I like to use difference maps between Fa and Fb .. It is a bit tricky now to set them up..but they do highlight changes.
Obviously 1) you need to have the same spacegroup and cell, and the same indexing convention. (Easy to check this in the data processing task when importing the second data set. - give the first data set as a reference) 2) Dont be tempted to run molecular replacement on the second structure - just start refinemen from structure 1) - it is MUCH simpler if both examples are on the same origin.. Now maybe you go back to the old fashioned ccp4i. Run CAD to put both sets (and associated phases for one of the structures) into a single mtz Run SCALEIT to a) put the two data sets on the same scale, and b) look for a sensible resolution to choose, and to pinpoint any unlikely differences that could dominate a difference map.. Then I run the old FFT task where you could input these cut offs easily, but maybe it is possible with the newer program?? No documentation though that I could find.. The FFT map can then be read into COOT (dont forget to mark it as a difference map) And a peak search will highlight large positive and negative regions Positive where there is something in structure 1) but not in 2) Negative where there is something in structure 2) but not in 1) Easy-peasy??? well - it really is informative! Eleanor On Tue, 9 Apr 2024 at 08:33, Briony Yorke <[email protected]> wrote: > Hi Murpholino, > > > > Helen Ginn is developing software to characterise changes in protein > structures (especially informative when the changes are small but > significant)– there is a web app and a download here: > > > > https://rope.hginn.co.uk > > > > I recommend watching the youtube tutorial. > > > > *From: *CCP4 bulletin board <[email protected]> on behalf of > Murpholino Peligro <[email protected]> > *Date: *Tuesday, 9 April 2024 at 02:39 > *To: *[email protected] <[email protected]> > *Subject: *[ccp4bb] How to compare the same protein crystallized in > different conditions? > > *Caution External Email:* Do not click any links or open any attachments > unless you trust the sender and know that the content is safe. > > Hi... > > Let's say I want to compare the same protein crystallized in different > conditions. Same space group, almost same resolution. The global RMSD will > be pretty small (around 0.3 Angstroms). There will be some changes in > rotamers in some residues and some extra waters here and there... Besides > local rsmd and contact maps (or differences in contact maps)... is there > anything else to get a decent view of these small changes? > > Thanks a lot. > > > > > ------------------------------ > > 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 > ######################################################################## 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/
