I agree with Harry, I suspect that embarrassment has no definition/ meaning in the context of Nature. ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Harry Powell <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> Sent: Tuesday, May 14, 2024 6:28 PM To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] Experimental phasing Selenomethionine data collection etc. tips
Hi With this in mind, I have found the easiest way to generate AlphaFold models (for those not in the DB) is actually in CCP4 Cloud-remote - makes MR using AF models a real doddle. See the Tutorials (in particular on MR) available with CCP4 Cloud. Harry > On 14 May 2024, at 09:20, Randy John Read <rj...@cam.ac.uk> wrote: > > Dear Marco, > > You don’t mention here or in the earlier thread whether you tried AlphaFold > models and, if you did, how you prepared them for MR. I’m happy to hear of > any case where we still need experimental phasing methods to solve new > protein structures, but we’ve seen very few examples where AlphaFold models > didn’t work! > > I’m probably not the only one who would be delighted to take a look at the > problem to see what we can learn from it, if AlphaFold models really aren’t > working. > > Now, back to your question: to prepare for a SAD phasing experiments one > place I would look would be Tom Terwilliger’s recent papers on planning and > analysing SAD experiments (https://doi.org/10.1107/S2059798315019269, > https://doi.org/10.1107/S2059798315019403) as well as other information on > this from the Phenix website, including the YouTube tutorials. > > Best wishes, > > Randy Read > >> On 14 May 2024, at 01:17, Marco Bravo >> <0000d0eb7bee83ae-dmarc-requ...@jiscmail.ac.uk> wrote: >> >> Hello all, >> I have a data collection trip next week and plan to collect data on >> selenomethionine derivative crystals at the al831 beamline. Are there any >> resources, tips, tutorials, literature etc. That you can recommend to help >> me prepare for these experiments. Also is there a way to plug in the >> experimental data into ccp4 cloud to do the automatic structure solution? Do >> I need native and derivative data to solve the structure? Last trip I >> collected a seemingly 2.8 angstrom resolution data on a crystal of the >> native protein but could not get a solution depsite extensive molecular >> replacement attempts. It seems that assigning a space group for the crystals >> has been troublesome as well. here is my last thread I posted about the >> issue for reference. >> >> https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=ind2402&L=CCP4BB&O=D&X=CCE6DFA19FA3D40346&Y=mbrav005%40ucr.edu&P=112302 >> >> ######################################################################## >> >> 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 http://www.jiscmail.ac.uk/CCP4BB, a >> mailing list hosted by http://www.jiscmail.ac.uk/, terms & conditions are >> available at https://www.jiscmail.ac.uk/policyandsecurity/ > > ----- > Randy J. Read > Department of Haematology, University of Cambridge > Cambridge Institute for Medical Research Tel: +44 1223 336500 > The Keith Peters Building > 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<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list > hosted by www.jiscmail.ac.uk<http://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&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk<http://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&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/
