Indeed, update 54 from Mar 29 seems to have messed up several monomer definitions and/or their handling in coot (the version distributed with ccp4): - GLU and ASP contain lines referencing GLN and ASN, respectively, preventing coot from finding any chi angles. - For GLN, chi angles appear twice in the coot torsion dialog. - Many amino acid definitions now contain main chain torsion angles, which are erroneously listed as chi in coot.
The coot version available from Paul Emsleys website comes with its own version of the monomer library, which seems to work fine. Best Oliver ================================================ PD Dr. Oliver H. Weiergräber Institute of Complex Systems ICS-6: Structural Biochemistry Tel.: +49 2461 61-2028 Fax: +49 2461 61-9540 ================================================ ________________________________________ From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Eleanor Dodson [0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk] Sent: Thursday, April 26, 2018 11:49 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving Oops - oh dear - GLN labels should NOT appear in a list devoted to GLU!! Well spotted.. Eleanor On 26 April 2018 at 10:34, Chris Richardson <chris.richard...@icr.ac.uk<mailto:chris.richard...@icr.ac.uk>> wrote: Many thanks for explaining where it is going awry. Looking at GLU.cif in the monomer library that is part of the CCP4 distribution, it contains the following lines: GLN chi1 N CA CB CG 180.000 15.000 3 GLN chi2 CA CB CG CD 180.000 15.000 3 GLN chi3 CB CG CD OE1 0.000 30.000 2 In the monomer library you link, it has: GLU chi1 N CA CB CG 180.000 15.000 3 GLU chi2 CA CB CG CD 180.000 15.000 3 GLU chi3 CB CG CD OE2 0.000 30.000 2 Which makes more sense. Thanks again, Chris ________________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Huw Jenkins <h.t.jenk...@me.com<mailto:h.t.jenk...@me.com>> Sent: 26 April 2018 09:47 To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] Coot 'Edit Chi Angles' on Mac misbehaving > On 26 Apr 2018, at 09:19, Chris Richardson > <chris.richard...@icr.ac.uk<mailto:chris.richard...@icr.ac.uk>> wrote: > > I've just compiled Coot on the same Mac using Fink, and the dialogue for this > version of Coot shows CA <--> CB, CB <--> CG, and CG <--> CD angles for the > same residue. >From a quick look at the Fink coot.info<http://coot.info> it appears to get >the monomer library from here: http://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/Dictionary/refmac_dictionary_v5.41.tar.gz Setting $CLIBD_MON to point to this and the 'Edit Chi Angles' dialogue for CCP4 distributed Coot 0.8.9.1 shows CA <--> CB, CB <--> CG and CG <--> CD of Glu 14 A from the RNase tutorial model. Huw The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------
