December 2011 - phenixbb - phenix-online.org

Problem with version 1.7.1-743 on OSX
by Miguel Ortiz Lombardía 06 Feb '12

06 Feb '12

Dear phenix developers, Last Friday (April 29) we upgraded phenix to its most recent version (1.7.1-743). Installation went smoothly on both Mac (10.6.7 64-bit) and Linux (Ubuntu 10.10 64-bit) machines. However, we observe that we cannot use phenix.refine (I don't know for the rest of the applications) from the GUI on the Macs. phenix.refine does work from the command line, though. So, whenever we try to add a pdb in the GUI, we get this error message: This application does not support the file type for /path/to/the/file.pdb (format: txt) If we try to open an mtz, it sometime works, but most often we get: PHENIX did not recognize the file type for /path/to/the/file.mtz! and on the terminal from where the GUI was started we can find: **SYMMETRY OPERATOR ERROR** Error in interpreting symop " X+2/3, Y+1/3, Z+1/3 " **SYMMETRY OPERATOR ERROR** Error in interpreting symop " -Y+2/3, X-Y+1/3, Z+1/3 " (and so on, so forth). Any clues ? Best regards, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:[email protected] http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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Chirality of Ribityl chain of FMN inverted
by Yuri 09 Jan '12

09 Jan '12

Hello Developers, When I built Ligand restraints using eLBOW, my resulting .pdb had an inverted chiral center in the ribityl chain of the flavin mononucleotide particularly C4'. In the database the ligand had an S configuration (correct), but after minimization and restraint generation the output had R configuration at that particular center. I wonder if there is a way to enforce the configuration for each center, although I suspect it could be a little bug, because I noticed my restraints have that center annotated as S eventhough it is R in the actual .pdb Cheers, -- Yuri Pompeu

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whether my following data are acceptable
by Dialing Pretty 02 Jan '12

02 Jan '12

Dear All, Following is the data range of my x-ray statistics by resolution bin: FOM between 0.84 to 0.86 Phase error between 17.90 to 24.14 scale factor from 0.88 to 1.07 SigmaA from 0.85 to 0.95 #work from 2688 to 2922 #test from 133 to 157 Do these data are within the acceptable range? Cheers, Dialing

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reference model restraints
by Ursula Schulze-Gahmen 24 Dec '11

24 Dec '11

I am refining a 3.1 A structure and are trying to use model restraints for this. There are 3 molecules in the asymmetric unit of my structure. I input the high resolution structure of one molecule of the reference structure to create restraints during the refinement. From looking at the log file, it seems to me that the reference structure is aligned to only one of my molecules, but not the other 2. How can I make sure the restraints are valid for all 3 molecules. Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

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eLBOW generates Mogul geometries
by Nigel Moriarty 23 Dec '11

23 Dec '11

Folks For a few weeks now eLBOW has been able to generate Mogul geometries. If you have CCDC's mogul installed and accessible at the command-line, eLBOW can request Mogul provide an experimentally accurate geometry. Simply use the --mogul option at the command-line and eLBOW will query Mogul for the geometry to use to generate a restraints file and a PDB file. Stay tuned for more details in the Computational Crystallography Newsletter. Happy Holidays, Merry Christmas and Happy New Year Nigel -- Nigel W. Moriarty, PhD Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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partial model in autobuild?
by Yarrow Madrona 21 Dec '11

21 Dec '11

Hello, I would like to use autobuild to start from a partial model. I have done Phaser EP with phases from MR. I can see the fourth molecule but it is not well defined and I am not exactly sure where to place it. Is it possible to run autobuild from the partial model to fill in the fourth model? Thanks. -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

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Re: [phenixbb] Reflection file woes phenix/ccp4/PDB
by Machius, Mischa Christian 20 Dec '11

20 Dec '11

Robbie, Yes, the thought that the anomalous R free flags could have something to do with it occurred to me as well, so I checked. As far as I can see, the test reflections are evenly distributed between the + and - sets; they were not selected from the + or - set only. For the vast majority of the test reflections, both Bijvoet mates were measured and both were flagged properly. For some, however, only one Bijvoet mate was measured and flagged. It probably wouldn't do any harm to consolidate the test flags, discarding the few with only one measured Bijvoet mate, but I really don't see why it should be necessary to do so. For now, I have converted the reflection file into the CNS format and sent to the PDB, hoping that they will be able to deal with that one properly. Bit surprised though that no one has run into that problem before. Thanks for your suggestion. MM On Dec 16, 2011, at 3:54 AM, Robbie P. Joosten wrote: > Hi Mischa, > > Your mtz file seems to contain 'anomalous' free R-flags (that is what I gather from Pavel's post). This is kind of weird. Do you really want I+ in the work set and I- in the test set? That would bias your R-free. If the two flags match (which I really hope), then you can leave one column out before you (re)deposit your data. This will hopefully solves the problem. > > Cheers, > Robbie Joosten > > Netherlands Cancer Institute > > On 12/15/2011 05:40 PM, Machius, Mischa Christian wrote: >> Y'all, >> >> While depositing a structure, the PDB 'complained' about my structure-factor file, saying they don't contain R-free flags or are otherwise incomplete. The comment was prompted by their Refmac R-factor test failing. >> >> The structure-factor file I submitted came from phenix.refine (xxx_data.mtz). I am using version 1.7.3-928. >> >> Indeed, using this file in CCP4 fails with the message: >> "CCP4MTZfile: Mtz column type mismatch: I-obs(+) K-J CCP4MTZfile: Mtz column type mismatch: SIGI-obs(+) M-Q" >> >> The file contains anomalous data. I have no problems with files that do not contain anomalous data. >> >> Needless to say that Phenix uses the structure-factor file just fine when reading it back into, say, its validation utility. >> >> When I use iotbx.reflection_file_reader, I cannot detect any anomalies. >> >> I am at a loss as to how to resolve this issue. I would like to deposit the data as prepared by Phenix so that the PDB tools can use them. >> >> Anybody ran into this issue before? Any ideas for how to resolve it? >> >> Many thanks in advance! >> >> MM >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb

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Failure in installing Phenix-1.7.3
by arka chakraborty 20 Dec '11

20 Dec '11

Hi all I am facing a problem while installing phenix 1.7.3 on Redhat Enterprise 5 OS. I have tried with fedora 3 binary as instructed in the download page and also with others but nothing works. I have tried installing from the root. Every time the error log is states that GLIB 2.4 is unavailable which is required by user/local/.. Please help! Thanks in advance, ARKO -- *ARKA CHAKRABORTY* *CAS in Crystallography and Biophysics* *University of Madras* *Chennai,India*

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SF-Tool check
by Dialing Pretty 19 Dec '11

19 Dec '11

Dear All, I have done the SF-Tool check for my protein crystal structure, and the result is as following. My 3 questions are (1) What does the following mean and how to solve the problem "Error! No labels are written for MTZ to mmCIF conversion Structure factor conversion is done?" (2)Where there is no "Calculated phenix R_factor(all data)"? (3) Where there is no "Correlation (Fo-Fc)"? I am looking forward to getting your reply. Dialing Error! No labels are written for MTZ to mmCIF conversion Structure factor conversion is done. Header of the mtz file can be seen from here Click here to see the converted mmCIF file Checking Xray Data by PHENIX (model_vs_data) ... PHENIX (model_vs_data) is done. Checking structure factor quality ... PHENIX.xtriage is done. Summary of Results (XXXX : ) Reported PHENIX Calculated phenix High resolution 2.829 2.83 Low resolution 50.937 50.94 Number of Reflection17446 17446 Completeness 99.98 100.0 R_factor (all data) 0.2134 ? R_factor (work set) 0.2106 0.2093 R_free 0.2668 0.2667 Correlation (Fo-Fc) ? ?

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Prevent MacPyMOL from registering as a valid pdb/pml/etc viewer.
by Francis E Reyes 19 Dec '11

19 Dec '11

Hi phenix developers I just installed 1.7.3-928. Apparently, OS X thinks the internally distributed pymol is my preferred pdb viewer (as opposed to my more recent build in /Applications). This may have something to do with the Info.plist registering document types. A small change in Finder for the user, but it was quite maddening to figure out why I had opened a pdb and pseudoatom was not working. Can future builds keep the internally distributed pymol as walled in as possible? Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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fwd: Annual CCP4 summer school in USA, at APS, June 19-26
by Nathaniel Echols 19 Dec '11

19 Dec '11

---------- Forwarded message ---------- From: "Sanishvili, Ruslan" <rsanishvili(a)anl.gov> To: "'phenixbb(a)phenix-online.org'" <phenixbb(a)phenix-online.org> Date: Mon, 19 Dec 2011 11:39:28 -0600 Subject: Annual CCP4 summer school in USA, at APS, June 19-26 Dear Colleagues, We are pleased to announce the fifth annual CCP4 summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2012/ Title: "CCP4 school: From data collection to structure refinement and beyond" Dates: June 19 to 26. Site: Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois (Near Chicago), USA The school content: Data collection workshop the first two days: beamline training and data collection on GM/CA-CAT beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used. Software workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. It will be organized in three Sections – lectures, tutorials and hands-on trouble-shooting. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. Applicants: Graduate students, postdoctoral researchers and young scientists at the assistant professor level are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection workshop and/or hands-on sessions. Application: Application deadline is April 17. The application form, the program, contact info and other details can be found at http://www.ccp4.ac.uk/schools/APS-2012/ Fees: There is no fee for the workshop. The students will be responsible for their transportation and lodging. The workshop organizers will arrange economical lodging at the Argonne Guest House. The workshop will also cover the expenses for all meals and refreshments. Garib, Ronan and Nukri Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishvili(a)anl.gov

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phenix.refine and ligands
by AFL 19 Dec '11

19 Dec '11

Hi, I'm facing an extremely annoying 'problem' when refining structures with ligands. When I try to refine a structure with a ligand inserted in coot from what I believe is refmac dictionary I'm getting following error: Number of atoms with unknown nonbonded energy type symbols: 13 "HETATM 3279 OG2 FLC B 1 .*. O " "HETATM 3280 CGC FLC B 1 .*. C " "HETATM 3281 OG1 FLC B 1 .*. O " "HETATM 3282 CG FLC B 1 .*. C " "HETATM 3283 CB FLC B 1 .*. C " "HETATM 3284 OHB FLC B 1 .*. O " "HETATM 3285 CBC FLC B 1 .*. C " "HETATM 3286 OB2 FLC B 1 .*. O " "HETATM 3287 OB1 FLC B 1 .*. O " "HETATM 3288 CA FLC B 1 .*. C " ... (remaining 3 not shown) When FLC (citrate anion) is exported via libcheck and cif file is generated with phenix.elbow everything works fine. Why is the phenix.refine not compatible with the refmac dictionary definitions? Or maybe I am doing something wrong? Cheers, Andrzej -- alnyds(a)gmail.com e-mail

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High B-factors after Phenix restrained refinement
by Da Duan 18 Dec '11

18 Dec '11

Hi all I am rather new to the crystallography so please bear with me, :-). I used Phenix AutoMR to solved a structure to 3.3A and after 1 round of rigidbody refinement with Phenix Refine I proceeded to restrained refinement. The R/Rfree from the refinement decreased nicely as expected but the B average is at ~100 (using Group B factor refinement option). I took the same model and mtz through Refmac and the B average is about ~40. Has anyone experienced this before? I am almost positive it maybe a setting issue in Phenix Refine that i should be looking at to get the B factors to refine correctly. Thanks in advance for your help! Da Duan

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Phaser problems
by Yarrow Madrona 18 Dec '11

18 Dec '11

Hello, Lately I have been having some trouble with phaser MR. For some reason even if I get a complete solution, it involves molecules from two different unit cells and it one case it picked up a symmetry related molecule as a crystallagraphic dimer. Recently I re-ran jobs from a sucessful run (over a year ago) in Phaser 2.1.4 where I get 4 molecules in the asymetric unit with plausable contacts that refined very well. Recently, however, I have re-run the job with the same search molecule and settings (all default). Although I get a solution, it involves molecules apparently from two asymetric units. The dimers formed are not the same contacts as what was seen in the earlier phaser run with Phaser 2.1.4. However if you turn on the symetry related molecues the tight crystallagraphic dimer seen previously shows up between one molecule and a symmetry mate. Has anyone had experiences like these recently with phaser? BTW my search model is 99% identical to my molecule (only one residue difference). Thanks. -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

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Re: [phenixbb] GUI MR_Rosetta without explicit search model?
by Gohlke, Ulrich 16 Dec '11

16 Dec '11

Dear Nat, I changed the .py file as you suggested, and for the moment, it seems to work. Thanks! Cheers, Uli --------------------------------------------------------------------------- dr ulrich gohlke staff scientist - macromolecular structure and interaction max-delbrück-center for molecular medicine (mdc) +49 30 9406 - 2725 (w) +49 30 9406 - 2548 (fax) ulrich.gohlke(a)mdc-berlin.de <mailto:[email protected]> http://www.mdc-berlin.de/en/research/research_teams/macromolecular_structur… <http://www.mdc-berlin.de/en/research/research_teams/macromolecular_structur…>

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Re: [phenixbb] WAS High B-factors after Phenix restrained refinement
by Bryan Lepore 16 Dec '11

16 Dec '11

This classic essay has excellent tips that are worth reviewing from time to time : http://catb.org/~esr/faqs/smart-questions.html -Bryan

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GUI MR_Rosetta without explicit search model?
by Gohlke, Ulrich 16 Dec '11

16 Dec '11

Dear colleagues, I am trying to set up an MR_Rosetta run using the GUI of Phenix 1.7.3. Unlike the command line version, it doesn't seem to accept either Robetta fragment files or alignment files from the hhpred server as the sole input but it keeps on asking for a pdb-file as search model. Is this behaviour intended or am I missing something? Best regards, Uli Gohlke --------------------------------------------------------------------------- dr ulrich gohlke staff scientist - macromolecular structure and interaction max-delbrück-center for molecular medicine (mdc) +49 30 9406 - 2725 (w) +49 30 9406 - 2548 (fax) ulrich.gohlke(a)mdc-berlin.de <mailto:[email protected]> http://www.mdc-berlin.de/en/research/research_teams/macromolecular_structur… <http://www.mdc-berlin.de/en/research/research_teams/macromolecular_structur…>

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Compilation problem rosetta MR on Fedora 10
by Martin Moche 16 Dec '11

16 Dec '11

Dear Phenix Users, I am trying to compile rosetta mr on my fedora 10 computer: http://www.phenix-online.org/documentation/mr_rosetta.htm#anch35 Compared to the instructions % tar xzf rosetta3.2_Bundles.tgz did not work for me, instead I run % tar xvf rosetta3.2_Bundles.tgz and subsequently % tar xvf BioTools-3.3.tgz % tar xvf protocol_capture-3.3.tgz etc etc >From the rosetta_source directory as an ordinary user (not root) I run: % python scons.py -j2 bin mode=release The compilation runs for a while but finally I got the termination message below. What should I try next? Best regards, Martin #################### my computer info ################## daffy-mochma 183% scons --version SCons by Steven Knight et al.: script: v1.0.0.d20080826.r3315, 2008/08/26 11:30:08, by scons on scons-dev engine: v1.0.0.d20080826.r3315, 2008/08/26 11:30:08, by scons on scons-dev Copyright (c) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 The SCons Foundation daffy-mochma 104% uname -a Linux daffy 2.6.27.41-170.2.117.fc10.i686 #1 SMP Thu Dec 10 11:00:29 EST 2009 i686 i686 i386 GNU/Linux daffy-mochma 105% python --version Python 2.5.2 ############# termination message ############################# g++ -o build/src/release/linux/2.6/32/x86/gcc/libutility.so -Wl,-rpath=/net/fileserver/xtal/rosetta3.3_bundles/rosetta_source/build/external/release/linux/2.6/32/x86/gcc/ -shared build/src/release/linux/2.6/32/x86/gcc/utility/pointer/ReferenceCount.os build/src/release/linux/2.6/32/x86/gcc/utility/pointer/ReferenceCountMI_.os build/src/release/linux/2.6/32/x86/gcc/utility/options/OptionCollection.os build/src/release/linux/2.6/32/x86/gcc/utility/options/mpi_stderr.os build/src/release/linux/2.6/32/x86/gcc/utility/tag/Tag.os build/src/release/linux/2.6/32/x86/gcc/utility/sql_database/DatabaseSessionManager.os build/src/release/linux/2.6/32/x86/gcc/utility/boinc/boinc_util.os build/src/release/linux/2.6/32/x86/gcc/utility/io/icstream.os build/src/release/linux/2.6/32/x86/gcc/utility/io/izstream.os build/src/release/linux/2.6/32/x86/gcc/utility/io/ocstream.os build/src/release/linux/2.6/32/x86/gcc/utility/io/ozstream.os build/src/release/linux/2.6/32/x86/gcc/utility/options/keys/OptionKeys.os build/src/release/linux/2.6/32/x86/gcc/utility/excn/Exceptions.os build/src/release/linux/2.6/32/x86/gcc/utility/file/file_sys_util.os build/src/release/linux/2.6/32/x86/gcc/utility/file/FileName.os build/src/release/linux/2.6/32/x86/gcc/utility/file/gzip_util.os build/src/release/linux/2.6/32/x86/gcc/utility/file/PathName.os build/src/release/linux/2.6/32/x86/gcc/utility/basic_sys_util.os build/src/release/linux/2.6/32/x86/gcc/utility/string_util.os build/src/release/linux/2.6/32/x86/gcc/utility/heap.os build/src/release/linux/2.6/32/x86/gcc/utility/integer_mapping.os build/src/release/linux/2.6/32/x86/gcc/utility/mpi_util.os build/src/release/linux/2.6/32/x86/gcc/utility/exit.os build/src/release/linux/2.6/32/x86/gcc/utility/LexicographicalIterator.os -Llib -Lexternal/lib -Lbuild/src/release/linux/2.6/32/x86/gcc -Lsrc -Lbuild/external/release/linux/2.6/32/x86/gcc -Lexternal -L/usr/local/lib -L/usr/lib -lObjexxFCL -lz -lcppdb -lsqlite3 /usr/bin/ld: cannot find -lz collect2: ld returned 1 exit status scons: *** [build/src/release/linux/2.6/32/x86/gcc/libutility.so] Error 1 scons: building terminated because of errors. Martin Moche, Ph.D. Head of Protein Crystallography Karolinska Institutet MBB/PSF Scheeles väg 2 171 77 Stockholm Sweden phone: +46-8-524 868 43 mobile: +46-73-322 93 27 fax: +46-8-524 868 68 email: Martin.Moche(a)ki.se

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Reflection file woes phenix/ccp4/PDB
by Machius, Mischa Christian 15 Dec '11

15 Dec '11

Y'all, While depositing a structure, the PDB 'complained' about my structure-factor file, saying they don't contain R-free flags or are otherwise incomplete. The comment was prompted by their Refmac R-factor test failing. The structure-factor file I submitted came from phenix.refine (xxx_data.mtz). I am using version 1.7.3-928. Indeed, using this file in CCP4 fails with the message: "CCP4MTZfile: Mtz column type mismatch: I-obs(+) K-J CCP4MTZfile: Mtz column type mismatch: SIGI-obs(+) M-Q" The file contains anomalous data. I have no problems with files that do not contain anomalous data. Needless to say that Phenix uses the structure-factor file just fine when reading it back into, say, its validation utility. When I use iotbx.reflection_file_reader, I cannot detect any anomalies. I am at a loss as to how to resolve this issue. I would like to deposit the data as prepared by Phenix so that the PDB tools can use them. Anybody ran into this issue before? Any ideas for how to resolve it? Many thanks in advance! MM

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Dec 16, 2011 deadline- User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 15 Dec '11

15 Dec '11

Dear Users, > > The deadline for Feb/April 2012 Collaborative > Crystallography proposals will be *Dec 16, 2011. * > > ---------------------------------------------------------------------------------------- > Through the Collaborative Crystallography Program (CC) at the > Advanced Light Source (ALS), scientists can send protein crystals > to Berkeley Center for Structural Biology (BCSB) staff researchers > for data collection and analysis. The CC Program can provide a > number of benefits to researchers: > > * Obtain high quality data and analysis through collaborating with > expert beamline > researchers; > * Rapid turn around on projects; and > * Reduced travel costs. > > To apply, please submit a proposal through the ALS General User > proposal review process for beamtime allocation. Proposals are > reviewed and ranked by the Proposal Study Panel, and beamtime is > allocated accordingly. BCSB staff schedule the CC projects on > Beamlines 5.0.1 and 5.0.2 to fit into the available resources. Only > non-proprietary projects will be accepted. As a condition of > participation, BCSB staff researchers who participate in data > collection and/or analysis must be appropriately acknowledged - > typically being included as authors on publications and in PDB > depositions. Please consult the website for additional information at: > > http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography > > ----------------------------------------------------------------------------------------- > How To Apply: > > To learn more, go to: > > http://www.als.lbl.gov/als/quickguide/becomealsuser.html > > To submit a proposal, go to: http://alsusweb.lbl.gov/. Scroll > down to "*Structural Biology beamlines (includes protein SAXS)*" > and click on "New Proposal." Enter your proposal information, with > attention to the following details: > > * For question 3/First choice, select "5.0.1 > (Monochromatic);" for question 3/Second choice, select "5.0.2 (MAD)." > * Check box (yes) in response to question (7) "Do you want collaborative > crystallography > (beamline 5.0.1 or 5.0.2 only) > * In question 4, please describe a specific research project with a > clear end point. > > In order to request CC time for Feb/April 2012 allocation period, > proposals must be submitted by *Dec 16, 2011.* > > The deadline for CC proposals for the time period May/June 2012 will be > Mar 15, 2012. > > Regards, > Banumathi Sankaran > >

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Re: [phenixbb] Compilation problem rosetta MR on Fedora 10
by Eugene Valkov 15 Dec '11

15 Dec '11

Hi Martin, I had encountered an issue with building Rosetta 3.2.1 on Ubuntu 11.04, specifically that SCons could not compile it because it used gcc 4.1 libraries, whereas there was gcc 4.4 installed. Could you check what version of gcc you have installed on your Fedora box? If it is the compiler issue then there are some workarounds documented on Rosetta forums: https://www.rosettacommons.org/node/2274 These worked for me, but you have to hack around in code a bit to make it happen. HTH, Eugene > On 15 December 2011 13:08, Martin Moche <Martin.Moche(a)ki.se> wrote: >> Dear Phenix Users, >> >> I am trying to compile rosetta mr on my fedora 10 computer: >> http://www.phenix-online.org/documentation/mr_rosetta.htm#anch35 >> >> Compared to the instructions >> % tar xzf rosetta3.2_Bundles.tgz >> >> did not work for me, instead I run >> % tar xvf rosetta3.2_Bundles.tgz >> >> and subsequently >> % tar xvf BioTools-3.3.tgz >> % tar xvf protocol_capture-3.3.tgz >> etc etc >> >> From the rosetta_source directory as an ordinary user (not root) I run: >> % python scons.py -j2 bin mode=release >> >> The compilation runs for a while but finally I got the termination message >> below. >> >> What should I try next? >> >> Best regards, >> Martin >> >> #################### my computer info ################## >> >> daffy-mochma 183% scons --version >> SCons by Steven Knight et al.: >> script: v1.0.0.d20080826.r3315, 2008/08/26 11:30:08, by scons on >> scons-dev >> engine: v1.0.0.d20080826.r3315, 2008/08/26 11:30:08, by scons on >> scons-dev >> Copyright (c) 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 The SCons >> Foundation >> >> daffy-mochma 104% uname -a >> Linux daffy 2.6.27.41-170.2.117.fc10.i686 #1 SMP Thu Dec 10 11:00:29 EST >> 2009 i686 i686 i386 GNU/Linux >> >> daffy-mochma 105% python --version >> Python 2.5.2 >> >> >> >> ############# termination message ############################# >> >> g++ -o build/src/release/linux/2.6/32/x86/gcc/libutility.so >> -Wl,-rpath=/net/fileserver/xtal/rosetta3.3_bundles/rosetta_source/build/external/release/linux/2.6/32/x86/gcc/ >> -shared >> build/src/release/linux/2.6/32/x86/gcc/utility/pointer/ReferenceCount.os >> build/src/release/linux/2.6/32/x86/gcc/utility/pointer/ReferenceCountMI_.os >> build/src/release/linux/2.6/32/x86/gcc/utility/options/OptionCollection.os >> build/src/release/linux/2.6/32/x86/gcc/utility/options/mpi_stderr.os >> build/src/release/linux/2.6/32/x86/gcc/utility/tag/Tag.os >> build/src/release/linux/2.6/32/x86/gcc/utility/sql_database/DatabaseSessionManager.os >> build/src/release/linux/2.6/32/x86/gcc/utility/boinc/boinc_util.os >> build/src/release/linux/2.6/32/x86/gcc/utility/io/icstream.os >> build/src/release/linux/2.6/32/x86/gcc/utility/io/izstream.os >> build/src/release/linux/2.6/32/x86/gcc/utility/io/ocstream.os >> build/src/release/linux/2.6/32/x86/gcc/utility/io/ozstream.os >> build/src/release/linux/2.6/32/x86/gcc/utility/options/keys/OptionKeys.os >> build/src/release/linux/2.6/32/x86/gcc/utility/excn/Exceptions.os >> build/src/release/linux/2.6/32/x86/gcc/utility/file/file_sys_util.os >> build/src/release/linux/2.6/32/x86/gcc/utility/file/FileName.os >> build/src/release/linux/2.6/32/x86/gcc/utility/file/gzip_util.os >> build/src/release/linux/2.6/32/x86/gcc/utility/file/PathName.os >> build/src/release/linux/2.6/32/x86/gcc/utility/basic_sys_util.os >> build/src/release/linux/2.6/32/x86/gcc/utility/string_util.os >> build/src/release/linux/2.6/32/x86/gcc/utility/heap.os >> build/src/release/linux/2.6/32/x86/gcc/utility/integer_mapping.os >> build/src/release/linux/2.6/32/x86/gcc/utility/mpi_util.os >> build/src/release/linux/2.6/32/x86/gcc/utility/exit.os >> build/src/release/linux/2.6/32/x86/gcc/utility/LexicographicalIterator.os >> -Llib -Lexternal/lib -Lbuild/src/release/linux/2.6/32/x86/gcc -Lsrc >> -Lbuild/external/release/linux/2.6/32/x86/gcc -Lexternal -L/usr/local/lib >> -L/usr/lib -lObjexxFCL -lz -lcppdb -lsqlite3 >> /usr/bin/ld: cannot find -lz >> collect2: ld returned 1 exit status >> scons: *** [build/src/release/linux/2.6/32/x86/gcc/libutility.so] Error 1 >> scons: building terminated because of errors. >> >> >> Martin Moche, Ph.D. >> Head of Protein Crystallography >> Karolinska Institutet >> MBB/PSF >> Scheeles väg 2 >> 171 77 Stockholm >> Sweden >> phone: +46-8-524 868 43 >> mobile: +46-73-322 93 27 >> fax: +46-8-524 868 68 >> email: Martin.Moche(a)ki.se >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> -- Eugene Valkov, D.Phil. MRC Career Development Fellow Division of Structural Studies MRC Laboratory of Molecular Biology Hills Road Cambridge CB2 0QH email: evalkov(a)mrc-lmb.cam.ac.uk tel: +44 (0)1223 402261

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loosening constraints on water addition
by Crystal VanderZanden 15 Dec '11

15 Dec '11

I'm trying to adjust the parameters on the water picking to allow for more waters to be found. I tried creating a solvent.params file with the code below, then I increased and decreased the primary map cutoff. When I ran the water picking command with the solvent.params file, it actually decreased the number of waters found, both at the high and low primary map cutoff. Does anyone know what I can do to relax the water finding criteria so more waters will be found? Thanks, Crystal refinement { ordered_solvent { low_resolution = 2.8 b_iso_min = 1.0 b_iso_max = 50.0 b_iso = 25.0 primary_map_type = mFobs-DFmodel primary_map_cutoff = 3.0 secondary_map_and_map_cc_filter { cc_map_2_type = 2mFobs-DFmodel } } peak_search { map_next_to_model { min_model_peak_dist = 1.8 max_model_peak_dist = 6.0 min_peak_peak_dist = 1.8 } } }

2 1

how to get the sf.ent file
by Dialing Pretty 15 Dec '11

15 Dec '11

Dear All, Will you please tell me how can I get the sf.ent file from a PDB enty? Cheers, Dialing

3 2

wilson scale
by Dialing Pretty 15 Dec '11

15 Dec '11

Dear All, For my structure, the wilson scale is 0.5, is it fine or not? Best regards. Dialing

2 1

phenix.superpose_pdbs and nucleic acids.. does it work?
by Francis E Reyes 14 Dec '11

14 Dec '11

Hi phenixer's. I need to do a superposition of two pdbs. I guess phenix.superpose_pdbs is my jiffy but it doesn't seem to work for nucleic acids (tried selection = 'name P' or selection = 'all'). LSQKAB seems to have the same limitation. They are the exact same PDBs (1 to 1 atom/residue mapping) but just shifted and rotated relative to the other. I need a superposition or the transformation matrix for all atoms. Traceback (most recent call last): File "/usr/local/phenix-1.7.1-743/phenix/phenix/command_line/superpose_pdbs.py", line 450, in <module> run(args=sys.argv[1:]) File "/usr/local/phenix-1.7.1-743/phenix/phenix/command_line/superpose_pdbs.py", line 434, in run m = manager(params.extract(), log) File "/usr/local/phenix-1.7.1-743/phenix/phenix/command_line/superpose_pdbs.py", line 171, in __init__ selection_moving = self.selection_moving) File "/usr/local/phenix-1.7.1-743/phenix/phenix/command_line/superpose_pdbs.py", line 306, in _alignment "bugs(a)phenix-online.org for help.") RuntimeError: Failed to identify corresponding atoms from sequence alignment. This is probably a bug - contact bugs(a)phenix-online.org for help. I may just strip it down to phosphate's and rename the residues to ALA but a quick phenix jiffy would be great. Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

2 1

on residue bond deviation
by Dialing Pretty 14 Dec '11

14 Dec '11

Dear All, After a key step refinement byPhenix refine, I find there are 2 residues (total about 450 residues) with bad angles as analyzed by MolProity (deviation ratio 0.46%, goal is 0.1% ), both of the 2 residues are Pro, and both of the deviation angles are C-N-CA. Will you please give the comment on what do the 2 deviations mentioned above mean for my whole protein structure, or should I continue to refine my protein structure? I am looking forward to getting your reply. Dialing

2 1

on the input file for the Phase and build
by Dialing Pretty 14 Dec '11

14 Dec '11

Dear All, For the Phenix Phase and build, the input mtz file is the scala mtz file, and the ouput mtz file will be the mtz file with phase, is this correct? I am looking forard to getting a reply from you. Cheers, Dialing

2 1

strange MR problem
by intekhab alam 13 Dec '11

13 Dec '11

Hi All I have a 3.0A dataset of a protein-protein complex. I used one of the protein structure solved previously as a template and used phaser in CCP4 as well as in phenix. I used the sca file in phenix which gave a solution with 6 monomers in ASU which are packed as a hexamer. In ccp4 phaser i used the converted .mtz file which gave 6 molecules in ASU but with a different packing. In both the cases map fits well in the model and there is some extra density that may correspond to second protein partner of the complex molecule. when i tried to use the MR solution generated in phenix with the mtz file from ccp4 the model shows a lot of clashes. what kind of approach should i take so as to resolve this ambiguity. Regards -- INTEKHAB ALAM LABORATORY OF STRUCTURAL BIOINFORMATICS KOREA UNIVERSITY, SEOUL

2 4

Phenix version 1.7.3 released
by Paul Adams 13 Dec '11

13 Dec '11

The Phenix developers are pleased to announce that version 1.7.3 of Phenix is now available. Binary installers for Linux, and Mac OSX platforms are available at the download site: http://phenix-online.org/download/ Some of the new features in this version are: Graphical interface: ==================== - New GUIs: MR-Rosetta - viewer for diffraction images (also available as phenix.image_viewer) - editable heavy-atom sites in HySS and AutoSol General: ======== - New commands: phenix.ncs_average, phenix.model_vs_sequence, phenix.image_viewer, phenix.find_alt_orig_sym_mate, phaser.MRage - support for CNS v1.3 reflection files Refinement: =========== - Reduced memory requirement for map related calculations - Improved handling of parameter files in the GUI - RNA geometry target now includes pucker & base type-specific Chi 1 parameters - TLS group definitions from PDB file header will be automatically used if no groups are provided by the user - Bug fix in clashscore calculation for large structures with duplicate chain IDs plus SEGIDs - Torsion NCS restraints uses SEGIDs if present in input PDB file Molecular Replacement: ====================== - phaser (version 2.4): - support for pseudo-translational non-crystallographic symmetry (tNCS) in molecular replacement - detects presence of tNCS from inspection of native Patterson - characterizes tNCS parameters (translation, small rotational difference between copies) - accounts for effect of tNCS in molecular replacement calculations - note: support currently limited to one tNCS operator relating two molecules (or sets of molecules) - FAST search method turned on by default, replacing FULL search method - MR possible with a model containing a single atom - B-factor refinement turned on by default in molecular replacement - Bug fix for occasional and irreproducible segmentation faults for 32 bit binary running on 64 bit Linux - Packing function accepts cases where an ensemble with internal point group symmetry is on a special position, and pdb file output deletes atoms overlapped due to the symmetry of special position - phaser.MRage (version 0.1.0) - automated MR: - New command-line switches for common actions, e.g. setting the verbosity, getting PHIL parameters, etc - Define component by sequence, but calculate molecular weight from available models if sequence is omitted - Calculate number of copies to find from Matthews coefficient - Ability to perform homology search (currently only BLAST is supported, either local installation or NCBI service) - alignments automatically generated for "template" if target sequence is known - various options for queueing systems, e.g. qslot - option to automatically write out solutions - fully parallel space group exploration - phenix.find_alt_orig_sym_mate (new command): - For different molecular replacement solutions from the same dataset, finds the copy of moving_pdb closest to reference_pdb with respect to all symmetry operations and alternative origin shifts permitted by the spacegroup in moving_pdb Experimental Phasing and Model Building: ======================================== - AutoSol: - Fixed problems with clean_up=True deleting overall_best.pdb - Allow data file names of any length - Use NCS in scoring by default if ncs copies > 2 - Correct anisotropy and sharpen by default - AutoBuild: - Automatic anisotropy correction and sharpening for all maps - phenix.multi_crystal_average: - Automatic anisotropy correction and sharpening - Automatic filling of reflections to highest resolution of any dataset - Masking heavy-atom sites from averaging - Inputs grouped by crystal Miscellaneous: ============== - phenix.ready_set/phenix.reduce: - Improved handling of alternate conformations - phenix.cif_as_mtz - Support for files containing multiple datasets - Extraction of Hendrickson-Lattman coefficients and anomalous arrays - New map_to_asu and remove_systematic_absences options - phenix.maps: - Added atom selection parameter for simple omit maps (omit.selection) - phenix.ligand_identification: - Implemented methods to generate custom ligand library based on parent protein's SCOP or CATH terms, Pfam accession numbers, GO accession numbers, or InterPro ID - Improved ligand geometry after real-space refinement For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this publication should be used to cite use of Phenix: PHENIX: a comprehensive Python-based system for macromolecular structure solution. P. D. Adams, P. V. Afonine, G. Bunkóczi, V. B. Chen, I. W. Davis, N. Echols, J. J. Headd, L.-W. Hung, G. J. Kapral, R. W. Grosse-Kunstleve, A. J. McCoy, N. W. Moriarty, R. Oeffner, R. J. Read, D. C. Richardson, J. S. Richardson, T. C. Terwilliger and P. H. Zwart. Acta Cryst. D66, 213-221 (2010). Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- 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 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 ] --

1 0

ncs_average output map
by Ursula Schulze-Gahmen 12 Dec '11

12 Dec '11

I am puzzled about my ncs-averaged output map. I determined the ncs relation using phenix.find_ncs with pdb and mtz input. The program finds 2 NCS groups with 3 molecules each and the rmsds are low. I then read in the ncs_spec file and an mtz file with map coefficients into phenix.ncs_average. I used the FOFCWT, PHFOFCWT coefficients. The output map seems cleaner than the unaveraged map and shows some of the same features, but the density around the 3 molecules is not identical. 2 of them look very similar, but the density around one of them is somewhat different. How is this possible if the map is averaged? Thanks for any suggestions or explanations. Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

2 3

AutoBuild Question
by Page, Rebecca 12 Dec '11

12 Dec '11

Dear phenix community: I ran AutoBuild.dat with a seq.dat file that has 3 separate sequences. Chains A and B were built, but chain C was not, even though there is density for the third chain. It occurred to me that only two of the three chains may have been read in. I seem to recall that seq.dat can be a maximum of two sequences, but am not sure. So, is there a limit to the number of sequences that can be present in seq.dat and if so, what is the limit. Thanks in advance, Rebecca

4 4

phenix.refine_failed
by Xue-Yuan Pei 12 Dec '11

12 Dec '11

Dear Phenix Experts: My phenix.refine has developped the following error (see below). I tried to check my PDB format, there is not B-factor error. so what could be wrong that stoped my phenix.refine without PDB and .def files in the output? Many thanks for your advice. Xue yuan Pei, Ph.D Department of Biochemistry University of Cambridge Cambridge CB2 1GA U.K > Error messages: > Traceback (most recent call last): > File > "/usr/local/xtal/phenix-1.7.2-869/phenix/phenix/command_line/refine.py", > line 11, in <module> > command_line.run(command_name="phenix.refine", args=sys.argv[1:]) > File > "/usr/local/xtal/phenix-1.7.2-869/phenix/phenix/refinement/command_line.py", > line 105, in run > refine_object.write_refined_pdb(f_pdb) > File > "/usr/local/xtal/phenix-1.7.2-869/phenix/phenix/refinement/driver.py", > line 1284, in write_refined_pdb > ignore_hd = not self.neutron_refinement) > File > "/usr/local/xtal/phenix-1.7.2-869/cctbx_project/mmtbx/model_statistics.py", > line 534, in __init__ > ignore_hd = ignore_hd) > File > "/usr/local/xtal/phenix-1.7.2-869/cctbx_project/mmtbx/model_statistics.py", > line 449, in __init__ > molprobity_scores=True) > File "/usr/local/xtal/phenix-1.7.2-869/cctbx_project/mmtbx/model.py", > line 1063, in geometry_statistics > molprobity_scores = molprobity_scores) > File > "/usr/local/xtal/phenix-1.7.2-869/cctbx_project/mmtbx/model_statistics.py", > line 112, in __init__ > self.clashscore_obj.analyze_clashes(hierarchy = pdb_hierarchy) > File > "/usr/local/xtal/phenix-1.7.2-869/cctbx_project/mmtbx/validation/clashscore.py", > line 167, in analyze_clashes > stdin_lines=tmp_r.as_pdb_string()) > File > "/usr/local/xtal/phenix-1.7.2-869/cctbx_project/iotbx/pdb/hierarchy.py", > line 527, in as_pdb_string > siguij=siguij) > RuntimeError: atom B-factor does not fit into F6.2 format: > "ATOM 1 N GLY A 1 " > B-factor: 111147.29 >

3 3

phenix.refine_failed
by Christian Roth 12 Dec '11

12 Dec '11

Hi, indeed your B-Factor shown in the error message for Gly A 1 is unrealistic. Is maybe in your pdb-file a space missing? I think a 8 digit B-Factor is not possible in the pdb format. Best Regards Christian

1 0

Phaser not writting out ligands
by Yarrow Madrona 09 Dec '11

09 Dec '11

Hello, I am having trouble with Phaser not writing out my ligands (HEME and small molecule) to it's output PDB even though they are in the input PDB. I am running through the GUI using Phenix version 1.7.3-921. Phenix refine recognizes HEME from the CCP4 library I think so I am not sure why I at least do not get a HEME in the output PDB. Thanks for your help. -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697 -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

2 1

Please apply for RapiData 2012, a course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 09 Dec '11

09 Dec '11

We are offering RapiData 2012, the fourteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 22-27 April 2012: http://www.bnl.gov/rapidata/. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. We encourage all students to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. You'll find the application materials on the Course Application tab at this site. For the tenth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 22 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (under 40 yrs). Please apply for the course, and then contact R. Sweet (sweet(a)bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Bob Sweet, Sonya Kiss, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ ========================================================================= Robert M. Sweet E-Dress: sweet(a)bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLS not 1) http://px.nsls.bnl.gov/ Biology Dept Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================

1 0

map output from ncs_average
by Ursula Schulze-Gahmen 09 Dec '11

09 Dec '11

I used ncs_average to create an averaged fo-fc map. From the manual I thought that the output map is a CCP4 map. I have however difficulties to read it into Pymol as ccp4 map. It is not recognized. Any suggestions? Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

3 4

print_sequence
by Bradley Hintze 09 Dec '11

09 Dec '11

Hi, I am analyzing many PDBs vai a script. Thus, I am feeding print_sequence the full path of the given PDB. This has the unfortunate effect of having a filename more than 80 char. As such the '>filename' line is split into two lines making parsing less than ideal. Is there a way I can avoid having the full path on the '>' line and still give print_sequence the full path? Or can that feature be added? Thanks, -- Bradley

2 1

excluding atoms from refinement
by Crystal VanderZanden 08 Dec '11

08 Dec '11

Does anybody know if there a general code that will allow us to exclude something from refinement? I would like to specify that there is a particular part of my structure that I don't want to refine the position. I've thought about deleting those atoms from the pdb file, but then that phasing information is excluded from the refinement. Any ideas? Thanks, Crystal

3 2

Re: [phenixbb] Autosol problems
by Tom Terwilliger 08 Dec '11

08 Dec '11

Hi Stacy, I'm sorry for the trouble! Normally autosol should not have problems with resolve, so this indicates that either (1) the data are unusual or (2) there is some problem in autosol. Can you possibly send along (terwilliger(a)lanl.gov) the log file from autosol and the LAST.log file if there is one? Also what version of phenix is this? (type "phenix.version") Thanks! -Tom T On Dec 8, 2011, at 8:55 AM, stacy William wrote: > Dear All... > I am new user for Phenix. I am right now working with SAD data. I had run Ausol in GUI interface with my SAD anamolous data. but when i am using the output file for my autobuild program it is giving problems with Resolve... n terminating with an error message suggesting to check resolve file. Do i need to change some parameters in Autosol to produce right output files which in turn can work as input files for Autobuild program > Thanks > Stacy > > Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: terwilliger(a)LANL.gov Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss

1 0

automr wizard: searching for all plausible space groups option
by Vitali Stanevich 08 Dec '11

08 Dec '11

Hi, I'm trying to solve structure by MR with phenix 1.6.1-357 version. I have 100% identity search model and can find solution without problem in ccp4i in P212121 sg. But, I can't do it in phenix.automr command line because program looks only for P222 space group (pointed out by Randy Read). I use .sca from hkl2000 and running program from parameters file. I tried: ... all_plausible_sg_list = True use_all_plausible_sg = True ... all_plausible_sg_list = P222 P2221 P21212 P212121 use_all_plausible_sg = True ... space_group = "P 21 21 21" ... They lead to report that no solution found or program being stalled (last variant). What should I do to make phaser search for all space groups in P222 point group? Thanks, Vitali

3 2

rosetta mr
by Shya Biswas 07 Dec '11

07 Dec '11

Hi all, I was wondering how to generate .ali file that I need to run rosetta MR. I have most of the files for the run except this one. the documentation did not help a lot. thanks, Shya

3 3

pseudo-merohedral twinning
by Zhou, Tongqing (NIH/VRC) [E] 07 Dec '11

07 Dec '11

Hi Pavel, I just collected a 2.85 A dataset with space group P212121, MR went well, however, the refinement was not fine: (eg: Rigid body r=48%, it won't go down anymore). I then ran xtriage, it turned out the my data was pseudo-merohedral twinned. The twin fraction is ~0.02. Twin_law=k,h,-l. It there a way to de-twin the data and then do the refinement or just use the twin_law="k,h,-l" at the command line? Is there a way to specify twin_fraction in the paramenter file? Also re-processed data in P41212 or P43212, the ~25% Rsym indicated the data should still be in P222. Thanks, Tongqing Tongqing Zhou, Ph.D. Staff Scientist Structural Biology Section Vaccine Research Center, NIAID/NIH Building 40, Room 4607B 40 Convent Drive, MSC3027 Bethesda, MD 20892 (301) 594-8710 (Tel) (301) 793-0794 (Cell) (301) 480-2658 (Fax) ****************************************************************************** The information in this e-mail and any of its attachments is confidential and may contain sensitive information. It should not be used by anyone who is not the original intended recipient. If you have received this e-mail in error please inform the sender and delete it from your mailbox or any other storage devices. National Institute of Allergy and Infectious Diseases shall not accept liability for any statements made that are sender's own and not expressly made on behalf of the NIAID by one of its representatives. ******************************************************************

4 3

pdbtools
by Bradley Hintze 06 Dec '11

06 Dec '11

Developers, I am doing some automated analysis on many pdbs. My analysis is contained to a single chain in a given pdb. Aa such, to cut down on computing time I am generating many pdbs cut to the desired chain. When using pdbtools I get the following Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 46 Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. Also note that phenix.ready_set and phenix.elbow are available for creating restraint definitions (CIF files). Is there a way around this without creating a CIF file or another tool to cut pdbs? Thanks, Bradley -- Bradley J. Hintze Duke University Graduate Student Department of Biochemistry

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Rfree flag transfer
by Zhang yu 06 Dec '11

06 Dec '11

Hi, I am using phenix_1.7.1-743 GUI. I would like to transfer Rfree tag from one dataset to the other one, but had the following error, "The uni cell for the Miller array /***/*** (186.326, 103.98, 297.48, 90, 98.465, 90)" is significantly different than the output unit cell (183.486, 103.5, 295.416, 90, 98.828, 90)" Two datasets are from same kind of crystal, but with slight different cells. I guess that is why "Reflection file editor" refused to do it. Could anyone tell me how to avoid the error? Thanks Yu

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autoMR wizard
by Vitali Stanevich 06 Dec '11

06 Dec '11

Hi, I'm trying to solve structure by molecular replacement. We already have structure for this protein and new is exactly the same thing with a ligand soaked. I can solve it without a problem with ccp4 gui (tfz=47.7), but not with phenix.automr, which is disappointing. Can somebody point me out what's wrong with my data input? I did it with this command: phenix.automr output.sca complex_search.pdb identity=90 mass=93500 copies=1 or with .eff file (attached) Thanks, Vitali

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H related bond deviaion
by Dialing Pretty 06 Dec '11

06 Dec '11

Dear All, I did a Phenix refine, and before the refine all the H were added. MolProbity analysis demonstrated that almost everything are acceptable after the refinement. However when I did the geometry analysis by the COOT validation, I find all the residues having a significant deviation bond involving H. with z score higher than 7. I am looking forward to getting an explanation from you on it,including how to avoid it. Cheers, Dialing

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bond deviation deected by Coot
by Dialing Pretty 05 Dec '11

05 Dec '11

Dear All, After Pheneix refine, the quality of the structure improved significantly as analyzed by Molprobity. However the bond deviation increased significantly after the refinement. Will you please tell me which refine function can be used to reduce the bond deviation detected by the Coot geometry analysis? Cheers, Dialing

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rotamer outlier reduction by coot
by Dialing Pretty 05 Dec '11

05 Dec '11

Dear All, I am leaning rotamer outlier reduction by Coot. After select a rotamer and acception, I find some hydrogens in the outlier rotamer will be isolated from the rotamer, and the rotamer will have new hydrogens at its new position. Is any influence by further refine by phenix? After new rotamer acception, I have did the rotamer auto-fit, I find there is a trend on that several oxygens can pack together. How to process this problem? After I save the new PDB file by coot after I selected the new rotamers to replace the outlier rotamers, I did a Phenix refine. There is an error message at the start says "Number of atoms with unknown nonbonded energy typensymbol: 2228". What does it mean and how to solve the problem? Is any simple method by which I can do the rotamer outlier reduction by Coot? I am looking forward to getting your reply. Dialing

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documents explaining parameter settings in phenix-1.7.2
by Ruan Wenjie 05 Dec '11

05 Dec '11

Hi, I want to know, about the new Phenix-1.7.2 version, whether I can find some detailed documents explaining how to set the parameters..since there are so many options and I'm not clear their meaning..Thanks~ best, wenjie

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Job Opportunity - Head of the Berkeley Center for Structural Biology
by Paul Adams 04 Dec '11

04 Dec '11

The Physical Biosciences Division at Lawrence Berkeley National Laboratory is seeking candidates for the Head of the Berkeley Center for Structural Biology. This position provides scientific, technical and operational oversight of the BCSB at the Advanced Light Source (ALS), a third generation synchrotron facility. The BCSB is a user resource for structural biology experiments and consists of 5 beamlines at 2 sectors of the ALS, with a staff of 16. This Staff Scientist position will provide leadership and direction to develop methodology and instrumentation for collecting and analyzing crystallographic data using synchrotron radiation, and on projects involving the structure determination of biological molecules using X-ray crystallography. This position focuses on the field of crystallography, and involves interactions and collaborations with researchers from multiple scientific disciplines including chemistry, crystallography, biochemistry, biology, physics and computational sciences. For full details please visit the job application link at: https://lbl.taleo.net/careersection/2/jobdetail.ftl?lang=en&job=73970 Lawrence Berkeley National Laboratory is a world leader in science and engineering research, with 13 Nobel Prize recipients over the past 75 years. LBNL conducts unclassified research across a wide range of scientific disciplines and hosts four national user facilities. AA/EEO employer committed to the development of a safe and diverse workforce. Learn more about the Lab at http://www.lbl.gov. -- 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 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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pdb hierarchy
by Bradley Hintze 04 Dec '11

04 Dec '11

Hi Phenix, I have a hierarchy question. I was using the hierarchy and got something that I did not expect. when running this: pdb_io = pdb.input(pdbfile) hierarchy = pdb_io.construct_hierarchy() for model in hierarchy.models(): print model.id for chain in model.chains(): print ' ' + chain.id When I do this I expect the chains in pdbfile to be printed once for each model in pdbfile. However, when I ran this I got, for example, chain 'A' printed four times under the same model. Why is this? Thanks, Bradley

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Writing PDB
by Bradley Hintze 04 Dec '11

04 Dec '11

Hi again, I am trying to take a pdb and write out a new pdb with just a specified chain. I am trying to do this with the hierarchy but am unfamiliar with its functions How do I do this? Thanks, Bradley

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the Ming dial
by Dialing Pretty 04 Dec '11

04 Dec '11

Dear All, In the Ming dial, there is a occupancy (%), which indication of excellent , good, etc. Does it mean if I choose the "occupancy" of excellent, the rotamer outlier ratio will be lowered? My crystal has a resolution of 2.8, and I find no matter how I turn the dial, the original fits the map best. Currently my rotamer outlier is 8%, thus I need the way to have it solved. In addition, for Coot and Ming, which is much convenient to reduce rotamer outlier? I am looking forward to getting your reply. Cheers, Fenghui

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on the rotamer optimization
by Dialing Pretty 03 Dec '11

03 Dec '11

Dear All, Besides Coot and Ming, is any software or server which could further optimize the side chain outliers? I am looking forward to getting your reply. Cheers, Dialing

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solvent model in phenix.refine
by Weiergräber, Oliver H. 01 Dec '11

01 Dec '11

Hello, the ordered_solvent option in phenix.refine apparently uses these parameters by default: min_model_peak_dist = 1.8 max_model_peak_dist = 6.0 min_peak_peak_dist = 1.8 I was wondering about the justification for this (extremely relaxed) set of limits. As far as I know, the shortest hydrogen bonds (if defined as donor-acceptor distance) are about 2 A, and even these are considered exceptional and rare. Similarly, anything in excess of 3.5 A is quite unlikely to be significant energetically, so why use 6 A as an upper limit? Even if max_model_peak_dist was only meant to limit the extent of the outer solvent shell, there is no such thing as max_peak_peak_dist to avoid unreasonably long individual bonds. My personal suggestion would be a range of about 2.3 - 3.2 A for a significant hydrogen bond, with the lower limit exemplified by charged interactions (carboxyl-water or oxonium-water), which tend to be shorter - and stronger - than average. On the other hand, I do frequently observe elongated densities which, in accordance with the default parameters, are typically interpreted by phenix.refine as two water molecules about 2 A apart. So the question arises whether this is a realistic assumption, compared to a "sliding water" model in which the position of a single molecule is just ill-defined in a certain direction (due to a competition of adjacent binding sites for example)? Best regards, Oliver ================================================ PD Dr. Oliver H. Weiergräber Institute of Complex Systems ICS-6: Structural Biochemistry Tel.: +49 2461 61-2028 Fax: +49 2461 61-1448 ================================================ ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDirig Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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Clashing alternative conformations
by Sozanne Solmaz 01 Dec '11

01 Dec '11

Dear all, I have the following problem: I have a homodimer of two protein chains A and B, which I refine in Phenix, and one residue has 2 alternate conformations (a and b) for each chain. If the residues of both chains A and B are in the alternative conformation b, they clash. However, I would expect that never both residues are in conformation b, and therefore only the combinations aa, ab and ba of alternative conformations exist. My problem is, that during the refinement, the two b conformations of the residues clash, which drives the clash-score of the overall structure to a very high value and repulsion pushes the two b-conformations apart during refinement, therefore I cannot model them properly. Is it possible in Phenix to define these two conformations as non-clashing and non-repulsive? Thank you, best regards, Sozanne Solmaz.

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