Error In Label Assignments In Labin Refmac
Jason -----Bruno Matias
Re: [ccp4bb] SigmaA LABIN error - Protein crystallographyMain steps: - Protein purification - CrystallisationSpecial: - Programs for crystallography - X-ray detectorsBasic tutorials: - Chemistry - Protein - Peptide - Amino AcidsXtal community: - CCP4BB CCP4bb navigationCCP4bb <-- 2011 <-- October 2011 <-- 29 October 2011Previous message:Subject: **Possible spam**Re: Low resolution refinementFrom: Kay Diederichs Kay {- dot -} Diederichs {- at -} UNI-KONSTANZ {- dot -} DEDate: 2011-10-29Next message:Subject: Post-doctoral position in membrane protein structure at the ESRFFrom: https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg20825.html Matthew BOWLER bowler {- at -} ESRF {- dot -} FRDate: 2011-10-29Subject: Re: SigmaA LABIN errorFrom: Ian Tickle ianjt05 {- at -} GMAIL {- dot -} COMDate: 2011-10-29Hi Yogesh, in your first run the problem is exactly what the errormessage says: the required columns are not present in the input MTZfile for SIGMAA, i.e. the file'/tmp/yogeshgupta/nme_phasecombination_11_1.tmp' http://proteincrystallography.org/ccp4bb/message20644.html contains only columnlabels 'H K L FP SIGFP FC PHIC' as shown in the file header listing inthe SIGMAA output. I guess what you wanted to do was copy over allthe columns from your original input MTZ file, not just 'H K L FPSIGFP'. According to the documentation for SFALL: "If you want tocopy everything over, use ALLIN on the LABOUT line." - there's also anoption in the CCP4I interface for SFALL to do this.Personally, I wouldn't use SFALL anyway for this, I would use REFMACwith refinement mode 'unrestrained' and 'NCYC 0'. You also need to besure to use the Fcalc columns with the solvent contribution included:FC_ALL & PHIC_ALL. The reason is that SFALL doesn't use a solventmodel which is likely to cause big problems with the low resolutionshells in SIGMAA (of course you could always cut them out, but that'shardly an ideal solution). Also SFALL can't handle TLS or ADP models.I also tried your second run - I had to make a couple of changes inyour
[ccp4bb] Molrep and Refmac5 errors - Protein crystallographyMain steps: - Protein purification http://proteincrystallography.org/ccp4bb/message33026.html - CrystallisationSpecial: - Programs for crystallography - X-ray detectorsBasic tutorials: - Chemistry - Protein - Peptide - Amino AcidsXtal community: - CCP4BB CCP4bb navigationCCP4bb http://www.img.bio.uni-goettingen.de/ms-www/internal/manuals/ccp4i/help/programmers/command_template.html <-- 2013 <-- October 2013 <-- 15 October 2013Previous message:Subject: Re: High Rsyms between 5-7 AFrom: Kay Diederichs kay {- dot -} diederichs {- error in at -} UNI-KONSTANZ {- dot -} DEDate: 2013-10-15Next message:Subject: POSTDOC POSITION at UC Irvine, SoCalFrom: Hudel Luecke hudel {- at -} UCI {- dot -} EDUDate: 2013-10-15Subject: Molrep and Refmac5 errorsFrom: Rajiv K Bedi rajiv_psn {- at -} HOTMAIL {- dot -} COMDate: 2013-10-15Dear all,I recently started using error in label CCP4i (Windows 8) software for data processing and model building but I get the following error messages whenever I use molrep and refmac5:MOLREP#CCP4I TERMINATION STATUS 0 " MOLREP(ccp4): Error in label assignments in LABIN"#CCP4I TERMINATION TIME 08 Oct 2013 16:27:56#CCP4I MESSAGE Task failedREFMAC5#CCP4I TERMINATION STATUS 0 Program received signal 11 (SIGSEGV): Segmentation fault.#CCP4I TERMINATION TIME 08 Oct 2013 16:26:50#CCP4I MESSAGE Task failedI get those error with every data set I tried, therefore, I would be really appreciative if you could help me with it.Thanks,RajivCCP4bb navigationCCP4bb <-- 2013 <-- October 2013 <-- 15 October 2013Previous message:Subject: Re: High Rsyms between 5-7 AFrom: Kay Diederichs kay {- dot -} diederichs {- at -} UNI-KONSTANZ {- dot -} DEDate: 2013-10-15Next message:Subject: POSTDOC POSITION at UC Irvine, SoCalFrom: Hudel Luecke hudel {- at -} UCI {- dot -} EDUDate: 2013-10-15 ProteinCrystallography.org: Copyright 2006-2010 by Quid United Ltd
into Components - Continuation Lines Sub-components and Double-Continuation The | character - an inline ELSE Undefined Parameters and Why Split Commands into Components Control Structures IF-ELSE-ENDIF LOOP-ENDLOOP CASE-CASEMATCH-ENDCASE LABELLINE - Writing LABIN and LABOUT Commands Hints for Programmers Appendix: Some Examples of Write Flags Introduction First read the Overview of the files required for a task interface. It is common in scripts to run CCP4 programs to redirect the command input from the script file using << but in CCP4i the commands are written to a separate file (chiefly to enable VMSsupport). Command templates are used to generate the command files for CCP4 (or other) programs. The procedure CreateComScript will substitute parameters into the template to create a command file. There is usually one command template file per program, though if program function is very modular it may be reasonable to have seperate templates for different functions (e.g. see the amore_*.com templates in $CCP4I_top/templates). Note that the templates are all kept in the directory $CCP4I_top/templates. Before writing a new task interface, check here for existing templates for program(s) you may want to use - particularly because the rest of the task interface must use the same parameter names that are used in the template. Using CreateComScript in a Script File The CreateComScript procedure is usually called from a run script - a few example lines of a run script might be: set TITLE "This should be a really good fiddle" set FACTOR_1 0.1 set FACTOR_2 400 set FACTOR_3 27.1 set EXTRA_FIDDLE 1 CreateComScript $CCP4I_top/templates/fiddleprog.com fp_script The first argument to CreateComScript is the name of the fiddleprog template file and the second argument returns the name of a temporary file which is created and will contain the command lines: title'This should be a really good fiddle' fiddlefactors 0.1 400 - 27.1 Note that the values of the parameters set in the run file are not passed to the C