Re: [ccp4bb] Measuring angles between domains
Well I do this by overlapping one domain of protein A onto protein B - you can do that in coot - then overlap the second domain of the shifted A onto the second domain of B. The coot log file tells you omega phi kappa applied and kappa is your angle of interest... is that clear enough - I could give more detail.. The worst problem is finding the coot log file but if you are using I2 it is available in the job directory.. Eleanor On Fri, 12 Nov 2021 at 19:37, Ishan Rathore wrote: > Hi Kyle > > I have used this pymol plugin to measure the angle between domains > > https://pymolwiki.org/index.php/Angle_between_domains > > Regards > Ishan > > > On Sat, Nov 13, 2021, 12:35 AM Kyle Gregory < > 3632e92fcc15-dmarc-requ...@jiscmail.ac.uk> wrote: > >> Dear CCP4 bulletin board, >> >> I have two domains connected by a helix and I want to measure tilt angles >> between domains, for comparison purposes to other structures of the same >> protein. >> >> Does anyone have any tools they'd recommend? >> >> Kind regards, >> Kyle >> >> >> >> -- >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 >> > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
Re: [ccp4bb] High-order oligomers vs robust crystals - references?
Hi, I think this paper might be useful for digging into oligomerization and crystallization: https://onlinelibrary.wiley.com/doi/pdf/10.1002/anie.201806092 I'm not sure they discuss prokaryotes but do have many interesting ideas. Best, Orly On Fri, Nov 12, 2021 at 7:20 PM Edwin Pozharski wrote: > One could use PISA to get a rough distribution of oligomerization states > of proteins in the PDB and compare bacterial vs mammalian... there always > will be a question though of whether any bias is inherent in proteins or > driven by crystallizability itself. > > Personally, I always though that bacterial proteins crystallize better > because they express better and are more stable. All of this is hand > waiving on my part, of course. > > --- > I don't know why the sacrifice didn't work. The science seemed so solid. > Julien XIII, Lord of the Lemurs > > On Fri, Nov 12, 2021 at 9:52 AM Frank von Delft < > frank.vonde...@cmd.ox.ac.uk> wrote: > >> Hello all >> >> Two decades ago, I remember (!) much talk about a reason that bacterial >> proteins crystallize "more easily" is that they tend to come as >> oligomers (dimers and up), and that this internal symmetry made them >> happier to crystallize. >> >> Did anybody ever publish hard evidence? Or even, is there a primary >> citation for the idea? >> >> Thanks >> Frank >> >> >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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=1 > -- Orly Avraham, Ph.D. Postdoctoral fellow The lab of Prof. Ora Schueler-Furman The Hebrew University of Jerusalem Israel To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
[ccp4bb] Open position: Structural Bioinformatics Pipeline Developer at Lonza (Cambridge UK)
Hi All, We are hiring again! Know someone that wants to join a fast growing team? We are seeking a highly motivated and skilled developer with experience in implementing structural bioinformatics tools/pipelines to join Lonza's Early Development Services (EDS) Bioinformatics team based in Cambridge, UK. To apply: https://www.lonza.com/jobs/R38474 Daphne Daphné Truan, PhD Senior Group Leader EDS Bioinformatics Lonza Biologics Chesterford Research Park Cambridge, United Kingdom www.pharma.lonza.com To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/
