Re: [COOT] rotamer selection
Hi Paul, Thank you for reading and taking time to answer my email. Please see my replies in blue below. Regards, Daniel From: Paul Emsley Date: Thursday, 31 August 2023 at 01:46 To: Daniel Larsson , Subject: Re: rotamer selection On 25/08/2023 06:56, Daniel Larsson wrote: Hi Paul, I have some suggestions/requests for facilitating sidechain modelling. 1. Option to have the rotamer tool default to the rotamer most closely resembling the current rotamer (now it defaults to the most common rotamer) That seems like a marginal improvement in the user interface. If you want to "just tighten up the probability to the closest rotamer" then turn on rotamer restraints so that they are used during refinement (set-refine-rotamers 1) The benefit of this would be that you could quickly “look-up” the closest documented rotamer. For example, in situations when you are refining multiple models in parallel and want to make one consistent (perhaps lower resolution) with another. Or for analysis/documentation purposes e.g. saying “in model 1 residue X has rotamer N and in model 2 it has rotamer M”. Thanks for the tip for how to use rotamer restraints. I have not been doing that in COOT before, but I think I looked for it before and could not find the feature. I will make a hot-key for that switch. Perhaps it would be nice to have that restrain in the R/RC menu so that more people would find it? 1. Option to have the rotamer tool default to the rotamer with the highest average map value for the atoms. Atoms closer to the Ca should be weight higher (as an option). This could be done quite easily. But it's getting quite close to auto-fit-rotamer functionality. Yes, but the distinction would be important to me. I first focus on CaBLAM and Ramachandran outliers and after that work is done I want to disturb the backbone as little as possible. To me, auto-fit-rotamer moves the backbone too much and the whole mainchain geometry usually gets distorted (beyond just tandem refine it back into shape). At first, I thought that “vanilla” auto-fit would not move the main chain atoms and that the backrub rotamer option was intended for this purpose, but both affect the backbone so I don’t understand the distinction and have stopped using auto-fit-rotamer altogether. 1. Perhaps also have an option to allow for a small rotation/translation. The devil, is as Phil would say, in the detail. That is very true. This suggestion moot, since it would be better to just enable rotamer restraints and refine “the normal way”. 1. Show all rotamers in the rotamer library at the same time and then you can click on the one that you want (“bouquet” mode) I don't see how this is an improvement over the use of the dot and comma keys. Yes, I do use the dot and comma keys and they are great. But the long sidechains have extensive rotamer libraries (I’m looking at you arginine) and often many rotamers go out of the plane when you are zoomed in, so you have to spin the structure around to see which ones can be ignored right-away and which ones are close contenders. And when you look at them in sequence, you would have to memorize the good ones (for example 7, 12 and 31) and then go back and flip back and forth between them a few times to decide which one fits the density the best while also makes biochemical sense. Here are even more feature requests for this non-existent feature: Perhaps you could shift/control click to deselect/select rotamers (maybe together with box selection) and then use delete to hide bad candidates. Another suggestion which might be easier to implement would be to color-code the options in the rotamer list according to density fit (and maybe also clash score)? Or maybe even color-code the rotamers in the bouquet view to take the analogy one step further! 1. Automatically select the best rotamer in a chain/molecule considering fit-to-density and clashes, but without touching the backbone and not doing any refinement. The backbone shrugs when the sidechain dances. There is no tool in Coot for rotamer fitting that doesn't move the mainchain. It could be done quite easily, but I am not convinced of the utility. It seems to me that it is quite possible the the backbone atom positions have already been compromised to account for the wrongly positioned sidechain rotamer and so without variation in backbone orientation, the wrong rotamer is more likely to be found. This is also true. I always do a tandem or sphere refine to a djust the backbone after selecting rotamer. But I prefer to do it in two independent steps to have more control. And if the density is weak, I would probably adjust the rotamer again after that (and then point 1 above would be helpful to quickly get an ideal rotamer) to get sound initial model restraints for the final global minimization. Paul. p.s. are you iDaniel? No, that must be another Daniel that you are thinking about
Re: [COOT] rotamer selection
On 25/08/2023 06:56, Daniel Larsson wrote: Hi Paul, I have some suggestions/requests for facilitating sidechain modelling. * Option to have the rotamer tool default to the rotamer most closely resembling the current rotamer (now it defaults to the most common rotamer) That seems like a marginal improvement in the user interface. If you want to "just tighten up the probability to the closest rotamer" then turn on rotamer restraints so that they are used during refinement (set-refine-rotamers 1) * Option to have the rotamer tool default to the rotamer with the highest average map value for the atoms. Atoms closer to the Ca should be weight higher (as an option). This could be done quite easily. But it's getting quite close to auto-fit-rotamer functionality. * Perhaps also have an option to allow for a small rotation/translation. The devil, is as Phil would say, in the detail. * Show all rotamers in the rotamer library at the same time and then you can click on the one that you want (“bouquet” mode) I don't see how this is an improvement over the use of the dot and comma keys. * Automatically select the best rotamer in a chain/molecule considering fit-to-density and clashes, but without touching the backbone and not doing any refinement. The backbone shrugs when the sidechain dances. There is no tool in Coot for rotamer fitting that doesn't move the mainchain. It could be done quite easily, but I am not convinced of the utility. It seems to me that it is quite possible the the backbone atom positions have already been compromised to account for the wrongly positioned sidechain rotamer and so without variation in backbone orientation, the wrong rotamer is more likely to be found. Paul. p.s. are you iDaniel? To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [COOT] rotamer selection
I can also add that “Auto Fit Rotamer” tool is probably intended to do #4, but to me it is not useful, since it moves the mainchain atoms. I have disable backrub rotamers (I think). Regards, Daniel From: Mailing list for users of COOT Crystallographic Software on behalf of Daniel Larsson Reply to: Daniel Larsson Date: Friday, 25 August 2023 at 07:56 To: Subject: rotamer selection Hi Paul, I have some suggestions/requests for facilitating sidechain modelling. * Option to have the rotamer tool default to the rotamer most closely resembling the current rotamer (now it defaults to the most common rotamer) * Option to have the rotamer tool default to the rotamer with the highest average map value for the atoms. Atoms closer to the Ca should be weight higher (as an option). Perhaps also have an option to allow for a small rotation/translation. * Show all rotamers in the rotamer library at the same time and then you can click on the one that you want (“bouquet” mode) * Automatically select the best rotamer in a chain/molecule considering fit-to-density and clashes, but without touching the backbone and not doing any refinement. Perhaps it is already possible to do some of these things already? Regards, Daniel När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[COOT] rotamer selection
Hi Paul, I have some suggestions/requests for facilitating sidechain modelling. * Option to have the rotamer tool default to the rotamer most closely resembling the current rotamer (now it defaults to the most common rotamer) * Option to have the rotamer tool default to the rotamer with the highest average map value for the atoms. Atoms closer to the Ca should be weight higher (as an option). Perhaps also have an option to allow for a small rotation/translation. * Show all rotamers in the rotamer library at the same time and then you can click on the one that you want (“bouquet” mode) * Automatically select the best rotamer in a chain/molecule considering fit-to-density and clashes, but without touching the backbone and not doing any refinement. Perhaps it is already possible to do some of these things already? Regards, Daniel När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT=1 This message was issued to members of www.jiscmail.ac.uk/COOT, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
