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&A=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&A=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&A=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] Coot 9.8.91 is still broken
On 24/08/2023 15:53, Helge Paternoga wrote: I just had the chance to try out the new Coot version 9.8.91 from CCP4 and I would like to report that RSR of ribosomes is still broken Thank you. I will get to this shortly. I had been hoping to solve the problem without a general-purpose (and more complex) link-filtering algorithm. It seems that I should not avoid it. Regards, Paul. To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=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] Coot 9.8.91 is still broken
Dear Helge, > G533 in chain a > C823 in chain A > G1186 in chain A > C1147 in chain A > A614 in chain a These are actually what I just reported to Paul - the "DNA-SER" link problem, while some of them are DNA-TYR, but the same issue. Coot tries to make these links when RNA/DNA residues are close to SER or TYR. It is related to the AA-RNA problem: https://pemsley.github.io/coot/blog/2023/06/05/AA-RNA.html > D2T > 3TD > 6MZ In the monomer library, they have been demoted to NON-POLYMER because they do not use the standard atom names. However, it is completely fine to change D2T and 3TD group names to peptide/RNA, as the problematic atom names are those that do not exist in polymers (OXT equivalent for example). Changing 6MZ group name to RNA would be suboptimal, because they use O1P/O2P/O3P names instead of the standard OP1/OP2/OP3, and restraints for these atoms would not be used in the refinement (if you change the group name to RNA). Best regards, Keitaro On Thu, 24 Aug 2023 at 16:03, Helge Paternoga wrote: > > Dear Paul, > > I just had the chance to try out the new Coot version 9.8.91 from CCP4 > and I would like to report that RSR of ribosomes is still broken (albeit > not as severely as before). > > You can have a look at PDB-7K00 for examples: > > https://www.rcsb.org/structure/7K00 > > https://www.ebi.ac.uk/emdb/EMD-22586 > > I went through the model with sphere refine to check for broken areas > and identified many, here are a few: > > G533 in chain a > C823 in chain A > G1186 in chain A > C1147 in chain A > A614 in chain a > > > In addition, there are three modified residues in that model that still > require edited restraints to make them work in Coot: > > D2T > 3TD > 6MZ > > Here, the group name is "NON-POLYMER", I changed that to RNA (3TD+6MZ) > or L-peptide (D2T) which makes it work in Coot. Is that ok to do? > > Many regards, > > Helge > > > > To unsubscribe from the COOT list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=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/ To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=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] Coot 9.8.91 is still broken
Dear Paul, I just had the chance to try out the new Coot version 9.8.91 from CCP4 and I would like to report that RSR of ribosomes is still broken (albeit not as severely as before). You can have a look at PDB-7K00 for examples: https://www.rcsb.org/structure/7K00 https://www.ebi.ac.uk/emdb/EMD-22586 I went through the model with sphere refine to check for broken areas and identified many, here are a few: G533 in chain a C823 in chain A G1186 in chain A C1147 in chain A A614 in chain a In addition, there are three modified residues in that model that still require edited restraints to make them work in Coot: D2T 3TD 6MZ Here, the group name is "NON-POLYMER", I changed that to RNA (3TD+6MZ) or L-peptide (D2T) which makes it work in Coot. Is that ok to do? Many regards, Helge To unsubscribe from the COOT list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=COOT&A=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/
