- phenixbb - phenix-online.org

Postdoctoral position in crystallography of the CFTR ion channel
by Machius, Mischa Christian 12 Dec '12

12 Dec '12

On behalf of a collaborator, I'd like to bring this open position to your attention. Postdoctoral position available in the laboratory of Jack Riordan, Dept of Biochemistry and Biophysics and Cystic Fibrosis Center, University of North Carolina at Chapel Hill. To join and provide a major contribution to a team working on the production, purification and characterization of the CFTR ion channel protein for crystallization and X-ray crystallography. Required experience working with membrane proteins and lipids and/or protein crystallization. Focus will be on crystallization in meso in collaboration with experts in that technology. Contact: jack_riordan(a)med.unc.edu<mailto:[email protected]> The University of North Carolina is an equal opportunity employer. ----------------------------------------------------------------------- Mischa Machius, PhD Director, Center for Structural Biology Assoc. Professor, Dept. of Pharmacology University of North Carolina 4079 Genetic Medicine CB#7365 120 Mason Farm Road Chapel Hill, NC 27599-7365, U.S.A. tel: +1-919-843-4485 fax: +1-919-966-5640 email: machius(a)med.unc.edu<mailto:[email protected]>

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SA Fo-Fc omit map
by Mengbin Chen 12 Dec '12

12 Dec '12

Dear Phenix Users, I have been playing around with Phenix AutoBuild GUI to generate a fo-fc sa omit map of the ligand in a protein structure, and I have the input files as follows: output.mtz (data type:experimental data) ligand.pdb (data type: omit box atoms & ligands) ligand.cif (data type: restraints of the ligand) protein.pdb (data type: starting model) omit map type: simulated annealing omit region: omit around PDB fie I have set the occupancies of all ligand atoms zero and deleted the ligand coordinates in my starting model. After the run finished and I checked the refined coordinates and map.mtz in COOT, I found that there was no electron density around the ligand while the protein model was in electron density, which was exactly opposite of what I wanted before. Furthermore, I have 3 Mg2+ ions in protein.pdb file, all of which moved away from where they were after the refinement run, which was not wanted either. Could anyone tell me how to do the sa omit map of ligand correctly? Thanks in advance! Mengbin -- Mengbin Chen Department of Chemistry University of Pennsylvania

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Re: [phenixbb] Fwd: parameters for averaged kick maps
by Pavel Afonine 11 Dec '12

11 Dec '12

Hi Jose, kick-map related parameters in ordered_solvent scope of parameters are leftover that I forgot to remove back when I was working on it. So you can see it as a minor bug. And yes, you can't change them. Sorry about delayed answer (I saw the email on phenixbb but did note reply immediately and it sank in the flood of other stuff). Pavel On 12/10/12 11:04 AM, Jose M de Pereda wrote: > Dear Phenix Team, > > Last week I sent an e-mail to the phenixbb regarding the parameters > that control de generation of averaged kick maps. Unfortunately, I > have not received any feedback from the community. > > I wonder if you could give me some help on this subject. > > Probably, the calculation of averaged kick maps is already very well > optimized in phenix.refine and phenix.maps. Yet, I am still curious. > > Thanks a lot in advance > All the best > > Jose > > > -------- Original Message -------- > Subject: [phenixbb] parameters for averaged kick maps > Date: Tue, 04 Dec 2012 10:12:46 +0100 > From: Jose M de Pereda <pereda(a)usal.es> > Reply-To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > To: PHENIX user mailing list <phenixbb(a)phenix-online.org> > > > > Dear all, > > I would like to compare averaged kick maps obtained using different “kick sizes”. > Is it possible to define the kick size and the number of kicks in phenix.refine and/or phenix.maps? > > In phenix.refine, the “ordered_solvent” section has keywords to control the generation of kick maps: > kick_map { > kick_size = 0.5 > number_of_kicks = 100 > } > But, it seems to me that these can not be used during the generation of maps or maps’ coefficients. > > Related with this issue, does phenix.refine always use the same kick > size or does it adjust it ad hoc (e.g. based on ML error estimates)? > > Thanks a lot, > Jose > > > -- > ------------------------------------------------------------ > Jose M de Pereda, PhD > Instituto de Biologia Molecular y Celular del Cancer (IBMCC) > Spanish National Research Council - University of Salamanca > Campus Unamuno s/n > E-37007 Salamanca, Spain > Phone: +34-923-294817 > Fax: +34-923-294795 > http://xtal.cicancer.org/ > ------------------------------------------------------------ > >

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Simulated annealing map
by Appu kumar 10 Dec '12

10 Dec '12

Thank you Terwilliger, Thomas for you quick reply, for guiding me on how to make simulated annealing omit map. Now i am able to make it but i have one question. i want to show the SA omit map of ligand with the map of omitted region around ligand. I tried it, i got the map also, but the omitted map of region around ligand is show in recatangular box which is not as great as of ligand inside the omitted region. Thank you

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Please apply for RapiData 2013, a course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 10 Dec '12

10 Dec '12

We are offering RapiData 2013, the fifteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 21-26 April 2013: http://www.bnl.gov/RapiData/. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. We encourage all students to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. You'll find the application materials on the Course Application tab at this site. For the eleventh time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 21 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be a small additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (under 40 yrs). Please apply for the course, and then contact R. Sweet (sweet(a)bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply or send your students to our course, Bob Sweet, Sonya Kiss, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ ========================================================================= Robert M. Sweet E-Dress: sweet(a)bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLS not 1) http://px.nsls.bnl.gov/ Photon Sciences and Biology Dept Mail Stop, Bldg 463 Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================

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Real Space CC Raw Data
by Eddie Pryor 08 Dec '12

08 Dec '12

Hi, All, To satisfy a reviewer, I would like to include a supplemental figure that contains, among other things, Real Space CC for each residue. I was wondering where this raw data might be stored so that I can parse and create a graph with it. The only thing I could find was in the Refine_###_info.txt log file, but that only included values less than 0.7. I know that all of the residues / CC values can be listed through the GUI, but with ~900 residues in my ASU, this is something I do not want to do manually! Thanks! --Eddie Pryor

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How to make simmulated annealing omit map
by Appu kumar 07 Dec '12

07 Dec '12

Dear Users, I am refining a enzyme structure with ligand. I want to make the simulated annealing omit map of ligand including with 4 Angestron radius around the ligand. I am seeking your valuable advice to help me out. I know how to make omit map but i have not come accross making simmulated annealing omit map. I would appreciate your help. Thank you Appu

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Is this a Phaser bug or am I misinterpreting ?
by Phil Jeffrey 05 Dec '12

05 Dec '12

Phaser from CCP4 6.3.0 built via fink running on OSX 10.6.8 in 64-bit mode. This is a snippet from a much larger run, ongoing. In multiple instances the order of the LLG and the Z-score in the translation function are not in sync: (42.16, 40.23, 40.18 vs 5.14, 5.24, 4.82) and looks like the Z-scores are still shown in the peak rank order before rescoring, while the LLGs are after rescoring. SET #5 of 6 TRIAL #60 of 115 ---------------------------- Search Euler = 263.0 82.1 85.7, Ensemble = ensemb3 ANNOTATION: RFZ=3.6 TFZ=3.8 PAK=0 LLG=26 LLG=30 Known MR solutions SOLU SPAC C 1 2 1 SOLU 6DIM ENSE ensemb3 EULER 30.6 65.7 246.9 FRAC 0.90 0.00 0.17 BFAC -5.14 Grid sampling: 0.825029 Angstroms Select peaks over 67.5% of top (i.e. 0.675*(top-mean)+mean) Top 360 translations before clustering will be rescored Calculating Likelihood for TF SET #5 of 6 TRIAL #60 of 115 0% 100% |=========================================================================| DONE Scoring 1 randomly sampled translations Generating Statistics for TF SET #5 of 6 TRIAL #60 of 115 0% 100% |==| DONE Top Peaks With Clustering ------------------------- # Rank of the peak after rescoring search points (#) Rank of the peak before rescoring search points LLG Log-Likelihood Gain Z-Score Number of standard deviations of LLG above the mean FSS Fast Search Score Select all peaks There were 159 peaks # (#) Frac X Frac Y Frac Z LLG Z-score Split #Group raw/top 1 6 0.842 0.923 0.779 +42.16 5.14 0 2 52.58/ 52.58 2 3 0.369 0.865 0.553 +40.23 5.24 37 2 53.18/ 53.18 3 10 0.743 0.937 0.261 +40.18 4.82 48 2 50.69/ 50.69 #SITES = 159: OUTPUT TRUNCATED TO 3 SITES

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Re: [phenixbb] log files for refinement (was: completeness using Intensities vs. structure factor)
by Pavel Afonine 05 Dec '12

05 Dec '12

Hi Yarrow, thanks for sending log files. Completeness reported in log files reflects the content of input MTZ data files: *32.log:* (...) F-obs: (...) Miller array info: (...)/reflectionsFreeR_1.38A.mtz:F_New(+),SIGF_New(+),F_New(-),SIGF_New(-),systematic_absences_eliminated Observation type: xray.amplitude Type of data: double, size=325598 Type of sigmas: double, size=325598 Number of Miller indices: 325598 Anomalous flag: True Unit cell: (64.3967, 68.0966, 103.663, 90, 96.1167, 90) Space group: P 1 21 1 (No. 4) Systematic absences: 0 Centric reflections: 4910 Resolution range: 43.7941 1.3786 Completeness in resolution range: 0.901282 Completeness with d_max=infinity: 0.901259 (...) and *35.log:* (...) I-obs: (...) Miller array info: (...)/reflectionsFandIFreeR_1.38A.mtz:IMEAN_New,SIGIMEAN_New,systematic_absences_eliminated Observation type: xray.intensity Type of data: double, size=181940 Type of sigmas: double, size=181940 Number of Miller indices: 181940 Anomalous flag: False Unit cell: (64.3967, 68.0966, 103.663, 90, 96.1167, 90) Space group: P 1 21 1 (No. 4) Systematic absences: 0 Centric reflections: 4910 Resolution range: 43.7941 1.3786 Completeness in resolution range: 0.992202 Completeness with d_max=infinity: 0.992164 (...) The numbers above are reported before anything else is done, that is they reflect exactly what's in input MTZ files. Somehow you managed to loose ~10% of data when converting Iobs into Fobs. How did you do this conversion? In theory this is possible since French&Wilson Iobs->Fobs conversion may result on some number of reflections lost. Note, when phenix.refine does IMEAN->Fobs conversion (35.log file) this does not result in ~10% loss. So based on looking at log files I can say it's not phenix.refine that manipulated your data or reported it wrong. You lost reflections at previous steps. Pavel On 12/4/12 4:57 PM, Yarrow Madrona wrote: > Hi, > > Here are the log files for refinement you asked for. > > 35.log is refined with Intensities. The MTZ file has a slightly different > name but it is the same MTZ. One had Intensities taken out of it because I > didn't think I needed them any longer. > > 32.log is refined with structure factors. Intensities were removed. > > Thanks for your help! > > -Yarrow > > >

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completeness using Intensities vs. structure factor
by Yarrow Madrona 05 Dec '12

05 Dec '12

Hi, (Phenix v.1.8.1-1168) I recently refined a structure using experimental Intensities and compared it to the same structure refined with calculated structure factors. I know if you provide intensities Phenix.refine will convert to structure factors. I am not sure if it runs truncate or what. Anyway, I get this in the log file which matches my completeness in the scala log file: Completeness in resolution range: 0.992202 Completeness with d_max=infinity: 0.992164 When I run using structure factors (Truncate run in Scala) I get the following: Completeness in resolution range: 0.901282 Completeness with d_max=infinity: 0.901259 Perhaps Scala did not merge anomolous and non-anomolous data? This does not may a whole lot of sense to me. Is some data thrown out? Can someone explain? Thank you. -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

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parameters for averaged kick maps
by Jose M de Pereda 04 Dec '12

04 Dec '12

Dear all, I would like to compare averaged kick maps obtained using different “kick sizes”. Is it possible to define the kick size and the number of kicks in phenix.refine and/or phenix.maps? In phenix.refine, the “ordered_solvent” section has keywords to control the generation of kick maps: kick_map { kick_size = 0.5 number_of_kicks = 100 } But, it seems to me that these can not be used during the generation of maps or maps’ coefficients. Related with this issue, does phenix.refine always use the same kick size or does it adjust it ad hoc (e.g. based on ML error estimates)? Thanks a lot, Jose -- ------------------------------------------------------------ Jose M de Pereda, PhD Instituto de Biologia Molecular y Celular del Cancer (IBMCC) Spanish National Research Council - University of Salamanca Campus Unamuno s/n E-37007 Salamanca, Spain Phone: +34-923-294817 Fax: +34-923-294795 http://xtal.cicancer.org/ ------------------------------------------------------------

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table 1
by So Jay 04 Dec '12

04 Dec '12

Hi, I was using generate table 1 utility in phenix-1.8.1-1168. The data was processed with HKL2000 and model was refined using Autobuster. In the table I find two entries for Multiplicity and R-sym were blank.I was wondering if there is any particular reason for this. ThanksJay

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Similar 2Fo-Fc maps, very different e/A^3 levels (absolute levels)
by Sam Stampfer 04 Dec '12

04 Dec '12

Dear Phenix group, I am trying to decide which electron density map to use for rebuilding my structure in Coot. Both 2Fo-Fc maps appear quite similar at the 1 sigma level but the absolute electrons per cubic Angstrom (e/A^3) is very different. When contoured at 1.00 rmsd in coot, these are the e/A^3 levels (Coot calls them absolute levels): Map #1 2Fo-Fc: 0.0044 e/A^3 Map #2 2Fo-Fc: 0.0832 e/A^3 Map #1 was generated using a twinning operator that is typically required for this crystal form. Map #2 was generated without the twinning operator and it tends to have slightly better 2Fo-Fc density, and there is a bit more density (or noise?) in the Fo-Fc map. The structure was refined in Phenix and gave a similar Rfree regardless of whether a twinning operator was used. What does it mean to have this 20-fold difference in electrons per cubic Angstroms for my maps? Which map should I use? Thanks for your help! -Sam PS: The Fo-Fc map in Map#2 also contours at a much higher absolute e/A^3 level.

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pseudotranslation and twinning problem
by Rajeshwer Sankhala 03 Dec '12

03 Dec '12

I am new to crystallography. I have collected data for 26 kDa protein with a maximum resolution of 2.25A in I 41 space group. I have a poor model for molecular replacement (~15-20% identical). When i did xtriage run, it suggested -h,k,-l twinning law and indicated about pseudo-translation. Now when i am running Phaser for molecular replacement i am getting very low LLG (less than 100) and TFZ score (5-6). Can anyone suggest which parameters or setting i should use to improve my LLG score and get a best model for refinement. Thanks Raj

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dev-1227: problem reading in tls parameters from refmac or tlsmd
by Boaz Shaanan 02 Dec '12

02 Dec '12

Hi, In the TLS pulldown I tried to upload tls parameters from either refmac (.tls) or tlsmd (.tlsin) through the 'load' button, according to the suggestion in this section, but it complains about wrong format of the file. Am I doing something wrong? Thanks, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaanan(a)bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710

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Specify particular columns from data files on the command line
by Brad C. Bennett 30 Nov '12

30 Nov '12

Hi all (again)- I'm trying to run DEN refinement in Phenix from the command line. How do I specify certain columns from multiple data files (in my case, 2 MTZ files) to be used? For example, the Rfree flags from one and the hkl data from the other. Thanks! Brad C. Bennett Research Associate- Mark Yeager Lab University of Virginia Molecular Physiology and Biological Physics 320 Snyder Building 480 Ray C. Hunt Drive Charlottesville, VA 22908 Email: bcb3b(a)virginia.edu Lab phone: 434-243-2520

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DEN refinement
by Morten Groftehauge 30 Nov '12

30 Nov '12

Hi guys, Two quick questions about DEN refinement: 1) If gamma refines to 0 does that mean that I should run DEN refinement again with the output model? Or should I do a refinement and then another DEN? Since gamma = 0 the refinement should be allowed a possibility of moving the structure further towards the reference restraints in my mind. 2) If gamma refines to 1 it means that my reference model is inappropriate, right? Not really much of a question, I know. And I know that DEN refinement is in beta but it would be nice if you outputted the optimal gamma and weight for the refinement to the GUI. Actually it would be nice if the did that for geometry weights and xray weights too when one optimizes them. Cheers, Morten -- Morten K Grøftehauge, PhD Pohl Group Durham University

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Error starting Phenix on Linux
by Brad C. Bennett 30 Nov '12

30 Nov '12

Hi all- After installing the latest version and release of Phenix (1.8.1-1168) onto our Linux workstation and setting the environment for bash, I get the following error upon trying to launch Phenix from the command line: ImportError: libjpeg.so.62: cannot open shared object file: No such file or directory I've never seen this before (previous versions of Phenix have run fine on this machine) and don't know what this file is exactly and where it should be located. Anyone come across this and know if there is a fix (or if I'm just doing something stupid!). Thanks! Brad C. Bennett Research Associate- Mark Yeager Lab University of Virginia Molecular Physiology and Biological Physics 320 Snyder Building 480 Ray C. Hunt Drive Charlottesville, VA 22908 Email: bcb3b(a)virginia.edu Lab phone: 434-243-2520

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Call for submissions for the Computational Crystallography Newsletter (CCN) January 2013
by Nigel Moriarty 30 Nov '12

30 Nov '12

Folks Calling for articles and short communications of interest to structural biologists. The deadline for publication in the January 2013 issue is 31 December, 2012 but if you can send me drafts before the 15th of December we can get started on generating proofs. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and the template are available at www.phenix-online.org/newsletter. Cheers Nigel -- Nigel W. Moriarty, PhD Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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choosing Rfree set with NCS and twinning
by vincent Chaptal 30 Nov '12

30 Nov '12

Dear phenixbb, I am using the "reflection file editor" in phenix 1.8.1-1168 to generate my test set (with the GUI). I have NCS so I ticked the box "assign test set in thin resolution shells". I also have twinning, and want to have my Rfree not biased by twin related reflections. I guess the option "use lattice symmetry to generate test set" is the one I should use for this purpose? I couldn't find much information online about this option. No log file has been generated so I can't check what happened. I am supposing xtriage is ran in the background and if a twin law is found, then used to generate the test set. My output from xtriage is: Statistics depending on twin laws ----------------------------------------------------------------- | Operator | type | R obs. | Britton alpha | H alpha | ML alpha | ----------------------------------------------------------------- | -k,-h,-l |PM| 0.249| 0.272| 0.246| 0.200| ----------------------------------------------------------------- And indeed if I check in mtzdmp the output mtz, reflections in the test set are related by (-k, -h, -l); disclaimer: I only checked in the plane (h,k,0). I would like to be sure my Rfree is generated correctly. Alternatively, what would happen when multiple twin laws are available? Is the most probale used? Is it possible to specify the editor which law to use? Thank you for your help. Vincent -- Vincent Chaptal, PhD Institut de Biologie et Chimie des Protéines Drug-resistance modulation and mechanism Laboratory 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.ibcp.fr

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DNA double helix with many molprobity bad clashes
by Benda, Christian 30 Nov '12

30 Nov '12

Hi, I am refining a protein-DNA complex at around 3 A with a standard b-form dsDNA. R-factors are around 24/20 (kinda low for the resolution). Originally, I placed the DNA using coot and now, after several rounds of refinement in phenix, I get a long list of bad clashes from molprobity validation (in phenix) that covers the whole length of the DNA and almost exclusively lists hydrogens from the ribose moiety (whether or not in contact with protein). My question is, - why is phenix.refine not taking care of these clashes (i.e. optimizes the structure such that they go away)?. Am I giving experimental contribution to high a weight (I have "optimize x-ray/stereochemistry" checked)? - if so, can I (and how) restrain geometry for the DNA a little more but leave the protein alone (and does that make sense)? thanks for any help Christian

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phenix.erraser error
by Russell Chan 29 Nov '12

29 Nov '12

Hi, I'm currently trying to use the new command, phenix.erraser, to refine my RNA structure. I generated a ccp4 map and removed the R-free flags, however it generates an error after its starts its first round of minimization. The command I use is: phenix.erraser <mypdb>.pdb <mymap>.ccp4 The error generated is: ################################### Starting SWA_rebuild_erraser.py... Output pdb will be...precursor_chi_erraser.pdb Create temporary directory /home/Russ/Desktop/erraser_test/precursor_chi_erraser_temp/... fixed_res_final in Rosetta pdb file = [] cutpoint_final in Rosetta pdb file = [1, 2, 3, 4, 12, 15, 19, 20, 21, 25, 30, 37, 38, 49, 54, 58, 68, 69, 72, 79, 83, 84, 105, 108, 109, 122, 124, 125, 130, 133, 134, 137, 140, 143, 146, 158, 160, 161, 168, 170, 176, 179, 187, 189, 201, 204, 205, 216, 217, 228, 237, 239, 241, 245, 246, 268, 269, 273, 279, 283, 292, 293, 302, 305, 309, 311] extra_res_final in Rosetta pdb file = [] Starting whole-structure minimization 1... ******************* ERROR ENDING *************** Command 'phenix.python /home/sbgrid/programs/x86_64-linux/phenix/1.8.1-1168/phenix-1.8.1-1168/phenix/phenix/erraser/full_struct_slice_and_minimize.py -binary_name linuxgccrelease -map /home/<Russ>/Desktop/erraser_test/erraser_map.ccp4 -map_reso 2.0 -new_torsional_potential True -pdb minimize_0.pdb -out_pdb minimize_1.pdb > minimize_1.out 2> minimize_1.err' returned non-zero exit status 1 ******************* ERROR ENDING *************** Any help would be greatly appreciated! Thanks, Russell

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Re: [phenixbb] [COOT] CCP4 - Coot in Applications
by Nathaniel Echols 28 Nov '12

28 Nov '12

---------- Forwarded message ---------- From: Paul Emsley <pemsley(a)mrc-lmb.cam.ac.uk> To: PHENIX user mailing list <phenixbb(a)phenix-online.org> Cc: Date: Wed, 28 Nov 2012 17:08:50 +0000 Subject: Re: [phenixbb] [COOT] CCP4 - Coot in Applications On 28/11/12 15:03, Antony Oliver wrote: > > Ok - annoying thing…. > > 1) using /Applications/coot.app/Contents/Resources/script to launch Coot from the command line (terminal window) works IF you don't have X11 open already. > 2) if you DO have X11 open, coot pretty much always crashes with the aforementioned "invalid window errors". It is not clear to me if you are, or are not using Bill Scott's binary... (it's the one I recommend for Macintosh). Paul.

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Re: [phenixbb] [COOT] CCP4 - Coot in Applications
by Antony Oliver 28 Nov '12

28 Nov '12

Ok - annoying thing…. 1) using /Applications/coot.app/Contents/Resources/script to launch Coot from the command line (terminal window) works IF you don't have X11 open already. 2) if you DO have X11 open, coot pretty much always crashes with the aforementioned "invalid window errors". >>> Nov 23 12:17:02 coot-real[80005] <Error>: kCGErrorIllegalArgument: CGSGetSurfaceBounds >>> Nov 23 12:17:02 coot-real[80005] <Error>: kCGErrorFailure: Set a breakpoint @ CGErrorBreakpoint() to catch errors as they are logged. >>> Nov 23 12:17:02 coot-real[80005] <Error>: kCGErrorIllegalArgument: CGSBindSurface: Invalid window 0x8da >>> Nov 23 12:17:02 coot-real[80005] <Error>: kCGErrorIllegalArgument: CGSBindSurface: Invalid window 0x8da >>> Nov 23 12:17:02 coot-real[80005] <Error>: kCGErrorIllegalArgument: CGSBindSurface: Invalid window 0x8da Ideas and suggestions welcome. I guess I could make sure that X11 is not running each time I invoke a script or run coot from the command line - but it's not exactly ideal. --> NB: Running Mac OS X, 10.7.5 - Lion. Please excuse the cross bulletin board posting, but I really do use quite a range of software across all program suites - and this method of delivering coot causes problems for many of the plugins/scripts (phenix and buster for example). With thanks, Antony. --- Dr Antony W Oliver Senior Research Fellow CR-UK DNA Repair Enzymes Group Genome Damage and Stability Centre Science Park Road University of Sussex Falmer, Brighton, BN1 9RQ email: antony.oliver(a)sussex.ac.uk tel (office): +44 (0)1273 678349 tel (lab): +44 (0)1273 677512 On Nov 27, 2012, at 11:32 AM, Antony Oliver wrote: > Thanks Charles - that seems to work..! > > Tony. > > --- > Dr Antony W Oliver > Senior Research Fellow > CR-UK DNA Repair Enzymes Group > Genome Damage and Stability Centre > Science Park Road > University of Sussex > Falmer, Brighton, BN1 9RQ > > email: antony.oliver(a)sussex.ac.uk > tel (office): +44 (0)1273 678349 > tel (lab): +44 (0)1273 677512 > > On Nov 26, 2012, at 10:19 AM, Charles Ballard wrote: > >> You could give >> >> /Applications/coot.app/Contents/Resources/script >> >> a go. >> >> Charles >> >> On 23 Nov 2012, at 12:20, Antony Oliver wrote: >>

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coordinate refinement and maps
by Subhani Bandara 27 Nov '12

27 Nov '12

Hi all, I am refining a protein with metal-ligand complexes. Is it possible to refine only y coordinates for an atom (on two fold) while keeping X and Z fixed using Phenix? Also is there a way to calculate something like anomalous difference-difference map (Anomalous Fobs - Anomalous Fcalc) to identify any additional atoms bound at metal sites. Thanks in advance for the help! Subhani

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