July 2010 - phenixbb - phenix-online.org

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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sum(occ)<1?
by Ed Pozharski 17 Jul '10

17 Jul '10

Let's say there are two orientations of a ligand for which occupancies need to be refined. By default, the sum of the two will be fixed at 1.0. From quick look at the manual, the only way to have the sum(occ) at lower level is to reset main.occupancy_max. However, this will probably affect all the atoms for which occupancies are refined, which is undesirable (while ligand may have total occupancy of <1, alternate conformers for protein residues should always add up to 1). Am I missing something or the only way to get this done is to refine twice - once only for ligand occupancy, and then for the rest of the model. And what if total occupancy of the ligand is unknown? Is there a way to allow sum(occ) to be anywhere between 0 and 1? -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs

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how to fix a secondary structure?
by xinghua qin 17 Jul '10

17 Jul '10

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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How to manually define NCS group for phenix.autobuild?
by J J 15 Jul '10

15 Jul '10

Hello everyone, It is easy to manually define NCS group in phenix.refine, but how to manually define it in phenix.autobuild? phenix.simple_ncs_from_pdb will generate an .ncs_spec file which can be used in autobuild, but what if I want to define ncs group myself, say removing some residues from the automatically detected one. I can manually remove them from the .ncs_spec file, but the operations defined in the .ncs_spec is no longer valid? Thanks in advance Jason U Pitt

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