Hi Murpholino, You could go the route of comparing refined models, as described by Dr. Yorke. As Dr. Dodson describes, isomorphous difference maps are another way to compare datasets. A benefit is that they do not require separate refinement of models for both states, which can render the comparison susceptible to differences in modeling choices. Isomorphous difference maps have been used for comparison of crystallographic datasets for decades.
Using CCP4’s utilities provides one way of doing so. Depending on your comfort with python and need to understand exactly what you are doing, you may also appreciate the following non-CCP4 options (apologies; this includes some self-promotion): 1. Use of PHENIX’s isomorphous difference map routine—it’s easy to use but could be better documented. 2. Use of reciprocalspaceship (rs), which is based on modern python. See here for an example: https://rs-station.github.io/reciprocalspaceship/examples/6_timeresolvedPYP.html (this was developed by Jack Greisman and Kevin Dalton, initially within my research group). In cases where the unit cells are similar but not quite the same, it may be helpful to try MatchMaps, developed by Dennis Brookner in my group: https://rs-station.github.io/matchmaps/quickstart.html. Matchmaps, rs, and its add-on rs-booster, are open-source and you and everyone else are welcome to adapt the code for your own purposes. Hope this helps, Doeke From: CCP4 bulletin board <[email protected]> On Behalf Of Murpholino Peligro Sent: Monday, April 8, 2024 9:39 PM To: [email protected] Subject: [ccp4bb] How to compare the same protein crystallized in different conditions? 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<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMFaQ&c=WO-RGvefibhHBZq3fL85hQ&r=DPfbtiuJFZDsaMqRC3wABRuP0iJZMKOIsdAAHocfxcg&m=cMD6L-aSuJB8Pn2hRWAhI4O_rB8womRPm9cQR_L-uuVm_w_IuO7CgiNxnt2eOYaR&s=C7zPtOeCi5fFM7KwpFINs6NmqNCIi_GTxhSvEFDxTV4&e=> ######################################################################## 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/
