- phenixbb - phenix-online.org

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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