- phenixbb - phenix-online.org

xtriage
by Francis E Reyes 13 Aug '09

13 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 08 Aug '09

08 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 07 Aug '09

07 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 07 Aug '09

07 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 06 Aug '09

06 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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