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/
