Hi all, Just to conclude on this - ARCIMBOLDO via CCP4 in coiled coil mode worked quite nicely in the end now that I finally had time to work through it - took a few days with 8 x 20 aa peptides as the search set on my old iMac but the end result was fine :). So didn't have to try other options really in the end. The pipe line worked quite nicely given there are 400 residues in the asymmetric unit.
Thanks for everyone for the suggestions and advice! Best, Tommi On Oct 8, 2019, at 12:00 PM, IRACEMA CABALLERO MUÑOZ <icm...@ibmb.csic.es<mailto:icm...@ibmb.csic.es>> wrote: Hi Tommi, as sent by Kay ARCIMBOLDO has a specific mode to solve coiled coils (http://scripts.iucr.org/cgi-bin/paper?cb5097). Here you can find the tutorial: http://chango.ibmb.csic.es/tutorial_coiled, it explains how to launch it through the command line and a summary explaining the improvements of the mode. It can also be launched through CCP4i, here you only need to activate "run coiled-coil mode" and put the search strategy (number of helices and helix length). In this supplementary table, you have examples of the search strategy for 150 cases https://doi.org//10.1107/S2059798317017582/cb5097sup2.xlsx [coiled_coil_mode_ccp4i.png] And please if you have any questions just let me know. Best wishes, Iracema El mar., 8 oct. 2019 a las 9:33, Daniel Rigden (<drig...@liverpool.ac.uk<mailto:drig...@liverpool.ac.uk>>) escribió: Hi Tommi Yes, AMPLE does well with coiled-coils. The QUARK route is the easiest to try. In your position I would simply trim a bit of sequence off either end. Maybe you can see homologs that are a bit shorter at one terminus? In any case, that's unlikely to affect the modelling and we've seen QUARK make good models of coiled-coil proteins. For Rosetta modelling we simply recommend you use the Robetta server http://robetta.bakerlab.org/fragmentsubmit.jsp for fragment libraries. Unless you're processing large numbers of sequences it's not worth getting to grips with local fragment library generation. At the moment CCP4online takes a file of ready-made models, not carrying out the actual modelling for you. Doing local Rosetta modelling via AMPLE is as described here https://ample.readthedocs.io/en/latest/examples/rst/abinitio.html#example-abinitio Recently, in collaboration with Owen Davies in Newcastle, we've made some big improvements to AMPLE's abilities with coiled-coils, involving more bespoke modelling protocols, both of a single chain and, where the information is known, of a parallel oligomer. I gather Owen has been in touch with you about these. The code is available but is not in the current CCP4 distribution. We're also planning to improve the AMPLE documentation in the next few months and we'll include an example of use of this new coiled-coil mode at that time. Best wishes Dan On 07/10/2019 22:33, Kajander, Tommi A wrote: > Hello, > > We have a bit tricky case of coiled coil protein with good data (2.05Å) for > dimeric coiled coil (dimer in AU) - looks like AMPLE might be a way > to solve such cases, if you know other good programs please suggest (Better > yet if there is a clear how-to manual) > > Some technical tips on usage for generation of fragments for AMPLE would be > of help, not completely on top of that… (running the QUARK server, the real > sequence is bit over 200 aa so not sure what is the best approach here? > Rosetta? any how-to for that.. well i am running Robetta fragments too). > > with AMPLE can I do this with the online server or better run locally (need > Rosetta installed I take it?) > > Suppose I could try Rosetta-MR also, but to my recollection that requires > some kind of a phaser hit first to be improved, and i dont think I am there. > > Thanks for any comments, > > Best, > Tommi > > > > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- Prof Daniel Rigden Institute of Integrative Biology Room 101, Biosciences Building University of Liverpool Crown St., Liverpool, L69 7ZB (+44) 151 795 4467 pcwww.liverpool.ac.uk/~drigden/<http://pcwww.liverpool.ac.uk/~drigden/> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 Tommi Kajander, PhD Principal investigator Structural Biology and Biophysics Institute of Biotechnology Biocenter 3, Viikinkaari 1 (PO Box 65) University of Helsinki tommi.kajan...@helsinki.fi<mailto:tommi.kajan...@helsinki.fi> +358 294158904 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
