Dear Paul, sorry for the delay.
I did not answer your previous questions in detail, because going back to coot 0.8 did solve the problem for me, which kept me busy. But of course, to do sth. about the situation you need to understand a lot better what is going on. What I have is a “phenotype” (coot 0.9) that presents differently than the previous generation (coot 0.8) and since it’s not possible for me to revert any of the mutations its hard to pinpoint the cause of the problem. The most general description I can come up with: in coot 0.9 the model moves “funny” – different from coot 0.8. Some (new?) restraints seem to act on the atoms preventing them to stay where I put them. This "hidden-thinking" coot 0.9 appears to apply confuses me. *I don’t think this description is a major improvement from before, maybe someone else (Georg?, Eleanor? Herman?) can give it a try? However, I have a hunch that the root of our communication trouble is that the way you and I are using coot is very different. Therefore, I think it maybe best if (a) I told you how I use it most of the time and (b) provide you with a specific example (off-list). Maybe you can reproduce the trouble if you follow my procedure. Staying in the picture of your Ferrari/bus metaphor, I think I am probably walking to work: I am predominantly using the real-space refine options, going through the structure bit by bit, putting the model where (I think) it belongs. I also make use of the stepped-refine procedure, but I know more than one colleague who considers that “cheating” already or do not know about that option at all. Of course, I am making use of the validation, measurement, map and model tools, but hardly of any automation (§). No special key-binding, no scripts - just out of the box, default settings, iterative cycles with refinement. That may not be what you have intended, but the people in my echo chamber just do the same. Eigen-flip, jiggle-fit, pepflip, JED-flip, backrub, interactive contact dots, acedrg – sorry I’ve never heard of them. You mentioned a blog and/or other coot info before. With coot 0.9 I tried finding more information but your coot-website and the included tutorials appear to be a bit older https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/. Is there a new source of info somewhere? - I am happy to look into it. Best, Eike § automatic building of alternate conformations for HR-structures would be really helpful though. -----Original Message----- From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Paul Emsley <pems...@mrc-lmb.cam.ac.uk> Reply to: Paul Emsley <pems...@mrc-lmb.cam.ac.uk> Date: Tuesday, 8. September 2020 at 17:44 To: "CCP4BB@JISCMAIL.AC.UK" <CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] AW: Going back to Coot 0.8 On 08/09/2020 16:25, Georg Zocher wrote: > > > we have the same experience in our lab. What experience is that? I am still in the dark about you think is now worse. > Personally, I did would not like to judge here, as so far, I did not > have had enough time to get into the new RSR of coot 0.9.x by myself. > But many colleagues did not like the new refinement module maybe just > as they are used to the method in all coot versions before. You have a Ferrari parked beside your house but you want to to take the bus to work because that's what you've always done. Or maybe the Ferrari is parked around the back and you don't know it's there? > > I just thought if it wouldn't be an option to let the user decide what > kind of RSR implementation she/he would like to use and give them the > choice via an option in coot preferences? That would be possible but not easy. Unlike much of the CCP4 suite, Coot is Free Software. But, again... why would you want to take the bus? Explain. regards, Paul. ######################################################################## 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/ ######################################################################## 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/
