- phenixbb - phenix-online.org

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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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

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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

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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

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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

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

19 Sep '14

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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

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Refining structure with overlapping conformations of different residues
by Igor Petrik 18 Sep '14

18 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

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calculate TLS contribution to total B-factor
by Michael Thompson 18 Sep '14

18 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

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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*

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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

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phenix.merging_statistics and resolution shells
by Murpholino Peligro 16 Sep '14

16 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?

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LABELIT and MOSFLM version
by Ngoc Anh Thu Ho 15 Sep '14

15 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

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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

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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

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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

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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

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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

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