- phenixbb - phenix-online.org

Re: [phenixbb] ramachanran plot refinement or restraint?
by Ralf W. Grosse-Kunstleve 26 Jul '07

26 Jul '07

Hi Jianghai, > I am refining a low resolution huge protein structure. There are > about 20% residues in the disallowed region of ramachandran plot. Is > there a way in phenix.refine to refine the phi, psi angles to get a > better ramachandran plot? or a phi, psi restraints in refinement? If you add discard_psi_phi=False to the phenix.refine command line the psi and phi dihedral angles are restraint according to the CCP4 monomer library definitions in mon_lib_list.cif (run phenix.where_mon_lib_list_cif to get the full path name). Look for data_link_TRANS and data_link_CIS, scroll down to _chem_link_tor.value_angle, to see the restraint definitions. We don't have much experience using the phi, psi restraints. If you don't mind, please let us know how it goes! Ralf

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ramachanran plot refinement or restraint?
by Jianghai Zhu 26 Jul '07

26 Jul '07

Hi, I am refining a low resolution huge protein structure. There are about 20% residues in the disallowed region of ramachandran plot. Is there a way in phenix.refine to refine the phi, psi angles to get a better ramachandran plot? or a phi, psi restraints in refinement? Thanks. Jianghai +++++++++++++++++++++++++++++++ Jianghai Zhu, Ph.D CBR Institute for Biomedical Research Department of Pathology Harvard Medical School 200 Longwood Ave., Boston, MA 02115 Ph: 617-278-3211 Fx: 618-278-3232 +++++++++++++++++++++++++++++++

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problems in installation of phenix
by tara kashav 25 Jul '07

25 Jul '07

Dear all, I am trying to install phenix but getting following error. My system specifications are: 2.6.5-1.358 i686. Can anyone suggest me how to troubleshoot and install the program. Traceback (most recent call last): File "/usr/local/phenix-1.3b/phenix/wxGUI/wxPhenix.py", line 11, in <module> import wx File "/usr/local/phenix-1.3b/build/intel-linux-2.6 /base/lib/python2.5/site-packages/wx-2.8-gtk2-ansi/wx/__init__.py", line 45, in <module> from wx._core import * File "/usr/local/phenix-1.3b/build/intel-linux-2.6 /base/lib/python2.5/site-packages/wx-2.8-gtk2-ansi/wx/_core.py", line 4, in <module> import _core_ ImportError: libXfixes.so.3: cannot open shared object file: No such file or directory Thanks, Tara Kashav, Dr. S. Gourinath's Lab, Lab No 430, School of Life Sciences, Jawaharlal Nehru University, New Delhi - 110067

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Re: [phenixbb] How to keep a custom bond planar ?
by Ralf W. Grosse-Kunstleve 24 Jul '07

24 Jul '07

Hi Mathieu, Also sorry for the late reply. > How can I define a plan or some dihedral ?? Sorry, this is not implemented (not hard, but never got to it). > Or as in the ligand .cif I defined a plan > LIG plan-2 C1 0.020 > LIG plan-2 C2 0.020 > LIG plan-2 C3 0.020 > > I could add the atoms NZ and CE of the lysine to the plan-2. You can define the bond, angles, dihedrals, chiralities and planarities with a cif link. Currently we don't generate such links automatically (it is in the works). To get a start, copy one of the links from the mon_lib_list.cif file; the command phenix.where_mon_lib_list_cif will give you the absolute path. Give the cif link a unique name and modify it for your situation. Then use "apply_cif_link" as described in the phenix.refine documentation, e.g. at the CCI Apps download page (http://www.phenix-online.org/download/cci_apps/). Let me know if you need more specific help. Ralf

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Re: [phenixbb] handling of alternate conformations
by Ralf W. Grosse-Kunstleve 24 Jul '07

24 Jul '07

Hi Ulrich, Sorry for the late reply. I was out of town for a week. > My first question is whether NCS constraints are also applied to alternate > conformations. Should be, but is not heavily tested. All NCS restraints are listed in the .geo file created by phenix.refine (assuming write_geo_file=True, which is the default). Look for the long lists following "NCS restraint group". Do your alternative conformation atoms appear in these lists? > My second question concerns the atom count of the conformers, where the > parts with non-alternating conformations seem to be included as well. Pavel's explanation from last week is correct. Internally a "conformer" is always a complete chain. The bond, angle, dihedral, chirality, and planarity restraints are determined independently for each conformer. This generates duplicate restraints which are checked for consistency and then reduced again. Ralf

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handling of alternate conformations
by Ulrich Baumann 16 Jul '07

16 Jul '07

Dear Phenix experts, we encounter the following "problem" when trying to refine alternating conformations: we have a complex with 4 chemically different polypeptide chains in the asymmetric unit, composition A3B3CD. For chains C and D we see additional density, which appears to belong to three alternating conformations which can be thought as rigid-body motions (for the whole chains C and D, let's call these conformers 1,2 and 3, but we label them conventionally in the file with the prefix A,B,and C) with roughly estimated occupancies of about 0.3, 0.3 and 0.4 (we can really see most of them). A and B have no visible alternating conformations (occupancies set to 1.0). From the atom count it appears that phenix reads in three conformers called A,B and C with A: A3B3C(1)D(1), B: A3B3C(2)D(2) and C: A3B3C(3)D(3). Phenix.refine says it has these 3 conformers: conformer A A:2700 atoms, conformer B:2700 atoms, common with A 2100, conformer C:2700 atoms, common with A 2100, common with B 2100. Refinement yields an R/Rfree of about 0.210/0.325. If we treat the three conformers of polypeptide chains C and D as independent chains with occupancy each 1.0 (this is possible 'cos there are no repulsive contacts between them, fortunately), we get R/Rfree of 0.243/0.291 and phenix applies NCS restraints to all chains. The resolution is about 2.9 A. We use phenix.refine from the CCI_APPS, version 2007-03-26-1903, SUSE Linux. My questions is: is the difference due to the lack of NCS between conformers or are the occupancies mistreated somwhow? I am asking because I would not consider the whole A3B3C(x)D(x) particle as a conformer but only chains C and D ...... Is there a possibility to apply NCS restraints to conformers? Many thanks in advance, Ulrich

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How to keep a custom bond planar ?
by Coincon Mathieu 16 Jul '07

16 Jul '07

Hi, I defined a bond (and angles) between my ligand and the NZ of a lysine in a file (bond.def). ..-C2-.. | -CE-NZ = C1-C3-.... This is a double bond. Everything work good except for the planarity of the lysine's atoms. For the bond I wrote in my bond.def: bond { action = *add atom_selection_1 = chain D and resname LIG and name C2 atom_selection_2 = chain A and resname LYS and resid 66 and name NZ distance_ideal = 1.340 sigma = 0.02 } For an angle: angle { action = *add atom_selection_1 = chain D and resname LIG and name C3 atom_selection_2 = chain D and resname LIG and name C2 atom_selection_3 = chain A and resname LYS and resid 66 and name NZ angle_ideal = 120.000 sigma = 3 } How can I define a plan or some dihedral ?? Or as in the ligand .cif I defined a plan LIG plan-2 C1 0.020 LIG plan-2 C2 0.020 LIG plan-2 C3 0.020 I could add the atoms NZ and CE of the lysine to the plan-2. Thanks by advance. And by the way phenix (with coot) is GREAT (I did my apo-enzyme in four days !!!!) -------- Mathieu Coicon PhD Student Biochimie Universite de Montreal (+1)514-343-6111 #5352

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Phaser
by john kryst 13 Jul '07

13 Jul '07

Hi all !!! Is it possible to fix one domain and search for the second one in phaser !!! What are the keywords to use for that. I have a protein with two domains. It i give both the domains together it is not finding the solution. If i give only one domain it is giving the solution and the R and Rfee is 28 and 33. But it is not finding the second one. Thanks in advance for your suggestions.. regards John

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Refinement use of Friedel pairs
by Mark A Saper 11 Jul '07

11 Jul '07

I am refining a structure containing SeMet with data collected at peak wavelength. Provided I give the f' and f'', will phenix.refine calculate F+ and F- structure factors and use the provided FOBS+ and FOBS- ? CNS does this. Refmac only uses f' and I get >6 sigma Fo-Fc peaks on the Se. Thanks for your help. _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry Biophysics Research Division, University of Michigan 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu (734) 764-3353 fax (734) 764-3323 http://www.biochem.med.umich.edu/biochem/research/profiles/saper.html

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setting resolution for 2 datasets in AutoSol
by Thomas C. Terwilliger 09 Jul '07

09 Jul '07

Hi Luca, It's easiest to do this in 2 steps: 1a. You can set the resolution separately for each dataset in the AutoSol Wizard. In the GUI, just go through each dataset and set the overall resolution to your desired values as you go. Ignore the density modification and building that occurs in this run. 1b. Then you'll get an output exptl_fobs_phases_freeR_flags_2.mtz or equivalent that is phased to the resolution you specified, but that has all the data (with no phases) to higher resolution. 2. Now run the AutoBuild wizard, and set the resolution to your high-resolution limit. That should use the phases you generated, and include the high-res data for density modification and refinement. Equivalently, you can run AutoSol at low resolution then run AutoBuild at higher resolution by supplying an input_hires_file with the hires data. A key point here is that the building in AutoSol is just a preliminary build...the building in AutoBuild is the real thing. You can also run 2 datasets and set the resolution for each in a script. Here is a script to read in 2 SAD datasets and solve them together as one, setting the resolution of phasing to 3 A for the first and 2.9 for the second, cat two_datasets.inp input_seq_file seq.dat resolution 2.9 # Resolution expt_type sad input_file_list se.sca ############## NEW DATASET ################ run_list start # run "start" method. run_list read_another_dataset # starting a new dataset here resolution 3.1 # Resolution input_file_list br.sca Let me know if that does not do it! -Tom T >> From: lp212(a)mole.bio.cam.ac.uk >> Date: July 9, 2007 3:38:28 PM PDT >> To: phenixbb(a)phenix-online.org >> Subject: script for Zn and Se phasing >> Hi, >> I have collected two peak datasets on two different crystals, for a protein that contains zinc: >> 1. peak dataset at the Zn edge (lambda=1.285A, 2.5A reso) >> 2. peak dataset at the Se edge (lambda=0.98A, 2.8A reso) >> The protein has 2 Zn and 11 SeMet, and 4/au. When I input both >> datasets in the AutoSol GUI, Hyss finds correctly 8/8 Zn sites, and ~34/44 Se sites, but only when I cut back the resolution (4.2A for Zn, and 4.7A for Se). What I can't figure out is how to tell the Autosol GUI to use a low-res cutoff for finding the sites, and then use all the data for model building. Could someone please explain how to do this in the GUI, or send me a script? >> Thanks a lot! Apologies if this is trivial... >> Luca >

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