Dear Eike,
This is not about me trying to convince you to change. I was pleased with Coot 0.8.9.2 when I released it and I am pleased that you like it too. I was trying to express that *I* think that the refinement in 0.9.x is across the board better and I am not seeing the problems that you see. Instead, this is about me trying to find out what you (and others) think is going wrong. This is about turning your email into a useful bug report. What I've got now is "it does not work any more and I don't like it" - and that is not helpful. You mentioned that you had problem with a ligand complex. I tried to investigate further by asking you if you were using Acedrg-Coot. You didn't answer. You suggest that atom clashes may be a problem. I tried to investigate further by asking you if you noticed a problem with Coot's description of non-bonded contacts. You didn't answer. To be clear, these were not rhetorical questions, they were an attempt to address the problems - or at least begin to do so. What I need is an example of *what* is going wrong. Just one example would be a start. It seems to me that if the problem is as pervasive as you seem to think it is, then it shouldn't be difficult for you to conjure up a problematic case. This is the sort of thing that I want: This model is based on 1xyz from the PDB, except that I've adjusted the model to create a problem. See the region of A501 - you can see that that model and the map do not correspond. It is hard for me to fix it in 0.9 because when I do X, Coot does Y, but in 0.8.9 all I had to do was A, B and C. It might be the case that Coot can trivially solve the problem, but you don't know about it - and that might be because I have insufficiently explained how to do it. Or made the means by which you can do so too opaque. Or maybe you have to type something. At the moment I have no clue. Normally, I would have taken to private correspondence by now. I recognise that your primarily interest is the latest and greatest of the 0.8 series, and you may think that this may not be worth your effort, so if you don't do this perhaps some of the other frustrated Coot users may do so? Hence the public continuation of our discussion. Regards, Paul. On 07/09/2020 10:28, Schulz, Eike-Christian wrote:
Dear Paul, Thanks for the detailed response. The reason for me being a bit annoyed is really simple: basic model building did work well in coot 0.8.x and (for me and others) it does not work anymore in coot 0.9. Because I like coot (and because most computer problems are usually 30cm in front of the screen) I have tried to get used to it for a few month, but on the weekend I have switched back to coot 0.8 * –> problem(s) solved, what a relief. I realize that I have not been particularly helpful in bug-fixing, but the changes appear to be rather comprehensive and thus I can only comment on the user experience. This is (naturally) a subjective experience but what I hear from my colleagues tells me that I am not alone with my frustration. Try to look at it from my point of view: - the previous version of coot does what I want, - I see few advantages of the new version, - the basic functionality (that I am used to) appears to be gone in the new version. Since I am not convinced - why should I switch ? Best regards, Eike * thanks to Bill Scott for the pre-compiled mac-binaries http://scottlab.ucsc.edu/xtal/wiki/index.php/Stand-Alone_Coot -----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: Saturday, 5. September 2020 at 02:05 To: "CCP4BB@JISCMAIL.AC.UK" <CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot 0.8 Dear Eike, Yes, it helps a little. Changing weights on switching refinement maps is inconvenient, but not a point of failure. Alternative conformations may need some assistance - pin an atom using anchoring. When Coot starts a refinement it tells you in the terminal about the bad bonds and non-bonded contacts that it found in the model. Do you perceive that to be wrong or missing interactions? There are many ways to skin a covalent ligand complex. I use the Acedrg-Coot interface (as described in my blog). Do you? If you wish, you can calculate an average map, the tool for that can be found in Calculate -> Map Tools -> Average Maps... Perhaps it would be useful to have an alert "You're not looking at the map into which you are trying to fit the model" - maybe the background should go pink - or something. I feel that you are annoyed but I still don't understand why. As Phil used to like to say, the devil's in the details. I see that previously I didn't answer your question. So let me correct that now: (i) You can turn on interactive contact dots ("Contact Dots On") using Refinement Tools from Curlew. This is a validation tool however and doesn't describe what is going on with the refinement energy inside Coot's head. I have it turned on by default for myself, FWIW. (ii) There is no way to turn on "Old Style" refinement in 0.9 - although "proportional editing" in 0.9.1 will bring some of that non-refined initial displacement of surrounding atoms [1] (iii) 0.8.2 is the best release for the 0.8.x series. I did quite a bit of work on 0.8.3 but I never released it. Most (not all) of the updates have been folded into 0.9.x. Paul. [1] it was seeing that Tristan had added to ISOLDE something like the tool I had intended that that actually made me write it for Coot [2] - it is a useful technique when shoving around domains in cryo-EM. [2] That and watching Blender tutorials. On 04/09/2020 19:04, Schulz, Eike-Christian wrote: > Dear Paul, > > thanks for your comprehensive response in spite of my rather general comment. And thanks for listening! I hope you see this as constructive criticism and not only as blunt complaining (a national tradition ;) ): > > Instead of a screencast I'd like to give at least a few more details on the trouble on my end. > > The problems mainly arise when: > > - switching maps e.g. from 2Fo-Fc to Fo-Fc, or omit maps (X-ray restraints ?) > - modelling alternative / low occupancy conformations > - modelling covalent ligand complexes (atom clashes ?) > - parts of the solution are in either of the maps (maybe map averaging would help?) > > --> which is practically all I am doing, and the result is often a model next to but not inside of the density. I am a long-term practitioner of ctrl-drag, but with little help in these cases. > > With respect to sophisticated solution and the "method developers’ intention", I would like to answer with some experience from our own serial crystallography method development. > > For even distribution of micro-crystal slurries, we developed a custom-multichannel pipette adapter, went through different iterations, adapted and improved the design added more features optimized parameters and it now works nicely as intended. However, users rather like to use a single empty pipette-tip and distribute a big puddle of slurry manually. Not half as pretty as the solution I intended, but admittedly easier, faster cheaper. Thus, in the end the user-perspective won over my intention. > > With respect to pull-atoms restraints, I don't think more visibility is going to help the case. The restraints themselves appear to be off (if that’s a statement that helps in any way). > > I hope this helps a little bit to narrow down the hard-to-describe problem. > > Best, > > Eike > > -----Original Message----- > From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of "Schreuder, Herman /DE" <herman.schreu...@sanofi.com> > Reply to: "Schreuder, Herman /DE" <herman.schreu...@sanofi.com> > Date: Friday, 4. September 2020 at 15:02 > To: "CCP4BB@JISCMAIL.AC.UK" <CCP4BB@JISCMAIL.AC.UK> > Subject: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot 0.8 > > Dear Paul, > Thank you for your explanation. I will try to adapt my way of working to the new coot. > Best, > Herman > > -----Ursprüngliche Nachricht----- > Von: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> Im Auftrag von Paul Emsley > Gesendet: Freitag, 4. September 2020 13:58 > An: CCP4BB@JISCMAIL.AC.UK > Betreff: [EXTERNAL] Re: [ccp4bb] AW: Going back to Coot 0.8 > > EXTERNAL : Real sender is owner-ccp...@jiscmail.ac.uk > > > > Dear Frustrated Coot 0.9 Users, > > I'd like to let you know that you I have heard similar reports in the recent past (including, as you can see, from EJD). I have taken what I believe to be remedial action to address the most pressing issue. > > I think the situation has arisen because Coot users are bringing previous experience of using RSR into their use of 0.9. Because the movement of the non-dragged atoms in 0.8.x was rather unsophisticated, many people learnt (I discovered, rather late in the day) to "flick" the dragged atom with a large and fast movement to get over a local energy barrier. (Needless to say, I hadn't intended for that to happen, the approved way to make such modifications was Ctrl-drag over-dragging.) Applying a large and fast flick to the dragged atom in > 0.9 often leads to an undesired result. If one then misses that fact that an atom pull restraint is still in effect and goes on to drag on another atom, then confusion and frustration ensues. > > For myself, by using eigen-flip and jiggle fit beforehand and then by combining pepflip, JED Flip and backrub rotamer during RSR I often don't even need to pull on the atoms. By adding in interactive contact dots, I can see what it is that's causing Coot to not move the atom to where I'm trying to drag it (the NBCs have been re-paramaterized and up-weighted in the 0.9.x rewrite). I have, from time to time in the past year, used Coot 0.8.x and to me it now feels painfully crippled. RSR in Coot 0.9.x is joyfully expeditious and pleasingly animated. > > For now (which is to say, before Coot 0.9.1 is available) I suggest keeping an eye out for unsatisfied atom pull restraints, and using the "Clear Pull Restraints" at moments of confusion. Also, use less flick and more smoothness when dragging atoms. For example, a 180 degree rotation of the ribose from the Coot tutorial would be difficult, if not impossible using 0.8.x, but in 0.9.x one can pull on the hydrogen atom of the O5' > to rotate it in a few seconds. I have added a (rather poor) video of me doing just that to my channel (I should make a better video). > > With all that said, I am still listening - I will add a change shortly that will make the pull atom restraints more obvious by making them fatter, pinker and more opaque. If there are still problems and you could somehow make a screencast available to me that illustrates the problem, then I would be very interested to view it. > > Regards, > > Paul. > > > On 04/09/2020 10:05, Schreuder, Herman /DE wrote: > > Dear Paul, > > > > Here I fully agree with Eike. With the real space refinement in the > > new coot the ligand often goes everywhere, except where it should go. > > Changing the Xray weight helps sometimes, but not always. In many > > cases I do not real-space refine and leave it to Buster to do the refinement. It would be very good if the old behavior could be reinstalled. > > > > Best regards, > > > > Herman > > > > *Von:*CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> *Im Auftrag von > > *Schulz, Eike-Christian > > *Gesendet:* Freitag, 4. September 2020 10:36 > > *An:* CCP4BB@JISCMAIL.AC.UK > > *Betreff:* [EXTERNAL] [ccp4bb] Going back to Coot 0.8 > > > > *EXTERNAL : *Real sender is owner-ccp...@jiscmail.ac.uk > > <mailto:owner-ccp...@jiscmail.ac.uk> > > > > Dear Paul, > > > > I have been working with coot for over 10 years now with little reason to complain. > > > > However, in spite of trying for a few months now, I am not getting warm with coot 0.9. > > > > I like the new eye-candy, and the more organized menus. But fitting > > residues and ligands into ED, has never before been so difficult, and > > frankly it annoys me that previously simple tasks have become an > > effort. It seems as if coot and I see different minima and we always disagree where to put the residue. At the moment all my data are at convenient resolutions of 1.7Å or better, so there is little ambiguity on that side. > > > > I am using all default settings, but maybe there is something that needs to be changed? > > > > * Is there a way to go back to the old (0.8-style) fitting functions in coot 0.9? If so how? > > * If not, which of the last coot versions > > (https://urldefense.proofpoint.com/v2/url?u=https-3A__www2.mrc-2Dlmb.cam.ac.uk_personal_pemsley_coot_binaries_release_&d=DwIDaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=JMRzXNjcC-4YR8SFJTyrf_aNVcxumHrqFuPyV9QJlUM&s=5NsBSHjvi7V_A6kImjIckNzc50syFHFMZyXcv7xVvNA&e= > > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www2.mrc-2Dlmb.cam.ac.uk_personal_pemsley_coot_binaries_release_&d=DwMGaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=3AflakQZ5Fz_M9sPnssJL3oU4C-u25224gN5ljs5KwA&s=_vveOeCJ42OXDKFFrxFP_yaBEA0xSQBIGW2RWy8kmAk&e=>) > > would you recommend? > > > > With best regards, > > > > Eike > > > > ---------------------------------------------------------------------- > > -------------------------------------- > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.u > > k_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1&d=DwIDaQ&c=Dbf9zos > > wcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8o > > HzZyRHMQu1AQ&m=JMRzXNjcC-4YR8SFJTyrf_aNVcxumHrqFuPyV9QJlUM&s=eaYXeWi77 > > kgDfJvtGBGRhDVnuYKmGhyagkOCVMZI02I&e= > > <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac. > > uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMGaQ&c=Dbf9zo > > swcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8 > > oHzZyRHMQu1AQ&m=3AflakQZ5Fz_M9sPnssJL3oU4C-u25224gN5ljs5KwA&s=75WQhZGY > > Otd4zWRp-4QbaftNeHjcD7TdnUNJCeafm8o&e=> > > > > > > > > ---------------------------------------------------------------------- > > -------------------------------------- > > > > To unsubscribe from the CCP4BB list, click the following link: > > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.u > > k_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1&d=DwIDaQ&c=Dbf9zos > > wcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8o > > HzZyRHMQu1AQ&m=JMRzXNjcC-4YR8SFJTyrf_aNVcxumHrqFuPyV9QJlUM&s=eaYXeWi77 > > kgDfJvtGBGRhDVnuYKmGhyagkOCVMZI02I&e= > > > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1&d=DwIDaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=JMRzXNjcC-4YR8SFJTyrf_aNVcxumHrqFuPyV9QJlUM&s=eaYXeWi77kgDfJvtGBGRhDVnuYKmGhyagkOCVMZI02I&e= > > This message was issued to members of https://urldefense.proofpoint.com/v2/url?u=http-3A__www.jiscmail.ac.uk_CCP4BB&d=DwIDaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=JMRzXNjcC-4YR8SFJTyrf_aNVcxumHrqFuPyV9QJlUM&s=WObQ0_zD2AkvVrmTBHIt0liSCRENbmeKP7NQJQfORwg&e=, a mailing list hosted by https://urldefense.proofpoint.com/v2/url?u=http-3A__www.jiscmail.ac.uk&d=DwIDaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=JMRzXNjcC-4YR8SFJTyrf_aNVcxumHrqFuPyV9QJlUM&s=MrY51xu69NDzoho1ql-Qe0SkcNY8eTjK5OyjAsr5os4&e=, terms & conditions are available at https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_policyandsecurity_&d=DwIDaQ&c=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo&r=HK-CY_tL8CLLA93vdywyu3qI70R4H8oHzZyRHMQu1AQ&m=JMRzXNjcC-4YR8SFJTyrf_aNVcxumHrqFuPyV9QJlUM&s=5tczq6xBwaqHxiS03OK4nvGKnbHGHUF6V61owlsnfNg&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/ > > > ######################################################################## > > 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/
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