December 2011 - phenixbb - phenix-online.org

Problem with version 1.7.1-743 on OSX
by Miguel Ortiz Lombardía 06 Feb '12

06 Feb '12

Dear phenix developers, Last Friday (April 29) we upgraded phenix to its most recent version (1.7.1-743). Installation went smoothly on both Mac (10.6.7 64-bit) and Linux (Ubuntu 10.10 64-bit) machines. However, we observe that we cannot use phenix.refine (I don't know for the rest of the applications) from the GUI on the Macs. phenix.refine does work from the command line, though. So, whenever we try to add a pdb in the GUI, we get this error message: This application does not support the file type for /path/to/the/file.pdb (format: txt) If we try to open an mtz, it sometime works, but most often we get: PHENIX did not recognize the file type for /path/to/the/file.mtz! and on the terminal from where the GUI was started we can find: **SYMMETRY OPERATOR ERROR** Error in interpreting symop " X+2/3, Y+1/3, Z+1/3 " **SYMMETRY OPERATOR ERROR** Error in interpreting symop " -Y+2/3, X-Y+1/3, Z+1/3 " (and so on, so forth). Any clues ? Best regards, -- Miguel Architecture et Fonction des Macromolécules Biologiques (UMR6098) CNRS, Universités d'Aix-Marseille I & II Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France Tel: +33(0) 491 82 55 93 Fax: +33(0) 491 26 67 20 mailto:[email protected] http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

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Chirality of Ribityl chain of FMN inverted
by Yuri 09 Jan '12

09 Jan '12

Hello Developers, When I built Ligand restraints using eLBOW, my resulting .pdb had an inverted chiral center in the ribityl chain of the flavin mononucleotide particularly C4'. In the database the ligand had an S configuration (correct), but after minimization and restraint generation the output had R configuration at that particular center. I wonder if there is a way to enforce the configuration for each center, although I suspect it could be a little bug, because I noticed my restraints have that center annotated as S eventhough it is R in the actual .pdb Cheers, -- Yuri Pompeu

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whether my following data are acceptable
by Dialing Pretty 02 Jan '12

02 Jan '12

Dear All, Following is the data range of my x-ray statistics by resolution bin: FOM between 0.84 to 0.86 Phase error between 17.90 to 24.14 scale factor from 0.88 to 1.07 SigmaA from 0.85 to 0.95 #work from 2688 to 2922 #test from 133 to 157 Do these data are within the acceptable range? Cheers, Dialing

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reference model restraints
by Ursula Schulze-Gahmen 24 Dec '11

24 Dec '11

I am refining a 3.1 A structure and are trying to use model restraints for this. There are 3 molecules in the asymmetric unit of my structure. I input the high resolution structure of one molecule of the reference structure to create restraints during the refinement. From looking at the log file, it seems to me that the reference structure is aligned to only one of my molecules, but not the other 2. How can I make sure the restraints are valid for all 3 molecules. Ursula -- Ursula Schulze-Gahmen, Ph.D. Assistant Researcher UC Berkeley, QB3 356 Stanley Hall #3220 Berkeley, CA 94720-3220

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eLBOW generates Mogul geometries
by Nigel Moriarty 23 Dec '11

23 Dec '11

Folks For a few weeks now eLBOW has been able to generate Mogul geometries. If you have CCDC's mogul installed and accessible at the command-line, eLBOW can request Mogul provide an experimentally accurate geometry. Simply use the --mogul option at the command-line and eLBOW will query Mogul for the geometry to use to generate a restraints file and a PDB file. Stay tuned for more details in the Computational Crystallography Newsletter. Happy Holidays, Merry Christmas and Happy New Year 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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partial model in autobuild?
by Yarrow Madrona 21 Dec '11

21 Dec '11

Hello, I would like to use autobuild to start from a partial model. I have done Phaser EP with phases from MR. I can see the fourth molecule but it is not well defined and I am not exactly sure where to place it. Is it possible to run autobuild from the partial model to fill in the fourth model? Thanks. -Yarrow -- Yarrow Madrona Graduate Student Molecular Biology and Biochemistry Dept. University of California, Irvine Natural Sciences I, Rm 2403 Irvine, CA 92697

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Re: [phenixbb] Reflection file woes phenix/ccp4/PDB
by Machius, Mischa Christian 20 Dec '11

20 Dec '11

Robbie, Yes, the thought that the anomalous R free flags could have something to do with it occurred to me as well, so I checked. As far as I can see, the test reflections are evenly distributed between the + and - sets; they were not selected from the + or - set only. For the vast majority of the test reflections, both Bijvoet mates were measured and both were flagged properly. For some, however, only one Bijvoet mate was measured and flagged. It probably wouldn't do any harm to consolidate the test flags, discarding the few with only one measured Bijvoet mate, but I really don't see why it should be necessary to do so. For now, I have converted the reflection file into the CNS format and sent to the PDB, hoping that they will be able to deal with that one properly. Bit surprised though that no one has run into that problem before. Thanks for your suggestion. MM On Dec 16, 2011, at 3:54 AM, Robbie P. Joosten wrote: > Hi Mischa, > > Your mtz file seems to contain 'anomalous' free R-flags (that is what I gather from Pavel's post). This is kind of weird. Do you really want I+ in the work set and I- in the test set? That would bias your R-free. If the two flags match (which I really hope), then you can leave one column out before you (re)deposit your data. This will hopefully solves the problem. > > Cheers, > Robbie Joosten > > Netherlands Cancer Institute > > On 12/15/2011 05:40 PM, Machius, Mischa Christian wrote: >> Y'all, >> >> While depositing a structure, the PDB 'complained' about my structure-factor file, saying they don't contain R-free flags or are otherwise incomplete. The comment was prompted by their Refmac R-factor test failing. >> >> The structure-factor file I submitted came from phenix.refine (xxx_data.mtz). I am using version 1.7.3-928. >> >> Indeed, using this file in CCP4 fails with the message: >> "CCP4MTZfile: Mtz column type mismatch: I-obs(+) K-J CCP4MTZfile: Mtz column type mismatch: SIGI-obs(+) M-Q" >> >> The file contains anomalous data. I have no problems with files that do not contain anomalous data. >> >> Needless to say that Phenix uses the structure-factor file just fine when reading it back into, say, its validation utility. >> >> When I use iotbx.reflection_file_reader, I cannot detect any anomalies. >> >> I am at a loss as to how to resolve this issue. I would like to deposit the data as prepared by Phenix so that the PDB tools can use them. >> >> Anybody ran into this issue before? Any ideas for how to resolve it? >> >> Many thanks in advance! >> >> MM >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb

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Failure in installing Phenix-1.7.3
by arka chakraborty 20 Dec '11

20 Dec '11

Hi all I am facing a problem while installing phenix 1.7.3 on Redhat Enterprise 5 OS. I have tried with fedora 3 binary as instructed in the download page and also with others but nothing works. I have tried installing from the root. Every time the error log is states that GLIB 2.4 is unavailable which is required by user/local/.. Please help! Thanks in advance, ARKO -- *ARKA CHAKRABORTY* *CAS in Crystallography and Biophysics* *University of Madras* *Chennai,India*

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SF-Tool check
by Dialing Pretty 19 Dec '11

19 Dec '11

Dear All, I have done the SF-Tool check for my protein crystal structure, and the result is as following. My 3 questions are (1) What does the following mean and how to solve the problem "Error! No labels are written for MTZ to mmCIF conversion Structure factor conversion is done?" (2)Where there is no "Calculated phenix R_factor(all data)"? (3) Where there is no "Correlation (Fo-Fc)"? I am looking forward to getting your reply. Dialing Error! No labels are written for MTZ to mmCIF conversion Structure factor conversion is done. Header of the mtz file can be seen from here Click here to see the converted mmCIF file Checking Xray Data by PHENIX (model_vs_data) ... PHENIX (model_vs_data) is done. Checking structure factor quality ... PHENIX.xtriage is done. Summary of Results (XXXX : ) Reported PHENIX Calculated phenix High resolution 2.829 2.83 Low resolution 50.937 50.94 Number of Reflection17446 17446 Completeness 99.98 100.0 R_factor (all data) 0.2134 ? R_factor (work set) 0.2106 0.2093 R_free 0.2668 0.2667 Correlation (Fo-Fc) ? ?

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Prevent MacPyMOL from registering as a valid pdb/pml/etc viewer.
by Francis E Reyes 19 Dec '11

19 Dec '11

Hi phenix developers I just installed 1.7.3-928. Apparently, OS X thinks the internally distributed pymol is my preferred pdb viewer (as opposed to my more recent build in /Applications). This may have something to do with the Info.plist registering document types. A small change in Finder for the user, but it was quite maddening to figure out why I had opened a pdb and pseudoatom was not working. Can future builds keep the internally distributed pymol as walled in as possible? Thanks! F --------------------------------------------- Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

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