- phenixbb - phenix-online.org

Number of atoms and average b-factors for specific chain IDs (with the option of specifying multiple chain IDs).
by Francis E Reyes 15 Mar '10

15 Mar '10

Is there anyway to get this quickly? Either by phenix util, web util, or whatever? Thanks! FR --------------------------------------------- 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

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gtk error
by Rafael Counago 15 Mar '10

15 Mar '10

Dear all, I am running PHENIX on ubunut (karmic koala, 32 bits). On start up I am getting the following message: Gtk-Message: Failed to load module "canberra-gtk-module": libcanberra-gtk-module.so: cannot open shared object file: No such file or directory Any ideas how to solve this issue? Another question... is there a way to automatically search the old messages from the bb? Cheers, Rafael. -- Rafael Couñago Research Fellow Department of Biochemistry University of Otago 710 Cumberland St Dunedin, New Zealand ph: (03) 479 5148

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Gap between R and Rfree
by Young-Jin Cho 13 Mar '10

13 Mar '10

Hi everyone, I recently got a diffraction data and am trying to refine it. The question is whatever I did the gap between R and Rfree stay far away: .2140/.2982 around 2.5 A resolution. (water added and isotropic(individual_adp) and so on). Although I am redoing with many different approaches, if anyone can give me any comments or suggestions, it would be helpful. Thanks in advance, Young-Jin

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Low resolution structure
by Kendall Nettles 13 Mar '10

13 Mar '10

I have a few questions related to a 3.5 angstrom structure. I have one helix that I am having trouble placing accurately. It does have a cysteine that disulfide bonds with the same residue in a symmetry related molecule. Can I restrain this distance during a rigid body refinement of the helix? How do I do this? What kind of parameters would be appropriate for the disulfide? My second question is whether someone can suggest appropriate distance_ideal, sigma, and slack for hydrogen bond restraints for a helix? Also, I have a 2 angstrom structure of this part of the complex for reference. Thanks! Kendall Nettles

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Re: [phenixbb] phenix gui freezes
by John Berrisford 12 Mar '10

12 Mar '10

Dear All Thanks for the suggestions on how to solve my GUI freezing issues. It looks like it was a communication problem with coot that was causing my problems. Editing App.py as below solved my problem. Adding a preference setting to do this would be useful. Thanks again John Message: 3 Date: Thu, 11 Mar 2010 09:48:29 -0500 From: Nathaniel Echols <NEchols(a)lbl.gov> To: PHENIX user mailing list <phenixbb(a)phenix-online.org> Subject: Re: [phenixbb] phenix gui freezes Message-ID: <49B2EAFF-6882-4118-8322-E3949BA490DE(a)lbl.gov> Content-Type: text/plain; charset=us-ascii I have one other thought - the GUI listens on a socket for incoming commands from Coot (this isn't used very much at present). Apparently this caused problems on Linux with the old GUI, which also used Python sockets. If something goes wrong here, it could certainly take down the entire program. To fix this, edit the file $PHENIX/phenix/wxGUI2/App.py, and comment out this line (in 1.6): self.start_xmlrpc_server() (if you're new to python, a comment starts with '#'.) I will add a preferences setting to do this. I can also try slowing down the GUI updates while a process is running (using detached processes should also take care of this). -- John Berrisford Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk TEL: +44 (01223) 252918

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naming of refinement runs
by John Berrisford 12 Mar '10

12 Mar '10

Dear All I've been running multiple refinement runs and they are named sequentially. I'm looking for a method to name the refinement runs with the GUI. I understand that I can edit the output file names, but is there anyway to give the refinement runs a title to describe the run as there is in CCP4i? I was thinking along the lines of eg. "Refine_10 - 20 cycles ADP scale 2...." Thanks John -- John Berrisford Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk TEL: +44 (01223) 252918

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Custom ligand - confirming the correct scattering definition
by George Phillips 12 Mar '10

12 Mar '10

Pavel, I am following up on this question of the oxidation state of metals. It is important to deal with this properly to get the most out of the data and to able to show difference maps in papers that make sense. Where are the scattering factors stored (it1992's for example)? One could hack an oxidation state in for the standard numbers to get it right (ugly but effective). Alternatively, maybe the scattering factor tables and element id's could be expanded? Is this all hard coded or are there libraries or tables that are parsed? THanks for any comments, as always. George N. Phillips, Jr., Ph.D. Professor of Biochemistry and of Computer Sciences University of Wisconsin-Madison 433 Babcock Dr. Madison, Wi 53706 Phone/FAX (608) 263-6140 Hi Andy, currently phenix.refine will not make difference between say "Fe" and "Fe+2". So if you see some artifacts at mFo-DFc map around your Fe, that might be explained by not taking "+2" into account. Refining occupancy of Fe would fix the map appearance (most likely), but I would not do that, since it will rather hide the problem than properly address it (and of course it would be misleading too). Regarding "n_gaussian table": it is just a dynamic approximation to the standard scattering factor table (mostly done to optimize runtime; the accuracy is not compromised). For more details see: Grosse-Kunstleve RW, Sauter NK, Adams PD: cctbx news Newsletter of the IUCr Commission on Crystallographic Computing 2004, 3:22-31. Pavel. On 11/25/09 12:37 PM, Andy Torelli wrote: > To the Phenix group: > > I've created a .cif file for a ligand that includes metal atoms. The > metal atoms are defined in the .cif file with their element name, but in > actuality, they should be defined according to their oxidation state so > that the correct scattering parameters are used during refinement. > > In CNS, this meant choosing an "atom type" that would be parsed to > match the correct scattering definition listed in the scatter.lib file. > I see that phenix uses the n_gaussian table for scattering values. > Where can I view this and the other scattering table options? Like CNS, > do I just need to use the name of the element with the correct > oxidation state from the table (e.g. "Fe+2") in my .cif file to ensure > that the correct scattering definition is used during refinement and map > calculation? > > Thanks, > -Andy Torelli > > _______________________________________________ > phenixbb mailing list > phenixbb at phenix-online.org > http://www.phenix-online.org/mailman/listinfo/phenixbb > Previous message: [phenixbb] Custom ligand - confirming the correct scattering definition Next message: [phenixbb] Confused by the output from Phenix autobuild jobs Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] More information about the phenixbb mailing list George N. Phillips, Jr., Ph.D. Professor of Biochemistry and of Computer Sciences University of Wisconsin-Madison 433 Babcock Dr. Madison, Wi 53706 Phone/FAX (608) 263-6142

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composite omit map command phenix 16
by John Bruning 11 Mar '10

11 Mar '10

Hi, How can I generate a composite omit map from the command line in Phenix16? Thanks, John

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

11 Mar '10

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

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does phenix.refine ignore F-obs, SIGF-obs?
by Scott Classen 11 Mar '10

11 Mar '10

Hi All, I have an mtz file that has: I-obs SIGI-obs F-obs SIGF-obs I want phenix.refine to use F-obs and SIGF-obs, but even though I provide : labels = "F-obs,SIGF-obs" I think phenix.refine is seeing the I-obs,SIGI-obs and recalculating the structure factors from those values instead of using the Fs that I provide in the mtz. Is this the case? Other than stripping the I-obs,SIGI-obs from the input mtz, is there a way to force phenix to use my structure factors? 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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phenix gui freezes
by John Berrisford 11 Mar '10

11 Mar '10

Dear All A little while ago I posted a message about the GUI freezing on linux systems, either run remotely (centos) or locally (ubuntu system). I never received a solution and I'm still having this problem despite upgrading to version 1.6. On my ubuntu system the GUI seems to freeze either when the screen saver comes on (set to turn the screen off) or I switch desktop - although not everytime I do this. The freezing GUI means that I have to force quit phenix after every refinement run (I haven't tried other tasks) and that the freeR is not reported to the GUI (not a major problem). Thankfully in version 1.6 the configuration and results for each refinement run are recorded and I can retrieve this information by loading a job through job history - a big improvement over version 1.5. Anyone else having this problem and does anyone know a solution? Thanks John -- John Berrisford Medical Research Council Mitochondrial Biology Unit Wellcome Trust / MRC Building Hills Road Cambridge CB2 0XY WEB: www.mrc-mbu.cam.ac.uk TEL: +44 (01223) 252918

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Re: [phenixbb] does phenix.refine ignore F-obs, SIGF-obs?
by Scott Classen 11 Mar '10

11 Mar '10

Here are some excerpts from the phenix.refine log file: Resolution range: 44.4024 1.8604 Completeness in resolution range: 0.995991 Completeness with d_max=infinity: 0.995862 Number of F-obs in resolution range: 92411 Number of F-obs <= 0: 3322 Refinement resolution range: d_max = 44.4024 d_min = 1.8604 Fobs statistics after all cutoffs applied: Miller array info: None Observation type: xray.amplitude Type of data: double, size=89089 Type of sigmas: double, size=89089 Number of Miller indices: 89089 Anomalous flag: False Systematic absences: 0 Centric reflections: 11672 Resolution range: 44.4024 1.8604 Completeness in resolution range: 0.960187 Completeness with d_max=infinity: 0.960063 This implies to me that phenix.refine is throwing out my very weak reflections. It appears that completeness goes from 99.6% to 96.0% Then further down in the log file I see: ============================== Outliers rejection ============================= Distribution of F-obs values before outliers rejection: 0.126 - 28.714 : 65519 28.714 - 57.302 : 13850 57.302 - 85.890 : 5625 85.890 - 114.478 : 2515 114.478 - 143.066 : 991 143.066 - 171.654 : 393 171.654 - 200.242 : 128 200.242 - 228.830 : 49 228.830 - 257.418 : 12 257.418 - 286.006 : 7 basic_wilson_outliers = 0 extreme_wilson_outliers = 0 beamstop_shadow_outliers = 0 model_based_outliers = 1 total = 1 Distribution of F-obs values after outliers rejection: 0.126 - 28.714 : 65519 28.714 - 57.302 : 13850 57.302 - 85.890 : 5624 85.890 - 114.478 : 2515 114.478 - 143.066 : 991 143.066 - 171.654 : 393 171.654 - 200.242 : 128 200.242 - 228.830 : 49 228.830 - 257.418 : 12 257.418 - 286.006 : 7 which makes it look like nothing is being rejected? So what is it? in the header of the resulting pdb file: REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.860 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.402 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.03 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.02 REMARK 3 NUMBER OF REFLECTIONS : 89088 which implies that indeed some reflections are being rejected. My hunch is that if F-obs = SIGF-obs then the reflection is rejected. Thanks, Scott

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Re: [phenixbb] phenixbb Digest, Vol 52, Issue 12
by Kay Diederichs 11 Mar '10

11 Mar '10

Am 11.03.2010 23:51, schrieb phenixbb-request(a)phenix-online.org: > Message: 4 > Date: Wed, 10 Mar 2010 16:52:35 -0500 > From: Nathaniel Echols<NEchols(a)lbl.gov> > To: PHENIX user mailing list<phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] autosol interface bug? selinux conflict? > Message-ID:<6BE2BD93-F43C-4D37-AD91-9F31BCE2C6F1(a)lbl.gov> > Content-Type: text/plain; charset=us-ascii > > On Mar 10, 2010, at 4:37 PM, Kay Diederichs wrote: >> > I wonder >> > - why do Fortran binaries give a SElinux problem, and C++ binaries don't? > Because we bundle the Intel Fortran shared libraries (which are required by SOLVE) with the binary installers. > if you simply link with -static-intel then you don't have to distribute those libraries. HTH, Kay

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Additional residue info in coot
by Brown, Breann 11 Mar '10

11 Mar '10

Hello, I am currently refining a model of a zinc-binding protein and after refinement there is additional positive Fo-Fc density at the zinc site. This is the fourth independent structure of this particular protein solved in my lab so we are confident the metal is in fact zinc. I noticed that after refinement the "residue info" in Coot has two lines for the zinc atom. The first line reads "G/121 ZN/ZN 1.00 44.30" while the second line reads G/121 ZN/ 0.00 0.00. The occupancy for the second line cannot be changed and it only appears after refinement. I carried out the same refinement using a previously solved structure of the same protein and the extra residue info line was not present. My question is where does this extra line in the residue info come from and could the zero occupancy be causing additional Fo-Fc density at the metal site? Thanks, Breann Breann L. Brown Page Laboratory Department of Molecular Pharmacology, Physiology and Biotechnology Brown University Providence, RI 02912

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Re: [phenixbb] autosol interface bug? selinux conflict?
by Kay Diederichs 10 Mar '10

10 Mar '10

Am 11.03.2010 07:00, schrieb phenixbb-request(a)phenix-online.org: > Message: 1 > Date: Wed, 10 Mar 2010 09:28:36 -0500 > From: Nathaniel Echols<NEchols(a)lbl.gov> > To: PHENIX user mailing list<phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] autosol interface bug? selinux conflict? > Message-ID:<E0B9BF9F-C96B-4F45-9D02-CC16197AFFF0(a)lbl.gov> > Content-Type: text/plain; charset=us-ascii > > On Mar 9, 2010, at 6:03 PM, Stuart Endo-Streeter wrote: >> After this repetitive route got autosol running, I ran into some kind of >> selinux security warning that blocked autosol and caused it to crash. I >> seem to have fixed that issue by switching temporarily to permissive mode, >> but disabling security to run phenix hardly seems the appropriate solution. >> I didn't manage to catch the autosol error message, I will try to recreate >> it later tonight if needed. > > SELinux breaks the Fortran binaries we distribute. There are two things to try: > > 1. If you installed to /usr/local, try installing to your home directory instead (if this is your computer rather than a shared system). For example: > > computer:~> ./install --prefix=/home/nat/software > > I don't know if this will help or not, but it's worth a try. I wonder - why do Fortran binaries give a SElinux problem, and C++ binaries don't? - does the phenix installer script treat (i.e. label) C++ binaries in any special way which cannot be done for other binaries? If it is known that SElinux is the problem, then this already half of the solution. In general, these problems can easily be found and fixed (on RedHat-derived distros at least) by labelling libraries and binaries in a specific way which is suggested by the output of the SEtroubleshoot- daemon (to be found in /var/log/messages). If that daemon doesn't run, you may have to install it with "yum install setroubleshoot-server". HTH, Kay

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python issues
by Patrick Loll 10 Mar '10

10 Mar '10

Hi, This is really a ccp4-provoked question, but it relates to phaser & cctbx (I think), so I'll try here as well: After an install of ccp4 on a MacBook Pro running Snow Leopard and on a MacPro running Leopard, the command: source /sw*/bin/init.csh (where /sw* is either /sw64 on the machine running 10.6, or /sw on the machine running 10.5) gives the error: ******************************************* Fatal Error: Incomplete libtbx environment! ******************************************* Please re-run the libtbx/configure.py command. If I go to ...ccp4.../src/phaser/phaser-2.1.4/libtbx/ and type python configure.py Then it tells me that the md5 module is deprecated, and that the cool kids use hashlib instead. Does this mean that I need to go to an earlier version of python? Will that mess up other things? Curiously, one machines giving this problem has python 2.5.1, while the other has 2.6. However, I currently have python 2.5.1 running on another machine (albeit with a slightly earlier version of ccp4) and it doesn't give me this problem. Ideas? Thanks, Pat --------------------------------------------------------------------------------------- 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

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Re: [phenixbb] autosol interface bug? selinux conflict?
by Nathaniel Echols 10 Mar '10

10 Mar '10

On Mar 9, 2010, at 6:03 PM, Stuart Endo-Streeter wrote: > Problem is, column labels are selected. "i_obs sigma" is showing in the > label field for each dataset. Clicking on the field to try to re-select > makes no difference, I still get the same error message. If I load just a > single anomalous dataset in addition to the native dataset, usually autosol > will run, sometimes not. It does not matter which anomalous dataset I am > using. If I load the native and only one of the anomalous datasets it > usually works. If I then repeat the process of adding a single anomalous > dataset, running autosol, aborting the run, then adding the next dataset, > eventually I can add all the datasets and start autosol. I'm not sure what to suggest, because I can't reproduce this (with 1.6 or the latest code), nor could I find anything in the code that indicates how it happens. Could you please send me a screenshot of the GUI before you click Run? > After this repetitive route got autosol running, I ran into some kind of > selinux security warning that blocked autosol and caused it to crash. I > seem to have fixed that issue by switching temporarily to permissive mode, > but disabling security to run phenix hardly seems the appropriate solution. > I didn't manage to catch the autosol error message, I will try to recreate > it later tonight if needed. SELinux breaks the Fortran binaries we distribute. There are two things to try: 1. If you installed to /usr/local, try installing to your home directory instead (if this is your computer rather than a shared system). For example: computer:~> ./install --prefix=/home/nat/software I don't know if this will help or not, but it's worth a try. 2. Install from source. This will take several hours, so if you have multiple cores we recommend adding the flag "--nproc=8" (or whatever) when you run the install script. If you have access to the Intel Fortran compiler we recommend installing and configuring that (I think the build script will switch to using it automatically), since g77/gfortran produce binaries that are *much* slower. This problem should go away in a few months when we purge the last FORTRAN code from PHENIX. -------------------- Nathaniel Echols Lawrence Berkeley Lab 510-486-5136 NEchols(a)lbl.gov

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autosol interface bug? selinux conflict?
by Stuart Endo-Streeter 09 Mar '10

09 Mar '10

Dear board... I am trying to run autosol with a native dataset and a mad experiment to extend the phases. Unfortunately I cannot even begin the actual process (without some weird convolutions) because phenix keeps giving the following message: "You must select a column label to use in each reflection file. If no labels are shown in the drop-down menu, it may not be a valid format." Problem is, column labels are selected. "i_obs sigma" is showing in the label field for each dataset. Clicking on the field to try to re-select makes no difference, I still get the same error message. If I load just a single anomalous dataset in addition to the native dataset, usually autosol will run, sometimes not. It does not matter which anomalous dataset I am using. If I load the native and only one of the anomalous datasets it usually works. If I then repeat the process of adding a single anomalous dataset, running autosol, aborting the run, then adding the next dataset, eventually I can add all the datasets and start autosol. After this repetitive route got autosol running, I ran into some kind of selinux security warning that blocked autosol and caused it to crash. I seem to have fixed that issue by switching temporarily to permissive mode, but disabling security to run phenix hardly seems the appropriate solution. I didn't manage to catch the autosol error message, I will try to recreate it later tonight if needed. My system is CentOS 5.4, gui is KDE, phenix is v1.6, installed just yesterday. Any suggestions/clues would be appreciated. Stuart Endo-Streeter ________________________________ Stuart Endo-Streeter, Ph.D Dept. Computer Science Duke University Medical Center 3245 French Family Sciences Building 919-660-4018 stuart.endostreeter(a)duke.edu

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anisotropic refinement water hydrogens and gui
by Christian Roth 09 Mar '10

09 Mar '10

Dear all, I did an anisotropic refinement with the gui for a 1.6 Ang. structure I think this is quite O.K. as the R-values seems to be reasonable(14/18.8). But for comparison I want exclude waters and hydrogens explicitly from the anistropic refinement. One could do this in the command line mode via adp.individual.anisotropic ="not water and not element H. I started from the gui and modified the .eff directly by icnluding: adp { individual { isotropic = None anisotropic = "not water and not element H" In the output pdb all waters have an anisou flag. So I assume phenix refined them anisotropically. How do I have to modify the .eff file to exclude the waters from the anisotropic refinement. I would like to use the gui, because you get this nice summary output with all statistics. Phenix started optionally anisotropic refinement at 1.7 Ang. As far as I understand one should keep in mind that the data to parameter ration should have certain value of app. 3 or 4. But restraints as paramters are not as solid as experimental data. Is this 1.7 Ang. borderline a rule of thumb, is there a strict rule at which point I could refine anisotropic, or maybe mixed isotropic anisotropic. Best regards Christian

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phenix.refine and multi-metals centers
by Carlos Frazao 09 Mar '10

09 Mar '10

Hi I have a doubt on the refinement of e doubled metal center. I know that: 1) one may fix the metals to their actual positions by using e.g. refine.sites.individual="not element Fe" 2) one may use "phenix.metal_coordination my.pdb" to obtain a dictionary for the actual metals coordinations but how does phenix.refine handels metal-to-metal interactions? How should one set the refinement of a metallo protein with a two metals centre, in order not to bias the final result (metal to metal distances) ? Thanks a lot, Carlos -- ************************************** Dr. Carlos Frazao Structural Biology Laboratory - Macromolecular Crystallography Unit ITQB-UNL, Av Republica, Apartado 127 2781-901 Oeiras, Portugal Phone: (351)-214469666 FAX: (351)-214433644 e-mail: frazao(a)itqb.unl.pt www.itqb.unl.pt

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molprobity todo list and coot integration in linux
by hari jayaram 09 Mar '10

09 Mar '10

Hi, Is a difference in the way the GUI molprobity TODO list is displayed between linux and Mac OSX . I am running 1.6.289 on both ...and have coot with scheme and python scripting installed, On mac OSX , phenix starts up coot with the molecule and maps loaded after a phenix.validate and a TO-DO list in a separate GUI window In Linux these separate To-do list windows dont seem to open . ..I have looked everywhere and the dont seem burried behind something else, Is there some setting I need to toggle to have these popup , sortable todo lists for molprobity assisted rebuilding on Linux systems? Thanks for your help Hari

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Autosol + MR
by Manoj saxena 07 Mar '10

07 Mar '10

Hi, I have partial solution from MR on a crystal with dimensions 52.729 60.364 142.908 90.00 90.00 90.00 P 21 21 21. I have SAD data from another crystal with dimension 53.860 61.470 142.492 90.00 90.00 90.00 P 21 21 21. My question is can I treat both as isomorphous and combine data from both of them and use my MR as model with Autosol. What is the maximum difference in unit cell dimensions allowed to consider two unit cell isomorphous? If you can point to some references/examples that will be highly appreciated. Thanks a lot. Marusa

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phenix.reduce segmentation fault with -trim option on Snow leopard Mac OSX
by hari jayaram 04 Mar '10

04 Mar '10

Hi I am running the phenix.reduce with the -trim option and getting a segmentation fault with phenix version 1.6.289 I will remove the molprobity introduced hydrogens using pdbtools ..but thought I will write in with this Thanks Hari $ phenix.reduce s3-3_2.1_refmac0-coot-15_refmac0FH.pdb -trim > s3-3_2.1_refmac0-coot-15_refmac0FnoH.pdb reduce: version 3.15 11/6/2009, Copyright 1997-2009, J. Michael Word Processing file: "s3-3_2.1_refmac0-coot-15_refmac0FH.pdb" Segmentation fault

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coot integration require coot with python?
by hari jayaram 03 Mar '10

03 Mar '10

Hi Is it likely that the phenix-coot integration with the new GUI requires a python infused coot ?. Although I have set the coot path correctly nothing happens after coot launches . I am using the ccp4 6.1.3 coot 0.6 (revision 2540) [with guile 1.8.3 embedded] and phenix 1.6.289 on OSX snow leopard 10.6.2. I know the ccp4 coot does not come with python scripting support ...the pymol integration seems fine , but coot just sits there with an empty window after a phenix.validate run. Any ideas on how to have them talking to each other? Thanks Hari

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autosol and NCS
by hli＠uci.edu 03 Mar '10

03 Mar '10

I have solved a structure by MR with Phaser. There are 4 copies of molecules per ASU. Parts of the search model are not agreeable with the new structure leading to messy density in some regions. Now a set of SAD data has been collected. I want to run Autosol (MRSAD) to combine the SAD and model phases, doing density modification including the NCS. Can I run simple_ncs_from_pdb to get the NCS operators from the MR solution pdb file and use them for Autosol? Thanks for help. Huiying UC Irvine

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