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 [image: 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>) 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/ > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
