[ccp4bb] error
Dear all, during conversion of .sca file to mtz in ccp4, i got this message (see below). *** * Information from CCP4Interface script *** The program run with command: /opt/ccp4i/destination/ccp4-6.4.0/bin/ctruncate -hklin "/tmp/gouri/tvpsat_akg_1_1_mtz.tmp" -hklout "/tmp/gouri/tvpsat_akg_1_3_mtz.tmp" -colin "/*/*/\[IMEAN,SIGIMEAN\]" -colano "/*/*/\[I(+),SIGI(+),I(-),SIGI(-)\]" -colout akg has failed with error message child killed: segmentation violation *** #CCP4I TERMINATION STATUS 0 "child killed: segmentation violation" #CCP4I TERMINATION TIME 17 Nov 2014 12:05:50 #CCP4I MESSAGE Task failed Can any one tell me, what does it means? or how can i overcome with this error? thank you -- WITH REGARDS Rohit Kumar Singh Lab. no. 430, P.I. Dr. S. Gourinath, School of Life Sciences, Jawaharlal Nehru University New Delhi -110067
Re: [ccp4bb] rosetta from sbgrid
Hi Ursula. I don't have any experience of sbgrid, but the executable that AMPLE needs will be called something along the lines of: AbinitioRelax.linuxgccrelease (the name after the dot will change depending on the platform and how Rosetta was compiled). If you can find that (try using whatever search/find commands your OS provides), then it should be possible to run AMPLE. Running AMPLE with CCP4i, you'll need to give AMPLE the name of the top Rosetta installation directory. This is not the name of the executable or the directory it sits in, but the directory that contains all of the rosetta files (binaries, database, documentation etc.). For Rosetta 3.5, this is called rosetta-3.5, and the path to the binary within it looks like this: rosetta-3.5/rosetta_source/bin/AbinitioRelax.linuxgccrelease For later Rosetta versions, the directory structure has changed, and it is more like the following: rosetta_2014.30.57114_bundle/main/source/bin/AbinitioRelax.linuxgccrelease AMPLE needs the full path to the rosetta-3.5 or rosetta_2014.30.57114_bundle directory. I'm not sure which version is shipped with sbgrid, but hopefully the above will help you find it. Best wishes, Jens From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Ursula Schulze-Gahmen [uschulze-gah...@lbl.gov] Sent: 14 November 2014 22:33 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] rosetta from sbgrid I am confused about the Rosetta program provided by sbgrid. Is this a standalone program that I can use by itself or is it called from within phenix? I would like to try AMPLE for molecular replacement in CCP4, but I am not sure if I have the Rosetta version I would need. I am not able find the executable in the rosetta directory in sbgrid. Could somebody give me a hint where to look? Thanks Ursula -- Ursula Schulze-Gahmen, Ph.D. Project Scientist UC Berkeley, QB3 360 Stanley Hall #3220 Berkeley, CA 94720-3220 (510) 643 9491
Re: [ccp4bb] How to run CCP4 without source command
Dear Peter, Put your source command in your ".bashrc" file. It's a hidden file (because of the dot in the start) in your home folder and will be run every time you open a terminal, so any command inside will be executed. You can edit the file by typing gedit .bashrc Just after opening a terminal. If you just started using Linux and you're interested in an introduction to how Linux works, I'd recommend the Linux Foundations free online course https://www.edx.org/course/linuxfoundationx/linuxfoundationx-lfs101x-2-introduction-5386 Especially if you are not working in a lab were people can help you with questions like the one you just asked. Venlig hilsen/Best regards Folmer Fredslund Den 16/11/2014 07.34 skrev "陈昂" : > Dear all: > > I have installed CCP4 suit on my computer. The OS IS fedora 18. Every time > I open the software, I have to > > use the command source. Does anyone else can run it in terminal without > that command? > > Thank u so much! > > best regards, > > Peter >
Re: [ccp4bb] How to run CCP4 without source command
read the documentation? Probably somewhere it should be mentioned to have the 'source ' command in your bash file? I might have misunderstood your question though. Leo > On 16 Nov 2014, at 07:30, 陈昂 wrote: > > Dear all: > > I have installed CCP4 suit on my computer. The OS IS fedora 18. Every time I > open the software, I have to > > use the command source. Does anyone else can run it in terminal without that > command? > > Thank u so much! > > best regards, > > Peter
