 |
 |
Thank you - that is a super useful tool. Of course alphafold should always do better when used for testing a known structure - it has used thst model presumably as part of the basis for its prediction. Eleanor On Sat, 4 Mar 2023 at 06:42, Ricardo Padua <[log in to unmask]> wrote: > Hi, > You can also use Theseus (https://theobald.brandeis.edu/theseus/) to > superimpose the NMR states using maximum likelihood. > By running: > theseus 4hiq.pdb > it will spit out the superimposed ensemble and also the average structure > which you can use as a guide to trim the flexible bits. That resulted in a > TFZ of 6.4 against the 4ey9 data in Phaser (2h run). The > Alphafold predicted model performed significantly better, Phaser found a > solution with a TFZ of 10.7 in a couple of minutes. > > > On Thu, Mar 2, 2023 at 1:25 PM Eleanor Dodson < > [log in to unmask]> wrote: > >> Thank you for all the excellent suggestions. (And the aligned models!) >> I am not ACTUALLY trying to solve the structure - it is insulin, which I >> have seen before.. >> It was a student project - solve 4ey9 using 1hiq.. which didn't work in a >> straightforward way. Hence my puzzlement.. >> Insulin MR is never easy - there is only 30% solvent, metal ions not in >> the model, two molecules in the asymmetric unit, each with two chains to >> position, >> and several different folds to choose from in the PDB (would be >> interesting to see what Alphafold predicts from sequence alone..) >> To add to the difficulty - the strong low resolution data for 4ey9 is >> missing which is never good for MR either. >> Will try to rationalise what I have learnt. >> Eleanor >> >> >> >> >> On Thu, 2 Mar 2023 at 16:53, Olson, Linda < >> [log in to unmask]> wrote: >> >>> Typically we only align regions within a certain rmsd for backbone heavy >>> atoms since regions lacking NOE’s are just randomly placed. The aligned >>> regions should be listed in the original manuscript in their statistics >>> table. You can just make these selections in pymol to get the best >>> alignment. We used to use a program called MolMol >>> >>> >>> >>> Best, >>> >>> Linda >>> >>> >>> >>> *From: *CCP4 bulletin board <[log in to unmask]> on behalf of Randy >>> John Read <[log in to unmask]> >>> *Date: *Thursday, March 2, 2023 at 10:19 AM >>> *To: *[log in to unmask] <[log in to unmask]> >>> *Subject: *Re: [ccp4bb] NMR structires >>> >>> ATTENTION: This email originated from a sender outside of MCW. Use >>> caution when clicking on links or opening attachments. >>> ------------------------------ >>> >>> Hi Eleanor, >>> >>> >>> >>> Normally they are aligned, but I guess not for really old ones. >>> >>> >>> >>> I tried to use Ensembler to align them, but it uses SSM, which didn’t >>> find enough to work with I guess. However, ChimeraX’s matchmaker tool did >>> manage, and you can see the ensemble isn’t very tight! >>> >>> >>> >>> >>> >>> Randy >>> >>> >>> On 2 Mar 2023, at 15:09, Eleanor Dodson < >>> [log in to unmask]> wrote: >>> >>> I have been looking at 1hiq - an NMR structure with 20 models. >>> I had always assumed that an attempt had been made to overlap the first >>> with the second, third etc, but this does not seem to be so for this >>> structure.. >>> Have I been labouring under a misapprehension? >>> Eleanor Dodson >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> <https://urldefense.com/v3/__https:/www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!H8mHWRdzp34!4GDBb8zAmQri-kX1gjNcW6WwuKz3HOkCrXXfzMrnioQWVB7HmFu2ZSBXr8f44TtnNFQaSYLyKYNtKQ$> >>> >>> >>> >>> ----- >>> Randy J. Read >>> Department of Haematology, University of Cambridge >>> Cambridge Institute for Medical Research Tel: +44 1223 336500 >>> The Keith Peters Building >>> Hills Road E-mail: >>> [log in to unmask] <[log in to unmask]> >>> Cambridge CB2 0XY, U.K. >>> www-structmed.cimr.cam.ac.uk >>> <https://urldefense.com/v3/__http:/www-structmed.cimr.cam.ac.uk__;!!H8mHWRdzp34!4GDBb8zAmQri-kX1gjNcW6WwuKz3HOkCrXXfzMrnioQWVB7HmFu2ZSBXr8f44TtnNFQaSYJ-aNoscA$> >>> >>> >>> >>> >>> ------------------------------ >>> >>> To unsubscribe from the CCP4BB list, click the following link: >>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >>> <https://urldefense.com/v3/__https:/www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!H8mHWRdzp34!4GDBb8zAmQri-kX1gjNcW6WwuKz3HOkCrXXfzMrnioQWVB7HmFu2ZSBXr8f44TtnNFQaSYLyKYNtKQ$> >>> >>> ------------------------------ >>> >>> 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 >> > > > -- > Ricardo Padua > HHMI Research Specialist > Kern Lab > Dept. of Biochemistry, MS009 > Brandeis University > Waltham, MA 02454, USA > > E-mail: [log in to unmask] > ######################################################################## 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/