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LigandFit parameters?
by Hermella Woldemdihin 27 Jul '10

27 Jul '10

Hi, I am using LigandFit on the GUI version of Phenix. In my electron density map there is a good density for my ligand. And I have my ligand in pdb format. As an input to LigandFit I gave my ligand file(pdb), an MTZ file from my data processing and my protein at some stage of refinement (@ a good R-values). I used the default settings (Resolution=0, Minimum CC of ligand to map=0.75 and Ligand map shape=Fo-Fc) and I got a bad result. My overall CC=0.33 and Score=68.68). What shall I do to get the best solution??? Thanks all! Hermi

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Planarity restraint for covalent linkage
by Elwood A. Mullins 24 Jul '10

24 Jul '10

I'm trying to refine a thioester linkage (CoA to glutamate). Is it possible to define planarity restraints in a refinement.geometry_restraints.edits file along with bonds and angles? If not, what would be the best way to restrain the linkage?

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questions about ncs copy in autobuild
by J J 23 Jul '10

23 Jul '10

Dear All, I am using phenix.autobuild .eff file to build a structure (version 1.6.1). For the input I have a pdb model file with 6 chains; a sequence file which contains residues of a single chain (the sequence file has a few more residues at N-terminal than the pdb model file); an mtz amplitude file; I also specified ncs_copies=6 (I know there are 6 copies in the au). What confuses me is the output pdb file only has one chain (huge Rwork&Rfree, >0.5). Should there be 6 chains? The other issue is that the output chain has fewer residues than my sequence file (both N&C-terminal). It also has fewer residues compared with the pdb model file. Is this because I do not have enough resolution to resolve those missing residues? Thanks in advance. Jason U Pitt

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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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