Dear Massimo, This was a bug in Refmac and has been fixed in Refmac5.8.0385 which will be hopefully released with the next CCP4 update.
However, local NCS restraints do not impose restraints on B-factors, so you do not have to worry about that. Best regards, Keitaro On Thu, 13 Oct 2022 at 14:05, Degano Massimo <degano.mass...@hsr.it> wrote: > > > 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 ######################################################################## 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/
