If there isn’t already a suitable model, this looks like a good opportunity to try out the powerful new RoseTTAFold deep learning algorithm by Minkyung Baek in David Baker’s lab. It can be used through the Robetta server (http://robetta.bakerlab.org, choose Structure Prediction->Submit and then choose the RoseTTAFold option). It’s already been used to solve a number of unsolved structures, including the ones discussed in a paper on the algorithm (https://www.biorxiv.org/content/10.1101/2021.06.14.448402v1) and others I’ve heard of through the grapevine.
Best wishes, Randy > On 2 Jul 2021, at 12:52, Eleanor Dodson > <0000176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > > Yes - nothing very significant in the self rotation list of peaks.. > Is the resolution really 2.6A though - if so it will be very difficult to > find a single helix which would be quite a small fraction of 70x2 residues > Iwould think.. > Is there no suitable model? > Eleabor > > On Fri, 2 Jul 2021 at 12:45, leo john <ljohn16012...@gmail.com> wrote: > Thank you all. > > I have tried both space groups. I am attaching the required file. > > Cheers > John > > On Fri, Jul 2, 2021 at 12:40 PM Eleanor Dodson <eleanor.dod...@york.ac.uk> > wrote: > I presume you have tested both P41 and P43 space groups? > It is a bit hard to check peak heights in the self rotation. Could you attach > the molrep output - I think it is called xxxmolrep.doc.txt in the > job directory.. > Eleanor > > > On Fri, 2 Jul 2021 at 12:33, leo john <ljohn16012...@gmail.com> wrote: > Hi Group; > > I have collected data at approximately 2 Ang and automated softwares at > Diamond have processed it in spacegroup P41. > My peptide is 70 residues long with 3 helices of minimum 17 residues in it. > According to Mat. Coeff. there are 2 molecules. I am also attaching the > self-rotation function output map (please give some opinion on it also i.e > number of molecules, symmetry). > > Since the molecule has mainly alpha-helices, I am trying to use Arcimboldo > but with no luck. > I have used both the coiled-coil mode and normal mode for it and maximum > value of CC after 5 cycles I get is closed to 20 that is not great for a > solution. Even upon looking the structure solution by Arcimboldo, I found a > lot of loops and I do not get any density for sidechains. A few of the parts > of the helices and loops are overlapping. > > I have used CCPi2 with the following options: > The assymmetric unit contains 1 molecule of mol wt 7300 > search for 3 helices of length 14 residues > > Any help will be appreciated. > <image.png> > > Thank you > John > > > 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 > ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Fax: +44 1223 336827 Hills Road E-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk ######################################################################## 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/
