October 2011 - phenixbb - phenix-online.org

Problem with version 1.7.1-743 on OSX
by Miguel Ortiz Lombardía 07 Feb '12

07 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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AutoBuild Question
by Page, Rebecca 13 Dec '11

13 Dec '11

Dear phenix community: I ran AutoBuild.dat with a seq.dat file that has 3 separate sequences. Chains A and B were built, but chain C was not, even though there is density for the third chain. It occurred to me that only two of the three chains may have been read in. I seem to recall that seq.dat can be a maximum of two sequences, but am not sure. So, is there a limit to the number of sequences that can be present in seq.dat and if so, what is the limit. Thanks in advance, Rebecca

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Molecule and maps will not load into coot from Phenix 1.7.1-743
by Jobichen Chacko 01 Nov '11

01 Nov '11

The same old problem, I tried to add the coot path using preferences. Coot version result: COOT_PREFIX is /usr/local /usr/local/bin/coot-real --version 0.6.1 (revision 2740) [with guile 1.8.7 embedded] [with python 2.6.0 embedded] The coot opens just after phenix-refine job starts and after the job finishes. But no maps and models are loaded. Thanks. Jobi

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"ATP" monomer in phenix_refine
by Zhang yu 29 Oct '11

29 Oct '11

Hi, I had a trouble of refining "ATP" in Phenix. I appreciate any help. ATP with tri-phosphate is in the 5' end of RNA chain. It is added to the RNA chain in coot as a monomer "ATP", and it could be connected to the downstream base after I changed the "_chem_comp.group" option to "RNA" in the cif file. But when I refine the model in Phenix, Phenix treated the "ATP' as a monomer and didn't connect it to the downstream base. I tried two ways to solve it 1. Add the the modified (chang the "_chem_comp.group" option to "RNA") cif file in phenix_refine, but Phenix doesn't recognize it. 2. In REEL, I found phenix has its own cif file for ATP, but the its header couldn't be edited. Any suggestions? Thanks. Yu

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Problem avoiding real space refinement
by Jerome Nwachukwu 28 Oct '11

28 Oct '11

Hi: We noticed that in some of our refinements, real space refinement was performed even though we chose not to do this. I tried to opt out of real space refinement as follows: " refine { strategy = *individual_sites individual_sites_real_space rigid_body \ *individual_adp group_adp *tls *occupancies group_anomalous ..." however, the R-free is identical whether we select real space refinement or not, and the logfile shows " Validate: |--------START--------| |--------FINAL--------| residue map_cc 2mFo-DFc mFo-DFc map_cc 2mFo-DFc mFo-DFc "LYS A 18 " 0.9359 16.78 0.00 0.9107 17.60 0.00 "ARG A 19 " 0.9513 21.82 0.00 0.9470 20.97 -6.52 <<< "ARG A 26 " 0.9440 26.72 0.00 0.9474 27.33 -2.43 "ARG A 69 " 0.9685 31.36 0.00 0.9659 32.58 0.00 "GLN A 86 " 0.9681 23.57 -5.81 0.8850 19.29 -18.27 <<< "GLU A 89 " 0.9689 26.30 -4.43 0.8977 23.67 -11.59 <<< "LYS A 93 " 0.9746 25.19 0.00 0.9682 26.47 2.90 ... " and suggesting that real space refinement was performed. Is there a way to correct this, or to ensure that real space refinement is not performed during refinement? Thank you, -Jerome Jerome C. Nwachukwu, PhD Dept. of Cancer Biology The Scripps Research Institute-Florida

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problem to add D atom on carbonyl group (enol) as alternate conformation
by Maxime Cuypers 27 Oct '11

27 Oct '11

Dear all, i have a problem that i block on for quite a while. i need to add a D atom on carbonyl group (enol) as alternate conformation to a main chain protein amide group to refine with phenix.refine. It is not something that the program phenix.reduce can perdeuterate as it is an unusual position. it actually perdeuterates all the rest of the protein successfully. Does anyone have an idea how to proceed? i tried so far to rename the residue and give .cif restraints generated with readyset for the new tautomer. phenix seemed to recognised it but it failed due to the fact it does not recognise the residue as being a residue to link to the other residues and bounds bounce off. A friend told me a cif_link was the problem. Then i tried to apply cif_modification in a parameter file with the corresponding .cif file as explained briefly on: http://www.phenix-online.org/documentation/refinement.htm#anch88 it does not solve the problem. the link between the new tautomer residue and the rest of the residues does not occur in refinement. Thanks for your help in advance. i am getting deseperate. Maxime

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exploring the conformational space of sidechains
by Francois Berenger 27 Oct '11

27 Oct '11

Hello, Is there a way to do this with Phenix? I.e., from a given model, obtain models with different but also reasonable sidechains conformations. N.b.: I don't have X-ray data so I am looking for a geometric thing, and I'm OK if the model's backbone undergoes some small movement because of the sidechains having moved. Thanks a lot, F.

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Molecule and maps will not load into coot from Phenix 1.7.1-743
by Yuri 27 Oct '11

27 Oct '11

Read the thread I waas just a part of maybe it is related -- Yuri Pompeu

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Re: [phenixbb] COOT not "connected" to PHENIX
by Yuri 26 Oct '11

26 Oct '11

I installed the version with python embedded in coot And it works!! Thanks a lot!! On Tue, 25 Oct 2011 11:41:38 -0700, Nathaniel Echols wrote: > On Tue, Oct 25, 2011 at 11:40 AM, Yuri <yuri.pompeu(a)ufl.edu> wrote: >> Now here comes the stupid question... >> How do I fix it? >> Install a different coot version or is it something in my >> architecture? > > Install a different Coot. If you're downloading from Paul Emsley's > page, you need a package with "python" in the file name. I have no > idea whether the Linux binaries distributed by CCP4 have Python or > not > (the Mac version definitely does). > > -Nat -- Yuri Pompeu

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