- phenixbb - phenix-online.org

Re: [phenixbb] R-factor difference between phenix and sftools
by Ed Pozharski 13 Oct '14

13 Oct '14

To be fair, I made the same mistake initially, but the question is about calculating Rs with sftools using output mtz from phenix.refine, not sfcheck. Thusly, bulk solvent explanation does not seem to apply. My other theory (impossible to check without actual data) was that phenix.refine outlier reflection rejection makes the difference here, although it's surprising if effect is so noticeable. Sent on a Sprint Samsung Galaxy S® III <div>-------- Original message --------</div><div>From: Pavel Afonine <pafonine(a)lbl.gov> </div><div>Date:10/13/2014 2:21 PM (GMT-05:00) </div><div>To: Tim Gruene <tg(a)shelx.uni-ac.gwdg.de>, phenixbb(a)phenix-online.org </div><div>Subject: Re: [phenixbb] R-factor difference between phenix and sftools </div><div> </div>Thanks Tim, yes missed this one! Hi Simon, the differences in R-factors you observe are most likely because we use improved bulk-solvent modeling and overall scaling procedure. This is described here: Bulk-solvent and overall scaling revisited: faster calculations, improved results. Afonine PV, Grosse-Kunstleve RW, Adams PD, Urzhumtsev A. Acta Cryst. D69, 625-34 (2013). Specifically, Figures 3-4 in this paper make your observations very expectable. Other contributions to differences are discussed here: phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics. P.V. Afonine, R.W. Grosse-Kunstleve, V.B. Chen, J.J. Headd, N.W. Moriarty, J.S. Richardson, D.C. Richardson, A. Urzhumtsev, P.H. Zwart, P.D. Adams J. Appl. Cryst. 43, 677-685 (2010). Pavel On 10/13/14 11:10 AM, Tim Gruene wrote: Dear Simon, I found this a very puzzling observation and given the high throughput of this board, it is likewise puzzling you have not received a reply yet - or have you? Best regards, Tim On 10/12/2014 08:25 PM, Simon Jenni wrote: Hi, we refined a structure in phenix.refine (dev-1810) and the R-factors are: Final R-work = 0.3221, R-free = 0.3638 phenix.cc_star agrees: phenix.cc_star com_001.pdb com_001.mtz \ f_obs_labels="F-obs,SIGF-obs" \ f_model_labels="F-model,PHIF-model" \ unmerged_data="xscale.hkl" r_work: 0.322 r_free: 0.364 so does phenix.model_vs_data: phenix.model_vs_data com_001.pdb com_001.mtz r_work : 0.3221 r_free : 0.3638 sigma_cutoff : None However, when I calculate the R-factors with sftools, I get a discrepancy between the phenix and sftools results: sftools << eof read com_001_f_model.mtz Y select col R_FREE_FLAGS > 0 correl col FOBS FMODEL select invert correl col FOBS FMODEL quit Y eof R-work: 33.6 R-free: 38.1 Does anyone perhaps know what causes this difference? With best regards, Simon PS: The structure is in spacegroup P212121 with strong pseudocentering tNCS (dimer in the asymmetric unit, native Patterson peak at 0.500 0.500 0.497). No indication for a P21 twin (L-test and refinement in P21 with twin law), not higher symmetry spacegroup I222 (alternating strong and weak reflections are visible in the diffraction patterns, resolved structural differences in the two protomers of the dimer). Two datasets from different beamlines. As might be expected, the R-factors after refinement are unusually high (e.g. 28/35 [conventional resolution cutoff at 3.1 A], 32/36 with Kay's CC cufoff at 2.6 A). I wanted to compare refinements between different programs to see how they cope with the unexpected bimodal amplitude distribution. _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

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Refine three alternate conformations of residues and two loop confirmations.
by AMIT 13 Oct '14

13 Oct '14

Hi All, I am unable to refine three alternate conformations of a residue provided in PDB file prefixed before resname as A,B and C in Phenix dev-1370. When I make it two alternate conformations it runs OK. Also I am not able to refine two loop confirmations, the refinement somehow puts both in the major 2Fo-Fc map peak and makes the almost same, even though the starting loop has different trace.Turning off siulated annealing or making temp. lower or just doing 1 cycle is not doing any good. Any suggestions will be helpful. Thanks, Amit. ------------------------------------------------------- AMIT DAS, Ph.D. PRESENT ---- BUILDING 8600, MS-6460 BIOLOGY AND SOFT MATTER DIVISION P O BOX 2008 OAK RIDGE NATIONAL LABORATORY 1 BETHEL VALLEY ROAD OAK RIDGE, TN 37831-6460 U.S.A. PROTEIN CRYSTALLOGRAPHY SOLID STATE PHYSICS DIVISION BARC, TROMBAY, MUMBAI-400085. INDIA. --------------------------------------------------------

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Test
by Paul Adams 11 Oct '14

11 Oct '14

-- 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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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

2 1

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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Target function for refinement in case of Pseudo-translational symmetry
by Varun Bhaskar 29 Sep '14

29 Sep '14

Hi, I collected a dataset for a binary complex (72kDa size) to 3.62A resolution which could be processed in P32 2 1 space group. Data quality analysis with phenix.xtriage showed a presence of Pseudotranslational symmetry (Non-origin peak in the patterson with 60% intensity at 0.33, -0.33, -0.013). I determined the structure with MR. I have 6 copies in ASU. I tried Zanuda for SG validation and this looks like the right space group. For refinement when I use Maximum likelihood (ML) as the target function, my Rfactor/Rfree is around 31.3/32 but when I change it to Least square (LS) my Rfactor/Rfree drops to 27.3/29.8. The map quality after ML or LS refinement looks very similar for most of the molecule, except for few places where the map from ML has slightly better features. I read people use LS instead of ML only in the case of twinning but I am not sure if it could also be used in the case of PST. Would the use of LS as the target function for refinement be right in this case? Thanks in advance Best Regards Varun

2 1

Histidine as a hydrogen bond acceptor in Phenix refine
by Phan, Jason 26 Sep '14

26 Sep '14

Hi All, I've been refining a 1.1 Å structure with explicit hydrogen atoms and noticed that the serine HG atom (hydrogen atom attached to oxygen gamma) is rotated more than 90 degrees from the OG - NE2 (histidine) line (5 cases observed). In this position, the HG is staggered with the two carbon beta hydrogens and should be the preferred configuration. However, there is a histidine nearby with atom NE2 at 2.7 Å from the serine OG and in good geometry for Hbond formation. The other nitrogen, ND1, is protonated and interacting with an aspartic acid (similar to the catalytic triad configuration). In this protomer, the NE2 atom has a lone pair and should act as an acceptor. Thus, the OG - H - NE2 angle should be as close to 180 as possible for an ideal hydrogen bond angle. The OG - H - NE2 angle of more than 90 degrees looks a little off to me. I checked the other program, e.g. Schrodinger Prime to see how it treats this situation and found that all the OG - H - NE2 angles are within 10-60 degrees from the ideal value of 180, certainly not 90 as observed in Phenix refine. My question is is NE2 or ND1 atom of the HID or HIE protomer treated as a potential hydrogen bond acceptor in Phenix? For other acceptors like the backbone carbonyl oxygen, carboxylic acid oxygen, and water oxygen, the hydrogen bond angle OG -H -O looks good. Not when it involves histidine atom NE2 or ND1 though. The pH of the crystallization is 7 by the way. Also, there's no water nearby that would draw the HG away from the histidine. Jason

4 5

Fo-Fc omit map for ligand in the protein-ligand structure
by Wei Shi 20 Sep '14

20 Sep '14

Hi all, I am working with a protein dimer-ligand structure (resolution: 2.8Å) and am going to make a figure showing the bound ligand superimposed with the electron density (Fo-Fc) map obtained after omit refinement. What I did is to make the ligand-free structure model and then use Phenix.refine using the following parameters plus simulated annealing (torsion angle) or (Cartesian): Default: XYZ coordinates + Real-space+ Individual B factors + Occupancies. Also click: Optimize X-ray/stereochemistry weight + Optimize X-ray/ADP weight + Secondary structure restraints + NCS. Contoured at 2σ, the Fo-Fc map generated show green density for most part of the ligand, but for several atoms in the middle of the ligand, the green density is missing... It's like this: some atoms have green density and the next few no green density and then a couple few has green density and then a couple more no green denisty.... The missing green density usually means that part is disordered in the structure, right? I am not sure why the density is missing for some atoms in the middle of the ligand. It would makes more sense if the missing green density is at the end of the ligand... Does anyone happen to have any clue about what it means for the green density missing in my case? Also, I am not sure whether I did the omit refinement right: (1). For simulated annealing, it has two options, one is Cartesian and the other is Torsion angle, and it's said that torsion angle is more suitable of low resolution data. Is there any difference about which one to choose in my case? (2). Is it Okay to run the omit refinement in the presence of the following parameters as I did: Optimize X-ray/stereochemistry weight + Optimize X-ray/ADP weight + Secondary structure restraints + NCS. Thank you so much! Best, Wei

5 24

Increase in R/R(free) after phenix.real_space_refine
by George Devaniranjan 19 Sep '14

19 Sep '14

Hi, I refined (phenix.refine) a 1.0Å structure but it had a few CB outliers and some rotamer outliers. I decided to try real_space_refine, to check if they could be fixed (given that it has a higher radius of convergence). (using run=local_grid_search+minimization_global in real_space_refine) But, the R/R(free) increased from 11.39/13.24( for the refine model) to 16.51/17.55 (real_space_refine model). It seemed a big increase, when I looked at the map against the structure the protein itself seemed fine. The rotamers outliers had decreased, the CB outliers were fixed..etc The solvent fit to the density had worsened in COOT. What am I doing wrong? Any suggestions, advice would be much appreciated. Thank you, George

3 2

RMS angles and comprehensive validation in phenix
by C 19 Sep '14

19 Sep '14

5 6

Problems getting rigid and tls to run
by David Shin 19 Sep '14

19 Sep '14

Hi - Running versions: Version: 1.9.1692 mac-intel-osx-x86_64 osx-10.6.8 Version: 1.9.1692 intel-linux-2.6-x86_64 redhat-e5.10 In both cases, I can run an input model I used previously and get rigid and tls to work. With a newer model, I cannot get either to work (and yes, there was a reason I tested rigid on a model that was refined once). Weirder is I have gone from gui on mac to produce an .eff file to transfer to linux - in the .eff file I get: strategy = *individual_sites *individual_sites_real_space rigid_body \ *individual_adp group_adp tls *occupancies group_anomalous despite having checked the rigid and tls boxes Weirder yet, is I hand edit the file to add *rigid *tls and run on the linux machine, and both still get turned off. I diff the input refine.eff files between using the older model and newer, and nothing appears very different. The only thing I can think of is that there could be some legacy .hidden files in the working directory that change something, but it makes no sense once I port everything to a different computer. Anyone have this trouble? Thanks, Dave

1 0

Refining structure with overlapping conformations of different residues
by Igor Petrik 19 Sep '14

19 Sep '14

Hi, I am trying to refine a structure in which there are two sets of linked conformations of two residues. Around half of the occupancy (altloc A) corresponds to the sidechain of residue 29 pointing into the pocket and residue 65 pointing out and the other conformation (altloc B) has the side chain of residue 65 in the pocket (where residue 29 is in altloc A) and residue 29 pointing out of the pocket. I am refining them by using occupancy refinement groups in, but phenix refine seems to think that altloc A of residue 29 and altloc B of residue 65 may exist at the same time and pushes them apart to avoid clashes. Is there any way around this? - Igor

2 1

calculate TLS contribution to total B-factor
by Michael Thompson 19 Sep '14

19 Sep '14

Hello All, I have a structure that was refined with phenix.refine using TLS, so my PDB file contains B-total in the isotropic B-factor column as well as ANISOU lines. For the sake of analysis, I am interested in determining the TLS contribution to these total B-factors. How can I split B-total into isotropic and TLS contributions? I'm fairly certain this is possible, as it is the inverse of what one would do after refining a structure with TLS in Refmac, which requires that the isotropic and TLS components be added together prior to deposition. I feel like perhaps there has been some discussion of this in the past, but I'm not able to dig anything up from the bb archives. Any help would be much appreciated. Thanks, Mike

2 1

Problem finding and running iotbx.explore_metric_symmetry
by Arka Chakraborty 17 Sep '14

17 Sep '14

Dear BB members, I am having a problem finding and running the iotbx.explore_metric_symmetry program. I have tried accessing it from the phenix cctbx directory and also from a separate installation of cctbx but could not locate the program. Could anyone point out how exactly to access it?. Thanks a lot in advance, Best regards, Arko -- *Arka Chakraborty* *ibmb (Institut de Biologia Molecular de Barcelona)* *BARCELONA, SPAIN*

2 1

Immediately available: Postdoctoral position in Computational Structural Biology
by David Sivak 17 Sep '14

17 Sep '14

Dear colleagues, This fall I start my own research group in the Physics Department at Simon Fraser University in Vancouver, British Columbia. In the near future, I hope to hire an exceptional, highly-motivated postdoctoral fellow to work on computational structural biology. Please forward this announcement to any interested parties. My group combines approaches from physics, information theory, and statistics to study the fundamental principles of biomolecular function under strong fluctuations. The postdoctoral position will focus on the development of model comparison methods to understand the conformational heterogeneity revealed by structural biology experiments, especially X-ray crystallography. Within this broad research thrust there is ample freedom to pursue particular areas of personal scientific interest. Our theoretical flights of fancy are tethered to reality through a close collaboration with the experimental group of Jaime Fraser at UC San Francisco. Postdoctoral fellows in my group will work in the intellectually-stimulating and interactive biophysics community within SFU Physics, with close ties to the Molecular Biology/Biochemistry department, home to several top-notch structural biology groups. In my own (possibly biased) opinion, the endless all-season outdoors opportunities, mind-blowing food from all ethnicities, and mild weather make Vancouver an enviable place to call home; slightly more objectively, it makes every official top 5 list of most livable cities in the world. The ideal candidate would have experience with computer programming, biomolecular modeling and statistics, and a PhD in a relevant field (broadly construed: physics, biophysics, chemistry, bio- or chemical-engineering, molecular biology, or relevant areas of statistics, computer science, applied math, etc). But most important is intellectual curiosity, enthusiasm for research in this area, and an excellent track record in whatever field they have pursued. Interested candidates should send me a cover letter and CV (including publication list and contact information for 2-3 references). Further information is available at: http://davidsivak.com/ Thank you in advance! David -- David Sivak Asst. Prof., Dept. of Physics, Simon Fraser U david.sivak(a)gmail.com davidsivak.com 778-928-7995

1 0

phenix.merging_statistics and resolution shells
by Murpholino Peligro 17 Sep '14

17 Sep '14

can I specify the ranges of the resolution shells in phenix.merging_statistics? (something like "XSCALE-word" RESOLUTION_SHELLS=) and how many resolution shells are ok? 10, 15, 20?

2 1

LABELIT and MOSFLM version
by Ngoc Anh Thu Ho 16 Sep '14

16 Sep '14

Hello, labelit.index command cannot start Mosflm and gives an error, which reads: "MosflmVersionError: mosflm versions after 7.0.9 not supported” Other than that, indexing seems to be working fine. Can this be fixed or updated somehow? I’m using the latest Phenix 1.9-1692 and Mosflm 7.1.0 (with iMosflm 7.1.1). Best regards, Thu

2 2

calculate CC*
by wei xia 15 Sep '14

15 Sep '14

Hi all:I have a set of data indexed with XDS (space group P222). When I use phaser, the MR solution was in space group P212121.I then changed the space group of mtz file to P212121 using phenix Reflection file editor and did the refinement. Now I use phenix to calculate CC*, in which I input unmerged data (from xds, P222) and merged data (mtz file, P212121) and final pdb file.It turned out to be "incompatible symmetry" error. Are there any easy ways to get the calculate CC* running?Thanks! Wei Xia

2 1

Re: [phenixbb] [ccp4bb] Autobuild in specific area
by Terwilliger, Thomas Charles 14 Sep '14

14 Sep '14

Hi Foggy, This is a situation that autobuild does not address very well yet. Yes, you want rebuild_in_place=False. And yes, if you do that it will remove your model and rebuild it. It will also try to build into the remainder of the map. In practice, you already have pretty much the best that autobuild is going to produce. Delete the protein A chains that autobuild built, and put in your original protein A. Now you have your original model plus whatever autobuild was able to build. An alternative is: select "consider_main_chain_list=True" . This will take your input model A and at each step it will check to see if parts of that model are better than any other model that it has built. This can help for keeping the input model that you put in. All the best, Tom T ________________________________ From: CCP4 bulletin board [CCP4BB(a)JISCMAIL.AC.UK] on behalf of Zhang Foggy [foggyccp4(a)GMAIL.COM] Sent: Saturday, September 13, 2014 10:40 AM To: CCP4BB(a)JISCMAIL.AC.UK Subject: [ccp4bb] Autobuild in specific area Hi, All, I am trying to use Autobuild to build a protein-protein complex model. I obtained partial phase solution (protein-A) through MR, and can see some density of protein-B near protein-A. I would like to use Autobuild to build protein-B model into this area. I load data file, initial density map file, sequence file (both of protein A and B), and protein A model, and run Autobuild. However, The "rebuild-in-place" function confused me a lot, no matter I set it to True or False. When I set to True, it only rebuilt protein A model without adding any additional residues; while I set it to False, it deleted the input protein-A model, and rebuilt a new one... Could somebody tell me how to build the protein B model with keeping the input protein A model in Autobuild? Thanks. [https://ssl.gstatic.com/ui/v1/icons/mail/images/cleardot.gif] Foggy

3 3

Autobuild in specific area
by Zhang Foggy 13 Sep '14

13 Sep '14

Hi, All, I am trying to use Autobuild to build a protein-protein complex model. I obtained partial phase solution (protein-A) through MR, and can see some density of protein-B near protein-A. I would like to use Autobuild to build protein-B model into this area. I load data file, initial density map file, sequence file (both of protein A and B), and protein A model, and run Autobuild. However, The "rebuild-in-place" function confused me a lot, no matter I set it to True or False. When I set to True, it only rebuilt protein A model without adding any additional residues; while I set it to False, it deleted the input protein-A model, and rebuilt a new one... Could somebody tell me how to build the protein B model with keeping the input protein A model in Autobuild? Thanks. Foggy

1 0

phenix rosetta installation
by Dan Lin 12 Sep '14

12 Sep '14

Hi all: This is kind of a silly problem, but I'm trying to get phenix.rosetta_refine running on my computer and I am having some difficulty getting rosetta.build_phenix_interface to run. I'm getting a permission denied error in the os.symlink(python_lib, lib_link_name) line in rosetta_build_phenix_interface.py script and presumably I could fix this by changing the write permissions to wherever this points to, but I don't know where. Could anybody point me towards the folder that needs to fixed? Thanks, Dan

2 1

restraints for dna planarity
by John Lee 12 Sep '14

12 Sep '14

Hi, I'm refining a low resolution structure of a dna-protein complex (3.7A) & wondering if someone could help me with setting restraints in Phenix to maintain the base-pair planarity of the dna? With the restraints I have, even with a reference model, I'm getting 'puckering' of the base-pairs. Although the h-bonding distances seem to hold over time, I can't seem to find a way to keep the planarity intact. Thanks in advance for your help. -John

3 2

Phenix-Rosetta integration tests fail with Rosetta MPI on RHEL 6.3
by Sina Masoud-Ansari 12 Sep '14

12 Sep '14

Hi there, I'm wondering anyone has managed to successfully run Phenix with Rosetta MPI on Red Hat Enterprise Linux 6.3 or similar? I currently have a non-MPI build of Rosetta that passes all of the tests in phenix_regression.wizards.test_command_line_rosetta_quick However when running these tests with the MPI build of Rosetta the following tests fail: Running test_relax ------------------------------------------------------------ Numbers do not match: 6 1 Relaxed solutions 6 --- Relaxed solutions 1 ------------------------------------------------------------ FAILED See log files test_relax/test_relax.log test_relax/test_relax_current.log ================================================================= Running test_relax_double ------------------------------------------------------------ Numbers do not match: 6 1 Relaxed solutions 6 --- Relaxed solutions 1 ------------------------------------------------------------ ------------------------------------------------------------ Numbers do not match: 6 1 Relaxed solutions 6 --- Relaxed solutions 1 ------------------------------------------------------------ FAILED See log files test_relax_double/test_relax_double.log test_relax_double/test_relax_double_current.log ================================================================= Running test_relax_no_sol ------------------------------------------------------------ Numbers do not match: 6 1 Relaxed solutions 6 --- Relaxed solutions 1 ------------------------------------------------------------ FAILED See log files test_relax_no_sol/test_relax_no_sol.log test_relax_no_sol/test_relax_no_sol_current.log I have attempted to attach an archive of the logs. I'm working with Rosetta 3.5, more recent versions of Rosetta fail other tests in phenix_regression.wizards.test_command_line_rosetta_quick , please see https://www.rosettacommons.org/node/3721 for details. Rosetta 3.5 was compiled with GCC 4.4.6 using OpenMPI 1.6.4 Any help or advice is appreciated. -- Sina Masoud-Ansari Centre for eResearch 409.G21 24 Symonds Street University of Auckland e: s.ansari(a)auckland.ac.nz p: +64 9 3737599 ext 89369 w: http://www.eresearch.auckland.ac.nz

3 4

phenix refine geometry restraints
by George Devaniranjan 12 Sep '14

12 Sep '14

Hi, I was trying to restrain the N-CA-C angle to 110.0 I updated the .def file as follows: angle { action = *add atom_selection_1 = name N atom_selection_2 = name CA atom_selection_3 = name C angle_ideal = 110.0 sigma = 2 I got the following: Sorry: More than one atom selected: "name N" Number of selected atoms: 86 I tried using N in quotes and it doesn't work either but the example in the website had this(below), what am I doing wrong? resname ALA and (name ca or name c or name n or name o) Thank you

2 1

refinement for non-standard DNA base
by John Cheong 11 Sep '14

11 Sep '14

Hi, I have 5-fluoro-Uracil in my DNA:protein complex. I modeled 5-F-dU into the map, ran eLBOW for geometry file and did refinement. After the refinement, 5-F-dU is not connected to the neighboring nucleotides and the phosphate oxygens are rotated to wrong positions. Can anyone teach me how to refine with non-standard DNA base ? Any help or advice would be appreciated. John

2 1

Occupancy refinement of anomalous scatters
by Chen Zhao 09 Sep '14

09 Sep '14

Hi all, I have a question about the occupancy refinement of the anomalous scatters. This is because when I went through all the HA sites, I found that some of them has too high B factor and too high occ. I manually adjusted the occ and fed the model into refinement, but the B factor and occ came back to around their original level again. It seems that those have a stronger peak in the anomalous difference Fourier map has a higher occupancy after refinement, but this does not necessarily equals to a strong density peak in 2Fo-Fc map (some of them even disappear after refinement), and this might be related to their high B factor. Am I doing something wrong in the refinement? I am basically using phenix.refine default setting, but with TLS+isotropic B factor refinement and occupancy refinement of a small region (5-8 residues). The resolution is 3 A, and the refinement is already at the final stage. I am still at the learning stage and your input will be greatly appreciated. Thank you! Sincerely, Chen

2 1

Refinement and Density modification
by Ashu S 09 Sep '14

09 Sep '14

Dear all, I am working on a 3.6A Se SAD data. Autosol followed by autobuild gave a decent map (as expected at this resolution) with a moderate trace. After building poly ala trace and assigning few resides in and around Se positions when I refine the model, all the sharp features of the electron density map are lost. For example, a nice looking helical density becomes a tube. I presume that this happens because wilson B is high (~110 A2) and the map requires modification, sharpening etc. Is there a way to get the map with similar sharp features after model building and refinement as auto build gives? How could I follow exactly the same steps of density modification etc which auto build does? Thanks, Ashu

2 1

Refinement and Density Modification
by Ashu S 08 Sep '14

08 Sep '14

Dear all, I am working on a 3.6A Se SAD data. Autosol followed by autobuild gave a decent map (as expected at this resolution) with a moderate trace. After building poly ala trace and assigning few resides in and around Se positions when I refine the model, all the sharp features of the electron density map are lost. For example, a nice looking helical density becomes a tube. I presume that this happens because wilson B is high (~110 A2) and the map requires modification, sharpening etc. Is there a way to get the map with similar sharp features after model building and refinement as auto build gives? How could I follow exactly the same steps of density modification etc which auto build does? Thanks, Ashu

1 0

refine anomalous
by Andreas Förster 08 Sep '14

08 Sep '14

Dear all, I've solved a structure from a SAD dataset collected at 1.54 Å. The structure contains a good number of sulfurs and also what I think is a potassium ion. To verify, I chose a refinement strategy including "Anomalous groups". This worked well in an important way - R values down by 2 percentage points - but the refined f' and f" values are way off. I start out with these parameters in *.eff: anomalous_scatterers { group { selection = (name SD or name SG) f_prime = 0.319342 f_double_prime = 0.557592 refine = *f_prime *f_double_prime } group { selection = name K f_prime = 0.365562 f_double_prime = 1.06736 refine = *f_prime *f_double_prime } } What I get back is: Anomalous scatterer group: Selection: "(name SD or name SG)" Number of selected scatterers: 15 f_prime: -1.15797 f_double_prime: 0.00577091 refine: f_prime f_double_prime Anomalous scatterer group: Selection: "name K" Number of selected scatterers: 1 f_prime: -4.41689 f_double_prime: 0.00271946 refine: f_prime f_double_prime I thought I'd get close to the book values for S and would be able to identify the other anomalous scatterer by the refined f'/f" values. Naiveté or stupidity? Thank you. Andreas -- Andreas Förster Crystallization and X-ray Facility Manager Centre for Structural Biology Imperial College London

2 1

Fwd: Re: Sculptor
by Gabor Bunkoczi 08 Sep '14

08 Sep '14

Apologies, this was meant for the BB. -------- Original Message -------- Subject: Re: [phenixbb] Sculptor Date: 2014-09-08 10:41 From: Gabor Bunkoczi <gb360(a)cam.ac.uk> To: Marie Elizabeth Fraser <frasm(a)ucalgary.ca> Hi Marie, please check the extension of your alignment. If it is .pir, the second line is supposed to be a comment line, and it is therefore ignored. You can either change the extension to .ali, or insert an empty line after the ones starting with ">". If this is not the problem, then this is not supposed to happen. Please send me the logfile in the first instance, although I may need the actual alignment and the PDB file as well (you can delete the target sequence if you wish, an alignment with a single sequence is perfectly valid). BW, Gabor On 2014-09-08 01:22, Marie Elizabeth Fraser wrote: > Hello, > I'm running Sculptor from the Phenix GUI, trying to improve a > molecular replacement model. I've given the pdb file and a sequence > alignment. Sculptor does not appear to accept the first residues > aligned in the sequence alignment. In the alignment, these residues > are residue numbers 42 to 60, so they are on the second line of the > fasta file (the first line after the title) and Sculptor starts at > residue 61 (the subsequent line). Residues 42 to 60 of the target are > to match the first residues of the pdb model, so in the alignment, > there are 41 dashes before the beginning of the sequence for the pdb > file. Am I giving an incorrectly formatted sequence alignment, > misinterpreting what Sculptor does or is Sculptor supposed to do this? > Thank you, Marie > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb

1 0

Sculptor
by Marie Elizabeth Fraser 08 Sep '14

08 Sep '14

Hello, I'm running Sculptor from the Phenix GUI, trying to improve a molecular replacement model. I've given the pdb file and a sequence alignment. Sculptor does not appear to accept the first residues aligned in the sequence alignment. In the alignment, these residues are residue numbers 42 to 60, so they are on the second line of the fasta file (the first line after the title) and Sculptor starts at residue 61 (the subsequent line). Residues 42 to 60 of the target are to match the first residues of the pdb model, so in the alignment, there are 41 dashes before the beginning of the sequence for the pdb file. Am I giving an incorrectly formatted sequence alignment, misinterpreting what Sculptor does or is Sculptor supposed to do this? Thank you, Marie

1 0

refine structure with mtz file in P212121 or P222?
by Wei Shi 05 Sep '14

05 Sep '14

Hi all, I am working with a protein-ligand complex structure. The data was indexed with XDS and mtz file is generated using Phenix---Reflection tools---Reflection file editor. The space group used was P222. Then, I used the Phenix---Molecular replacement to find a solution (try all possible in same pointgroup), and the MR solution was in space group P212121. And then, I reindexed the data in XDS using space group P212121 and then generate the mtz file in space group P212121. So, I have two mtz file, in space group P212121 and P222. When I refine the MR solution with the different mtz files, the map generated is not same for the ligand. The statisitcs is better with P222 mtz file than P212121 mtz file. I am wondering why the density for the ligand and the statistics is different using mtz file in different space groups and which mtz file should I use to get the final structure model. Thank you so much! Best, Wei

2 3

phenix.refine and R free values
by PC 03 Sep '14

03 Sep '14

3 4

OMIT map
by abhishek jamwal 02 Sep '14

02 Sep '14

Dear phenixbb members, I want to build a SA-OMIT map for a ligand present in xtal structure of a protein. I am using "AutoBuild-create omit map" module of PHENIX ver. 1.8.4-1496 (graphical interface) for this purpose. However, when I run the program after adding requisite input files, it gives an error: " The map file parameter is not supported for omit map calculation" Q: What is this "file parameter" and way to fix this error/parameter ? waiting for answers many thanks in advance Abhishek Jamwal Structural Biology Group ICGEB, New Delhi

2 1

Phasing using CryoEM Map
by Alexander Kintzer 02 Sep '14

02 Sep '14

Hello All, I trying to phase my 4Å data with low resolution cryoEM maps (various 12-18Å). There is some documentation, but not really for dealing with EM data. I am having trouble converting the EM data from mrc to suitable F's for phaser. One would want to try different density contours of the cryoEM map, but I haven't found a good way to accomplish this. I also have been unable to search for Ta6Br12 clusters using Autosol even though the documentation seems to suggest that it is possible using the "TX" or "XX" designation for heavy atom search. Any guidance would be extremely helpful. best, Alex

4 3

Tau angles
by George Devaniranjan 02 Sep '14

02 Sep '14

Hi, Is there a way of extracting the tau (and omega) angles of residues in phenix ? Thank you

2 1

Re: [phenixbb] following on the anomalous map
by Kay Diederichs 29 Aug '14

29 Aug '14

Hi Charles, > Date: Thu, 28 Aug 2014 09:59:30 -0400 > From: CPMAS Chen <cpmasmit(a)gmail.com> > To: Gabor Bunkoczi <gb360(a)cam.ac.uk> > Cc: "PHENIX user mailing list $phenixbb(a)phenix-online.org$" > <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] following on the anomalous map > Message-ID: > <CAAU4GKbzA37j=51X4jMOJjq3t4rKW7Jz9+CQrPxO-HN1kFOOiQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > HI, Gabor, > > Thanks for you suggestion. > > I tried this method, it did not give out NO sites for Br. > > why there is apparent anomalous signal and I cannot identify any Br sites? are you sure that your data processing used the correct parameters? E.g. in XDS you should definitively be using "FRIEDEL'S_LAW=FALSE". If you use XSCALE after XDS, it automagically picks up this setting from XDS_ASCII.HKL i.e. you don't have to specify this again. If you, by mistake, use FRIEDEL'S_LAW=TRUE, then the large intensity differences of Friedel pairs will be judged as outliers by XDS, and these reflections will be rejected - that might lead to featureless maps. If the anomalous signal is very strong, and the multiplicity is high, and the Chi^2 values are >1.5, you may also want to use (additionally) "STRICT_ABSORPTION_CORRECTION=TRUE" . But this is rarely necessary. There are similar options in other data processing programs. If you mix and match data processing programs (e.g. XDS integration and aimless scaling) you have to be careful to have the right settings in all programs. best, Kay > > As Nat pointed out, other atoms should have very weak anomalous signal > diffracted at Br absorption peak (3.8e- for Br, versus 0.2e- for the > sulfurs). In the difference map, I can clearly see some peaks at high sigma > (> 6), but the anomalous difference map(they are all generated by > phenix.refine or phenix.maps) is almost featureless, or the peaks has > no overlaps. The anomalous difference gives the possible place of Br while > the difference map gives the possible place of the whole ligand, and I > assume there should be some overlaps between them. Am I right? > > Charles >

1 0

Re: [phenixbb] following on the anomalous map
by CPMAS Chen 29 Aug '14

29 Aug '14

HI, Gabor, Thanks for you suggestion. I tried this method, it did not give out NO sites for Br. why there is apparent anomalous signal and I cannot identify any Br sites? As Nat pointed out, other atoms should have very weak anomalous signal diffracted at Br absorption peak (3.8e- for Br, versus 0.2e- for the sulfurs). In the difference map, I can clearly see some peaks at high sigma (> 6), but the anomalous difference map(they are all generated by phenix.refine or phenix.maps) is almost featureless, or the peaks has no overlaps. The anomalous difference gives the possible place of Br while the difference map gives the possible place of the whole ligand, and I assume there should be some overlaps between them. Am I right? Charles On Wed, Aug 27, 2014 at 6:28 AM, Gabor Bunkoczi <gb360(a)cam.ac.uk> wrote: > Hi Charles, > > I could be totally misunderstanding what you are trying to achieve, but I > think what you need to do is an MR-SAD calculation. First, solve the > structure with MR (use the macromolecule from the non-Br structure, or use > your current model if you have done refinement on it), and use the > Phaser-EP GUI, and select "SAD starting from MR model". This should > highlight any Br you may have, and gives you a PDB-file with all the peaks > (you can also get a proper anomalous map, but this is only useful for > visualization - the peak search will identify any peaks you may have). > > Let me know if you need more details! > > BW, Gabor > > > On 2014-08-26 14:49, CPMAS Chen wrote: > >> Thanks. Nat. >> >> Since I have some MET and CYT in the protein, could I try to supply >> their sulfur as the initial anomalous scatters? >> >> As for the anomalous isomorphous difference map, would it be useful I >> compare the datasets acquired at 1A wavelength and at the Br >> absorption peak (~0.92A)? >> >> Appreciate your help >> >> Charles >> >> On Mon, Aug 25, 2014 at 5:08 PM, Nathaniel Echols <nechols(a)lbl.gov> >> wrote: >> >> On Sun, Aug 24, 2014 at 6:46 AM, CPMAS Chen <cpmasmit(a)gmail.com> >>> wrote: >>> >>> Here is the point I am not clear. If I am using phenix.refine to >>>> generate LLG map, how do I pick the anomalous group since I have >>>> not placed them in the model yet? >>>> >>> >>> You can't. The LLG map only becomes really useful once you have >>> some anomalous scatterers placed and refined - this is how Phaser >>> substructure completion works. If your molecules have no other >>> significant anomalous scatterers other than the expected Br, the LLG >>> map won't do you much good. >>> >>> By the way, when I choose ion_placement and specify Br, the result >>>> comes with no Br. >>>> >>> >>> Not too surprising, since the code is tuned to look for ions, not >>> part of a covalent molecule, and halides also tend to bond >>> non-specifically and we haven't figured out how to deal with that >>> yet. >>> >>> I want to find whether the Br-containing ligand is seen in my >>>> protein which I have a high resolution structure available. >>>> >>>> I have data collected at Br wavelength, peak or higher position. >>>> Phenix.xtriage reported that the anomalous signal is present to >>>> about 4A. However, both AutoSol or MR-SAD cannot identify the Br >>>> position. Simply say, AutoSol or MR-SAD can not generate any >>>> solution. Well, of course, the simple answer would be that there >>>> is no such ligand cocrystallized. >>>> >>> >>> The simplest explanation is that you just don't have enough >>> anomalous signal to determine the substructure, which can be true >>> even if your ligand is bound. Running experimental phasing to >>> figure this out is unnecessary and time-consuming. >>> >>> Anyway, I am trying to see if the anomalous difference map or >>>> LLG(generated by phenix.maps, this would be the initial one I >>>> assume) can tell me anything more useful. >>>> >>>> So, my question on this topic would be what is a better way you >>>> guys would recommend to identify these Br-ligands? By the way, I >>>> did have the native datasets for the same protein with ligand. >>>> >>> >>> I think in this case I would start with the simple anomalous >>> difference map. If you run phenix.find_peaks_holes (it's in the >>> GUI, of course) and give anomalous data as input, it can pick out >>> the highest peaks in the anomalous map. If the ligand really is >>> bound and the Br site is ordered I would expect this to be >>> detectable. Another alternative is to compute an anomalous >>> isomorphous difference map between a dataset collected at or above >>> (in eV) the Br peak, and a dataset collected below the peak. This >>> will allow you to visualize the wavelength-dependent difference in >>> anomalous scattering, and it's going to be specific for elements >>> with absorption edges within that energy range. But I really don't >>> think this should be necessary to answer your question. >>> >>> -Nat >>> >> >> -- >> >> *************************************************** >> >> Charles Chen >> >> Research Associate >> >> University of Pittsburgh School of Medicine >> >> Department of Anesthesiology >> >> ****************************************************** >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> > > -- > ################################################## > > Dr Gabor Bunkoczi > > Cambridge Institute for Medical Research > Wellcome Trust/MRC Building > Addenbrooke's Hospital > Hills Road > Cambridge CB2 0XY > ################################################## > -- *************************************************** Charles Chen Research Associate University of Pittsburgh School of Medicine Department of Anesthesiology ******************************************************

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How to tighten ligand geometry in phenix.refine?
by Blankenfeldt, Wulf 28 Aug '14

28 Aug '14

Dear all, I am currently trying to refine a cacodylate ion that partially occupies the phosphate binding site of a PLP cofactor – partially meaning ~90%, in fact I am leaving the PLP out altogether. When I am refining this in phenix. refine, the cacodylate becomes “ugly”: the tetraeder gets slightly squashed and the atoms are flying apart a bit such that they are not automatically connected in Coot any more. I am now wondering if I can tighten the geometry just for the cacodylate to prevent this from happening, either by sending a magical command or by fiddling with the dictionary. Can anyone advise me, please? Regards, Wulf ________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Das HZI ist seit 2007 zertifiziertes Mitglied im "audit berufundfamilie" Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Franziska Broer Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

2 1

phenix.refine abort
by sujata halder 27 Aug '14

27 Aug '14

Hi, I am trying to refine a protein with 60 chains (a T=1 virus; 5-3-2 symmetry) and each chain has 520 amino acids. I am using version 1.9 (Release tag: 1692). The job stopped midway and gave the error below followed by "Cannot allocate memory". I have run a similar job (i.e using a similar sized protein) before on an older version (version 1.7) and that had worked. Looking at the error I can't really figure out if the problem is related to installation or a missing module or something different about the code. I can share my files off-list. Here is the error: ====================== XYZ individual (reciprocal space) ====================== R-FACTORS RMSD CLASH RAMA ROTA CBET WEIGHT TARGETS work free delta bonds angl data restr 28.80 29.29 0.49 0.016 1.6 11.9 0.8 7.4 60 none 0.093 160.8996 Traceback (most recent call last): File "/usr/local/phenix-1.9-1692/build/intel-linux-2.6-x86_64/../../phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/command_line.py", line 163, in run call_back_handler=call_back_handler) File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/driver.py", line 1577, in run reference_model_manager = self.reference_model_manager).result File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/strategies.py", line 183, in __init__ ion_placement_manager = ion_placement_manager) File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/macro_cycle.py", line 114, in __init__ self.call(self.xyzrec, "XYZ individual (reciprocal space)") File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/macro_cycle.py", line 142, in call func(prefix = prefix) File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/macro_cycle.py", line 374, in xyzrec prefix = prefix) File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/xyz_reciprocal_space.py", line 204, in __init__ call_back=(len(trial_weights)==1)) File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/xyz_reciprocal_space.py", line 314, in try_weight result = self.show(weight=wt, print_stats=print_stats, call_back=call_back) File "/usr/local/phenix-1.9-1692/phenix/phenix/refinement/xyz_reciprocal_space.py", line 365, in show molprobity_scores = self.main.use_molprobity) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/model.py", line 1341, in geometry_statistics molprobity_scores = molprobity_scores) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/model_statistics.py", line 99, in __init__ self.clashscore = clashscore(pdb_hierarchy=pdb_hierarchy).get_clashscore() File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/validation/clashscore.py", line 133, in __init__ verbose=verbose) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/validation/clashscore.py", line 257, in __init__ self.run_probe_clashscore(self.h_pdb_string) File "/usr/local/phenix-1.9-1692/cctbx_project/mmtbx/validation/clashscore.py", line 341, in run_probe_clashscore stdin_lines=pdb_string).raise_if_errors().stdout_lines File "/usr/local/phenix-1.9-1692/cctbx_project/libtbx/easy_run.py", line 158, in __init__ close_fds=not subprocess.mswindows) File "/usr/local/phenix-1.9-1692/build/intel-linux-2.6-x86_64/base/lib/python2.7/subprocess.py", line 709, in __init__ errread, errwrite) File "/usr/local/phenix-1.9-1692/build/intel-linux-2.6-x86_64/base/lib/python2.7/subprocess.py", line 1222, in _execute_child self.pid = os.fork() OSError: [Errno 12] Cannot allocate memory ------------------------------------------------------------------------------------------------------------- Thanks, Sujata

2 1

Missing sanity check of duplicate resids within one chain?
by Schubert, Carsten [JRDUS] 27 Aug '14

27 Aug '14

Hi, this is a bit of an esoteric issue I just stumbled over, but I'd like to flag this up anyhow. For some reason (most likely boneheaded error on my side) I wound up with duplicate resids for two ion-atoms: TER HETATM 9325 CL CL S 1 10.578 23.153 35.662 1.00 75.71 Cl1- HETATM 9326 CL CL S 2 -6.546 32.210 31.507 1.00 80.31 Cl1- HETATM 9327 CL CL S 3 21.899 28.037 25.883 1.00 86.22 Cl1- HETATM 9328 K K S 3 7.259 -0.149 19.530 1.00 91.09 K1+ TER Phenix (1.9-1692) seemingly happily accepted the input and proceeded with refinement and validation. After upgrading my coot installation to the latest build the error was flagged. I think this sort of mistake should have at least been flagged in the validation stage or is this out of scope for phenix? Cheers, Carsten

3 3

phenix.maps command line arguments
by Ryan McGreevy 26 Aug '14

26 Aug '14

When using phenix.maps from the command line, passing any arguments for the "map" layer of parameters does not seem to work. For example the command: phenix.maps input.pdb_file_name=input.pdb input.reflection_data.file_name=input.mtz works just fine, but parameters under the "map" section don't seem to have any effect, such as: map.file_name=map.ccp4 map.kicked=True Could I be doing something wrong, or does this not actually work? I know I can set these parameters in a maps.params file, but I would like to be able to pass them on the command line for scripting and automation purposes.

1 0