[ccp4bb] Phaser gives error in 6.4.0 version
Dear All, Installed the CCP4 6.4.0 version recently on CentoS 5. When I try to run phaser I get the following error. Apparently I can reproduce the error for different reflection file. This happens after getting the rotation, translation and packing function. Any suggestions to this problem is highly appreciated. -- REFINEMENT -- Protocol cycle #1 of 1 Refinement protocol for this macrocycle: ROTATION : REFINE TRANSLATION : REFINE BFACTOR : REFINE MODEL VRMS : FIX MAP CELL SCALE: FIX LAST ONLY : FALSE There are 2 solutions to refine Spreading calculation onto 2 threads. Refining solutions 0% 100% |*** * Information from CCP4Interface script *** The program run with command: /home/programs/linux/ccp4/ccp4-6.4.0/bin/phaser has failed with error message terminate called after throwing an instance of 'cctbx::error' what(): cctbx Error: Lattice type not specified. *** Thanking you With regards -Karthik -- * Dr.Karthikeyan Subramanian, Ph.D Scientist, Protein Crystallography Lab Institute of Microbial Technology Council of Scientific and Industrial Research (CSIR) Sector 39-A, Chandigarh - 160036, INDIA email:skart...@imtech.res.in, skarthi...@gmail.com Phone: +91-172-6665193 Fax: +91-172-2690585 *
[ccp4bb] Problem in running ARP_WARP in CCP4i
Dear CCP4BB members, I am trying to run arp_warp classic (7.3 version) through ccp4i (CCP4 6.3) in CentOS system. However, it gives the following error even for the example files provided with Arp/Warp. Any suggestions are welcome. --- BFONT COLOR=#FF!--SUMMARY_BEGIN-- QUITTING ... ARP/wARP module stopped with an error message: /home/programs/linux/ccp4/arp_warp_7.3/bin/bin-x86_64-Linux/warp_tracing.sh !--SUMMARY_END--/FONT/B If I try to run through command line it gives the following error: auto_tracing.sh datafile ../psp.mtz Thu Mar 7 19:09:18 IST 2013 Word too long. QUITTING ... ARP/wARP module stopped with an error message: /home/programs/linux/ccp4/arp_warp_7.3/bin/bin-x86_64-Linux/auto_tracing.sh --- Thanking you With regards S. Karthikeyan __ सूक्ष्मजीव प्रौद्योगिकी संस्थान (वैज्ञानिक औद्योगिक अनुसंधान परिषद) Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) सैक्टर 39 ए, चण्डीगढ़ / Sector 39-A, Chandigarh पिन कोड/PIN CODE :160036 दूरभाष/EPABX :0172 6665 201-202
Re: [ccp4bb] SFCHECK produces incomplete postscript
If you have break in the protein chain, this problem will occur. Put TER card in the PDB file where ever the chain break is there, then run SFCHECK. The .ps output now will be complete and should be able to see in the viewer. HTH -Karthik Dear all, I have been trying to compare a model that I'm refining against the native SFs using SFCHECK. SFCHECK finishes normally (no errors in log file, seemingly complete list of output .ps files), but produces a postscript file with only the first page of output (and it is mostly blank). There is the typical light-grey panels on a dark-grey background format that I'm used to for SFCHECK postscript files, but there are no figures or data. Also, my mouse icon indicates it is hung trying to load/read the file (i.e. it's a moving busy icon under Linux). I've tried other postscript viewers without luck. I can successfully run SFCHECK on a completely different model/MTZ pair without problem though. So does anyone know of circumstances that would lead to a hung postscript file from SFCHECK? Thanks for your help, -Andy
Re: [ccp4bb] ccp4-6.1.3 phaser sigmaa weighted maps problem
Hi, Similar problem occured even in CCP4-6.1.0 in our case. So, we used to take the phaser output model and do rigid body refinement with REFMAC and see the density (in coot), which normally much better than output from PHASER mtz. I am not sure whether it is for case to case or it is general problem? -Karthik Hi , I just switched to ccp4-6.1.3 and ran the phaser which is bundled with the ccp4-6.1.3 release. After molecular replacement I get a pretty good solution (TFZ 59.2) and output pdb and mtz files. I am then looking at the maps from the phaser output mtz i.e the FWT , PHWT map and the FWT PHIC map . Both maps look very crappy and look like noise. I tried the fft inside of coot and separately as a FFT inside ccp4 and these maps look bad. So the FWT PHWT calc seem to be off. However , if I take the phaser solution output model and do the sigmaa myself. The map looks normal and sensible. It seems like phaser inside of ccp4-6.1.3 is not generating the output mtz correctly . Anyone else seeing this or is there something wrong with my setup. Hari
[ccp4bb] Request for def.site for HKL2000 for ESRF-BM14 MAR 225 CCD
Dear All, I am looking for def.site file for HKL2000 used in ESRF-BM14 beam line. We collected the data using MAR 225 CCD detector. The following link does not seem to work for me. http://www.esrf.fr/exp_facilities/BM14/runexperiment/bm14-def.site We need this file to process our data in the home lab. If anybody has one, can you please share with us. Thanking you With regards S.Karthikeyan * Dr.Karthikeyan Subramanian, Ph.D Scientist Institute of Microbial Technology (CSIR) Sector 39-A, Chandigarh - 160036, INDIA email:skart...@imtech.res.in, skarthi...@gmail.com *
Re: [ccp4bb] Request for def.site for HKL2000 for ESRF-BM14 MAR 225 CCD
Dear All, I got the file. Thanks a lot for the same. I apologize for posting a 'non-CCP4' question to the CCP4BB. With regards S.Karthikeyan Dear All, I am looking for def.site file for HKL2000 used in ESRF-BM14 beam line. We collected the data using MAR 225 CCD detector. The following link does not seem to work for me. http://www.esrf.fr/exp_facilities/BM14/runexperiment/bm14-def.site We need this file to process our data in the home lab. If anybody has one, can you please share with us. Thanking you With regards S.Karthikeyan * Dr.Karthikeyan Subramanian, Ph.D Scientist Institute of Microbial Technology (CSIR) Sector 39-A, Chandigarh - 160036, INDIA email:skart...@imtech.res.in, skarthi...@gmail.com *
Re: [ccp4bb] space groups not supported by Refmac5
Hi, Following mail (retrived from ccp4bb archieve) may help for intechanging the cell axis. HTH S.Karthikeyan == I have a CCP4 script for this: http://bl831.als.lbl.gov/~jamesh/elves/scripts/reindex.com If you run the script like this: reindex.com yourdata.mtz P22121 Then you will get a file called reindexed.mtz that has the space group P21212 with the cell permuted so that the shortest edge is b. Specifying P21221 will give you P21212 with the shortest edge at c, and P21212 will give you the shortest edge at a, like it is supposed to be. Like George said, this way you are always working in a cannonical space group so you will have much less portability issues between programs. -James Holton MAD Scientist = For the latter, P21221, you could reindex to get P21212, which is supported. - === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu On Mon, 2009-08-17 at 17:37 +0100, Arefeh Seyedarabi wrote: Hi, I have a question; recently I have encountered a few space groups which are not supported by Refmac5. Examples include I2 and P21221. Both these space groups have been identified as the best solutions for the two different datasets I am working on using Pointless. However, I am faced with difficulties in Refmac5, and the program fails to complete when I select refinement cycles with Arp-waters...with the message saying 'space group not supported'. Any suggestions on how this problem could be overcome? Regards, Arefeh Arefeh Seyedarabi, PhD Postdoctoral research assistant School of Biological and Chemical sciences Queen Mary, University of London Mile End road London E1 4NS Based at Joseph Priestley Building G.35 020 78828480
