Agreed, ANIS is the command to try. Sent from ProtonMail mobile
-------- Original Message -------- On 3 Jun 2021, 20:18, Philip D. Jeffrey wrote: > R1 of 17% is bad for small molecule. > 0.8 Å is in the eye of the beholder - if you're using macromolecular cutoffs > then these might be too aggressive for small molecule-type refinement stats - > try a more conservative cutoff lie 0.9 and see how that changes R1. However I > suspect it's more to do with how your model is fitting the data. > > Have you refined anisotropic Bfactors ? > Have you added hydrogens ? > > I would suggest non-CCP4 programs like Olex2 or SHELXLE as the interface for > the refinements - I use the latter and it's somewhat Coot like with useful > features that are particular to small molecule. Also PLATON has some things > (like expand-to-P1 and Squeeze) that, respectively, might be useful to > explore space group issues and disordered solvent. PLATON also has a means to > check for some forms of twinning. > > Phil Jeffrey > Princeton > > --------------------------------------------------------------- > > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Jacob Summers > <000060a137e4bf3a-dmarc-requ...@jiscmail.ac.uk> > Sent: Thursday, June 3, 2021 2:49 PM > To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> > Subject: [ccp4bb] Lowering R factor from small molecule structure > > Greetings! > > I am currently trying to reduce the R factor of a cyclic small molecule > peptoid in ShelXle. The max resolution of the molecule is 0.8 angstroms. The > molecule itself fits the density very well, but there are a few unexplained > densities around the molecule which do not seem to be anything in the > crystallization conditions. The R1 factor of the refinement is 17.07% but I > am unsure how to lower this value. Any ideas on how to better refine this > molecule or fill densities to lower the R1 factor? I do not have much > experience working with small molecule refinement or with ShelX. > > Thanks so much, > Jacob Summers > > ######################################################################## > > 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/ > > --------------------------------------------------------------- > > 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/
