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Job Openings: Industrial Post Doc - Structure Based Drug Design Method R&D
by Lance Westerhoff 12 Jun '10

12 Jun '10

Hello All- Good news! We have the following new position available. We are particularly interested in folks who have experience with xray refinement method research and development, so I figured this list would probably be a good fit. Please contact me if you know of anyone who might be interested: ================= Contact: Dr. Lance M Westerhoff - careers(a)quantumbioinc.com Based at: QuantumBio Inc., 200 Innovation Boulevard, State College, PA 16803 On the Web: http://www.quantumbioinc.com/careers/ Job Purpose: Beginning immediately, QuantumBio Inc, headquartered adjacent to The Pennsylvania State University in State College, PA, is in need of a post doctoral computational Biochemist/Chemist interested in continuing his or her career within a dynamic, small-company environment. Under the direction of Dr. Lance M. Westerhoff, General Manager of QuantumBio, the successful candidate will work with both academic and industrial partners to help transition and validate the novel, quantum mechanically based structure-based drug discovery technologies recently developed in the academic laboratory of Dr. Kenneth M. Merz Jr. to QuantumBios product line. The successful candidate will be integral to this project and will focus his or her efforts on the research and software development aspects necessary to validate and deploy this novel technology across the pharmaceutical industry. The position requires the candidate to have a Ph.D. in Chemistry, Biochemistry, or related field along with experience with the methods and software in the field. Due to the limited number of new work visas available, only American citizens or candidates with valid work permits will be considered at this time. A willingness to publish is required, and experience with C++, high performance programming, or xray refinement methods is a plus. Opportunities for advancement may be available through additional SBIR/STTR-style projects, and industry-supported collaborations. Further, in addition to the research and development duties of the project, the position will afford the successful candidate with access to and experience with QuantumBio's industry partners including a number of pharmaceutical, biotech, and computational firms. To apply, submit cover letter, CV, and one or two representative publications to the Contact above. About QuantumBio: QuantumBio Inc is accelerating drug discovery efforts by providing pharmaceutical, biotechnology companies and life science research organizations with a next generation of Computer-Assisted Drug Design (CADD) and Computer-Assisted Molecular Modeling (CAMM) solutions based on the increased accuracy and power of quantum mechanics. These solutions include a number of options tailored to each customers specific requirements including software licensing, services, and customization. See http://www.quantumbioinc.com/ for more! ================= Thank you for your time! -Lance ____________________ Lance M. Westerhoff, Ph.D. General Manager QuantumBio Inc. WWW: http://www.quantumbioinc.com Email: lance(a)quantumbioinc.com Phone: 814-235-6908 Fax: 814-235-6909

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large coordinate and map shift after simulated annealing
by fn1＠rice.edu 12 Jun '10

12 Jun '10

Hi everyone, I am wondering why large coordinate shift could happen after simulated annealing (no rigid body refinement). Although it helps decreasing R values, it looks like the whole molecule shifts together by about 3 A. Is this normal? I read a post in previous phenixbb, but I still not understand it. Thank you very much! Regards, Fengyun

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Persistant high average B-factor.
by Joseph Brock 11 Jun '10

11 Jun '10

Dear Phenix users, I am currently using version 1.6.1-353 and I'm working on a 1.7A structure that has refined quite well using Individual_sites+individual_adp(isotropic)+occupanices+TLS: Final R-work = 0.1776, R-free = 0.2262 However, I noticed that the average B-factor reported by polygon with these settings was quite high ( < 0.1 of other structures with a similar resolution). Discovering I could not change the value of wxu_scale when using individual_adp+TLS, I went about trying to reduce the average B using the method described here: http://phenix-online.org/pipermail/phenixbb/2007-September/000511.html However, I still can't seem to reduce the average B-factor. I've just done a refinement with the following non-default (extreme) target weight settings: target_weights { wxc_scale = 1.5 fix_wxc = 2 fix_wxu = 0.1 (wxu_scale = 1) But if anything, reducing wxu to such low values makes the avergae B-even higher while concuretnly making the gap between R-values much worse: Final R-work = 0.1602, R-free = 0.2457 This suggests to me that I'm obviously over fitting the data but I'm at a loss on how to proceed. Should i just accept that the automatic scaling used for Phenix TLS wxu is doing a good job and that my structure actually does have an unusually high avergae B? I'm fitting two ligands into density, which is at several places ambiguous, so I would like the most unbiased difference density possible. Many thanks in advance, Joe. _________________________________________________________________ New, Used, Demo, Dealer or Private? Find it at CarPoint.com.au http://clk.atdmt.com/NMN/go/206222968/direct/01/

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Autobuild error message, please help!!!
by 신인철 10 Jun '10

10 Jun '10

Hi, everyone I have a problem in running phenix.automr I started AutoMR with the command: ---------------------------------------------------------------------------- ----- phenix.automr build=True data=ZZZZZZ_H-Nat_x22_P3221_from_P321.sca \ coords='1_SMsp.pdb 2_SMsp.pdb 3_SMsp.pdb 4_SMsp.pdb' \ identity='40 32 29 27' seq_file=ZZZZZZ_seq.dat input_seq_file=ZZZZZZ_seq.dat \ copies=4 ---------------------------------------------------------------------------- ------ AutoMR process seems to be done without any error but during autobuild process, I encounterd an error message as follows ---------------------------------------------------------------------------- ----- Re-using input PDB coordinates in build this cycle Running 3 parallel build jobs Standard build in parallel starting with refine.pdb_1 This is the first try at building this model Setting background=False as nproc=1 Try: 1 building 1 model Try: 2 building 1 model Try: 3 building 1 model Running up to 1 jobs in parallel... with total of 3 jobs Splitting work into 3 jobs and running 1 at a time with csh in /data1/disk02/icshin/UGI/MR/PHENIX_MR_8/AutoBuild_run_1_/TEMP0 Starting job 1... **************************************************************************** **** Failed to carry out AutoBuild_build_cycle: child process stderr output: command: 'csh /data1/disk02/icshin/ZZZ/MR/PHENIX_MR_8/AutoBuild_run_1_/TEMP0/RUN_FILE_1' icshin_com: No such file or directory. **************************************************************************** **** ---------------------------------------------------------------------------- ---------------------------------------------------------- What am I supposed to do? Please, help me! ------------------------------------------------------- Inchul Shin Structural Biology Lab. CALS. Seoul Nationl Univ.

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how-to change resolve keywords using phenix.multi_crystal_average
by Bjørn Panyella Pedersen 09 Jun '10

09 Jun '10

Dear board I am doing a difficult case of density modification. I get good results using resolve after optimising some keywords. I now want to use multicrystal averaging. This works ok in dmmulti, but I would like to combine it with resolve. For this I have tried phenix.multi_crystal_average, which also runs phenix.resolve, but it uses default keywords for resolve, and I can't find documentation on how to change these keywords. Current maps from phenix.multi_crystal_average are worse that the optimized resolve maps, and I believe this is because of the default resolve settings. Is it possible to control resolve keywords using phenix.multi_crystal_average? And how can I do it? Thanks in advance -Bjørn -- Bjørn Panyella Pedersen, PhD Postdoc PUMPKIN, Centre for Membrane Pumps in Cells and Disease University of Aarhus, Dept. Molecular Biology Gustav Wieds Vej 10C DK-8000 Aarhus C, Denmark Phone: +45 89425261 E-mail: bjopp(a)bioxray.au.dk http://www.bioxray.au.dk

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Re: [phenixbb] phenixbb Digest, Vol 55, Issue 7
by ak2197＠columbia.edu 08 Jun '10

08 Jun '10

Ok Alex Sent from my Verizon Wireless BlackBerry -----Original Message----- From: phenixbb-request(a)phenix-online.org Date: Mon, 07 Jun 2010 12:00:01 To: <phenixbb(a)phenix-online.org> Subject: phenixbb Digest, Vol 55, Issue 7 Send phenixbb mailing list submissions to phenixbb(a)phenix-online.org To subscribe or unsubscribe via the World Wide Web, visit http://phenix-online.org/mailman/listinfo/phenixbb or, via email, send a message with subject or body 'help' to phenixbb-request(a)phenix-online.org You can reach the person managing the list at phenixbb-owner(a)phenix-online.org When replying, please edit your Subject line so it is more specific than "Re: Contents of phenixbb digest..." Today's Topics: 1. Robert Ng wants to stay in touch on LinkedIn (Robert Ng) ---------------------------------------------------------------------- Message: 1 Date: Mon, 7 Jun 2010 08:57:29 -0700 (PDT) From: Robert Ng <ubi(a)ufl.edu> To: PHENIX list <phenixbb(a)phenix-online.org> Subject: [phenixbb] Robert Ng wants to stay in touch on LinkedIn Message-ID: <1916754023.4088196.1275926249246.JavaMail.app(a)ech3-cdn13.prod> Content-Type: text/plain; charset="utf-8" LinkedIn ------------ PHENIX, I'd like to add you to my professional network on LinkedIn. - Robert Ng Robert Ng Graduate Research Assistant at Department of Biochemistry and Biophysics Gainesville, Florida Area Confirm that you know Robert Ng https://www.linkedin.com/e/isd/1366202655/UCksvc1y/ ------ (c) 2010, LinkedIn Corporation -------------- next part -------------- An HTML attachment was scrubbed... URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20100607/f95d09c5/a…> ------------------------------ _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb End of phenixbb Digest, Vol 55, Issue 7 ***************************************

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Robert Ng wants to stay in touch on LinkedIn
by Robert Ng 07 Jun '10

07 Jun '10

LinkedIn ------------ PHENIX, I'd like to add you to my professional network on LinkedIn. - Robert Ng Robert Ng Graduate Research Assistant at Department of Biochemistry and Biophysics Gainesville, Florida Area Confirm that you know Robert Ng https://www.linkedin.com/e/isd/1366202655/UCksvc1y/ ------ (c) 2010, LinkedIn Corporation

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A couple of questions regarding twinning
by Pietro Roversi 04 Jun '10

04 Jun '10

Dear all, A couple of questions regarding twinning: 1. The structure I work with has multiple twinning domains (4 to be exact, with pseudo-orthorhombic 222 symmetry induced by twinning in P1). I feed the autobuild script the operators using a keyord: input_files.refine_eff_file_list=mytwinrefinement.eff (see attached file) but only the last one seems to be used. Do I guess correctly that there is only provision for two domains adn therefore the last twinning definition overrides any previously defined one? If so, is there a way of specifying and using multiple twinning domains/operators? 2. Output structure factor amplitudes: are they detwinned? Are they detwinned before the density modification in resolve? and during it? Thanks for any clarification/suggestions Regards Pietro

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Re: [phenixbb] NAG-NAG description
by Chris Ulens 03 Jun '10

03 Jun '10

Thanks for the feedback. I would like to refine a NAG-NAG chain attached to residue Asn122 in my structure. There are 5 identical subunits. Could you verify my .params file? I get the following error: Empty atom selection refinement .pdb_interpretation.apply_cif_link.residue_selection_1="chain A and resname NAG and resid 122" Thanks. -Chris On 31 May 2010, at 21:34, Georg Mlynek wrote: > Dear Chris, this did it for me. > > > Create a file which you can call whatever you want even the extension > doesn't matter. E.g.: cif_link.params > > Put in this file your links: (Which Atom of residue1 will be > connected to > which Atom in residue2 is already defined in mon_lib_list.cif) > > > > refinement.pdb_interpretation.apply_cif_link { > data_link = NAG-ASN > residue_selection_1 = chain A and resname NAG and resid 500 > residue_selection_2 = chain A and resname ASN and resid 297 > } > refinement.pdb_interpretation.apply_cif_link { > data_link = BETA1-4 > residue_selection_1 = chain A and resname NAG and resid 500 > residue_selection_2 = chain A and resname NAG and resid 501 > } > refinement.pdb_interpretation.apply_cif_link { > data_link = BETA1-4 > residue_selection_1 = chain A and resname NAG and resid 501 > residue_selection_2 = chain A and resname BMA and resid 502 > } > refinement.pdb_interpretation.apply_cif_link { > data_link = ALPHA1-3. > > residue_selection_1 = chain A and resname BMA and resid 502 > residue_selection_2 = chain A and resname MAN and resid 503 > } > > 4) add this file in the GUI > > > Or run % phenix.refine model.pdb data.hkl cif_link.params > > > 5)Trouble shooting > > a)run iotbx.phil cif_link.params (this checks if the syntax is > right) > > b) check .eff file the links should be added there. You can also > check the . > geo file if you see anything strange. > > c)Having unknown to phenix.refine item in PDB file (novel ligand, > etc... > (BMA is also not there) ). phenix.refine uses the CCP4 Monomer > Library as > the source of stereochemical information for building geometry > restraints > and reporting statistics. If phenix.refine is unable to match an > item in > input PDB file against the Monomer Library it will stop with "Sorry" > message > explaining what to do and listing the problem atoms. If this > happened, it is > necessary to obtain a cif file (parameter file, describing unknown > molecule) > by either making it manually or having eLBOW program to generate it: > > phenix.elbow model.pdb --do-all --output=all_ligands > > this will ask eLBOW to inspect the model_new.pdb file, find all > unknown > items in it and create one cif file for them all_ligands.cif. > Alternatively, > one can specify a three-letters name for the unknown residue: > > phenix.elbow model.pdb --residue=MAN --output=man > > !Check the file if everything is ok! > > > Please correct if this is not ok, or there is an easier way now. > > Kind regards George. > > > -----Ursprüngliche Nachricht----- > Von: phenixbb-bounces(a)phenix-online.org > [mailto:[email protected]] Im Auftrag von Chris Ulens > Gesendet: Monday, May 31, 2010 9:14 PM > An: PHENIX user mailing list > Betreff: Re: [phenixbb] NAG-NAG description > > Dear glycobiologists and phenixfriends. > > I am trying to refine a NAG-NAG chain attached to an Asn122 in my > (pentameric) structure. > What is the proper description in the cif_link.params that is the > equivalent of the pdb description pasted below that phenix so kindly > ignores? > Also, what is the proper way to define the cif_link.params file in the > GUI? > > Thank you. > -Chris > > > LINK ND2 ASN A 122 C1 NAG A 834 1555 > 1555 1.37 > LINK O4 NAG A 834 C1 NAG A 835 1555 > 1555 1.43 > LINK ND2 ASN B 122 C1 NAG B 834 1555 > 1555 1.37 > LINK O4 NAG B 834 C1 NAG B 835 1555 > 1555 1.43 > LINK ND2 ASN C 122 C1 NAG C 834 1555 > 1555 1.37 > LINK O4 NAG C 834 C1 NAG C 835 1555 > 1555 1.43 > LINK ND2 ASN D 122 C1 NAG D 834 1555 > 1555 1.37 > LINK O4 NAG D 834 C1 NAG D 835 1555 > 1555 1.43 > LINK ND2 ASN E 122 C1 NAG E 834 1555 > 1555 1.37 > LINK O4 NAG E 834 C1 NAG E 835 1555 > 1555 1.43 > > --------------------------------------------------- > Chris Ulens, Ph.D. > Lab of Structural Neurobiology > Department of Molecular Cell Biology > Campus Gasthuisberg, ON1 > Herestraat 49, PB 601 > B-3000 Leuven > Belgium > e chris.ulens(a)med.kuleuven.be > t +32 16 345812 > f +32 16 345699 > w http://www.xtal.be > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb

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segmentation fault
by Harry M. Greenblatt 02 Jun '10

02 Jun '10

BS"D Dear All, We had the phenix 1.6.1 GUI running on a fedora core 12 machine; it was thought, for different reasons, that a kernel upgrade would address certain issues unrelated to phenix. The machine is now running 2.6.32.12-115.fc12 (64 bit) and phenix now gives a segmentation fault. Any suggestions? Thanks Harry ------------------------------------------------------------------------ - Harry M. Greenblatt Associate Staff Scientist Dept of Structural Biology harry.greenblatt(a)weizmann.ac.il Weizmann Institute of Science Phone: 972-8-934-3625 Rehovot, 76100 Facsimile: 972-8-934-4159 Israel

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Weight optimization
by Jianghai Zhu 29 May '10

29 May '10

Hi, I am using the optimize_wxc=true and optimize_wxu=true in my last refinement. The R and Rfree went down but the RMSDs were way too large. I wonder if phenix.refine still targets the geometry when it optimizes the R and Rfree. Here are the results from almost two identical runs except the weight optimization. 1) optimize_wxc = False optimize_wxu = False wxc_scale=0.08 wxu_scale=1.66 results: R=0.2294 R-free=0.2709 angl=1.087 bond=0.006 2) optimize_wxc = True optimize_wxu = True wxc_scale=0.08 wxu_scale=1.66 results: R=0.2141 R-free=0.2628 angl=2.894 bond=0.033 I am using the dev-412 version. Thanks. -- Jianghai

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offtopic: Problem with Pymol showing maps
by Tatyana Sysoeva 29 May '10

29 May '10

Hi all, if somebody is still not on the memorial day weekend, I have a short question off-topic for Pymol-users I have several maps from Phenix and want to draw some pictures in Pymol. I am opening the files, renamed to ccp4 or map, or not, and all I am getting is just a box, which is not even a unit cell boundary. If you know some nice simple program to do nice pictures of the electron densities- share your knowledge please! Sincerely Tanya

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Super: Rotation and translation
by J. Fleming 29 May '10

29 May '10

Hello, I've been using 'super' to align the c-alphas within one domain of two different models of the same protein while leaving the second domain to move freely. I can do this using: super (A and resid 1-100 and name ca), (B and resid 1-100 and name ca) What I would like to do is determine the rotation and translation of model B's second domain as it moves away from A's second domain. I can output a matrix after running super using: print cmd.get_object_matrix("A") How do I go from the matrix to an angle and distance? Thanks for any thoughts, Jon

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Re: [phenixbb] Autobuild submitted jobs
by Mark A Saper 27 May '10

27 May '10

Tom -- It turns out that each of the omit region's jobs submits another job, but that latter job is only the "test run_command" job. Why test the run_command if no subsequent jobs are submitted? Our solution, thanks to an extremely savvy cluster manager, was to install the qsub (Torque?) package on each of the computing nodes (117). Also we ran the top-level process on the head (scheduler) node, so as not to tie up a computing node while it waits for its sibling jobs (the omit regions) to finish the calculation. Overall wall-time with a separate node allocated for each omit region was about 50 minutes. Interestingly, although each node has 8 processors, the OMIT region jobs seems to only use one processor! Interestingly when phenix.refine jobs are run on my Macbook Pro, the operating system is savvy enough to spread it over 2 processors. -Mark ______________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry University of Michigan Biophysics, 3040 Chemistry Building 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323 http://www.biochem.med.umich.edu/?q=saper http://www.strucbio.umich.edu/

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How to turn off mask optimization
by Schubert, Carsten [PRDUS] 27 May '10

27 May '10

Hi, Is there a way to turn off the mask optimization step in 393? I tried 'main.optimize_mask = False' but that does not work. The program spends a substantial amount of time in repeated mask optimizations and I am trying to shave off a couple minutes for each run... Cheers, Carsten

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Autobuild submitted jobs
by Mark A Saper 27 May '10

27 May '10

Dear Tom and colleagues, We're running Autobuild composite omit on a large cluster, each node has 8 processors. Autobuild submits jobs with the "run_command". And it appears that each of those jobs submit other jobs. Are the latter jobs necessary? That is, are there situtations where they wouldn't be submitted as separate jobs but run as subprocesses? Currently nodes in our cluster don't have capability of qsubing new jobs, but we are in the process of changing this. Thanks, Mark _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry University of Michigan Biophysics, 3040 Chemistry Building 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323 http://www.biochem.med.umich.edu/?q=saper http://www.strucbio.umich.edu/

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atom selection syntax for ALT atoms?
by Scott Classen 26 May '10

26 May '10

This is the selection for the atom I'm interested in: atom_selection_2 = "name OE1 and chain A and resname GLU and resseq 160" I want to try a refinement with an alternate conformation at GLU160 . Can someone please help me with the proper syntax. Thanks, Scott ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Scott Classen, Ph.D. SIBYLS Beamline 12.3.1 http://bl1231.als.lbl.gov Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Rd MS6R2100 Berkeley, CA 94720 C) 510.206.4418 O) 510.495.2697 Beamline) 510.495.2134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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PDB Deposition Question
by Alexander Hirschi 26 May '10

26 May '10

Hi all - I refined a structure using Phenix 1.4-3 and now I need to submit it to the PDB. When I try to run sfcheck on the .mtz that Phenix generated, sfcheck can't read the file. I also tried to convert the .mtz to .cns using phenix.reflection_file_converter. This time, sfcheck could "not find IOBS or FOBS in your file". Any advice would be greatly appreciated. -Alex

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Installation problem, please help
by Tiberman Danny 24 May '10

24 May '10

Hello, while trying to install I get the following Error message: "======================================================================== Installing from binary bundle ========================================================================== bundle file: bundle-1.6.1-357-intel-linux-2.6-x86_64.tar.gz PHENIX installation source directory set to: /root/phenix-installer-1.6.1-357 PHENIX installation target directory <PHENIX_LOC > set to: /usr/local/phenix-1.6.1-357 PHENIX installation build directory set to: <PHENIX_LOC > /build/intel-linux-2.6-x86_64 PHENIX temporary build directory set to: build-binary/intel-linux-2.6-x86_64/monst/tmp PHENIX installation log directory set to: build-binary/intel-linux-2.6-x86_64/monst/log ==== warning: "/usr/local/phenix-1.6.1-357" already exists ==== ==== warning: cannot determine installation time-stamp, proceeding ==== installing binary components removing existing files in build-binary/intel-linux-2.6-x86_64/monst/tmp/binary finding installed versions finding binary versions binary components up-to-date the binary package will not be installed setting environment configuring PHENIX components /root/phenix-installer-1.6.1-357/bin/install-from-binary: line 347: 19650 Floating point exception$PHENIX_BUILD/base/bin/python $PHENIX_LOC/cctbx_project/libtbx/configure.py --current_working_directory="$PHENIX_BUILD" $PHENIX_COMPONENTS >>$PHENIX_LOG/binary.log 2>&1 Error configuring: see /root/phenix-installer-1.6.1-357/build-binary/intel-linux-2.6-x86_64/monst/log/binary.log for details" Thanks

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Re: [phenixbb] Restraining altloc related atoms during refinement
by John Pascal 21 May '10

21 May '10

>I have my doubts about supporting NCS restraints of alternative >conformations; the two seem to be mutually exclusive. But maybe >I don't understand your situtation. Here are some more details on the refinement situation: it is possible for a piece of duplex DNA to be positioned in two conformations in the crystal, and it appears that both conformations are occupied with roughly the same occupancy. The sequence is not completely palindromic, so at some positions a different base is present depending on the random orientation of the DNA. However, the phosphate and ribose atoms occupy the same positions regardless of the orientation, and I want to enforce this. >I can see that NCS restraints of backbone atoms only are useful, >even if the residue names are different. >The trouble is that atoms in two chains need to be matched >unambiguously while allowing for chain breaks. >I could try to simply remove the requirement that the residue names >have to match and go by residue sequence number + insertion code >only. Would that work in your case? Yes, that sounds like it would work. >A potential downside is that people have to be careful >excluding non-matching sidechain atoms. Perhaps it could be that there is an override option after an error message. Thanks for your help. -John -- John Pascal, PhD ph 215.503.4596 Assistant Professor fx 215.923.2117 Thomas Jefferson University Biochemistry & Molecular Biology 233 South 10th Street, BLSB 804 Philadelphia, Pennsylvania 19107 ----- Forwarded message from John.Pascal(a)mail.jci.tju.edu ----- Date: Thu, 20 May 2010 11:54:33 -0400 From: John Pascal <John.Pascal(a)mail.jci.tju.edu> Reply-To: John Pascal <John.Pascal(a)mail.jci.tju.edu> Subject: Restraining altloc related atoms during refinement To: phenixbb(a)phenix-online.org Hello All, I would like to restrain the positions of ribose/phosphate atoms of altloc 'A' to the positions of those in altloc 'B'. Problem is, altloc A and altloc B are different residue types, so phenix.refine exits stating that there are no common atoms when I enter the following NCS-type restraint: selection: chain I and altloc A and resid 1 and (phosphate or ribose) restrain: chain I and altloc B and resid 1 and (phosphate or ribose) I am using the phenix GUI. Is there a better place to enter this type of restraint (rather than NCS) that does not care if a P atom is from a Cd or from a Gd residue type? thanks. Best, John -- John Pascal, PhD ph 215.503.4596 Assistant Professor fx 215.923.2117 Thomas Jefferson University Biochemistry & Molecular Biology 233 South 10th Street, BLSB 804 Philadelphia, Pennsylvania 19107 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program. ----- End forwarded message ----- ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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Restraining altloc related atoms during refinement
by John Pascal 21 May '10

21 May '10

Hello All, I would like to restrain the positions of ribose/phosphate atoms of altloc 'A' to the positions of those in altloc 'B'. Problem is, altloc A and altloc B are different residue types, so phenix.refine exits stating that there are no common atoms when I enter the following NCS-type restraint: selection: chain I and altloc A and resid 1 and (phosphate or ribose) restrain: chain I and altloc B and resid 1 and (phosphate or ribose) I am using the phenix GUI. Is there a better place to enter this type of restraint (rather than NCS) that does not care if a P atom is from a Cd or from a Gd residue type? thanks. Best, John -- John Pascal, PhD ph 215.503.4596 Assistant Professor fx 215.923.2117 Thomas Jefferson University Biochemistry & Molecular Biology 233 South 10th Street, BLSB 804 Philadelphia, Pennsylvania 19107 ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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Re: [phenixbb] all reflections are equal, but some more than others
by Frank von Delft 20 May '10

20 May '10

Are you sure? It's the sigma estimation he talked about, and that does assume it's the same foe both strong and weak, doesn't it? ----- Reply message ----- From: "Phil Evans" <pre(a)mrc-lmb.cam.ac.uk> Date: Wed, May 19, 2010 21:22 Subject: [phenixbb] all reflections are equal, but some more than others To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> If by "scaling" you mean scaling unmerged observations together, I don't think it is right that it assumes a unimodal intensity distribution. In refinement I believe the underlying distributions are assumed to be unimodal, but in data reduction scaling there is no such assumption. That scaling just assumes that the experiment (mainly the diffraction geometry) can be parameterised in such a way that reflections close together in reciprocal space and in measurement time have similar and parameterisable scales. This is independent of the intensity distribution. Phil On 19 May 2010, at 08:44, esko.oksanen(a)helsinki.fi wrote: > Frank, > > Having had a case of such hectic pseudosymmetry, it turns out that the problem originates already from the scaling that assumes a unimodal intensity distribution. The weak reflections then have their sigmas heavily overestimated and the strong ones overestimated. I had to scale the weak and strong reflections separately and ridig-body refine against the weak ones... Of course this type of problem has little to do with issue of treating negative intensities. > > Esko > > Quoting "Frank von Delft" <frank.vondelft(a)sgc.ox.ac.uk>: > >> The philosophical arguments are fine, but is Pavel not justified in asking for real cases where it matters? It's not like he hasn't spent time thinking about it, and it's not like the whole phenix community isn't sitting in his ear about their own favourite missing fix. >> >> I suppose what comes to mind is a case with hectic pseudotranslation causing half the reflections to be systematically almost but not quite zero. But then again, I understand that even if you don't toss the weak ones out, current algorithms don't deal with this well anyway, so it needs special treatment (for now: refine in smaller cell, then rigid-body refine in super-cell). >> >> phx. >> >> >> >> >> >> On 18/05/2010 18:33, Ed Pozharski wrote: >>> On Mon, 2010-05-17 at 16:20 -0700, Peter Zwart wrote: >>> >>>> You make it sound like it is a bad thing. The effect of restraint >>>> weights (ADP, geometry) has most likely a much bigger impact on the >>>> final structure then a small fraction of smallish intensities (*) >>>> >>> Peter, >>> >>> I think discarding data has to be justified. Two points: >>> >>> 1. The fraction of negative intensities is not necessarily small. It >>> depends on resolution cutoff (and you make an excellent point about >>> PTS), but looking at scalepack log-files I can tell that in my hands the >>> fraction is often 10% or more (DISCLAIMER: I belong to I/sigma=1 >>> resolution cutoff cult). >>> >>> 2. Just because these reflections are weak does not mean that they are >>> insignificant. Their contribution to the maps may be small (now I fear >>> another round of "fill-in missing Fobs with Fc for map calculation" >>> discussion), but keeping Fc close to zero for these reflections during >>> refinement seems to be just as important as to keep Fc close to whatever >>> values the strong reflections have. >>> >>> The weak reflections are not fundamentally worse than strong(er) >>> reflections in the same resolution range. They are measured with >>> roughly the same precision. Moreover, the practice of setting negative >>> intensities to zero and then ignoring them in refinement discards those >>> that are barely negative and leaves in those that were (quite randomly) >>> barely positive. >>> >>> You are absolutely right that other factors will have impact on the >>> model. But that does not mean that discarding weak data is justified. >>> Crystallographic refinement is a Rube Goldberg machine, and all the >>> components should be as good as we can make them. Perhaps there could >>> be something better than French&Wilson, but discarding negative >>> intensity reflections is hardly the solution. >>> >>> Cheers, >>> >>> Ed. >>> >>> PS. Personally I have no stake in this, since I always use truncate. >>> >>> >>> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> >> > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb

1 0

View DM map from AutoSol gui?
by Francis E Reyes 20 May '10

20 May '10

I'm not a GUI kind of person but today I'm messing around with it. After AutoSol (with build=False... errr AutoBuild unchecked), I have an opportunity to 'View sites and experimental map' in coot or PyMOL. Wouldn't it be more useful if the gui loaded the DM maps as well? F --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

2 3

changing TLS groups mid refinement
by Scott Classen 20 May '10

20 May '10

Hello Phenixers, Are there any considerations to changing TLS groups mid refinement? Can I rest assured that after a few rounds of refinement with the new TLS definitions everything will sort itself out or should I do something drastic, like remove all the ANISOU records, reset B factors to some constant value, and start over? Thanks, Scott

14 34

phenix distorts ligand
by Mustafa Koksal 19 May '10

19 May '10

Hi, I have a problem in phenix refinement at 2.25 A resolution, data is 80% complete. I have protein, water, and ions in the .PDB file, and a ligand molecule that is distorted during refinement. I generated the pdb (with H atoms) with ChemDraw3D, edited the atom names etc. I used phenix.elbow to generate the .CIF file. Here is the first problem: Ligand has trans double bonds, which are written out by phenix.elbow as single rotatable bonds although I had correct connect records and H atoms in the .PDB file. I ran phenix.refine, it distorted the ligand, making double bonds not planar and nearly cis. Here is what I have tried: I edited the .CIF file to change these torsion agles to be CONSTANT and 180 or 0 deg. Here is the second problem: phenix.refine still distorted the ligand. Here is what I have tried: I used optimize_wxc/wxu in phenix.refine to optimize the weight, to see if I overweighed the data. Here is the third problem: phenix.refine still distorted the ligand. Is there a way to solve this problem? Is there a way to tighten the constraints for the ligand only? I still do not understand why it even cannot keep the double bonds planar (and trans). I do not want to move back to good old CNS... Thanks to all, Mustafa -- Mustafa Koksal Postdoctoral Fellow University of Pennsylvania Department of Chemistry Roy and Diana Vagelos Laboratories Office: 2090 IAST Office Phone: (215) 898-2227 Mobile Phone: (267) 319-6443 Mail Address: 231 S. 34th St, Philadelphia 19104, USA -- "If you grant me a pen, I shall destroy swords and spears" Mawlana Jalal-ad-Din Rumi --

2 1

geometry_restraints between sym mates?
by Scott Classen 18 May '10

18 May '10

Hi all, Is this possible? # on working model bond { atom_selection_1 = "name SM and chain M and resname SM and resseq 1" atom_selection_2 = "name OE1 and chain A and resname GLU and resseq 313" distance_ideal = 2.5 sigma = 0.2 } # on SYM mol bond { atom_selection_1 = "name SM and chain M and resname SM and resseq 1" atom_selection_2 = "name OE1 and chain A and resname GLU and resseq 285" distance_ideal = 2.5 sigma = 0.2 } I'll find out in a few minutes when I run it through phenix.refine, but I thought to ask anyways. Thanks, Scott

3 4

Looking at omit maps in coot
by xaravich ivan 18 May '10

18 May '10

Hi, Again this is pretty novice and I would apologize in advance. I ran Simulated annealing omit map in PHENIX and it gave me a bunch of files. I started with a partially built model ( I would say most of it was built) and it gave me an edited pdb that I can open in coot but I the composite omit mtz file is not opening in coot. In fact I cannot open any mtz file from the phenix output /OMIT directory and cannot see any map. I am pretty clueless. Thanks, Ivan

2 3

An easier explanation of the regions in omit map
by xaravich ivan 18 May '10

18 May '10

Hi Nat, So I have quite a few regions build by the SA_omit map of phenix. But How do I go about looking at these maps. What am I looking for here. Should I look at the regions where the occupancy was set zero in all these outputs and find if I could build some thing from one of the maps? I guess I am asking, How do I use this information to move forward in refinement? There are 24 regions map and .pdb output in the /OMIT directory. Thanks, Ivan On Fri, May 14, 2010 at 5:52 PM, Nathaniel Echols <nechols(a)lbl.gov> wrote: > On Fri, May 14, 2010 at 5:40 PM, xaravich ivan <xaravich.ivan(a)gmail.com>wrote: > >> Again this is pretty novice and I would apologize in advance. >> I ran Simulated annealing omit map in PHENIX and it gave me a bunch of >> files. I started with a partially built model ( I would say most of it was >> built) and it gave me an edited pdb that I can open in coot but I the >> composite omit mtz file is not opening in coot. In fact I cannot open any >> mtz file from the phenix output /OMIT directory and cannot see any map. >> I am pretty clueless. >> > > Some clarification: > > 1. Which version of Phenix, and which platform? > 2. GUI or command-line? > 3. If you're really making a composite omit map (as opposed to a simple > omit map, e.g. for a ligand), ignore the PDB file output by AutoBuild and > stick to the original. > > One common problem is that on Mac, if you try to open the MTZ file in Coot > (using the "Open MTZ", not auto-open), it will open a window to choose > column labels in the file, but it opens *behind* the main window, which you > need to move to the side temporarily. > > -Nat > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > >

2 1

Building DNA
by Rajagopalan, Senapathy 16 May '10

16 May '10

Dear Phenix developers, I am solving a protein-dna complex and Autobuild is able to build both the protein as well as DNA chain (one at a time). However, when I try to do the refinement, I get an error saying "Phenix could not find the geometry restraints in the standard monomer library for one or more residues in the pdb file... DG: 6 copies, DA: 3 copies, DT: 43 copies". It seems like Autobuid uses the nomenclature DA, DC, DG and DT for the DNA bases while Phenix.Refine either doesn't like the nomenclature or the restraint files uses a different one. It still however lets me do the refinement...although I don't know if it just ignores the DNA part. Can someone enlighten me on this. Also, the nomenclature Coot seems to like is Ad, Cd, Gd, Td for the DNA and doesn't like the above phenix style. In order to manipulate in coot, I had to rename all the bases...is it possible to have a format that is compatible both in Phenix and Coot or am I missing something obvious here. Thanks and Have a great weekend! Sena Methodist. Leading Medicine. Recognized by U.S.News & World Report as an "Honor Roll" hospital Named to FORTUNE magazine's "100 Best Companies to Work For" list five years in a row Designated as a Magnet hospital for excellence in nursing Visit us at methodisthealth.com Follow us at twitter.com/MethodistHosp and www.facebook.com/methodisthospital ***CONFIDENTIALITY NOTICE*** This e-mail is the property of The Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

4 3

Improved refinement method for low resolution data
by Florian Nachon 15 May '10

15 May '10

Hi all, Axel Brunger just published a paper in Nature (http://www.nature.com/nature/journal/v464/n7292/abs/nature08892.html) about a new method to improve models despite low-resolution data. It is implemented in CNS 1.3. It might be a bit early, but is there any plan to implement that method in phenix? Florian.

10 21

where do phenix.metal_coordination ideal bond lengths come from?
by Scott Classen 14 May '10

14 May '10

Hello, I have a structure with several water/carboxylate-coordinated metal ions and I am using phenix.metal_coordination to generate the restraints parameter file for phenix.refine. Can someone please tell me where phenix.metal_coordination is getting the ideal bond length/angle values from. Thanks, Scott Classen

2 1

Gordon Conference on Diffraction Methods
by A Leslie 14 May '10

14 May '10

Just a reminder that there is still time to register for the Gordon Conference on Diffraction Methods in Structural Biology, that will be held at Bates College in Lewiston, Maine from 18-23rd July. The program (see below) covers all aspects of macromolecular crystallography, from crystallization to structure solution and refinement, and includes sessions on complementary techniques and the potential of free electron lasers. Many of the leading methods developers will be present and the format of the meeting, with free afternoons, provides ample opportunities for informal discussions. Further details, including a full program and details on the application procedure can be obtained from: http://www.grc.org/programs.aspx?year=2010&program=diffrac We hope to see you there ! Andrew Leslie (Chair) & Ana Gonzalez (Vice Chair) Outline Program: Sunday pm: Macromolecular Structures, Pushing the boundaries Discussion leader: Michael Rossmann 1. ABC Transporters: Doug Rees 2. The Spliceosome : Kyoshi Nagai Monday am: Crystallisation and the diffraction experiment Discussion leader: Zbyszek Dauter 1. Nanolitre crystallisation: Seth Harris 2. Twinning and disorder: Todd Yeates 3. Simulating the diffraction experiment: James Holton 4. Microcrystallography: Gwyndaf Evans Monday pm: Radiation damage and data collection strategies Discussion leader: Vivian Stojanoff 1. Radiation damage, experimental: Elspeth Garman 2. Microbeams: Yanhui Zou 3. Testing data collection strategies with the Pilatus: Marcus Mueller Tues am: Synchrotron developments and automated data processing Discussion leader: Thomas Schneider 1. Synchrotrons, latest developments: Sean Mc Sweeney 2. Synchrotrons, latest developments: Janet Smith 3. Data processing with Xia2/CHEF: Graeme Winter 4. Data processing with AUTOPROC: Clemens Vonrhein Tues pm: Complementary techniques Discussion leader: Ana Gonzales 1. Electron tomography: Sriram Subramaniam 2. SAXS: Hiro Tsuruta 3. Spectroscopy: Carrie Wilmot Weds am: Structure solution and refinement Discussion leader: Paul Adams 1. SAD Phasing: Randy Read 2. Molecular replacement with BALBES: Garib Murshudov 3. PHENIX: Tom Terwilliger 4. TLS: Ethan Merritt Weds pm: Challenging problems/Membrane Proteins Discussion leader: TBC 1. Using cubic lipidic phase: Martin Caffrey 2. Membrane Proteins: Stephen White 3. The Bacterial Ribosome: Venki Ramakrishnan Thurs am: Selected Posters and Map improvement and Model building Discussion leader: Tassos Perrakis 1. COOT: Paul Emsley 2. Modelling nucleic acids: Johan Hattne Thursday pm: Future Methods, FELs, Diffraction imaging Discussion leader: Ed Lattman 1. Anton Barty 2. Serial Crystallography: John Spence and Petra Fromme

1 0

question about free energy calculation in protein complex
by crystallogrphy 14 May '10

14 May '10

Hi, I am trying to calculate the free energy of association for structure of a protein complexes based on the salt bridges, H-bonds and van der waals interaction? Does any one know how to do it? Thanks!

3 2

phenix.model_vs_data
by Young-Jin Cho 14 May '10

14 May '10

Dear Phenix users, This might be trivial questions though... 1. When you did phenix.model_vs_data, I see the discrepancy between R/Rfree. 'After applying resolution and sigma cutoffs' seems more accurate one though, could someone explain why it has such-even small though- discrepancy? 2. Also, when you do phenix.polygon, I used to seeing many branches from old version. With my current version(phenix-1.6.1-343), I normally see only 5 branches. Is there any reasons for that? Thanks in advance as always. Young-Jin

4 6

Refinement with partial model - question
by Peter Grey 14 May '10

14 May '10

Dear Phenix Users, I have a partial model at low resolution. Is there a way let Phenix.refine know the model is not complete and that when a mask is calculated for bulk solvent correction it should take this fact into consideration ? Alternatively, can I use a solvent mask from density modification program in Phenix.refine somehow ? Alternatively, is there a program that will build dummy atoms (zero occupancy) automatically in a map in all peaks above a certain sigma (i.e. atoms just for mask calculation). Thank you in advance, Peter.

14 32

Can simulated annealing remove model bias after MR?
by Francis E Reyes 14 May '10

14 May '10

Just curious.... Thanks F --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

2 1

B factors of zero after refinement
by Kyle Dolan 14 May '10

14 May '10

Hello all, I have been performing standard refinement of atomic coordinates and B factors (ADP) in phenix.refine using NCS and bulk solvent correction without anisotropic scaling. The program has been returning a handful of atoms with B factors of zero after refinement, and I'm not sure why. I tried using adp.set_b_iso to reset all B factors before refinement but some still come back down to zero. Has anyone else noticed something similar, or has a suggestion on what to do? Thanks, Kyle Kyle T. Dolan Department of Biochemistry and Molecular Biology The University of Chicago ktd(a)uchicago.edu

2 1

Phenix Ligand Identification error
by Rajan 14 May '10

14 May '10

Dear All Greetings I was searching for a ligand present in the active site of my protein using Ligand Search in "PHENIX" but i stuck in between with an error : A Python error was detected. This may be a problem with the program settings, an error in your data, or a bug; click "OK" to send a bug report to the PHENIX developers. AttributeError : ligand_identification instance has no attribute 'connections' Traceback: File "/home/programs/linux/phenix- 1.6.1-357/cctbx_project/libtbx/thread_utils.py", line 137, in run return_value = self._target(self._args, self._kwargs, self._c) File "/home/programs/linux/phenix-1.6.1-357/cctbx_project/libtbx/runtime_utils.py", line 55, in __call__ result = self.target() File "/home/programs/linux/phenix-1.6.1-357/phenix/phenix/command_line/ligand_identification.py", line 1769, in __call__ identify_ligands = ligand_identification(args=list(self.args), quiet=False) File "/home/programs/linux/phenix-1.6.1-357/phenix/phenix/command_line/ligand_identification.py", line 308, in __init__ ligand_identification.Run(self, params) File "/home/programs/linux/phenix-1.6.1-357/phenix/phenix/command_line/ligand_identification.py", line 1454, in Run return self.connections['STOP '] I am not able to identify the problem? Please let me know if some one can identify the problem, i don't know whether it is a bug or problem in my files. Thanks for your suggestions in advance. Rajan -- ************************************************ Current Address: Rajan Vyas Research Scholar Deptt. of Biotechnology Panjab University Chandigarh, India 160014 Mob. +919417374197 Fax: +91-172-2625254 ************************************************

5 4

Re: [phenixbb] General user proposal deadline May 15, 2010
by Peter Zwart 13 May '10

13 May '10

Dear All, Just a reminder that May 15, 2010 is the deadline for the July-August 2010 Rapid Access Proposal cycle for PX beamtime at the ALS. The BCSB beamlines (5.0.1,5.0.2, 5.0.3, 8.2.1 & 8.2.2) can all be operated remotely and are all equipped with ADSC Q315(R) detectors. Beamlines 8.2.2, 8.2.1 and 5.0.2 are tuneable stations whereas 5.0.1 and 5.0.3 are fixed-wavelength beamlines. Control software for the beamlines features an interface allowing ultra high-throughput screening, automated annotation of diffraction quality and on the fly indexing and collection strategy feedback. The automounters in use on sector 5 support the unipuck and the ALS puck (both commercially available at http://www.crystalpositioningsystems.com). Beamlines 8.2.1 and 8.2.2. support in addition to the uni- and ALS puck the Rigaku system (http://www.rigaku.com/) To submit a proposal, please go to the ALS website link listed below: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize Thank you, Stacey Ortega 510-495-2450

1 0

suggested change to OS X GUI ?
by Mark Saper 13 May '10

13 May '10

Dear Nate, Not a major problem, but would you consider changing the keyboard shortcut for "View all settings..." from command-A to option-command-A? I keep typing command-A to select all which is the usual binding for this key. Thanks, Mark

4 4

May 15, 2010 deadline- User proposal submission for Collaborative Crystallography at BCSB
by Banumathi Sankaran 11 May '10

11 May '10

Dear Users, The deadline for May/June 2010 Collaborative Crystallography proposals will be *May 15, 2010. * ------------------------------------------------------------------------ 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 July/August 2010 allocation period, proposals must be submitted by *May 15, 2010.* The deadline for CC proposals for the time period Sep/October 2010 will be July 15, 2010. Regards, Banumathi Sankaran

1 0

mac os x installation binary files
by xaravich ivan 08 May '10

08 May '10

Hi Phenix users, I am trying to install phenix in my Mac OS X and after getting the .tar file and running install i get this message (screen shot attached) Could anyone help the newbie? Thanks, Ivan

4 6

Rigid body refinement question
by Simon Kolstoe 07 May '10

07 May '10

Dear phenixbb, What do I need to change in my .def file if I want to refine chain A-E of a structure as per the defaults but specify a single chain (in my case chain L) for just rigid refinement in all cycles? I had a look at the manual page (http://www.phenix-online.org/documentation/refinement.htm ) but didn't find it too clear. Thanks, Simon --------------------------------------------------------------- Dr Simon Kolstoe Laboratory for Protein Crystallography Centre for Amyloidosis & Acute Phase Proteins UCL Medical School Rowland Hill Street, London NW3 2PF Tel: 020 7433 2765 http://www.ucl.ac.uk/~rmhasek --------------------------------------------------------------

5 4

weight non-bonded contacts during rigid body refinement
by Kenneth Verstraete 07 May '10

07 May '10

Dear all, I wonder how I can set the weight for non-bonded contacts to zero to prevent clashes during rigid body refinement. Thank you for your comments. Kenneth Verstraete

4 3

phenix-dev-386 Sorry: Sorry, unknown file or keyword: refinement_eff_file=refinement.eff for AutoBuild
by Francis E Reyes 06 May '10

06 May '10

Was this keyword removed/renamed for the command line version of AutoBuild? http://www.phenix-online.org/documentation/autobuild.htm says I should be able to specify refine_eff_file. Thanks F --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

1 1

sugar behaving sourly
by Patrick Loll 06 May '10

06 May '10

Hi, I'm refining a structure with an unusual monosaccharide. I generated a library for this sugar from PRODRG, and it looks OK, at least to my eye. Certainly the obvious parameters like bond angle restraints seem normal. However, when I refine with phenix, the sugar's C6 methyl group gets pushed out of density and assumes a very unnatural angle. Now, it turns out that there are two copies of this molecule in the AU, and the other copy looks fine after refinement. Moreover, I can load my library into Coot, and when I use it to refine the sugar's position or regularize its geometry, it works just fine; and when I run phenix.pdbtools --geometry_regularization and supply my library, the resulting structure has nice geometry. These three observations lead me to believe that there's nothing inherently wrong with my library. There are no steric clashes that would tend to push this methyl group out of whack (but just to be sure, I removed all nearby atoms and repeated the refinement, with the same result). I should mention that this refinement is at ca. 1.8 Å, and the density for the sugar looks quite nice. Any suggestions? Cheers, Pat Loll --------------------------------------------------------------------------------------- Patrick J. Loll, Ph. D. Professor of Biochemistry & Molecular Biology Director, Biochemistry Graduate Program Drexel University College of Medicine Room 10-102 New College Building 245 N. 15th St., Mailstop 497 Philadelphia, PA 19102-1192 USA (215) 762-7706 pat.loll(a)drexelmed.edu

2 1

Input NCS operators for AutoBuild
by Mark A Saper 06 May '10

06 May '10

This questions may be best answered by Tom. Does anyone know how to generate a custom NCS definition file that AutoBuild will read from the refinement format? The parameter is input_ncs_file = I used phenix.simple_ncs_from_pdb to generate 3 ncs format files. But I could not figure out how to make the program use my definitions. In any case simple_ncs_from_pdb outputs 3 formats in ./phenix/tmp: simple_ncs_from_pdb.ncs simple_ncs_from_pdb.ncs_spec simple_ncs_from_pdb.resolve I tried the last one, but it has no residue or chain specification. Should I use the .ncs_spec? The first one is for phenix.refine. Thanks, Mark _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry University of Michigan Biophysics, 3040 Chemistry Building 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323 http://www.biochem.med.umich.edu/?q=saper http://www.strucbio.umich.edu/

3 2

Re: [phenixbb] NCS problems using phenix GUI on a Mac
by Mark A Saper 05 May '10

05 May '10

John, I am having the exact same problem. I need the NCS parameters in a format suitable for AutoBuild which I think is different than phenix.refine. Are you trying to use phenix.simple_ncs_from_pdb routine in GUI? Let me know if you have made any progress. Thanks, Mark > Hello, > > I am having difficulties defining NCS parameters using the GUI > interface (Mac 10.4.11; phenix 1.6-289). > > Phenix will automatically select NCS restraint groups and use them > during refinement. But if I edit the automated selections to my > liking then click on Update and Save, the refinement runs with the > original parameters unedited. I have tried reading in a ncs.param > file, but it does not get read during the refinement run. Also, an > intermittent problem with this GUI is that I am not allowed to "Add" > a new restraint group. When I click this button, it just clears out > the selections on the last group, and does not add a new group. Any > ideas? > > Thanks. > > Best, > John > > -- > John Pascal, PhD ph 215.503.4596 > Assistant Professor fx 215.923.2117 > Thomas Jefferson University > Biochemistry & Molecular Biology > 233 South 10th Street, BLSB 804 > Philadelphia, Pennsylvania 19107 _________________________________ Mark A. Saper, Ph.D. Associate Professor of Biological Chemistry University of Michigan Biophysics, 3040 Chemistry Building 930 N University Ave Ann Arbor MI 48109-1055 U.S.A. saper(a)umich.edu phone (734) 764-3353 fax (734) 764-3323 http://www.biochem.med.umich.edu/?q=saper http://www.strucbio.umich.edu/

1 0

Job Opening for Industrial Post Doc in Xray Crystallography Software Development
by Lance Westerhoff 05 May '10

05 May '10

Hello All- We have an opening at QuantumBio Inc. for an Industrial Post Doc in Xray Crystallography Software Development. Below is the short job description. The position is based at QuantumBio Inc. headquarters in State College, PA (home of Penn State), and begins immediately. We expect that the successful candidate will have a good understanding of the innards of PHENIX (hence the present audience) and be willing to work with our software engineers as needed to integrate PHENIX and QuantumBio's linear scaling QM offerings and of course validate the resulting method both on proprietary and public data. A good understanding of C++ and/or Python will go a long way. We will be validating the software on-site at at least one of our pharma collaborators along the way, so this is also a good opportunity to get to know practitioners in the field. Contact: Dr. Lance M. Westerhoff, lance(a)quantumbioinc.com, 814-235-6908 Job Description: Beginning immediately: QuantumBio Inc., headquartered adjacent to The Pennsylvania State University in scenic State College, PA, is in need of a post doctoral computational Biochemist/Chemist or Xray Crystallographer interested in continuing his or her career within a dynamic, small-company environment. Under the direction of Dr. Lance M. Westerhoff, General Manager of QuantumBio Inc., the successful candidate will work with both academic and industrial partners to help transition and validate the novel, quantum mechanically based Xray refinement technologies recently developed in the academic laboratory of Dr. Kenneth M. Merz Jr. to QuantumBio’s product line. The successful candidate will be integral to this project and will focus his or her efforts on the research and software development aspects necessary to validate and deploy this novel technology across the pharmaceutical industry. The position requires the candidate to have a Ph.D. in Chemistry, Biochemistry, or related field and have extensive experience with PHENIX and/or other similar xray refinement packages along with an understanding of modern software development principles. Due to the limited number of new work visas available, only American citizens or candidates with valid work permits will be considered at this time. A willingness to publish, and experience with C++ and high performance programming is a plus. Opportunities for advancement may be available through additional SBIR/STTR-style projects, and industry-supported collaborations. Further, in addition to the research and development duties of the project, the position will afford the successful candidate with access to and experience with QuantumBio’s industry partners including a number of pharmaceutical, biotech, and computational firms. Interested candidates should submit at their earliest convenience their CV, one or two representative publications, and a cover letter capturing the following items: * Outline of the types of structures you have worked with and your experiences in the field. * Summary your method research and software development experiences to date. * Discussion of your level of experience with QM, semi-empirical QM, and molecular mechanics. * Also, will you require sponsorship to legally work for a for-profit company in the US and when will you be available? About QuantumBio: QuantumBio Inc is accelerating drug discovery efforts by providing pharmaceutical, biotechnology companies and life science research organizations with a next generation of Computer-Assisted Drug Design (CADD) and Computer-Assisted Molecular Modeling (CAMM) solutions based on the increased accuracy and power of quantum mechanics. These solutions include a number of options tailored to each customer’s specific requirements including software licensing, services, and customization. See http://www.quantumbioinc.com/ for more! Thank you for your time. Please feel free to contact me if you have any questions or comments about the position. -Lance ____________________ Lance M. Westerhoff, Ph.D. General Manager QuantumBio Inc. WWW: http://www.quantumbioinc.com Email: lance(a)quantumbioinc.com Phone: 814-235-6908 Fax: 814-235-6909 This message and any attachments are solely for the intended recipient and should be considered confidential. If you are not the intended recipient, please immediately and permanently delete.

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Re: [phenixbb] AUTOSOL for MAD data with error message-'Need a symfile for solve'
by Thomas C. Terwilliger 05 May '10

05 May '10

Hi Peter, I am a little puzzled...I would have thought that it was fixed in phenix 1.6.1. Can you possibly send me your data and exact command so that I can fix this? I'm sorry about that! -Tom T >> I am also having this problem, has this been corrected? I am using phenix-1.6.1 through the phenix GUI. >> >> Cheers >> Peter Czabotar >> >> >>>Hi again Frank and Graeme and Mohan, >>> >>>This is now fixed and should be available in tomorrow's build of PHENIX. Most setting should now be available in Autosol (this bug only affected Autosol, not Autobuild or any other PHENIX routines). >>> >>>Thanks for pointing out the problem (and Mohan if this does not solve it in your case, please let me know and I'll continue to fix it). >>> >>>All the best, >>>Tom T >>> >>>> Hi Frank and Graeme and Mohan, >>>> >>>> Yes, P 2 21 21 should be allowed in autosol. I see that it doesn't work and I'll fix that. >>>> >>>> All the best, >>>> Tom T >>>> >>>> >>>>>> Um, this one has been hacked to death on ccp4bb: there is in fact nothing wrong or "non-standard" with that setting. If the program won't >>>>>> handle it, email the authors and ask them to fix it. >>>>>> >>>>>> Reindexing is an almighty pain in the butt. >>>>>> >>>>>> That said: it sounds like you may be pointing at an out-of-date symmetry operator file; I forget which environment variable it is, check the manual, but point it to an up-to-date ccp4 installation, and >>>>>> I >>>>>> suspect it will be fine. >>>>>> >>>>>> phx >> >> >> >> ______________________________________________________________________ The information in this email is confidential and intended solely for the addressee. >> You must not disclose, forward, print or use it without the permission of the sender. >> ______________________________________________________________________ _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >>

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