- phenixbb - phenix-online.org

Trouble with occupancy refinement
by Chris Fage 09 Feb '16

09 Feb '16

Hello, I've built several glucose molecules from my cryosolution into regions of weaker electron density. Attempting to refine the occupancies of the corresponding atoms, I set the value of each to 0.25 in the pdb file. However, after running phenix.refine, most of the atoms still have occupancies of 1.00: 14 atoms with occ = 0.00 5 atoms with 0.00 < occ < 1.00 74 atoms with occ = 1.00 Is this unusual? Thank you! Best, Chris

3 6

Re: [phenixbb] sequence independent model building possible?
by Kay Diederichs 09 Feb '16

09 Feb '16

To check if you crystallized a contaminant, use https://strube.cbrc.kaust.edu.sa/contaminer/ HTH, Kay > >On 02/05/2016 01:01 AM, Kaushik Hatti wrote: >> Hello, >> >> Is abinitio model building possible for a map with poly alanine model >at 1.9A resolution? >> >> We thought we had crystallised our protein of interest X, collected >data at 1.9 A and all attempts to solve protein X (which has many >homologs) through MR failed. All attempts to re-crystallise the same >protein also failed. >> >> Now, we think the initial protein which got crystallised could be a >contaminant (we don't have any crystals left from this batch to check >for the sequence of the crystallised protein). Through various methods >(and a bit of luck) we have arrived at a decent map with LLG : 3600 and >TFZ: 22 and R/Rfree : 37/41 (for a poly alanine model). >> >> I believe these scores indicate right fold. As I still don't know >the sequence information, is it possible to build sidechains directly >from the map (I could only identify a couple of residues and the model >largely remains PolyAla)? Autobuild with Rebuild-in-place didn't help >in identifying any more residues. >> >> I have also searched PDB database for similar structures. But, none >of those are either from our expression system (E. coli) or organism of >our protein of interest. Neither did I find any similar sequences from >E. coli or our organism of interest. >> >> Any leads/suggestions would be helpful. >> Thanks, >> Kaushik, >> MRN Murthy lab, >> MBU, >> IISc, India >> >> -- > -- Diese Nachricht wurde von meinem Android-Mobiltelefon mit K-9 Mail gesendet.

3 4

Dual conformation on symmetry axis
by Jan Abendroth 07 Feb '16

07 Feb '16

Hi all, I am running into the following problem during the refinement of a rather small structure at 2.15Å resolution: An Arg side chain is located very close to a crystallographic 2-fold. There is good evidence that the side chain has two conformations. However, because of the 2-fold, conformer A overlaps with its symmetry mate A*, as does conformer B. Phenix wants to avoid this 'clash' and moves A and A* out of the density, same for B and B*. Is there a way to avoid this without reducing the symmetry? In the real crystal, of course the two side chains are agnostic as to if they are called A or B and will avoid one another ... Thanks! Jan -- Jan Abendroth Emerald Biostructures Seattle / Bainbridge Island, WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com

5 10

sequence independent model building possible?
by Kaushik Hatti 06 Feb '16

06 Feb '16

Hello, Is abinitio model building possible for a map with poly alanine model at 1.9A resolution? We thought we had crystallised our protein of interest X, collected data at 1.9 A and all attempts to solve protein X (which has many homologs) through MR failed. All attempts to re-crystallise the same protein also failed. Now, we think the initial protein which got crystallised could be a contaminant (we don't have any crystals left from this batch to check for the sequence of the crystallised protein). Through various methods (and a bit of luck) we have arrived at a decent map with LLG : 3600 and TFZ: 22 and R/Rfree : 37/41 (for a poly alanine model). I believe these scores indicate right fold. As I still don't know the sequence information, is it possible to build sidechains directly from the map (I could only identify a couple of residues and the model largely remains PolyAla)? Autobuild with Rebuild-in-place didn't help in identifying any more residues. I have also searched PDB database for similar structures. But, none of those are either from our expression system (E. coli) or organism of our protein of interest. Neither did I find any similar sequences from E. coli or our organism of interest. Any leads/suggestions would be helpful. Thanks, Kaushik, MRN Murthy lab, MBU, IISc, India -- Stupidity is everyone’s birthright. However, only the learned exercise it! --Kaushik (28Oct2014)

6 6

scaling in Fo-Fo maps
by Xun Lu 05 Feb '16

05 Feb '16

Hello everyone, I have a question on how the scaling is done when generating Fo-Fo maps in Phenix. So I want to compare three datasets (of the same protein of course): A,B,C. I generated three maps: A-B, A-C, B-C, and I can see the differences. But I also want to compare the peaks in the three maps, so I want to make sure the maps are generated using the same scaling. Thanks, Xun p.s. Any other ideas to compare three datasets?

4 4

Feature enhanced map with twinned data
by Matthias Uthoff 05 Feb '16

05 Feb '16

Hi all, I am processing the data of a twinned crystal (fraction approx. 40%) and I was wondering if the FEM module as implemented in Phenix can cope with twinned data? Or should I use a detwinned dataset? Best regards, Matthias -- Matthias Uthoff, PhD Student Institute for Biochemistry University of Cologne Otto-Fischer-Str. 12-14 D-50674 Cologne Phone: +49 221 470 3211 E-Mail: matthias.uthoff(a)uni-koeln.de Internet: http://px.uni-koeln.de

2 1

CORRECTION: refinement of peptide links in mmcif coordinates (multi character chain identifiers)
by wtempel 04 Feb '16

04 Feb '16

Hello all, thanks to Nigel Moriarty, I realized that the problem I encountered had nothing to do with PHENIX, but everything with less-than-careful analysis on my part. The relevant peptide bonds do in fact appear well-restrained by PHENIX. I apologize for the confusion. Wolfram

1 0

refinement of peptide links in mmcif coordinates (multi character chain identifiers)
by wtempel 04 Feb '16

04 Feb '16

Dear PHENIX users, for a structure with approx. 30 instances of an N-terminal AYA (N-acetylalanyl) residue, I have noticed that PHENIX did not restrain planarity of the peptide bond with the next residue. What is the recommended way of restraining those peptide bonds' dihedral angles and bond distances? Thank you, Wolfram Tempel

2 1

Rosetta refine
by Nigel Moriarty 03 Feb '16

03 Feb '16

Folks There has been a problem with the interface between Phenix and Rosetta when running phenix.rosetta_refine due to the randomness involved in the models created by Rosetta. We (mostly Frank DiMaio) have tracked and corrected it. After two weeks of testing, I feel comfortable recommending that users move to 2016.02.58402 bundle. This version update relates only to Rosetta refinement. If you are only using MR Rosetta or ERRASER you may continue using the previous versions. If you wish to use (or even hope to use) programs from both piles, you can follow the installation notes for Rosetta refinement and simply point your environmental variables used (which are common to all three programs) to the new bundle. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

1 0

Problems installing 1.10.1 on RHEL 6.3
by David Briggs 03 Feb '16

03 Feb '16

Hi Phenix, We are trying to upgrade Phenix on our Linux box running RHEL 6.3, kernel 2.6.32-279.14.1.el6.x86_64. I have attempted to install the Centos 5 build and I get an error message during installation: Configuring Phenix components... Traceback (most recent call last): File "./bin/install.py", line 262, in <module> installer(sys.argv[1:]).install() File "/home/public/packages/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos5/lib/libtbx/auto_build/install_distribution.py", line 185, in install self.install_from_binary() File "/home/public/packages/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos5/lib/libtbx/auto_build/install_distribution.py", line 295, in install_from_binary self.reconfigure(log=log) File "/home/public/packages/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos5/lib/libtbx/auto_build/install_distribution.py", line 460, in reconfigure call(args=args, log=log, verbose=self.options.verbose) File "/home/public/packages/phenix-installer-1.10.1-2155-intel-linux-2.6-x86_64-centos5/lib/libtbx/auto_build/installer_utils.py", line 81, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to '/home/public/packages/phenix-1.10.1-2155/base/bin/python /home/public/packages/phenix-1.10.1-2155/modules/cctbx_project/libtbx/configure.py --current_working_directory /home/public/packages/phenix-1.10.1-2155/build --command_version_suffix 1.10.1-2155 phenix phaser solve_resolve labelit' failed with exit code -11 When I attempt install the CentOS6 build I can install Phenix, but when I try and launch it I get a different error message: Traceback (most recent call last): File "/home/public/packages/phenix-1.10.1-2155/build/../modules/phenix/wxGUI2/command_line/main.py", line 23, in <module> run(sys.argv[1:]) File "/home/public/packages/phenix-1.10.1-2155/build/../modules/phenix/wxGUI2/command_line/main.py", line 16, in run from wxGUI2 import App File "/home/public/packages/phenix-1.10.1-2155/modules/phenix/wxGUI2/App.py", line 15, in <module> import wx File "/home/public/packages/phenix-1.10.1-2155/base/lib/python2.7/site-packages/wx-2.8-gtk2-unicode/wx/__init__.py", line 45, in <module> from wx._core import * File "/home/public/packages/phenix-1.10.1-2155/base/lib/python2.7/site-packages/wx-2.8-gtk2-unicode/wx/_core.py", line 4, in <module> import _core_ ImportError: /home/public/packages/phenix-1.10.1-2155/base/bin/../lib/libXrender.so.1: undefined symbol: _XGetRequest Should I give up and attempt to compile from the source, or is there a fix for these issues? Kind regards, Dave -- -- David Briggs about.me/david_briggs

2 1