- phenixbb - phenix-online.org

anomalous difference map
by CPMAS Chen 10 Oct '14

10 Oct '14

Hi, phenix users, A difference map is used to identify whether there is anything not-modeled, say some ligands, ions. Then when I generate anomalous difference map, I should not put the ligand(which contains Br) in the model, right? Or in phenix, after I put the Br-ligand in the model, I should not see the anomalous difference density at the site, right? Could anyone give me a confirmation of this? Thanks! Charles -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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Re: [phenixbb] (no subject)
by Sneha Rangarajan 08 Oct '14

08 Oct '14

After running autobuild, the Rfactors were 26/39 (autobuild removed the first 30 residues from the Nter!) but the maps look much better. I ran a quick refinement with default settings and the Rfactors are now 31/39 and can now see the density for my peptide (absent in the model) coming up. I have a few questions- 1) When is a good time to start building the peptide into the density (should I wait until Rfactors improve significantly)? 2) If so, should I be masking the peptide density somehow so that further refinement doesn't flatten out that density? 3) What is a general good strategy for lowering Rfactors? (Esp if the gap between Rwork and Rfree is high..like 28/40 or so)? Thanks a lot, S -----Original Message----- From: Sneha Rangarajan Sent: Wednesday, October 01, 2014 12:54 PM To: 'Paul Adams' Cc: phenixbb(a)phenix-online.org Subject: RE: I think my problem in MR has been one of the chains. Anyway I tried the ideas you suggested and seems like they worked! I used ensembler to create a merged pdb of the problematic chain and used phaser giving both chains as multiple ensembles. It gave me a solution with LLG=474 (highest I have got so far) and TFZ=18.8. I also tried MRage and got a solution with LLG=294. In both these maps, the density for chain1 ("bad chain") is not as good as the other chain but is nonetheless far better than what I have got before. I am currently running autobuild on the solution hoping my Rfactors would be reasonable this time. Thanks a lot for your inputs. They really helped!! S -----Original Message----- From: Paul Adams [mailto:[email protected]] Sent: Tuesday, September 30, 2014 7:51 PM To: Sneha Rangarajan Subject: Re: This likes normal orthorhombic data. In this case I suggest that the most likely issue is the search model (I assume your molecule is fairly small given the unit cell dimensions). I would look at ways to create the best search model using using tools like sculptor and ensembler. You can get Phaser to search for the two domains in the same run but using multiple ensembles. You might also want to try MRage in Phenix, where you can just provide the data file and the sequence and it will try to make the best model and solve the MR problem. On Sep 30, 2014, at 3:32 PM, Sneha Rangarajan <rsneha(a)umd.edu> wrote: > Oh I see. I tried to repeat xtriage with the scala.mtz file and am attaching the log file. > > ________________________________________ > From: Sneha Rangarajan > Sent: Tuesday, September 30, 2014 5:58 PM > To: Paul Adams > Cc: help(a)phenix-online.org > Subject: RE: > > Even i thought so but after i run mosflm and process the data in p21 or p1 and run quicksymm/quickscale it always suggests that the chosen space group is not correct and that it should be p212121. > > I will try looking into Zanuda. Thanks. > > S > ________________________________________ > From: Paul Adams [pdadams(a)lbl.gov] > Sent: Tuesday, September 30, 2014 5:36 PM > To: Sneha Rangarajan > Cc: help(a)phenix-online.org > Subject: Re: > > It looks like your R-merge etc in P222 is very high, what leads you to think this is the correct point group? Can you send the xtriage output for the unmerged P2 data? > > On Sep 30, 2014, at 2:29 PM, Sneha Rangarajan <rsneha(a)umd.edu> wrote: > >> Hi Nat, >> >> I am attaching the Xtriage log file from p222.mtz. >> Would you need anything else (mtz,pdb)? >> >> Thanks, >> Sneha >> <xtriage_237.log> > > -- > Paul Adams > Deputy Division Director, Physical Biosciences Division, Lawrence > Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, > Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, > U.C. Berkeley Vice President for Technology, the Joint BioEnergy > Institute Laboratory Research Manager, ENIGMA Science Focus Area > > Building 64, Room 248 > Building 80, Room 247 > Building 978, Room 4126 > Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul > > Lawrence Berkeley Laboratory > 1 Cyclotron Road > BLDG 64R0121 > Berkeley, CA 94720, USA. > > Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ > 1-510-495-2506 ] > -- > > > > > > > > > > > > > <xtriage_264.log> -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Building 80, Room 247 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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PDBe workshop on programmatic access to macromolecular structure information, 20-21 Nov 2014, Cambridge UK
by swanand＠ebi.ac.uk 05 Oct '14

05 Oct '14

=============================================================== Programmatic Access to the Macromolecular Structure Information =============================================================== -------- PDBe Workshop for Programmers, 20-21 Nov 2014 -------- ============= What? The Protein Data bank in Europe (PDBe; http://pdbe.org) is organising a hands-on, interactive workshop for developers interested in using primary and value-added information about the 3D structures in PDB and EMDB. Programmatic access to macromolecular structure data as well as information about assemblies, structure quality, literature and citations, and up-to-date cross-references to other biomedical resources (UniProt, Pfam, CATH, SCOP, etc.) is a critical requirement for integrative bioinformatics analyses and workflows. PDBe has developed a set of REST APIs (http://wwwdev.ebi.ac.uk/pdbe/api/doc) that provide easy access to high-quality information regarding biomacromolecular structures archived in PDB and EMDB. They provide a simple, reliable, light-weight mechanism to query macromolecular structure data, select entries or molecules of interest, and access targeted information about them, including information about the molecules, experimental details, assemblies, motifs, function, taxonomy, structure quality, etc. The API is used by the PDBe services and is also integrated in Jmol/Jsmol. We will also present Solr/Lucene based query API for macromolecular structure information including PDB, EMDB and value added information on assemblies, structure quality and up-to-date cross-reference infromation to other biomedical databases based on SIFTS (http://pdbe.org/sifts) . ============= Is it for me? Do you (plan to) develop software or on-line resources that use or need access to information about structures in PDB or EMDB? Would you rather not maintain your private infrastructure for retrieving, parsing, storing and updating such information? If so, then this workshop is for you! In the workshop, we will explain what information is available through the API and how you can access it from your own software or resource. There is plenty of time for hands-on work where experienced PDBe developers will try to help you use the API for your specific needs. ============= When? 20 & 21 November 2014. ============= Where? EMBL-EBI (http://www.ebi.ac.uk) , Cambridge. ============= How much does it cost? We expect you to pay for (and arrange) your own travel to and from Cambridge. However, there is no fee for the workshop, and we will provide free accommodation (Holiday Inn Express; http://www.hiexpresscambridgeduxford.co.uk), transportation between the hotel and the EMBL-EBI, coffee/tea, lunches and a workshop dinner on the 20th. This is all thanks to generous funding from the Wellcome Trust to PDBe. ============= How can I apply? E-mail Swanand Gore (swanand(a)ebi.ac.uk) or Jose Dana (dana(a)ebi.ac.uk) at PDBe no later than 20 October 2014 with the following details: * a brief description of the software you have developed or are developing - i.e. what it does, in which field, how many users, relevant publications, etc. * programming language(s) you are specifically interested in (python examples and tutorials will be provided). * how you would benefit from this workshop. * any specific topics or questions you would like to see addressed in the workshop. If the workshop is oversubscribed, we will select participants based on the information provided. You will be informed by the end of October if you have been selected or not, or whether you are on the stand-by list. ============= Prerequisites? Basic programming experience in use of REST API’s. Bring your own laptop with git and iPython notebook pre-installed if you want to follow the python tutorial and examples. If you need to make plots, make sure that matplotlib is also installed. ============= Questions? Swanand Gore (swanand(a)ebi.ac.uk) or Jose Dana (dana(a)ebi.ac.uk) at PDBe will be happy to answer your queries.

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Re: [phenixbb] Calculate average B-factor?
by Ed Pozharski 05 Oct '14

05 Oct '14

grep "^ATOM " filename.pdb | cut -c 61-66 | awk '{s+=$1;} END {print s/NR;}' "Nobody likes a show off, Private" Skipper Cheers Sent on a Sprint Samsung Galaxy S® III <div>-------- Original message --------</div><div>From: Chen Zhao <c.zhao(a)yale.edu> </div><div>Date:10/04/2014 4:03 PM (GMT-05:00) </div><div>To: PHENIX user mailing list <phenixbb(a)phenix-online.org> </div><div>Subject: [phenixbb] Calculate average B-factor? </div><div> </div>Dear all, I am just wondering whether there is a command line tool in phenix that calculates the average B-factor of a PDB file? Can it deal with the ANISOU records (from TLS refinement or not) properly? I looked into previous posts but the --show-adp-statistics option in phenix.pdbtools seems to be no longer available in the version (1.9-1678) I installed. Thank you so much, Chen

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Calculate average B-factor?
by Chen Zhao 04 Oct '14

04 Oct '14

Dear all, I am just wondering whether there is a command line tool in phenix that calculates the average B-factor of a PDB file? Can it deal with the ANISOU records (from TLS refinement or not) properly? I looked into previous posts but the --show-adp-statistics option in phenix.pdbtools seems to be no longer available in the version (1.9-1678) I installed. Thank you so much, Chen

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Off Topic: Calculating accurately RMSD
by PC 03 Oct '14

03 Oct '14

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Problems building source
by Jason Swails 01 Oct '14

01 Oct '14

Hi everyone, I'm a new user that is trying to get Phenix installed. I'm trying the source build since I want to poke around with a little development. I haven't had much luck in this endeavor (I'm fairly competent when it comes to building especially scientific software from source). What I tried was untarring the 1.9-1692 release tarball and running ./install in that directory. The first thing to fail was Imaging, and the build log complained of a missing freetype/fterrors.h header. On my machine, that file is located in /usr/include/freetype2/fterrors.h. OK, so I symlinked /usr/local/include/freetype to /usr/include/freetype2 and tried again. Imaging succeeded, but then I noticed that Phenix tried to compile its own version of freetype later (!). I'm curious as to why it would either a) not build freetype first so Imaging could use it or b) why it would try to build freetype at all when it already has to be installed. Anyway, after that was done, I got another problem when the install process got to Pango. Then I get the error: fribidi_config.h:1:18: fatal error: glib.h: No such file or directory But glib has already been installed according to the Phenix install log (and I have it installed on my system, too). There's a glib.h in tmp/glib-2.12.11/glib/glib.h (but that directory is never added to the include search path), and also in /usr/include/glib-2.0/glib.h. I admit that the install process has me puzzled (for instance, I can't figure out how to augment CFLAGS for the Pango install to make it find glib.h), and I feel that I'm playing a bit of whack-a-mole with the build problems here... Any help or advice regarding getting the source code built is appreciated. Thanks! Jason -- Jason M. Swails BioMaPS, Rutgers University Postdoctoral Researcher

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Re: [phenixbb] (no subject)
by Sneha Rangarajan 01 Oct '14

01 Oct '14

I think my problem in MR has been one of the chains. Anyway I tried the ideas you suggested and seems like they worked! I used ensembler to create a merged pdb of the problematic chain and used phaser giving both chains as multiple ensembles. It gave me a solution with LLG=474 (highest I have got so far) and TFZ=18.8. I also tried MRage and got a solution with LLG=294. In both these maps, the density for chain1 ("bad chain") is not as good as the other chain but is nonetheless far better than what I have got before. I am currently running autobuild on the solution hoping my Rfactors would be reasonable this time. Thanks a lot for your inputs. They really helped!! S -----Original Message----- From: Paul Adams [mailto:[email protected]] Sent: Tuesday, September 30, 2014 7:51 PM To: Sneha Rangarajan Subject: Re: This likes normal orthorhombic data. In this case I suggest that the most likely issue is the search model (I assume your molecule is fairly small given the unit cell dimensions). I would look at ways to create the best search model using using tools like sculptor and ensembler. You can get Phaser to search for the two domains in the same run but using multiple ensembles. You might also want to try MRage in Phenix, where you can just provide the data file and the sequence and it will try to make the best model and solve the MR problem. On Sep 30, 2014, at 3:32 PM, Sneha Rangarajan <rsneha(a)umd.edu> wrote: > Oh I see. I tried to repeat xtriage with the scala.mtz file and am attaching the log file. > > ________________________________________ > From: Sneha Rangarajan > Sent: Tuesday, September 30, 2014 5:58 PM > To: Paul Adams > Cc: help(a)phenix-online.org > Subject: RE: > > Even i thought so but after i run mosflm and process the data in p21 or p1 and run quicksymm/quickscale it always suggests that the chosen space group is not correct and that it should be p212121. > > I will try looking into Zanuda. Thanks. > > S > ________________________________________ > From: Paul Adams [pdadams(a)lbl.gov] > Sent: Tuesday, September 30, 2014 5:36 PM > To: Sneha Rangarajan > Cc: help(a)phenix-online.org > Subject: Re: > > It looks like your R-merge etc in P222 is very high, what leads you to think this is the correct point group? Can you send the xtriage output for the unmerged P2 data? > > On Sep 30, 2014, at 2:29 PM, Sneha Rangarajan <rsneha(a)umd.edu> wrote: > >> Hi Nat, >> >> I am attaching the Xtriage log file from p222.mtz. >> Would you need anything else (mtz,pdb)? >> >> Thanks, >> Sneha >> <xtriage_237.log> > > -- > Paul Adams > Deputy Division Director, Physical Biosciences Division, Lawrence > Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, > Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, > U.C. Berkeley Vice President for Technology, the Joint BioEnergy > Institute Laboratory Research Manager, ENIGMA Science Focus Area > > Building 64, Room 248 > Building 80, Room 247 > Building 978, Room 4126 > Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul > > Lawrence Berkeley Laboratory > 1 Cyclotron Road > BLDG 64R0121 > Berkeley, CA 94720, USA. > > Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ > 1-510-495-2506 ] > -- > > > > > > > > > > > > > <xtriage_264.log> -- Paul Adams Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 64, Room 248 Building 80, Room 247 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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PHENIX installation errors with CentOS 6
by Mark A. White 01 Oct '14

01 Oct '14

Hello, I am getting install errors with several phenix installations after upgrading to CentOS 6. I started with the nightly-build ========================================================================== PHENIX Installation version: dev release tag: 1807 machine type: intel-linux-2.6-x86_64 OS version: 2.6.32-431.29.2.el6.x86_64 user shell: /bin/tcsh destination: /usr/local ========================================================================= Warning: /usr/local/phenix-dev-1807 already exists, will be overwritten removing existing temporary directory... ok finding existing installations... Removing out-of-date lib directory... ok Removing out-of-date base software directory... ok Installing new binary package... ok Configuring PHENIX components... ******************************************************************************** configuration step incomplete! See the log file for detailed error messages. ******************************************************************************** The log contains only a list of files ending with (./docutils/._MANIFEST.in) and no error messages. Then I went back to the latest stable version, which was installed on my server when it ran CentOS 5. Both my server and WS now produce the same error (CentOS 6). ========================================================================== PHENIX Installation version: 1.9 release tag: 1692 machine type: intel-linux-2.6-x86_64 source machine type: intel-linux-2.6-x86_64 OS version: redhat-e6.5 user shell: /bin/tcsh destination: /usr/local ========================================================================= ========================================================================== Installing from binary bundle ========================================================================== bundle file: bundle-1.9-1692-intel-linux-2.6-x86_64.tar.gz PHENIX installation source directory set to: /home/white/downloads/phenix-installer-1.9-1692 PHENIX installation target directory <PHENIX_LOC > set to: /usr/local/phenix-1.9-1692 PHENIX installation build directory set to: <PHENIX_LOC > /build/intel-linux-2.6-x86_64 PHENIX temporary build directory set to: build-binary/intel-linux-2.6-x86_64/marvin/tmp PHENIX installation log directory set to: build-binary/intel-linux-2.6-x86_64/marvin/log ==== warning: "/usr/local/phenix-1.9-1692" already exists ==== ==== warning: cannot determine installation time-stamp, proceeding ==== installing binary components removing existing files in build-binary/intel-linux-2.6-x86_64/marvin/tmp/binary finding installed versions finding binary versions binary components up-to-date the binary package will not be installed setting environment configuring PHENIX components /home/white/downloads/phenix-installer-1.9-1692/bin/install-from-binary: line 361: 19688 Segmentation fault $PHENIX_BUILD/base/bin/python $PHENIX_LOC/cctbx_project/libtbx/configure.py --current_working_directory="$PHENIX_BUILD" $PHENIX_COMPONENTS $CONFIG_OPTS >> $PHENIX_LOG/binary.log 2>&1 Error configuring: see /home/white/downloads/phenix-installer-1.9-1692/build-binary/intel-linux-2.6-x86_64/marvin/log/binary.log for details The log contains only a list of files ending with (./docutils/._MANIFEST.in) and no error messages. Then I tried installing phenix-dev-1810 from source: Installing cairo... log file is /home/white/downloads/phenix-installer-dev-1810/install_tmp/intel-linux-2.6-x86_64/marvin/cairo_install_log getting package cairo-1.8.10.tar.gz... using /home/white/downloads/phenix-installer-dev-1810/gui/cairo-1.8.10.tar.gz Traceback (most recent call last): File "./bin/install.py", line 815, in <module> run(sys.argv[1:]) File "./bin/install.py", line 72, in __init__ self.install_from_source() File "./bin/install.py", line 292, in install_from_source log=out) File "/home/white/downloads/phenix-installer-dev-1810/lib/libtbx/auto_build/install_base_packages.py", line 113, in __init__ self.build_cctbx_dependencies() File "/home/white/downloads/phenix-installer-dev-1810/lib/libtbx/auto_build/install_base_packages.py", line 168, in build_cctbx_dependencies self.build_wxpython_dependencies() File "/home/white/downloads/phenix-installer-dev-1810/lib/libtbx/auto_build/install_base_packages.py", line 425, in build_wxpython_dependencies self.build_wxpython_dependencies_linux() File "/home/white/downloads/phenix-installer-dev-1810/lib/libtbx/auto_build/install_base_packages.py", line 504, in build_wxpython_dependencies_linux self.build_compiled_package_simple(pkg_name=pkg, pkg_name_label=name) File "/home/white/downloads/phenix-installer-dev-1810/lib/libtbx/auto_build/install_base_packages.py", line 377, in build_compiled_package_simple log=pkg_log) File "/home/white/downloads/phenix-installer-dev-1810/lib/libtbx/auto_build/install_base_packages.py", line 196, in configure_and_build self.call("make -j %d %s" % (self.nproc, " ".join(list(make_args))), log=log) File "/home/white/downloads/phenix-installer-dev-1810/lib/libtbx/auto_build/install_base_packages.py", line 192, in call return call(args, log=log) File "/home/white/downloads/phenix-installer-dev-1810/lib/libtbx/auto_build/installer_utils.py", line 53, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to 'make -j 8 ' failed with exit code 2 I would like to install the latest developmental version. Any idea what could be going wrong? I have the latest updates installed. -- Yours sincerely, Mark A. White, Ph.D. Associate Professor of Biochemistry and Molecular Biology, Manager, Sealy Center for Structural Biology and Molecular Biophysics Macromolecular X-ray Laboratory, Basic Science Building, Room 6.630 University of Texas Medical Branch Galveston, TX 77555-0647 Tel. (409) 747-4747 Fax. (409) 747-1404 mailto://[email protected] http://xray.utmb.edu QQ: "Life is no brief candle to me. It is a sort of splendid torch which I have got a hold of for the moment, and I want to make it burn as brightly as possible before handing it on to future generations. " - George Bernard Shaw

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refinement problem
by Sneha Rangarajan 30 Sep '14

30 Sep '14

Hello, I have a 1.9A dataset for a single chain Fv-peptide complex that shows psedomerohedral twin operators in Xtriage (1 in p212121, 3 in p21 and 7 in p1). Although most programs (in CCP4) identify the best SG to be p212121, MR cannot find a solution with p212121 due to packing clashes. I tried reprocessing it in p21 and MR can find only one molecule in the asu. The map looks quite good with good density for the sidechains. However the Rfactors wont come down. After a few rounds of refinement (rigidbody, Xray, TLS and Ind B fac) it is still 38/48. I tried processing it in p1 and have managed to find 3 molecules in the asu (missing one molecule). The map looks good. While the Rfactors are lower, the gap between Rwork and Rfree is still high (27/40). I don't know what space group I should choose to ultimately refine it and get the Rfactors low. If you need any more information, I would be happy to provide it. Does anyone have any suggestions? Thanks a lot, Sneha

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