Dear all, I have crystal with a protein homotetramer in the asymmetric unit, and I suspect from the electron density that the average B-factor of one chain may be substantially different than the others. Thus I would like to see the effect, if any, of changing the B-factor restraints between the NCS-related copies on the refinement statistics and maps. The question is: when using local NCS restraints in Refmac5, is there a way to change the weight restraining the B-factors of the NCS-related molecules? I went through the manual pages, but I am still confused as to which instruction I should use.
I also tried to approach the problem differently by defining manually the regions (using the old or new syntax): ncsr nchains 2 chain A D nspans 1 2 346 6 ncsr nchains 2 chain B C nspans 1 2 346 2 OR ncsr group 1 chain A D residue 2 346 sigx 0.002 sigb 10.0 ncsr group 2 chain B C residue 2 346 sigx 0.002 sigb 5.0 OR using the ccp4i GUI (that of course generates a command file with the syntax as in the first example) but Refmac5 always stops with the following error: The program run with command: /Applications/ccp4-8.0/bin/refmac5 XYZIN "/Users/degano.massimo/Desktop/Projects/NH/Marco_Ribose/ownref/refine9-coot-0.pdb" XYZOUT "/Users/degano.massimo/Desktop/Projects/NH/Marco_Ribose/refine9-coot-0_refmac1.pdb" HKLIN "/Users/degano.massimo/Desktop/Projects/NH/Marco_Ribose/XDS_ASCII_scaled2_sftools1.mtz" HKLOUT "/Users/degano.massimo/Desktop/Projects/NH/Marco_Ribose/XDS_ASCII_scaled2_refmac23.mtz" LIBIN "/Users/degano.massimo/Desktop/Projects/NH/Marco_Ribose/RIB_mon.cif" LIBOUT "/Users/degano.massimo/Desktop/Projects/NH/Marco_Ribose/UNHR_104_lib.cif" has failed with error message At line 5576 of file /Users/jenkins/workspace/CCP4/series-8.0-osx/devtools/co/refmac5.8/lsq_exp2.f (unit = 7, file = '/tmp/degano.massimo/refmac5_temp1.35666_NCS_R') Fortran runtime error: I/O past end of record on unformatted file Error termination. Backtrace: #0 0x15af88579 #1 0x15af89235 #2 0x15af89999 #3 0x15b054b40 #4 0x10c15a251 #5 0x10c4cb7ed #6 0x10c184856 #7 0x10c0653c4 #8 0x10c59a6de It appears that the lsq_exp2 subroutine takes exception to the input, most likely the contents of the binary temp file that is written by Refmac5. I installed ccp4-8.0 from the MacOSX distribution and I have the 8.0.005 update. Any help would be greatly appreciated! Massimo -- Dr. Massimo Degano Biocrystallography Unit Dept. of Immunology, Transplantation, and Infectious Diseases IRCCS Scientific Institute San Raffaele via Olgettina 58 20132 Milan - Italy email: degano.mass...@hsr.it phone: +39-0226437152 fax: +39-0226434153 skype: maxdegano ORCID: 0000-0002-0787-1883 http://research.hsr.it/en/divisions/immunology-transplantation-and-infectious-diseases/biocrystallography.html Rispetta l’ambiente: non stampare questa mail se non è necessario. Respect the environment: print this email only if necessary. ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
