- phenixbb - phenix-online.org

AutoBuild help
by Timothy C. Umland 18 Aug '09

18 Aug '09

I am new to running the AutoMR and AutoBuild Wizards, and I am having a problem getting AutoBuild to run. I have run AutoMR and it appeared to run fine, yielding a solution. However, when it did the default hand-off of the MR solution to AutoBuild, AutoBuild crashed. I then tried to run AutoBuild by itself, using the MR solution as the input model. Again, AutoBuild crashed. The error was the same in both cases. I was running AutoMR and AutoBuild from the command line. I am running Phenix version 1.4-3 on an Intel Mac (OS X 10.5.8). The AutoBuild error was **************************************************************************** **** Failed to carry out AutoBuild_build_cycle: child process stderr output: command: 'csh /AutoBuild_run_3_/TEMP0/RUN_FILE_1' sort: invalid option -- 4 Try `sort --help' for more information. **************************************************************************** **** I tried the suggested "sort --help", but at least to me it wasn't helpful. I am guessing that I have some incompatibility with my local installation of "sort" and Phenix? Any help is appreciated. Thanks, Tim

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1-2 October: What is a Macromolecular Complex ? meeting at the NKI, Amsterdam
by Anastassis Perrakis 18 Aug '09

18 Aug '09

Dear all, This is a reminder and some news for the meeting: "What is a macromolecular Complex? Shades of Meaning Across Cellular, Systems, and Structural Biology" http://xtal.nki.nl/Oct2009 - Registration closes on Monday 7th September at 12:00 noon. No exceptions after the deadline. - There will be eight (8) fellowships for attending the meeting, 500 Euro (max) each (*) Best regards on behalf of the organizers, Tassos (*) Only available if your lab is NOT part of the EU programs that support the meeting (SPINE-2-Complexes, TEACH-SG, 3D-Repertoire) and you really wanted to attend but could not for financial reasons, but 500 Euro will make it possible for you to join us, please email a.perrakis.AT.nki.nl with a short motivation and research interests, 10-15 lines max (no attachments please, simple text). Preference will be given to people not yet registered, since we might well assume that people that already registered had the money already sorted. The amount is the MAXimum available per person for ALL expenses, and it will be reimbursed after the meeting, *** based on receipts ***!

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Re: [phenixbb] Error in running Autosol....
by Thomas C. Terwilliger 15 Aug '09

15 Aug '09

Hi Karthikeyan, I'm sorry for the trouble! I see that you are running the very latest phenix from last night. This version passed our automated tests and it appears fine in general. Somehow the solve scaling step is not working in your run. I haven't seen this happen before, but my guesses are: 1. I have been making small changes in the autosol printout and it is possible that there is a place where solve is printing something out and the format does not match the variable type, and I didn't catch it in our tests. If this is the case you should be able to find it by running from the command-line and adding the keyword debug=true and it should print out a clearer error message for you that you can send me. You can run from the command line in the same place you ran from the GUI by saying phenix.autosol autosol.eff debug=True because the GUI writes out autosol.eff when it runs, saving your inputs. Then you can override those values by putting debug=True on the command line. Other less-likely possibilities: 2. your input datafiles are of a type that was unexpected (normally .sca, .mtz are fine, but perhaps the columns in an mtz are unusual). 3. Your structure is very large or high-resolution. 4. Something is unusual in your setup so that not much memory is available. If none of these helps, you are welcome to send me the files and I'll check it out. All the best, Tom T >> Dear All, >> >> I am using phenix-1.4-138 in RHEL5 Xeon-64 bit workstation. >> >> I am trying to solve a structure of Se-Met through phenix.autosol_gui. >> Once the >> programs starts it goes to several stages including converting from mtz to >> sca, >> xtriage and so on. >> Finally it gives an error message as follows: >> >> ******************************************************************************** >> Failed to carry out AutoSol_scale_and_analyze_mad: >> >> None of the solve versions worked >> See overall log file and also solve log file (in AutoSol_run_2_/LAST.LOG) >> ******************************************************************************** >> I found the LAST.LOG file is empty. >> >> I am trying to find out what could be problem? Any suggestions or help is >> much >> appreciated! >> >> Thanking you >> >> S.Karthikeyan >> >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >>

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Re: [phenixbb] low resolution data/parameter ratio
by Pavel Afonine 14 Aug '09

14 Aug '09

Hi Gerwald, > Two more quick questions: > how would you identify the best strategy? I would look at Rfree and Rfree-Rwork, and maps of course. To help in deciding what are the "good / reasonable" values, use POLYGON (Acta Cryst. D65, 297-300 (2009)) (phenix.polygon), local real-space correlation (phenix.real_space_correlation). I think Nat bundled them all into his magic tool called phenix.validation with will do this and more (it is GUI based). > I would aim for the lowest number of parameters with reasonably low > Rfree? Yes, this sounds right in general. > Does phenix report the total number of parameters refined anywhere in > the log? It's trivial and not at the same time (at least the way I understand it, of course I might be very wrong). It's trivial to compute the number of refinable parameters given the strategy you choose, but how you will count the restraints which are kind of quasi-observables, and what about weight that if chosen too strong so it can turn the restraints into quasi-constraints? Pavel.

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low resolution data/parameter ratio
by gerwald jogl 14 Aug '09

14 Aug '09

Hi All, I am struggling with low resolution data (3.6 A) and I am concerned about overfitting. I have a ratio of about 3 reflections per atom. Possible refinement scenarios would be a) coordinates+tls, b) coordinates, group_adp, tls or c) coordinates, individual_adp, tls. The last scenario seems to be pushing the limits. I wonder if there are studies, thoughts or opinions out there on which refinement scenario to use. Thanks for any comment on this, Gerwald

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adding sutrates in phenix.refine
by Rune wederkinck Andersen 14 Aug '09

14 Aug '09

Hi everyone I'm running a refinement in phenix.refine. I'm now trying to ad two subtrates AMP and RP5. The phenix.refine seams to reconise AMP but not the RP5 molecules. It seams as if this molecules is well known for the program (phenix-1.4-3/ext_ref_files/chemical_components/r/data_RP5.cif). In my PDB file the two molecules are described like this: ... HETATM 19 C6 AMP A 301 35.852 19.986 36.427 1.00 22.32 A HETATM 20 N6 AMP A 301 35.448 19.736 37.693 1.00 24.44 A HETATM 21 N7 AMP A 301 36.400 17.540 35.616 1.00 23.01 A HETATM 22 C8 AMP A 301 36.853 17.097 34.416 1.00 21.98 A HETATM 23 N9 AMP A 301 37.034 18.126 33.560 1.00 19.84 A HETATM 1 P' RP5 A 302 30.291 24.910 31.815 0.25 10.66 A HETATM 2 C5' RP5 A 302 32.348 25.416 30.301 0.25 14.76 A HETATM 3 O5' RP5 A 302 31.481 24.448 30.868 0.25 12.67 A HETATM 4 C4' RP5 A 302 33.260 24.753 29.307 0.25 15.58 A HETATM 5 C3' RP5 A 302 33.017 25.227 27.872 0.25 15.17 A HETATM 6 O3' RP5 A 302 33.951 26.264 27.522 0.25 14.15 A HETATM 7 C2' RP5 A 302 33.282 23.935 27.083 0.25 16.11 A HETATM 8 O2' RP5 A 302 34.571 23.963 26.478 0.25 13.68 A HETATM 9 C1' RP5 A 302 33.351 22.848 28.160 0.25 16.92 A HETATM 10 O1' RP5 A 302 32.775 23.415 29.296 0.25 16.62 A HETATM 11 O1 RP5 A 302 32.631 21.639 27.867 0.25 20.12 A HETATM 12 O1X RP5 A 302 29.112 25.373 30.809 0.25 10.53 A HETATM 13 O2X RP5 A 302 29.912 23.844 32.781 0.25 10.59 A HETATM 14 O3X RP5 A 302 30.793 26.258 32.567 0.25 9.63 A ATOM 1 N MET B 1 63.305 2.511 45.667 1.00 64.80 B ATOM 2 CA MET B 1 62.528 3.463 46.463 1.00 68.29 B ATOM 3 C MET B 1 62.555 4.863 45.882 1.00 65.73 B ATOM 4 O MET B 1 63.607 5.325 45.446 1.00 64.47 B ... I have tried with phenix.elbow as well but didn't work... Please help... Rune _________________________________________________________________ More than messages–check out the rest of the Windows Live™. http://www.microsoft.com/windows/windowslive/

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Running Autobuild after Autosol
by Katya Heldwein 14 Aug '09

14 Aug '09

Hi, how do I specify running Autobuild after Autosol, in the command line mode? I see the "phenix.autobuild after_autosol" option in the manual, but how will Autobuild know which Autosol run to use? Katya -- Ekaterina Heldwein, Ph.D. Assistant Professor Department of Molecular Biology and Microbiology Tufts University 136 Harrison Ave Boston, MA 02111 phone: 617-636-0858 fax: 617-636-0337 e-mail: katya.heldwein(a)tufts.edu

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CC beamtime application deadline this saturday
by Banumathi Sankaran 14 Aug '09

14 Aug '09

Dear Users, The deadline for October/November/December 2009 Collaborative Crystallography proposals will be August 15, 2009. Thumbnail Description: 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/independinvest.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 "Do you want collaborative crystallography (beamline 5.0.1 or 5.0.2 only ?) * In question 9, please describe a specific research project with a clear end point. In order to request CC time for October/November/December 2009 allocation period, proposals must be submitted by August 15, 2009. Please note that the ALS will be shut down in September, 2009. The deadline for CC proposals for the time period January/February 2010 will be November 15, 2009. Regards, Banumathi Sankaran

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Re: [phenixbb] phenix.refine special positions
by Ralf W. Grosse-Kunstleve 13 Aug '09

13 Aug '09

Hi Simon, To add to the previous answers, note that phenix.refine currently doesn't work well if you want to allow symmetry copies of your ligands to overlap. If you move to individual coordinate refinement you have to fix such ligands; i.e. it won't automatically repair bonds distorted by rigid-body refinement. Removing this limitation is on my to-do list. Ralf

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phenix.refine special positions
by Simon Kolstoe 13 Aug '09

13 Aug '09

Dear Pavel et al. Is there any way of defining a residue for rigid body refinement if a couple of the atoms are sitting on a symmetry axis? i.e. can I define the rigid body to be chain L but not the atoms that are giving the problems? I keep on getting the error: ================== Extract refinement strategy and selections ================= Some atoms selected for rigid body refinement are in special positions (listed below). Please remove these atoms from the rigid body selection and run refinement again. "ATOM 4 C4 A12 L 2 .*. C " Sorry: Atoms at special positions are within rigid groups. Thanks, Simon

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Shake
by esmael 13 Aug '09

13 Aug '09

Hi, Would be possible to only add "Shake" to the side-chain atoms during the refinement with Phenix? Thanks, Esmael

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phenix.xtriage says that entire res range contains anomalous signal but chart says differently?
by Francis E Reyes 13 Aug '09

13 Aug '09

Hi all I ran xtriage on my dataset to 4.5.here's the relevant section pertaining to anomalous signal Analyses of anomalous differences Table of measurability as a function of resolution The measurability is defined as the fraction of Bijvoet related intensity differences for which |delta_I|/sigma_delta_I > 3.0 min[I(+)/sigma_I(+), I(-)/sigma_I(-)] > 3.0 holds. The measurability provides an intuitive feeling of the quality of the data, as it is related to the number of reliable Bijvoet differences. When the data are processed properly and the standard deviations have been estimated accurately, values larger than 0.05 are encouraging. Note that this analyses relies on the correctness of the estimated standard deviations of the intensities. unused: - 90.6596 [ 0/1 ] bin 1: 90.6596 - 9.2614 [1371/1382] 0.0375 bin 2: 9.2614 - 7.3520 [1369/1376] 0.0033 bin 3: 7.3520 - 6.4230 [1380/1388] 0.0000 bin 4: 6.4230 - 5.8358 [1353/1359] 0.0016 bin 5: 5.8358 - 5.4176 [1367/1371] 0.0000 bin 6: 5.4176 - 5.0982 [1361/1369] 0.0000 bin 7: 5.0982 - 4.8429 [1378/1382] 0.0000 bin 8: 4.8429 - 4.6321 [1351/1359] 0.0000 bin 9: 4.6321 - 4.4538 [1383/1389] 0.0000 bin 10: 4.4538 - 4.3001 [1390/1393] 0.0000 unused: 4.3001 - [ 0/0 ] The full resolution range seems to contain a useful ammount of anomalous signal. Depending on your specific substructure, you could use all the data available for the location of the heavy atoms, or cut the resolution to speed up the search. If values larger than 0.05 are encouraging why is it telling me that the entire resolution contains a useful amount of anomalous signal? Did I process this incorrectly? 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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General User Proposal Deadline for PX/SAXS at the ALS: August 15, 2009
by Peter Zwart 12 Aug '09

12 Aug '09

Dear All, August 15, 2009 is the deadline for the October - December 2009 Rapid Access Proposal cycle. (!!!!Please note that the ALS will be shut down in September, 2009.!!!!) Remote data collection is available on all beamlines at the Berkeley Center for Structural Biology (BCSB). The NX remote desktop technology provides the remote user with the full complement of sample visualization, sample manipulation, beamline control, data acquisition and data analysis tools exactly as they would see them if they were stationed at the beamline. This enhanced remote operation capability is coupled with 24hr onsite support by BCSB staff who are able to assist immediately with loading additional samples for remote users or troubleshoot any issues that might arise. Beamlines 8.2.1 and 8.2.2: Both beamlines are now fully remote capable, which means that users are able control sample mounting, data collection and analysis from their home labs. This has dramatically increased the efficiency of data collection and significantly reduced the cost of protein crystallography experiments, since users no longer have to travel to the synchrotron. To facilitate studies on small crystals, a microdiffractometer was installed in the beamline 8.2.1 endstation. The new equipment allows precise sample positioning to within 2 microns, excellent sample viewing of very small crystals, and an off-axis crystal positioning stage. As part of the beamline optics upgrades, a new toroidal focusing mirror was purchased and installed in beamline 8.2.1; new parabolic mirrors are currently being polished. When completed, the new optics will increase the brightness of beamline 8.2.1 by a factor of 4 to 5 and decrease the spot size to 30 microns, greatly facilitating structure solution on large macromolecular complexes. Beamlines 5.0.1, 5.0.2, 5.0.3: On Sector 5, improvements to the existing Berkeley Automounter sample handling system have dramatically improved both total capacity and reliability. Upgrades to the 5.0.1 and 5.0.3 monochromators have been completed. The operational energy of both beamlines has been increased, taking them above the Se K-edge and thus introducing a significant new Se SAD capability for experiments on Se derivatized proteins. The new monochromators also provide significantly better beam focus and performance under the increased power loads of ALS topoff operation. These improvements have been coupled with the introduction of enhanced positional feedback, diagnostic tools, and auto-alignment systems for the beamline components to improve the overall stability and quality of the beam delivered to users. Another mode of access to the BCSB beamlines is through the Collaborative Crystallography (CC) Program. Users apply for beamtime via the general user program, and collaborate with an expert crystallographer who will conduct the experiments and data reduction on behalf of the researchers. Depending on the users, structure solution, model building and refinement can be carried out as well. Please visit http://bcsb.lbl.gov/ for more details about the Center and its beamlines. To find out more, click on: http://www.als.lbl.gov/als/quickguide/independinvest.html Scroll down to "Structural Biology/Small Angle X-Ray Scattering (SAXS)." We invite you to submit a proposal at: http://alsusweb.lbl.gov/4DCGI/WEB_GetForm/PXProposalEntry.shtml/Initialize If you'd like to apply for January-February 2010 beamtime at the Advanced Light Source, please submit a General User proposal by November 15, 2009. If you have any questions or would like to request open beamtime, please e-mail BCSBBeamtime(a)lbl.gov. Please note that executed user agreements must be received by LBNL prior to beamtime. Proprietary fees, if applicable, must be received by LBNL at least five working days prior to scheduled beamtime. -- ----------------------------------------------------------------- P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -----------------------------------------------------------------

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xtriage
by Francis E Reyes 12 Aug '09

12 Aug '09

Hi all I love the fact that xtriage can measure anomalous signal, but can it also do a quick check for isomorphous differences (with and without anomalous signal) similar to scalepack? Is there a phenix utility that can do this? 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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duplicated label
by Jianghai Zhu 12 Aug '09

12 Aug '09

Hi, I am using phenix.refine-125 to do a MLHL refinement. I got an error at the end of the refinement while it was trying to exporting results. "Sorry: Duplicate mtz_label_amplitudes:FOFCWT". The output map_coeffs.mtz file is corrupted and the next def file is blank. The refined pdb file seems to be fine. Anyone knows how to fix this problem? Thanks. -- Jianghai

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where are the optimized wxc_scale and wxu_scale when optimize_wxc_scale and optimize_wxu_scale = True?
by Francis E Reyes 07 Aug '09

07 Aug '09

Hi all I went through the time to optimize_wxc and optimize_wxu to help pull out some density for ligands (i.e. all sequence assigned residues are built). However, it would be nice if the resulting .def was updated with the optimized wxc and wxu. Where are those values? I didn't think for wxc it was scale=XX in the following lines.. r_work= 0.2167 r_free= 0.2525 bonds= 0.003 angles= 0.70 scale= 7.00 r_work= 0.2097 r_free= 0.2502 bonds= 0.004 angles= 0.96 scale= 8.00 ... etc Refining with the scale= value that phenix ultimately chose didn't work form me (resulted in awful geometry and high r/rfree). 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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Re: [phenixbb] Let's talk about maps...
by Dr. Mark Mayer 07 Aug '09

07 Aug '09

Hi Pavel, It would be really nice if the Electron density maps section in the online docs for phenix.refine http://www.phenix-online.org/documentation/refinement.htm#anch70 was updated to decribe all the different map options people have been asking about. Its much harder to find this info by digging through the Q&A on the bb. Mark --

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Re: [phenixbb] Autobuild error (FIXED)
by youssef ben ammar 07 Aug '09

07 Aug '09

Thanks for all replies, Autobuild error linked to the long path was solved based on the suggestion of Ben Eisenbraun (thanks Ben). I reinstalled tcsh, but only that did not solve the problem. So, I deleted csh from the path and kept only the newly installed tcsh after that everything is running perfectly. Youssef

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Re: [phenixbb] phenix.refine 1.3 vs. 1.4 map quality ?
by William G. Scott 06 Aug '09

06 Aug '09

Hi Paul et al: The yellow map is filled and the blue map is no-fill from the phenix- generated mtz file: http://sage.ucsc.edu/~wgscott/mystuff/filled_vs_unfilled.pdf So I think this is clearly what is going on. Thanks. Bill

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Segmentation Fault
by Waight, Andrew 06 Aug '09

06 Aug '09

Hello All, I've recently solved a membrane protein structure largely with the help of phenix refine. I also have been using the autobuild programs recently for ligand fitting and whatnot. The program during this time has been running flawlessly on my machine (Ubuntu 9.04 E8400 3.0ghz etc etc) However this weekend Autobuild and AutoMR spontaneously started throwing this error. (boost_adaptbx_segmentation_fault_backtrace+0x1f) [0xb7de2e27] Segmentation fault (Python and libc call stacks above) This crash may be due to a problem in any imported Python module, including modules which are not part of the cctbx project. To disable the traps leading to this message, define these environment variables (e.g. assign the value 1): BOOST_ADAPTBX_FPE_DEFAULT BOOST_ADAPTBX_SIGNALS_DEFAULT This will NOT solve the problem, just mask it, but may allow you to proceed in case it is not critical. Memtest 86 says my RAM is good. I have reinstalled phenix and am still getting the same error. I can't seem to find any other information on this error (segmentation faults are tricky I know) and am just wondering if anyone else has seen or solved this type of problem, thanks for your help. Andrew Waight Wang Lab Skirball Institute of Biomolecular Medicine NYU school of medicine </PRE> <html> <body> ------------------------------------------------------------<br /> This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.<br /> ================================= </body> </html> <PRE>

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Re: [phenixbb] Autobuild error
by youssef ben ammar 06 Aug '09

06 Aug '09

Thanks for your quick reply, I tried again to fix the problem as suggested by Thomas but this did not solve the problem. Actually I have two machines running phenix, one with the old version 1.3, and the other with 1.4-3 version. With the old version I have also coot, ccp4, and arp-warp, and all things are running without any problem in this machine. But in the other computer, I don't have arp-warp in it (ccp4 and coot exist also), and everything was running OK until I updated phenix to 1.4-3. But now even if I downgrade it to 1.3, autobuild does not work. If I compare echo $PATH results from both machines, I can notice that the path in the one with "defected" autobuild is too long. I will review again my path and try to fix it, or see if there are other recently-installed programs that interfere with phenix. Thanks Youssef.

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Autobuild error -
by Gino Cingolani 05 Aug '09

05 Aug '09

Dear Youssef and Tom, I had the same problem. I also emailed the Phenix classified and got a similar response from Tom. In reality, Tom suggestion didn't solve my problem. The funny thing is that in my case PHENIX.Autobuild worked fine for months before suddenly giving the 'Word too long' error. Weird!!! Believe it or not, the only thing I had to do to fix the problem was to uninstall the ARP/wARP package (sorry about that Tassos!). I realized that PHENIX.Autobuilt stopped working properly right when I installed ARP/wARP. I guess there may be a conflict between the two programs (could Phenix read some ARP/wARP library in the wrong directory?), or something like that. I'm not sure. I'm not claiming this is a general solution, but it worked in my case. I hope it will help you! Cheers, Gino ****************************************************************************** Gino Cingolani, Ph.D. Associate Professor Thomas Jefferson University Dept. of Biochemistry & Molecular Biology 233 South 10th Street - Room 826 Philadelphia PA 19107 Office (215) 503 4573 Lab (215) 503 4595 Fax (215) 923 2117 E-mail: gino.cingolani(a)jefferson.edu ****************************************************************************** "Nati non foste per viver come bruti, ma per seguir virtute e conoscenza" ("You were not born to live like brutes, but to follow virtue and knowledge") Dante, The Divine Comedy (Inferno, XXVI, vv. 119-120)

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Re: [phenixbb] Autobuild error
by Thomas C. Terwilliger 05 Aug '09

05 Aug '09

Hi Youssef, I'm sorry for the trouble! If you update to a recent "nightly build" such as 1.4-129 then this should go away. If it still doesn't, then have a look at your path: echo $PATH which is probably quite long....and identify a few things (perhaps ccp4 and coot for example) that you don't need while running phenix...and then add the keyword: remove_path_word_list="coot ccp4" All the best, Tom T remove_path_word_list = None .help = "List of words identifying paths to remove from PATH " "These can be used to shorten your PATH. For example..." "cns ccp4 coot would remove all paths containing these " "words except those also containing phenix. Capitalization" "is ignored." ">> Dear all, >> >> Recently I have problem with Autobuild. The process fails with the >> following >> message: >> Failed to carry out AutoBuild_build_cycle: >> child process stderr output: >> command: 'csh /home/phenix/p21/AutoBuild_run_1_/TEMP0/RUN_FILE_1' >> Word too long. >> Even if I set the path only to things related to phenix, the process fails >> with the same error. >> >> Any idea? >> >> Youssef >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://www.phenix-online.org/mailman/listinfo/phenixbb >>

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Autobuild error
by youssef ben ammar 04 Aug '09

04 Aug '09

Dear all, Recently I have problem with Autobuild. The process fails with the following message: Failed to carry out AutoBuild_build_cycle: child process stderr output: command: 'csh /home/phenix/p21/AutoBuild_run_1_/TEMP0/RUN_FILE_1' Word too long. Even if I set the path only to things related to phenix, the process fails with the same error. Any idea? Youssef

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Using phenix.pdbtools to strip multiple conformations out of a PDB file?
by Stephen Graham 04 Aug '09

04 Aug '09

Dear all, Apologies if this is a dumb question, but I couldn't find the answer in the docs or by asking the googlebrain. Is there a simple way in phenix.pdbtools to strip "alternate conformations" of side chains, etc, from an input PDB file? By removing "alternate conformations" I mean I would like to keep the conformation with the highest occupancy (not necessarily denoted 'A' in the altLoc column) unless all conformations have an equal occupancy, in which case I'd arbitrarily keep conformation 'A'. I think it should be possible by a clever atom_selection command, but the correct syntax has thus-far eluded me! Thanks, Stephen -- Dr Stephen Graham Division of Structural Biology Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Phone: +44 1865 287 549

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