- phenixbb - phenix-online.org

Only three weeks left to apply for RapiData 2012, a course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 06 Jan '12

06 Jan '12

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) =========================================================================

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CCI-Apps - Cygwin incompatibility after upgrade
by Schubert, Carsten [JRDUS] 05 Jan '12

05 Jan '12

Hi, After upgrading my cci_apps install on Windows from 1.7-718 to 1.7.3-928 the interoperability with cygwin is gone. Calling phenix.refine just gives a 'Command not found' error. Turns out that the little .exe files for each subprogram were replaced by .bat files. That is fine if one just wants to use the DOS CLI, but cygwin is not able to call programs via .bat files as far as I know. Is there a workaround for this problem besides working in the DOS CLI (yuk)? Thanks Carsten

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phenix.metal_coordination
by Young-Jin Cho 03 Jan '12

03 Jan '12

Hi everyone and wish your happy new year. I have a question regarding phenix.metal_coordination. when I typed my pdb file that has two alternative conformations of different species including metal such as a metal(B) and a water(A). It seems like, in this case, phenix.metal_coordination doesn't read the metal. Otherwise, is there other way I can let make .edits file for this pdb file? Thanks always in advance, Young-Jin

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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 15 Dec '11

15 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 } } }

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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

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