- phenixbb - phenix-online.org

Fitting ligand using coot
by bsubedi＠btk.fi 01 Apr '13

01 Apr '13

Hi all, I tried to fit the ligand using the coot -> calculate-> other modeling tools-> Find ligands. I have imported cif to coot and also opened the pdb file of my ligand. However, coot do not identify the ligand and asks to adjust r.m.s.d. I can see the density for my ligand. Could anyone suggest me what could be the problem or if I am missing anything here. Best regards. Bishwa

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Re: [phenixbb] question about FFT map coefficients
by Michael Thompson 29 Mar '13

29 Mar '13

Hi Nat, The FFT didn't work out, but I'm not sure if it's due to negative Fs. When I set up the FFT map coefficients utility with my mtz file, after picking my input I get a warning that "The reflections file does not appear to contain any suitable map coefficients." Then if I try to run it anyway I get the error message "There are no map coefficients in this MTZ file." An mtz dump confirms that I have columns FP and SIGFP. Additional info: these Fs were generated using a python script that I wrote, and there are not meaningful values for SIGFP. My script simply wrote out 0.000 to the SIGFP column for each reflection essentially as a place holder. I thought that maybe 0 was not a valid entry for SIGFP so I changed it to 0.001 so there would be some value there, but I get all the same errors. Could this be the problem? Any suggestions? Thanks for the help. Sorry to bug you. Mike ----- Original Message ----- From: "Nathaniel Echols" <nechols(a)lbl.gov> To: "PHENIX user mailing list" <phenixbb(a)phenix-online.org> Sent: Thursday, March 28, 2013 3:42:31 PM GMT -08:00 US/Canada Pacific Subject: Re: [phenixbb] question about FFT map coefficients On Thu, Mar 28, 2013 at 3:28 PM, Michael Thompson <miket(a)chem.ucla.edu> wrote: > I have an mtz file with map coefficients that are essentially Fo-Fo for two data sets. I would like to generate a map using these coefficients, but because the subtraction of Fs has already been done, there are some values of FP that are negative. Is "FFT map coefficients" able to handle negative values for FP? My guess would be that the answer is yes, because internally the amplitudes and phases for map calculation are combined to form a single array of complex numbers, and this effectively converts the amplitudes to be all-positive. Also, if this were not the case, the isomorphous or anomalous difference maps would never work. But I haven't actually tried what you're wanting to do with real data - if the result isn't what you expect, let us know. -Nat _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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question about FFT map coefficients
by Michael Thompson 28 Mar '13

28 Mar '13

Hello All, A quick question about the "FFT map coefficients" utility in the GUI: I have an mtz file with map coefficients that are essentially Fo-Fo for two data sets. I would like to generate a map using these coefficients, but because the subtraction of Fs has already been done, there are some values of FP that are negative. Is "FFT map coefficients" able to handle negative values for FP? If not, I can always change the sign of negative Fs and add 180 to the corresponding model phases, but I was hoping I could avoid this. Thanks in advance for the help! Mike P.S. I do know there is an Fo-Fo map option in phenix, but the origin of my map coefficients is more complicated than simply Fo-Fo, so I cannot use this option. -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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suggested usage of qsub?
by Scott Classen 28 Mar '13

28 Mar '13

Hi all, We have a HPC cluster configured with TORQUE/MAUI. I see in the Phenix GUI that there is some sort of ability to queue jobs to run via qsub. I can't find any documentation on how to set this up. If I'm working at my office computer and I want to submit to a remote server cluster for refinement, is this possible? Or is it assumed that qsub is available on the local machine? Thanks, Scott

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fwd: Deadline for the CCP4 Summer School application is approaching
by Nathaniel Echols 26 Mar '13

26 Mar '13

> ---------- Forwarded message ---------- > From: "Ruslan Sanishvili (Nukri)" <nukri(a)aps.anl.gov> > To: phenixbb(a)phenix-online.org > Date: Tue, 26 Mar 2013 11:52:44 -0500 (CDT) > Subject: Deadline for the CCP4 Summer School application is approaching > Dear Colleagues, > > The deadline for applications for the 6th annual CCP4 Summer School “From data collection to structure refinement and beyond” is only ten days away. Please submit your applications before April 5, 2013. The school will take place from June 18 to June 26, 2013 at the Advanced Photon Source (APS) near Chicago. > > There is no registration fee for the school. The students will be responsible for their own travel and lodging expenses. These and other details (the program, the list of speakers, the application process, accommodations, site access, contacts etc) can be found at the workshop website at http://www.ccp4.ac.uk/schools/APS-2013/index.php > > The school will include data collection, processing, structure solution, model building, refinement, validation, automation of many steps etc. Participants are encouraged to bring their own crystals, raw data or processed data for hands-on problem solving under the guidance of software developers and other experts. > We hope to see you in June > > Garib, Ronan and Nukri > > > > Ruslan Sanishvili (Nukri) > Macromolecular Crystallographer > GM/CA@APS > X-ray Science 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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low-res. real-space refinement
by "Weiergräber, Oliver H." 26 Mar '13

26 Mar '13

Hello, when refining a protein structure against a low-resolution dataset (5 A), I wanted to also attempt real-space refinement. However, in the log file I find: |-real space refinement (target=simple)---------------------------------------| rejected... | | | --------------------------------------------------------------------------- | Changing the target to, e.g., diff_map does not change anything; the message will still refer to the "simple" target. I guess this is due to an internal resolution limit, but that's only speculation since it seems to be undocumented. Indeed, there is probably not much to be gained by real-space refinement at this resolution (at least not in terms of side-chain conformations), but I wanted to give it a try anyway. Any comments on this issue? Regards, Oliver ================================================ PD Dr. Oliver H. Weiergräber Institute of Complex Systems ICS-6: Structural Biochemistry Tel.: +49 2461 61-2028 Fax: +49 2461 61-9540 ================================================ ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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Drag drop files
by Colin Levy 25 Mar '13

25 Mar '13

Hi all, I am running 1.8.2-1309 under OSX 10.7.5 but I lost the ability to drag and drop files between various phenix windows. Anyone else experiencing this or is it something specific to my setup? Thanks, Colin Manchester Protein Structure Facility MIB 1.025 Tel 0161 306 5185 c.levy(a)manchester.ac.uk<mailto:[email protected]>

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Refinement of B-factors at low resolution
by Florian Brückner 25 Mar '13

25 Mar '13

Dear all I am refining a structure at 3.2 A with phenix.refine using automatic optimization of target weights, solved by molecular replacement with a 2.1A structure of the same crystal form. Rwork=26%, Rfree=28%. I use individual atomic B-factor refinement. The obtained distribution of B-factors after refinement looks reasonable and quite similar to the distribution in the higher resolution model, which I suppose would be expected, since it is the same crystal form. However, the average B-factor does not change substantially, i.e. if I start with the B-factors from the high resolution model (average B-factor around 32 A**2) after 6 macrocycles the average B-factor is still around 32 A**2. If I set all B-factors to the Wilson B-factor determined by phenix.refine (66 A**2), after 6 macrocycles the distribution of B-factors looks again very similar to the high resolution MR model, but the average B-factor is still around 65 A**2. What should I make of this? Is this an expected behavior at this resolution, i.e. the fact that the absolute values of B-factors cannot be determined during refinement, although a reasonable distribution can be obtained as judged by plotting average B-factors vs. residue#? Since the average B-factor does not change much during refinement, which average B-factor should I start refinement with to end up with reasonable absolute values? I have manually determined the Wilson B-factor from the linear part of the Wilson plot (4.5-3.2 A) to be 97 A**2. This seems high to me. Would that be expected for the given resolution, given that the 2.1A structure of the same crystal form has 32 A**2? I should add, that there is not a substantial effect of the average refined B-factor on Rfree. Thanks for any comments or suggestions. Best regards Florian ------------------------------------------------------------- Dr. Florian Brückner Laboratory of Biomolecular Research (LBR) OFLG/102 Paul Scherrer Institut CH-5232 Villigen PSI Switzerland Tel.: +41-(0)56-310-2332 Email: florian.brueckner(a)psi.ch

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molecular replacemnt problem
by Appu kumar 24 Mar '13

24 Mar '13

Dear members, I am doing a molecular replacement of a transcription factor whose ligand binding structure(24000 Da) is available in PDB but not for the DNA binding(13000 Da). When i am searching for the two copies from ligand binding domain as a template model, i am getting very good solution but i am not getting any density for the DNA binding domain to build up in density. The space gorup is P 1 21 1 (4) and unit cell parameters are Unit Cell: 57.43 69.36 105.99 90.00 90.00 90.00. Please guide me how to get the complete model structure. Table below show the matthews statistics For estimated molecular weight 37000. Nmol/asym Matthews Coeff %solvent P(2.20) P(tot) _____________________________________________________________ 1 5.71 78.46 0.00 0.01 2 2.85 56.91 0.62 0.70 3 1.90 35.37 0.37 0.29 4 1.43 13.82 0.00 0.00 _____________________________________________________________ The phaser molecular replacement gives the following table. istogram of relative frequencies of VM values ---------------------------------------------- Frequency of most common VM value normalized to 1 VM values plotted in increments of 1/VM (0.02) <--- relative frequency ---> 0.0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 | | | | | | | | | | | 10.00 - 8.33 - 7.14 - 6.25 - 5.56 - 5.00 - 4.55 - 4.17 - 3.85 -- 3.57 --- 3.33 ------ 3.12 ---------- 2.94 **************** (COMPOSITION*1) 2.78 ----------------------- 2.63 -------------------------------- 2.50 ----------------------------------------- 2.38 ------------------------------------------------ 2.27 -------------------------------------------------- 2.17 ----------------------------------------------- 2.08 -------------------------------------- 2.00 -------------------------- 1.92 --------------- 1.85 ------- 1.79 --- 1.72 - 1.67 - 1.61 - 1.56 - 1.52 - 1.47 * (COMPOSITION*2) 1.43 - 1.39 - 1.35 - 1.32 - 1.28 - 1.25 - TABLE : Cell Content Analysis: SCATTER :N*Composition vs Probability:0|3x0|1:1,2: $$ N*Composition Probability $$ loggraph $$ 1 0.306066 2 0.00141804 $$ Most probable VM for resolution = 2.27817 Most probable MW of protein in asu for resolution = 92664.2 I have initially indexed the data in C2221 but Rfree was not decreasing so i reindexed the data in data in P121 space group keeping the Rfree flag of C2221. While analysing the symmetry mates , i found large space but no density. structure of Ligand binding domain is almost identical with 90% identity in sequence. I am stuck with this problem and don't know how to process further. I run the phenix.xtriage to evaluate the twining but it suggest no twining. When i reindex from C2221 to P21, the completeness of data reduced from 95 % to 35% whereas the map is very good and Rwork and Rfree are 26/31 for 2.2 resolution. I do not understand why the completeness of data reduced so much on reindexing. please Can anyone explain this phenomenon. Please give me your valuable suggestion. I will appreciate your effort. Thank you

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one or more errant TER cards
by jp d 20 Mar '13

20 Mar '13

hi, i am trying to refine using a reference model and keep getting this error *** Adding Reference Model Restraints *** Sorry: chain ' ' in start.pdb contains one or more errant TER cards. Please remove and try again i've tried various things including removing all the TER lines my models (reference and working) has many chains identified by segid's any suggestions ? thanks jpd

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install on ubuntu 12.04?
by Alastair Fyfe 19 Mar '13

19 Mar '13

Hi, I've installed previous phenix builds on ubuntu without problem, but with both 1.8.1-1168 and dev-1269 installers on 12.04, the command "./install --prefix=/home/afyfe" ends with "Error configuring: see /home/afyfe/phenix-installer-dev-1269/build-binary/intel-linux-2.6/svr/log/binary.log for details" and the tail of the binary.log file suggests: -- Creating files in build directory: "/home/afyfe/phenix-dev-1269/build/intel-linux-2.6" dispatcher_include_template.sh dispatcher_head.sh Please re-configure from scratch your cctbx_build:cd cctbx_build; /your/path/to/python ../cctbx_project/libtbx/configure.py [options] [modules] --- I don't see a cctbx_build directory under either the installer or destination directories. Any clues/suggestions? many thanks, Alastair

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International Conference on Structural Genomics - Structural Life Science, Sapporo, Japan, July 29-Aug 1, 2013
by Terwilliger, Thomas C 18 Mar '13

18 Mar '13

Dear Colleagues: On behalf of the organizing committee of the International Conference on Structural Genomics 2013 – Structural Life Science – (ICSG2013-SLS), we cordially welcome you to the conference, to be held in Sapporo, Hokkaido, Japan, July 29th – August 1st, 2013. ICSG2013-SLS is intended to provide an overview for the most recent developments in Structural Genomics and its impact on research in biology, medicine and disease, and to foster international collaboration among researchers. You can see all the details of the conference at: http://www.c-linkage.co.jp/ICSG2013 . Registration for the conference is now open. The scientific topics covered in ICSG2013-SLS include the wider life science research fields with particular attention to drug discovery (small molecules and biopharmaceuticals), biotechnology and industrial issues while keeping strength in the high-throughput technologies and integration of hybrid methods. These technologies are now leading to the new field of “Structural Life Science”. ICSG2-13-SLS is partially supported by the Grant-in-Aid for Scientific Research on Innovative Areas; “Structural Cell Biology”, “Intrinsically Disordered Protein” and “Transient Macromolecular Complexes”, from Ministry of Education, Culture, Sports, Science and Technology (MEXT) . In order to widen the opportunity to young and enthusiastic fellows to study more, we have organized several satellite workshops before ICSG2013- SLS. The topics will include “Small molecule screening”, “Automation of X-ray Structure Determination”, “Cell-free Protein Production”, “Automated NMR methods”, "Eukaryotic expression", “Interaction analyses" and "Bioinformatics”. We hope you also find the satellite workshops are informative and productive. The conference will be held in Keio Plaza Hotel Sapporo, in walking distance of Hokkaido University's main campus and Sapporo station. The summer in Sapporo is a great time to stay and enjoy the cool summer night of Japan. We are looking forward to welcoming you to Sapporo in the summer of 2013. Sincerely yours, Katsumi Maenaka, Ph.D. Chair, International Conference on Structural Genomics 2013 -Structural Life Science- (ICSG2013-SLS) Laboratory of Biomolecular Science and Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Japan Soichi Wakatsuki Chair of Program Committee, ICSG2013-SLS Photon Science, SLAC National Accelerator Laboratory Department of Structural Biology School of Medicine Stanford University

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MR_rosetta and disulphides
by Morten Groftehauge 18 Mar '13

18 Mar '13

Hi guys, Phenix version 1323 Rosetta version 3.4 I try to run phenix.mr_rosetta rosetta_command="-MR::disulf 129:411 228:281 279-615" mr_rosetta_228.eff but I get the following error in rebuild.log ERROR: Option matching -MR:disulf not found in command line top-level context I lifted the rosetta_command directly from the Version Documentation. Any clues as to why this doesn't work? Sincerely, -- Morten K Grøftehauge, PhD Pohl Group Durham University

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Tutorial of low resolution data?
by 李翔 17 Mar '13

17 Mar '13

Hi everyone, I will work on some low resolution data but have very little experience. (Data are about 4 A to 8 A) Does anyone know where I could find a tutorial for low resolution data please? It is best to work with Phenix, other software is fine. MIR or SAD or MR method will be appreciated and it is very helpful if the tutorial can talk about some details of the data processing. Cheers, Frank

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Phenix DEN-twin-refinement
by Ethayathulla A.S 14 Mar '13

14 Mar '13

hi all I want to do DEN twin-refinement using phenix. For my data phenix.DEN works better than CNS DEN. I want to DEN with twinning. Is there script for adding twinning operator for DEN refinement in phenix phenix.den_refine model.pdb data.mtz den.reference_file=reference.pdb Thank you Abdul --

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Re: [phenixbb] problems installing latest phenix on mac osx lion
by Alejandro Buschiazzo 14 Mar '13

14 Mar '13

Thanks Nat! read your message a bit later (I think I need to change from the digest format, so I receive each message as it comes), looking at http://phenix-online.org/pipermail/phenixbb/2013-March/thread.html Actually, your suggestion worked all right. (and by sourcing the phenix_env.sh as you point out, it's actually the same as the command line -installer of course) Don't know why the errors appeared before, but in any case, now it's running fine. Thank you for your help Alejandro > Not sure what's going on here - I will check it out today. There's > one more option however that should be the safest: did you try the > graphical installer yet? The destination can't be changed, but you > can still use the command line if you want by doing this: > > source /Applications/PHENIX-1.8.2-1309/Contents/phenix-1.8.2-1309/phenix_env.sh > > (or the csh equivalent) > > But I will see if there's an explanation for these errors. > > -Nat On Tue, Mar 12, 2013 at 4:26 AM, Alejandro Buschiazzo <alebus at pasteur.edu.uy <http://phenix-online.org/mailman/listinfo/phenixbb>> wrote: >/ I 'm trying to install phenix 1.8.2-1309 on a Macbook Pro (os x 10.7.5). />/ />/ First tried the binary installer proposed (which is indicated for os x />/ 10.6.7) />/ It didn't work, ending with "fix_mac_python: caught error - exiting." />/ />/ I spotted in the bb that this could've happened because the downloaded />/ installer was somehow corrupted, tried downloading it again, but same />/ result. />/ />/ Tried then the source installer: everything OK - except for wxPython, giving />/ this error />/ />/ WXPYTHON: />/ Using wxOSX_Cocoa build of wxPython 2.9 alpha version />/ />/ building wxPython-src-2.9.4.1 />/ ERROR: installation of wxosx_cocoa failed />/ />/ ERROR: installation of wxpython failed />/ />/ ...now I can work with command lines, but the GUI won't work of course. />/ />/ Your help is appreciated />/ />/ Alejandro />/ />/ />/ -- />/ Alejandro Buschiazzo, PhD />/ Research Scientist />/ Unit of Protein Crystallography />/ Institut Pasteur de Montevideo />/ Mataojo 2020 />/ Montevideo 11400 />/ URUGUAY />/ Phone: +598 25220910 int. 120 />/ Fax: +598 25224185 />/ http://www.pasteur.edu.uy/pxf/ -- Alejandro Buschiazzo, PhD Research Scientist Unit of Protein Crystallography Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 int. 120 Fax: +598 25224185 http://www.pasteur.edu.uy/pxf

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Fwd: 4th Edition of the ISBC2013
by Nathaniel Echols 14 Mar '13

14 Mar '13

---------- Forwarded message ---------- From: Jose A. Gavira <gavirius(a)gmail.com> Date: Thu, Mar 14, 2013 at 11:20 AM Subject: 4th Edition of the ISBC2013 Dear Colleague, The Laboratory of Crystallographic Studies is pleased to announce the 4th International School on Biological Crystallization (ISBC2013), to be held in Granada (Spain) during May 26-31, 2013. ISBC2013 is intended for postgraduate/postdoctoral students and research scientists from industrial and academic backgrounds. The International School will provide five days of lectures, posters and practical demonstrations focused on the fundamentals of crystallization from solution and their applications to the field of crystallization of biological materials, including biological macromolecules, biominerals and biomimetic materials. One day will be fully devoted to case studies on the crystallization of membrane proteins, viruses and large macromolecular complexes. For more information, please visit http://www.isbcgranada.org/<http://www.linkedin.com/redirect?url=http%3A%2F%2Fwww%2Eisbcgranada%2Eorg%2…> . Best regards, ISBC2103 Organizing Committee --- Gavi http://isbcgranada.org/

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problems installing latest phenix on mac osx lion
by Alejandro Buschiazzo 12 Mar '13

12 Mar '13

Hello, I 'm trying to install phenix 1.8.2-1309 on a Macbook Pro (os x 10.7.5). First tried the binary installer proposed (which is indicated for os x 10.6.7) It didn't work, ending with "fix_mac_python: caught error - exiting." I spotted in the bb that this could've happened because the downloaded installer was somehow corrupted, tried downloading it again, but same result. Tried then the source installer: everything OK - except for wxPython, giving this error > WXPYTHON: > Using wxOSX_Cocoa build of wxPython 2.9 alpha version > > building wxPython-src-2.9.4.1 > ERROR: installation of wxosx_cocoa failed > > ERROR: installation of wxpython failed ...now I can work with command lines, but the GUI won't work of course. Your help is appreciated Alejandro -- Alejandro Buschiazzo, PhD Research Scientist Unit of Protein Crystallography Institut Pasteur de Montevideo Mataojo 2020 Montevideo 11400 URUGUAY Phone: +598 25220910 int. 120 Fax: +598 25224185 http://www.pasteur.edu.uy/pxf

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GUI display items
by Luca Pellegrini 10 Mar '13

10 Mar '13

Hello, Is there a way to change/select the column items displayed in the PHENIX home window, under the 'Job history' tab? At the moment, mine shows: ID/Program/Date/Job title or directory/R-free. I would like to add things like the Overall score from MolProbity etc. I looked under Preferences but couldn't find anything. Thanks, Luca Luca Pellegrini Department of Biochemistry University of Cambridge 80 Tennis Court Road Cambridge CB2 1GA - UK Email: lp212(a)cam.ac.uk Tel: 0044-1223-760469 Fax: 0044-1223-766002 Sanger building, room 3.59

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fwd: EMBO 2013 Practical Course - Exploiting Anomalous Scattering in Macromolecular Structure Determination ESRF-EMBL, Grenoble, France, 10 - 14 June 2013
by Nathaniel Echols 09 Mar '13

09 Mar '13

(Note that the registration deadline is tomorrow.) ---------- Forwarded message ---------- From: Daniele de Sanctis <desancti(a)esrf.fr> To: phenixbb(a)phenix-online.org Date: Sat, 9 Mar 2013 12:51:54 +0100 Subject: EMBO 2013 Practical Course - Exploiting Anomalous Scattering in Macromolecular Structure Determination ESRF-EMBL, Grenoble, France, 10 - 14 June 2013 DEADLINE Tomorrow COURSE ANNOUNCEMENT EMBO 2013 Practical Course - Exploiting Anomalous Scattering in Macromolecular Structure Determination ESRF-EMBL, Grenoble, France, 10 - 14 June 2013 The EMBO 2013 Practical Course on Exploiting Anomalous Scattering in Macromolecular Structure Determination will be hosted by the ESRF in Grenoble, France from 10 to 14, June 2013. The course aims to impart the theoretical and practical basis for the 3-dimensional structure determination of bio-macromolecules using Anomalous Dispersion techniques (SAD & MAD) to young scientists who intend to apply these methods in macromolecular crystallography. Through a series of lectures, software demonstrations, practicals on the ESRF beamlines and tutorials, participants will get insights into all aspects of the structure determination process including beamline instrumentation, data collection and processing, heavy atom substructure determination, phasing and model building. There will also be sessions focusing on automated structure solution procedures and newer methods. Additional sessions will include presentations of distinguished structures solved with these techniques. The number of participants is limited to 20 and the deadline for application is March 10th, 2013. Additional information, course programme and instructions to apply to the course can be found in the course webpages: http://events.embo.org/13-crystallography/ Confirmed invited speakers include: Andreas Bracher, Kay Diederichs, Rita Giordano, Adrian Goldman, Wolfgang Kabsch, Gordon Leonard, Airlie McCoy, Sean McSweeney, Christoph Müller-Dieckmann, Max Nanao, Alexander Popov, Harry Powell, Thomas Terwilliger, Andrew Thompson, Isabel Uson, Clemens Vonhrein -- ἀρετή --------------------------------------- Daniele de Sanctis, PhD Structural Biology Group ESRF, Grenoble, France Tel 33 (0)4 76 88 2869

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map woes from refine
by Machius, Mischa Christian 08 Mar '13

08 Mar '13

Y'all, Recently, I've run into an issue with the maps from refine. All during the refinement cycles, the autoupdated maps in the associated coot window look great as refinement progresses. However, the final maps look horrible; completely chopped up. It's not a matter of contouring levels; it's essentially unrecognizable, and phenix acknowledges that by stating very low correlation coefficients at the end of the log file. I have downloaded the latest builds in an attempt to address B-value issues that were recently discussed and that I am (still) struggling with. The map issue happens with all of them. Is it possible that there is some crossfire from different versions, or any other reason? Any help appreciated. Cheers, MM

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selection of different residue ranges for a NCS group
by Andres PALENCIA 07 Mar '13

07 Mar '13

Dear All, I am trying to select different regions of the same protein to be included in the same NCS group before refinement. This correspond to the core of a protein. Additionally, I would define other NCS groups for external domains. I have 4 protein/RNA complexes in the asu, P1. Here are the residue ranges for the NCS group corresponding to the core of the protein (invariant): Chain A and resseq: 1:156, 188-227, 413:568, 629:794 this should be the reference group, to match the same region in the other 3 monomers (C, E. G). Other NCS groups will include the RNA, as well as other external domains: Chain B and resseq: 1: 87 This is the RNA molecule, that should match the other 3 monomers (D, F, H) Chain A resseq: 157:187 this is a external domain, to match the other protein monomer (C, E, G) and so on.... for other external domain I have seen that there is the possibility to use user-defined NCS groups, by using: * ncs_groups.params * or modifying the GUI by editing the atom selection For the external domains I think is easy as the syntax is only one line, however for the core of the protein I do not manage to select properly the different residue ranges. Could anybody please help on that? what would be the easiest way to do that? Can I for example creat a ncs_groups.params file and add it to phenix.refine in the GUI? Thanks in advance, Andres

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map scaling: sigma or volume scaled
by Edward A. Berry 07 Mar '13

07 Mar '13

map scaling can be defined: sigma or volume scaled Maybe another dumb question, but what is volume scaling? For 2mFo-DFc and mFo-DFc maps. Thanks, Ed

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quick clashlist or molprobity in batch mode
by jan 07 Mar '13

07 Mar '13

Hi all, I want to analyze a whole bunch of structures with molprobity, and I am looking for a convenient way to do this. phenix.quick_clashlist seems to be a handy tool. However, when I use the following command line: "phenix.quick_clashlist model=mypdb.pdb" ... the output tells me: # run_clashlist # # Run reduce and molprobity # type phenix.run_clashlist: --help for help Parameters used: run_clashlist { model = "4iuj.pdb" build = True summary_file = None output_file = None temp_dir = None remove_temp_dir = None verbose = False raise_sorry = False debug = False dry_run = True } ************************************************ 'str' object has no attribute '_anchor' ************************************************ Any ideas what I need to do differently? thanks, Jan -- Jan Abendroth Emerald BioStructures Seattle / Bainbridge Island WA, USA home: Jan.Abendroth_at_gmail.com work: JAbendroth_at_embios.com http://www.emeraldbiostructures.com

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Using Phenix Refine for Hypothetical Models
by Sam Stampfer 06 Mar '13

06 Mar '13

Dear Phenix Community, Is it possible to use phenix.refine to do simulated annealing and energy minimization of a hypothetical model? I am currently using pyrosetta relax for minimization; however, my hypothetical model is based on a homologous protein whose structure is a crystallographic trimer. I would like to preserve my model's symmetry, which I know is possible in phenix.refine but not in pyrosetta (the symmetry controls are only supported in regular rosetta, as far as I know). Is there a way to have phenix ignore x-ray data and just do energy minimization functions? How would I go about doing that? Would I need a file containing fake/dummy x-ray data? Thanks for your help! -Sam Stampfer

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