You've spoiled us all, Paul! I have noticed lately that I get false-alarm "red lights" when Ramachandran restraints are on, despite that the restraints seem to be working just fine. In well-behaved regions of the structure, changing the Rama weight or restraints type gives identical good results but different scores.
-- Kevin Jude, PhD (he/him/his) Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305 Phone: (650) 723-6431 On Mon, Jun 14, 2021 at 2:04 PM Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote: > On Mon, 2021-06-14 at 15:51 +0100, Phong Nguyen wrote: > > Hello, > > > > I am using Coot 0.9.5, installed from CCP4 package. It was working well > until today I decided to install ccp4 again > > because I have some trouble of trying to install ARP package. So I guess > that Coot also get reinstall after I > > reinstall the package. Coot runs normally, having some warning like in > the attachment file ¨coot_warning.txt¨ but I am > > able to open the pdb, the map and most of the function are working > normally. There is only one problem is that when I > > tried to refine the model with Ramachandran, it always give me the red > ramachandran, even if I tried to refine in a > > place that according to coot validation, the ramachandran there was > good, it also gave me only the red ramachandran. > > > > I think I have seen something similar. Some prolines are extremely > reluctant to turn green, despite considerable > provocation to do so. Sometimes, upping the weight on the Rama Restraints > helps... > > https://pemsley.github.io/coot/blog/2021/03/11/dynamic-weights.html > > ... sometime not. > > There may be a bug in the proline rotamer validation - or its > representation. > > There are two types of target function for the Ramachandran restraints. > You might like to try the other one: > > set_refine_ramachandran_restraints_type(0) # pythonically speaking > > > Could anybody can help with this situation? it is not possible for me to > refine a model with out ramachandran option. > > Teehehe! Modern notions for modern scientists. > > Paul. > > ######################################################################## > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 > > This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing > list hosted by www.jiscmail.ac.uk, terms & conditions are available at > https://www.jiscmail.ac.uk/policyandsecurity/ > ######################################################################## To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
