August 2010 - phenixbb - phenix-online.org

Constraining carbohydrate conformation
by Kenneth Verstraete 19 Aug '10

19 Aug '10

Dear phenixbb users, I wonder how I can constrain the conformation of a NAG-residue during refinement. I have a dataset to 4.2 Angstrom. After refinement some sugars end up in the boat conformation. I would like to run the refinement so that the Asn side chain and the Asn-NAG linkage is refined (using xyz or torsion angle dynamics) but that the NAG-residue itself is considered as a rigid group. Maybe one way of doing this is constraining the bonds and angles of the NAG residue by the defining them as "custom bonds and angles" with sigma=0? Is there a possibility in phenix to generate these constraints from an ideal NAG-residue automatically? Thank you very much for you advice, Kenneth Verstraete

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clean up temporary files
by Jianghai Zhu 18 Aug '10

18 Aug '10

Hi, I realize that after a phenix run, especially autobuild and autosol, there are a lot of temporary files. Is there a way to clean up the disk? Even the .geo file can be removed after some time, because it is huge and can be easily regenerated. -- Jianghai

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ubuntu 10.04 phenix installation
by vincent rao 18 Aug '10

18 Aug '10

Dear Phenix bb user, i'm trying to install the latest version of phenix (1.6.4-486) on my pc with Ubuntu 10.04 installed. I'm using the*phenix-installer-1.6.4-486-intel-linux-2.6-x86_64-fc13.tar * installer. The installer complains that the * bundle-1.6.4-486-intel-linux-2.6-x86_64.tar.gz* is missing in the phenix-installer-1.6.4-486/bundles folder, and requires *bundle-1.6.4-486-intel-linux-2.6.tar.gz *to be present in this folder. So i simply renamed *bundle-1.6.4-486-intel-linux-2.6-x86_64.tar.gz *to *bundle-1.6.4-486-intel-linux-2.6.tar.gz *and this allowed the installation to complete without any further errors. However, when trying to start Phenix, i get the following error: laptop:~/Documents/installers/phenix-installer-1.6.4-486> phenix Traceback (most recent call last): File "/usr/local/phenix-1.6.4-486/phenix/wxGUI2/command_line/main.py", line 13, in <module> run(sys.argv[1:]) File "/usr/local/phenix-1.6.4-486/phenix/wxGUI2/command_line/main.py", line 7, in run from wxGUI2 import App File "/usr/local/phenix-1.6.4-486/phenix/wxGUI2/App.py", line 6, in <module> import wx.lib.dialogs File "/usr/local/phenix-1.6.4-486/build/intel-linux-2.6/base/lib/python2.6/site-packages/wx-2.8-gtk2-ansi/wx/__init__.py", line 45, in <module> from wx._core import * File "/usr/local/phenix-1.6.4-486/build/intel-linux-2.6/base/lib/python2.6/site-packages/wx-2.8-gtk2-ansi/wx/_core.py", line 4, in <module> import _core_ ImportError: /usr/local/phenix-1.6.4-486/build/intel-linux-2.6/base/lib/python2.6/site-packages/wx-2.8-gtk2-ansi/wx/_core_.so: wrong ELF class: ELFCLASS64 Not sure if this is of any use in solving the problem, but i typed the following command phenix.wxpython -c "import sys; print sys.path" and got the following output; ['', '/usr/local/phenix-1.6.4-486', '/usr/local/phenix-1.6.4-486/cctbx_project', '/usr/local/phenix-1.6.4-486/reel', '/usr/local/phenix-1.6.4-486/phaser', '/usr/local/phenix-1.6.4-486/tntbx', '/usr/local/phenix-1.6.4-486/phenix', '/usr/local/phenix-1.6.4-486/elbow', '/usr/local/phenix-1.6.4-486/PyQuante', '/usr/local/phenix-1.6.4-486/docutils', '/usr/local/phenix-1.6.4-486/PyCifRW', '/usr/local/phenix-1.6.4-486/cctbx_project/boost_adaptbx', '/usr/local/phenix-1.6.4-486/cctbx_project/libtbx/pythonpath', '/usr/local/phenix-1.6.4-486/build/intel-linux-2.6/lib', '/usr/local/phenix-1.6.4-486/build/intel-linux-2.6/base/lib/python26.zip', '/usr/local/phenix-1.6.4-486/build/intel-linux-2.6/base/lib/python2.6', '/usr/local/phenix-1.6.4-486/build/intel-linux-2.6/base/lib/python2.6/plat-linux2', '/usr/local/phenix-1.6.4-486/build/intel-linux-2.6/base/lib/python2.6/lib-tk', '/usr/local/phenix-1.6.4-486/build/intel-linux-2.6/base/lib/python2.6/lib-old', '/usr/local/phenix-1.6.4-486/build/intel-linux-2.6/base/lib/python2.6/lib-dynload', '/usr/local/phenix-1.6.4-486/build/intel-linux-2.6/base/lib/python2.6/site-packages', '/usr/local/phenix-1.6.4-486/build/intel-linux-2.6/base/lib/python2.6/site-packages/Numeric', '/usr/local/phenix-1.6.4-486/build/intel-linux-2.6/base/lib/python2.6/site-packages/PIL', '/usr/local/phenix-1.6.4-486/build/intel-linux-2.6/base/lib/python2.6/site-packages/wx-2.8-gtk2-ansi'] thanks

4 3

geometry weight and rmsd bonds - angles
by Lionel Costenaro 17 Aug '10

17 Aug '10

Hello, I'm using phenix.refine for the first time and have some problem to get it reach reasonable rmsd bonds (0.012-0.015) and angles (1.5-1.8). I set the bonds rmsd_max and angles rmsd_max to these values and try different values for: wxc_scale (from default 0.5 downto 0.015), wxu_scale (from default 1 down to 0.03), wc (from default 1 up to 8), with and without optimising wxc wxu. Whatever the parameters, phenix never reached final rmsd better than 0.022 and 2.2. I refine the structure with refmac so far, but need to refine the occupancies (so phenix). Am I doing something wrong? Should I just use phenix to refine only the occupancy (I am actually doing it)? Any help or comment are welcome. Some information: space group: P21, 2 molecules (180 aa) / au, 510 waters, about 20% alternate conformations, ligand covalently link to the protein (correct dictionary and link parameters for refmac or phenix -add link to cif), resolution: 1.32, refine xyz for all, Baniso for all (refmac), ncs not used, R 13.6 Rfree 17.7 fom 0.913 rmsd 0.012 1.56 (last refmac) phenix version 1.6 289 (gui) Best regards, Lionel

8 20

HKL_base
by Ed Pozharski 17 Aug '10

17 Aug '10

MTZ-files generated by phenix (at least some of them) are missing the base dataset (HKL_base) which is a requirement since CCP4 5.0. Is this deliberate? Ed. -- "I'd jump in myself, if I weren't so good at whistling." Julian, King of Lemurs

3 6

AutoSol scaling error
by Yogesh Gupta 17 Aug '10

17 Aug '10

I got following error while running MIR in phenix: "Failed to carry out AutoSol_scale_and_analyze_MIR: list index out of range". Could some one tell me how to fix this? Thanks, Yogesh

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Re: [phenixbb] Restraints file for a new amino acid residue
by Joseph Noel 16 Aug '10

16 Aug '10

Pavel, I sent you the associated pdb file as an attachment. The site in question is 169 in both monomer A and monomer B. I think one way around the problem for me is to create alternative conformations for the residues on either end of the modified cysteine. In that way I can refine each as a section of alternative conformations and then I think things should link up both in Phenix and COOT. COOT is particularly problematic. It only recognizes conformer A and not any additional conformers for a particular position if the name of the amino acid changes. I guess my case is not that common - ie a mixture of oxidation states of a regular amino acid. Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

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Re: [phenixbb] Restraints file for a new amino acid residue
by Joseph Noel 13 Aug '10

13 Aug '10

Thanks all for the advice. Basically that is what I have been doing. It is actually an oxidized cysteine to sulfenic acid. I am refining the site as alternative conformers with the normal Cys, the single oxidation state to sulfenic acid (CSO) and the double to sulfinic acid (CSD). I know that CSO is in the phenix library but it adds hydrogens to the amino group every time I run elbow or ready set. I then I have to edit the PDB file to delete the hydrogen or Phenix will not refine. I also have problems in COOT. It will not let me move the residues torsional angles. I have checked other structures in the PDB and the density fits perfectly with the structures of many such oxidized systems but for some reason Phenix is giving me some problems. I was going to create a "new" residue and explicitly define the oxygen as charged rather then protonated since the pKa of sulfenic acid is quite low. Maybe the problems all stem from refining this particular position with three alternative "conformers", each conformer of which is chemically distinct. For now, I have CSO labeled as convention BCSO for conformer B. Cys is ACYS. Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

2 1

Autobuild error message
by bschmidt＠berkeley.edu 13 Aug '10

13 Aug '10

Hello all, I am trying to use phenix.autobuild from the command line to generate either composite omit maps or prime and switch maps. In either case, when I try, the program starts to run for a while before failing and giving me the following error message: "Failed to carry out AutoBuild_build_cycle: Sorry...the file AutoBuild_run_2_/TEMP0/refine_pdb_in.mtz is missing..." I'm not sure why that would be the case, or where that mtz is supposed to come from. Can anyone explain what might be the problem? Thanks, Bryan

2 2

Phaser SAD module - resolution question
by Peter Grey 13 Aug '10

13 Aug '10

Dear Phenix community, I am using Phaser SAD module with a poor MR model to locate the initial heavy-atom sub-structure. I have a 3A dataset but the anomalous signal is weak at the higher resolution shells. I would like to ask for your advice regarding the resolution I should use in Phaser. I thought that for the sake of just locating the sites I should use relatively low resolution (let's say 3.5 or even 4A) and then run Phaser a second time. In this second run I would use the highest-resolution and let Phaser only refine the sites (located in the first run) during one cycle and calculate the combined phases. Thank you in advance for your suggestions and advice, Peter

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