> ADP values are constrained to be positive, because negative values do not > have physical meaning.
Negative B-factors have physical meaning. It means Hell has frozen over. Regards, BR ------------------------------------------------------ Bernhard Rupp http://www.hofkristallamt.org/ b...@hofkristallamt.org +1 925 209 7429 +43 676 571 0536 --------------------------------------------------------- Doors and corners – that’s where they get you --------------------------------------------------------- On Wed, 23 Aug 2023 at 16:04, Adwaith Bini Bose Uday <adwaith.biniboseu...@mail.mcgill.ca> wrote: > > Hi Keitaro, > > Thank you for the answer. I will try that. > > Also, does using unsharpened half maps apply to PHENIX real space refine as > well? What is the advantage of using that instead of sharpened maps? > > Thank you > Adwaith > > ---------------------------------------------------------------------- > - > Adwaith B Uday > Ph.D student > Zeytuni lab, Department of Anatomy and Cell Biology McGill University, > Canada ________________________________ > From: Keitaro Yamashita <kyamash...@mrc-lmb.cam.ac.uk> > Sent: Friday, August 18, 2023 11:43 AM > To: Adwaith Bini Bose Uday <adwaith.biniboseu...@mail.mcgill.ca> > Cc: cc...@jiscmail.ac.uk <cc...@jiscmail.ac.uk> > Subject: Re: [ccpem] CCPEM Refmac servalcat error > > [You don't often get email from kyamash...@mrc-lmb.cam.ac.uk. Learn > why this is important at https://aka.ms/LearnAboutSenderIdentification > ] > > Dear Adwaith, > > This is a bug of the old version (up to 0.6.0 I think) of the gemmi > library that Servalcat heavily uses. It happens while reading the CCP4 > monomer library, and "." value in new_period causes the problem. We > just recently also fixed the monomer library for an old gemmi user > https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgith > ub.com%2FMonomerLibrary%2Fmonomers%2Fpull%2F29&data=05%7C01%7Cadwaith.biniboseuday%40mail.mcgill.ca%7Ced8073dc380044322d2008dba0023c2d%7Ccd31967152e74a68afa9fcf8f89f09ea%7C0%7C0%7C638279703797578781%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=sUaid30ECNCDPBgVdhwBCEaqResSfzmUkCmijvu9r0A%3D&reserved=0 > but it has not yet been distributed by CCP4. > > So the problem can be solved either by using a newer gemmi or the > latest monomer library. The latter should be easier. > > To the CCP-EM people: does Refmac/Servalcat job in the CCP-EM use the > monomer library in the CCP-EM package or from external? Would it work > if one downloads the new library and sets CLIBD_MON? > > By the way, please always use unsharpened half maps as an input! > > Best regards, > Keitaro > > On Fri, 18 Aug 2023 at 16:20, Adwaith B Uday > <adwaith.biniboseu...@mail.mcgill.ca> wrote: > > > > Hi, > > > > I am trying to use a sharpened map from cryosparc and a model in CCPEM > > Refmac. However, the job fails just after starting with the following error. > > > > Traceback (most recent call last): > > File "/home/adwaith/ccpem/lib/python2.7/runpy.py", line 174, in > > _run_module_as_main > > "__main__", fname, loader, pkg_name) > > File "/home/adwaith/ccpem/lib/python2.7/runpy.py", line 72, in _run_code > > exec code in run_globals > > File > > "/home/adwaith/ccpem/lib/python2.7/site-packages/servalcat/command_line.py", > > line 126, in <module> > > main() > > File > > "/home/adwaith/ccpem/lib/python2.7/site-packages/servalcat/command_line.py", > > line 116, in main > > modules[args.command].main(args) > > File > > "/home/adwaith/ccpem/lib/python2.7/site-packages/servalcat/spa/run_refmac.py", > > line 245, in main > > stop_for_unknowns=True, check_hydrogen=(args.hydrogen=="yes")) > > File > > "/home/adwaith/ccpem/lib/python2.7/site-packages/servalcat/utils/restraints.py", > > line 95, in load_monomer_library > > monlib = gemmi.read_monomer_lib(monomer_dir, resnames, > > ignore_missing=True) > > ValueError: not an integer: . > > > > Error in sys.excepthook: > > Traceback (most recent call last): > > File > > "/home/adwaith/ccpem/lib/python2.7/site-packages/servalcat/utils/logger.py", > > line 78, in handle_exception > > atexit.unregister(exit_success) > > AttributeError: 'module' object has no attribute 'unregister' > > > > Original exception was: > > Traceback (most recent call last): > > File "/home/adwaith/ccpem/lib/python2.7/runpy.py", line 174, in > > _run_module_as_main > > "__main__", fname, loader, pkg_name) > > File "/home/adwaith/ccpem/lib/python2.7/runpy.py", line 72, in _run_code > > exec code in run_globals > > File > > "/home/adwaith/ccpem/lib/python2.7/site-packages/servalcat/command_line.py", > > line 126, in <module> > > main() > > File > > "/home/adwaith/ccpem/lib/python2.7/site-packages/servalcat/command_line.py", > > line 116, in main > > modules[args.command].main(args) > > File > > "/home/adwaith/ccpem/lib/python2.7/site-packages/servalcat/spa/run_refmac.py", > > line 245, in main > > stop_for_unknowns=True, check_hydrogen=(args.hydrogen=="yes")) > > File > > "/home/adwaith/ccpem/lib/python2.7/site-packages/servalcat/utils/restraints.py", > > line 95, in load_monomer_library > > monlib = gemmi.read_monomer_lib(monomer_dir, resnames, > > ignore_missing=True) > > ValueError: not an integer: . > > > > I have also tried with the unsharpened map and a mask. However, it still > > gives me the same error. I am on the latest version of CCPEM. > > > > Has anyine else faced this issue? I would really appreciate any tips on > > solving this issue. > > > > Thank you > > Adwaith > > > > #################################################################### > > #### ######################################################################## To unsubscribe from the CCPEM list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCPEM&A=1 This message was issued to members of www.jiscmail.ac.uk/CCPEM, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ ######################################################################## 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/
