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Re: [phenixbb] Phenix version 1.7-650 and coot - SOLVED!
by Leonid Flaks 01 Feb '11

01 Feb '11

On 02/01/2011 04:20 AM, phenixbb-request(a)phenix-online.org wrote: > Message: 11 > Date: Mon, 31 Jan 2011 16:37:14 -0800 > From: Nathaniel Echols<nechols(a)lbl.gov> > To: PHENIX user mailing list<phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] Phenix version 1.7-650 and coot > Message-ID: > <AANLkTim6ux3V6FcfhXr_0vhNf2P9GWXfBh3aexbZcZ41(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > On Fri, Jan 28, 2011 at 8:00 AM, Leonid Flaks<flaks(a)bnl.gov> wrote: >> > Hi! >> > I just installed phenix version 1.7-650 on fedora 14 64-bit and noticed that >> > if I start coot from within phenix interface, most of the icons on the right >> > hand side of the coot window are not displayed. >> > There is a lot of messages like this: >> > >> > Error loading icon: Couldn't recognize the image file format for file >> > '/usr/share/coot/pixmaps/residue-info.png' > Okay, apparently we missed an important environment variable in the > script that launches Coot from Phenix - several library paths need to > be cleansed to prevent conflicting with the libraries we distribute. > The one we didn't know about (because it never caused problems before) > appears to be XDG_DATA_DIRS. The crude fix for this is to edit > $PHENIX/phenix/phenix/command_line/start_coot.sh and add this line at > the end of a list of "unset" commands: > > unset XDG_DATA_DIRS > > It'll be fixed in the next build too. If this doesn't totally solve > the problem, let me know - I'm going to unset several other paths too, > but those didn't appear to have any effect on our Fedora 14 machine. > > -Nat Nat, Just to confirm - your fix worked! Thank you very much, Leon -- Leonid Flaks Phone: (631) 344-2682 Fax : (631) 344-2741

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(no subject)
by Shuchi 01 Feb '11

01 Feb '11

hello, i have solved one structure and after solving the average B factor of the model is 107 and average B factor from wilson plot of DATA is 85.5 . is this fine or i did some wrong while fitting and refinement. resolution is 3.0 Angstroms . -- vandana kukshal CSIR-senior research fellow X ray lab ,MSB division central drug research institute lucknow

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Phenix version 1.7-650 and coot
by Leonid Flaks 31 Jan '11

31 Jan '11

Hi! I just installed phenix version 1.7-650 on fedora 14 64-bit and noticed that if I start coot from within phenix interface, most of the icons on the right hand side of the coot window are not displayed. There is a lot of messages like this: Error loading icon: Couldn't recognize the image file format for file '/usr/share/coot/pixmaps/residue-info.png' for png and svg files in the console window. I can see all of the icons if I start coot directly. I am using coot version 1.6.2-pre1 rev 3213 which is installed on 64-bit fedora 14 as a rpm file. I did not see this issue on a phenix version 1.6.4-476 with the same version of coot. Thanks, Leon -- Leonid Flaks Phone: (631) 344-2682 Fax : (631) 344-2741

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phenix.mr_rosetta paths
by Ben Eisenbraun 31 Jan '11

31 Jan '11

Hi, I'm testing Rosetta 3.2+PHENIX 1.7-650, and in the phenix.mr_rosetta output, I see: Checking rosetta paths: rosetta binary: /programs/l/rosetta/3.2/rosetta_source/bin/mr_protocols.default database_dir: /programs/l/rosetta/3.2/rosetta_database script_dir: /programs/l/rosetta/3.2/rosetta_source/src/apps/public/electron_density pilot_script_dir: /programs/l/rosetta/3.2/rosetta_source/src/apps/pilot/frank/ In the script directory, the C++ files were not built along with the regular Rosetta build. Do those need to be compiled for the target platform? Also, the pilot_script_dir is empty. Is there supposed to be something in there? Thanks. -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |

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translation/rotation matrix
by Yogesh Gupta 31 Jan '11

31 Jan '11

Dear PhenixBB members, I calculated two maps one using 3 wavelengths Se to 4.2A, and 3 wavelength Ta to ~3.9A for ~100kDa protein in space group P62 with 1 molecule in A.U. These crystals are non-isomorphous. Ta MAD map is better than Se MAD map. There is no model available at this point. Is there a way to transform Se sites accurately to the Ta map? Thanks for your help. Yogesh -- -------------------------------------------------- Yogesh K. Gupta, Ph.D. Dept of Structural & Chemical Biology Mount Sinai School of Medicine Icahn Medical Institute 1 Gustave L. Levy Place, Box 1677 New York, NY, USA 10029 Tel:+1 212-659-8639 --------------------------------------------------

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Re: [phenixbb] Phenix version 1.7-650 and coot
by Leonid Flaks 31 Jan '11

31 Jan '11

On 01/29/2011 03:00 PM, phenixbb-request(a)phenix-online.org wrote: > Message: 1 > Date: Fri, 28 Jan 2011 12:09:01 -0800 > From: Nathaniel Echols<nechols(a)lbl.gov> > To: PHENIX user mailing list<phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] Phenix version 1.7-650 and coot > Message-ID: > <AANLkTini0jaSAh9KKv1xZGbtE4ABtdU2_G5KMxWP0c4p(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > On Fri, Jan 28, 2011 at 8:00 AM, Leonid Flaks<flaks(a)bnl.gov> wrote: >> I just installed phenix version 1.7-650 on fedora 14 64-bit and noticed that >> if I start coot from within phenix interface, most of the icons on the right >> hand side of the coot window are not displayed. >> There is a lot of messages like this: >> >> Error loading icon: Couldn't recognize the image file format for file >> '/usr/share/coot/pixmaps/residue-info.png' >> >> for png and svg files in the console window. I can see all of the icons if I >> start coot directly. I am using coot version 1.6.2-pre1 rev 3213 which is >> installed on 64-bit fedora 14 as a rpm file. I did not see this issue on a >> phenix version 1.6.4-476 with the same version of coot. > Could you please send me the complete console output from Coot under > these conditions: > > a) when launching from Phenix 1.7 > b) when launching from Phenix 1.6.4 > c)when launching from the command line? > > Very little has changed in the Coot-related parts of Phenix since > 1.6.4, so I'm not sure how it's possible for one to work but not the > other. In the past, errors like this were due to conflicts with the > shared libraries distributed with Phenix, but we largely reset the > environment when starting Coot to avoid the problem, and I'm pretty > sure we started that a year and a half ago. > > thanks, > Nat > Nat, first of all - my apologies for the incorrect report. It turned out this problem exists in phenix 1.6.4 under fedora 14 also - just nobody noticed it on the current setup! Fedora 14 is about 2 month old and we are coming out of the winter shutdown. We had a mixture of fedora 12 and 13 before and did not see that problem. Of course, python version has been changed to python-2.7 for Fedora 14. Console output for all 3 conditions are saved. I'll mail them to you directly - I don't want to flood the list. Thanks, Leon -- Leonid Flaks Phone: (631) 344-2682 Fax : (631) 344-2741

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cis peptides
by Timothy Springer 30 Jan '11

30 Jan '11

Is there an easy way to specify unwanted cis-peptides and remove them in refinement or with torsion dynamics or SA? Tim

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Re: [phenixbb] Global refinement parameters - use statistical model for missing atoms
by Joseph Noel 30 Jan '11

30 Jan '11

Hi Pavel! Thanks for the reply. It does seem to be working though in the current version as long as I choose advanced level in the gui. Does it make sense though that it is lowering my Free-R? Also, the upshot is that the Fo-Fc maps are much flatter. I can see waters to build but only in the 2Fo-Fc sigmaa weighted maps so it does certainly seem to be doing something. Anyway, I look forward to the docs on it when you officially release it. Seems useful! Best- Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

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selection string for omit maps
by Alexandra Deaconescu 28 Jan '11

28 Jan '11

Hi: I am new to Phenix and I am currently using the GUI. I would like to compute a sa-omit map by leaving out residues 204-209 of my chain C. In the GUI, what is the proper syntax for this selection string? I tried a few obvious formats but the jobs failed. Thank you very much in advance, Alexandra ----- Original Message ----- From: phenixbb-request(a)phenix-online.org To: phenixbb(a)phenix-online.org Sent: Tue, 25 Jan 2011 15:00:01 -0500 (EST) Subject: phenixbb Digest, Vol 62, Issue 25 Send phenixbb mailing list submissions to phenixbb(a)phenix-online.org To subscribe or unsubscribe via the World Wide Web, visit http://phenix-online.org/mailman/listinfo/phenixbb or, via email, send a message with subject or body 'help' to phenixbb-request(a)phenix-online.org You can reach the person managing the list at phenixbb-owner(a)phenix-online.org When replying, please edit your Subject line so it is more specific than "Re: Contents of phenixbb digest..." Today's Topics: 1. Problem with loop fitting (Kendall Nettles) 2. Re: Problem with loop fitting (Tom Terwilliger) 3. Re: Problem with loop fitting (Kendall Nettles) 4. Ligandfit bug report (Kendall Nettles) 5. Re: Ligandfit bug report (Nigel Moriarty) 6. ADP: fix_wxu and wxu_scale (fulvio saccoccia) 7. Re: Problem with loop fitting (Tom Terwilliger) 8. Re: ADP: fix_wxu and wxu_scale (Pavel Afonine) 9. Re: adp values (Pavel Afonine) ---------------------------------------------------------------------- Message: 1 Date: Mon, 24 Jan 2011 15:47:02 -0500 From: Kendall Nettles <knettles(a)scripps.edu> To: PHENIX user mailing list <phenixbb(a)phenix-online.org> Subject: [phenixbb] Problem with loop fitting Message-ID: <C9634F76.F559%knettles(a)scripps.edu> Content-Type: text/plain; charset="iso-8859-1" Dear PHENIX developers, I am trying fit_loops for the first time and getting error message: "No suitable gap found matching residues" I'm not sure what the problem is. Best regards, Kendall Nettles knettles$ phenix.fit_loops pdb_in=Liganded_overall_best-coot-1.pdb mtz_in=cycle_best_refine_map_coeffs_1.mtz seq_file=seq.dat start=331 end=336 chain_id=A # fit_loops # # Fit loops in a PDB file with gaps # Type phenix.doc for help Input sequence file is seq.dat Reading sequence from seq.dat Fit_loops: Fit a missing loop in a model. Map from: TEMP_cycle_best_refine_map_coeffs_1.mtz using labin FP=2FOFCWT PHIB=PH2FOFCWT Model from: Liganded_overall_best-coot-1.pdb LABIN LINE: FP=2FOFCWT PHIB=PH2FOFCWT No suitable gap found matching residues 331 - 336 chain: A No final model obtained

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Global refinement parameters - use statistical model for missing atoms
by Joseph Noel 28 Jan '11

28 Jan '11

Hi All, Does it make sense that when the box for "use statistical model for missing atoms" is picked under the GUI's "Global refinement parameters options" that one might obtain "better" Free-R values? I seem to be seeing that for a 2.3 A refinement of a crystal with a monomer of 550 residues in the asymmetric unit and 68% solvent content. When I uncheck the box I get about a 3% increase in Free-R. Is there more information about what this option is actually doing and when it might be useful to employ? Joe ___________________________________________________________ Joseph P. Noel, Ph.D. Investigator, Howard Hughes Medical Institute Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics The Salk Institute for Biological Studies 10010 North Torrey Pines Road La Jolla, CA 92037 USA Phone: (858) 453-4100 extension 1442 Cell: (858) 349-4700 Fax: (858) 597-0855 E-mail: noel(a)salk.edu Web Site (Salk): http://www.salk.edu/faculty/faculty_details.php?id=37 Web Site (HHMI): http://hhmi.org/research/investigators/noel.html ___________________________________________________________

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