2.copies_to_find=1 \ > component_2.mass=13410 \ > component_2.component_copies=2 > > > essentially I'm not really using an ensemble of search models, I only > have a single PDB for each domain. So should ensemble_1.copies_to_find > and ensemble_2.copies_to_find be set to 1 or 2? > > > Thanks, > Scott > > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > Scott Classen, Ph.D. > SIBYLS Beamline 12.3.1 > http://bl1231.als.lbl.gov > Advanced Light Source > Lawrence Berkeley National Laboratory > 1 Cyclotron Rd > MS6R2100 > Berkeley, CA 94720 > C) 510.206.4418 > O) 510.495.2697 > Beamline) 510.495.2134 > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb >

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writing composite omit maps in .xplor
by Susan Tsutakawa 23 Jul '10

23 Jul '10

Hi all, Continuing the conversation on looking at Phenix maps in pymol, what is the best way to generate .xplor maps in Autobuild. I would like to generate a figure in pymol with an omit map. I wasn't able to find documentation explicitly stating how this can be done. Sincerely, Susan

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Questions about sequence file vs pdb model file in Autobuild
by J J 22 Jul '10

22 Jul '10

Dear All, Facts: -input: a sequence file, a pdb model file, an mtz file; the sequence file is the same as the pdb model except that the sequence file has 6 more residues at N-terminal; the pdb model is almost the same as my protein structure. (In a word, I just want to add a few more residues to the current pdb model. Of course I can do it in coot by manually placing residues at the N-terminal, but why not autobuild?) -problem: the output chain sequence is not the same as the sequence file (not the same as the input model file either). It misses some residues at the N-terminal and it adds some residues at the C-terminal (but disconnected from the C-terminal). Is it normal in autobuild? How to correct it? Thanks. Jason U Pitt

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Hydrogen bonds
by Owen Pornillos 21 Jul '10

21 Jul '10

Hi - Is it possible to explicitly declare a hydrogen bond restraint for non- backbone atoms, e.g., one between a helix capping Ser Ogamma atom and a backbone NH? Thanks, Owen

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Re: [phenixbb] Selecting ellipsoid of data
by Kay Diederichs 20 Jul '10

20 Jul '10

Hi Frank, "such a tool" is at http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Aniso_cutoff where it's meant to be applied to INTEGRATE.HKL which comes out of XDS. Doing it this way has the benefit that the statistics printed out by XDS' CORRECT (or SCALA/TRUNCATE; there are people who prefer that route) match the data you refine agains. HTH, Kay > Message: 1 > Date: Thu, 15 Jul 2010 06:32:40 +0100 > From: Frank von Delft<frank.vondelft(a)sgc.ox.ac.uk> > To: PHENIX user mailing list<phenixbb(a)phenix-online.org> > Subject: [phenixbb] Selecting ellipsoid of data > Message-ID:<4C3E9D78.5030203(a)sgc.ox.ac.uk> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi, is there a tool in phenix that allows me to select an ellipsoid of > data -- specified e.g. by the highest resolutions in three reciprocal > lattice directions. (Yes, I'm playing with anisotropy, "playing" being > the operative word.) > > phx > > > ------------------------------ > > Message: 2 > Date: Wed, 14 Jul 2010 22:47:30 -0700 > From: "Ralf W. Grosse-Kunstleve"<rwgk(a)cci.lbl.gov> > To: phenixbb(a)phenix-online.org > Subject: Re: [phenixbb] Selecting ellipsoid of data > Message-ID:<201007150547.o6F5lUoL018490(a)cci.lbl.gov> > Content-Type: text/plain; charset=us-ascii > > Hi Frank, > >> Hi, is there a tool in phenix that allows me to select an ellipsoid of >> data -- specified e.g. by the highest resolutions in three reciprocal >> lattice directions. (Yes, I'm playing with anisotropy, "playing" being >> the operative word.) > > I'm not aware of such a tool. > > Ralf > > > ------------------------------ > > Message: 3 > Date: Thu, 15 Jul 2010 07:15:58 +0100 > From: Frank von Delft<frank.vondelft(a)sgc.ox.ac.uk> > To: "Ralf W. Grosse-Kunstleve"<rwgk(a)cci.lbl.gov>, PHENIX user mailing > list<phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] Selecting ellipsoid of data > Message-ID:<4C3EA79E.2030503(a)sgc.ox.ac.uk> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Ralf > > Yeah, I figured. So if I want to use cctbx, where do I start? Just a > pointer to a) package and b) function where I'll see the syntax. > > So equation for ellipsoid is x^2/a^2 + y^2/b^2 + z^2/c^2 = 1; so I > imagine I take each reflection, convert each of h,k,l to 1/reso, and > with a = 1/res(a*), I just check whether the above is< 1. > > The main thing I still need is to convert h,k,l into orthogonal > coordinates.... or do I? I suppose I don't, as what I care for is not > whether it's "really" an ellipsoid, only whether it cuts through miller > index space anisotropically. > > Hmmmm... I may be able to do it in sftools; but if you can in<1minute > give me a link to where to look to get started in cctbx, that would be > awesome. > > (Thanks for listening :) > > > > >> Hi Frank, >> >> >>> Hi, is there a tool in phenix that allows me to select an ellipsoid of >>> data -- specified e.g. by the highest resolutions in three reciprocal >>> lattice directions. (Yes, I'm playing with anisotropy, "playing" being >>> the operative word.) >>> >> I'm not aware of such a tool. >> >> Ralf

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Iodide scattering factor
by Owen Pornillos 20 Jul '10

20 Jul '10

Hi BB, I am refining a structure that contains iodide ions. I remember some previous posts that PHENIX does not take into account the charge state and uses scattering factors for neutral atoms only. Is this still true? Thanks, Owen

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error on the latest phenix
by Jian Wu 20 Jul '10

20 Jul '10

Hi all, Today, I download the latest version phenix-1.6.3-473 and everything is ok during the installation. However, when I open the graphical phenix, something wrong has happened showed as below: Traceback (most recent call last): File "/local/prog/phenix-1.6.3-473/phenix/wxGUI2/command_line/main.py", line 13, in <module> run(sys.argv[1:]) File "/local/prog/phenix-1.6.3-473/phenix/wxGUI2/command_line/main.py", line 7, in run from wxGUI2 import App File "/local/prog/phenix-1.6.3-473/phenix/wxGUI2/App.py", line 6, in <module> import wx.lib.dialogs ImportError: No module named wx.lib.dialogs Any suggestions and comments will be appreciated. Best, Jian -- Jian Wu Ph.D. Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences (CAS) Tel: 0086-21-54921217 Email: protease(a)gmail.com

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Whic mtz file to use and parameters for phenix.refine (GUI) to set?
by Hermella Woldemdihin 20 Jul '10

20 Jul '10

Hi, I am new to phenix.refine. I'm using the graphical interface. I hav processed my dfiffraction data and used Phaser MR for molecular replacement. And I goyt a result: a solution pdb file and the associated mtz file. 1. So I use the mtz file from this Phaser MR solution or the original file from my data processing in phenix.refine? 2. I have set parameters for phenix.refine like this: Is there other settings for the parameter which I should do for a better result? PDB data: my solution from Phaser MR XRAY DATA= ???? Simulated Annealing=1000 Update waters Refine Target weights: Wxc=0.8 Wxu=1.6 Cycles=5 Fix rotamers Fix bad side chains

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modify the helices
by xinghua qin 19 Jul '10

19 Jul '10

hi everyone: Thanks for all the response! what I said last time may be chinglish and lead to some misunderstanding, the word I said fix a helix means that the model quality of the helix is not very good, I want to modify it manually.It is so hard to do this in low resolution.I modified the helix according to the electron density map, after refinement, large red areas appear in the difference map. That made me crazy! Are there any suggestions or any reviews about this point? I am new beginner to structural biology, any suggestions are welcomed ! Best regards Xinghua Qin Xinghua Qin College of Biological Sciences No.2, Yuan Ming Yuan West Road Haidian District?Beijing?China?100094 Tel: +86-10-62732672 > > > Message: 2 > Date: Fri, 16 Jul 2010 22:10:32 -0700 > From: Pavel Afonine <pafonine(a)lbl.gov> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] sum(occ)<1? > Message-ID: <4C413B48.305(a)lbl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hi Ed, > > > Reset occupancies that are outside the [0,1] range at every step of > > minimization. > > this simply will not work: this will invalidate the internal memory of > LBFGS minimizer that we use in phenix.refine and as result it will drive > it crazy. > > Pavel. > > > > ------------------------------ > > Message: 3 > Date: Fri, 16 Jul 2010 22:24:35 -0700 > From: Pavel Afonine <pafonine(a)lbl.gov> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] how to fix a secondary structure? > Message-ID: <4C413E93.6010002(a)lbl.gov> > Content-Type: text/plain; charset=UTF-8; format=flowed > > Hi Xinghua, > > you can use secondary structure restrains that are available in > phenix.refine. It will automatically figure out secondary structure and > apply proper restrains. This should preserve your helix geometry and > still refine it. > > Example: > > phenix.refine model.pdb data.mtz main.secondary_structure_restraints=true > > > Recently I am trying to fix a helice, but found that it is so hard > > for me because of the poor resolution(3.2A) and also a unvisible loop > > near it, so is there any way to just fix a helice ? can I get it out > > of the whole structure to refine it? > > If you still prefer not refining that helix over applying > secondary-structure restrains, then you can do that too: > > phenix.refine model.pdb data.mtz refine.sites.individual="not (chain A > and resseq 123:156)" > > where atom selection > > chain A and resseq 123:156 > > selects your helix, and prefix "not" means you exclude it from refinement. > > Of course you can do all this from PHENIX GUI. > > Let me know if you have any questions. > > Pavel. > > > ------------------------------ > > Message: 4 > Date: Fri, 16 Jul 2010 22:48:52 -0700 > From: Pavel Afonine <pafonine(a)lbl.gov> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] how to fix a secondary structure? - P.S. > Message-ID: <4C414444.8080208(a)lbl.gov> > Content-Type: text/plain; charset="utf-8"; Format="flowed" > > By the way, more information about secondary structure restraints in > phenix.refine you can find in recent PHENIX Newsletter (pages 12-17): > > http://www.phenix-online.org/newsletter/CCN_2010_07.pdf > > Pavel. > > > On 7/16/10 5:52 PM, xinghua qin wrote: > > Hi phenixers: > > Recently I am trying to fix a helice, but found that it is so hard > > for me because of the poor resolution(3.2A) and also a unvisible loop > > near it, so is there any way to just fix a helice ? can I get it out > > of the whole structure to refine it? > > > > Best regards > > > > Xinghua Qin > > > > -- > > Xinghua Qin > > College of Biological Sciences > > No.2, Yuan Ming Yuan West Road > > Haidian District?Beijing?China?100094 > > Tel: +86-10-62732672 > > > > > > ------------------------------ > > >

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