Re: [COOT] [EXTERNAL] Re: Bug in coot to change torsion angles?
Hi Paul, I think it is a bug. I was able to rotation O10 along the C07-N08 bond, but not the O9. Here is what I got: [cid:image001.png@01D8BCB0.38CC78E0] Color-by-chain seems normal to me. Zhen From: Paul Emsley Date: Tuesday, August 30, 2022 at 20:25 To: Gong, Zhen , COOT@JISCMAIL.AC.UK Subject: Re: [EXTERNAL] Re: Bug in coot to change torsion angles? On 31/08/2022 01:17, Gong, Zhen wrote: Hi Paul, Thank you very much for your timely reply. There are still some puzzles for me. I would like to change some torsion angles of a ligand in coot but it did not work as what I expected. I was able to play with the torsion angles formed by C06 C07 N08 O10 but not C06 C07 N08 O09 (shown in the figure below). One implies the other, it seems to me. I do not agree. One changes the position of O10, while the other changes O9. What I would like to do is to manually make the O9 and O10 in the same plane with aromatic ring if possible. I was able to rotate O10 along the C07-N08 bond but not 09, which I shall be able to do in coot? If I understand correctly what you are saying then that's a bug. C06-C07-N08-O09 defines a rotatable bond (C07-N08) about which one side of the fragment (the smaller side) is rotated - i.e. you cannot move O10 without moving O09 also. That's how it should work. It seems that you are saying that that is not how it's working for you. By the way, I was able to make O9 and O10 in the same plane with the aromatic ring by adding planar restraint. I would like to know why I could not rotate O9 along the N08-C07 bond if possible. Me too. It does seem very curious. Is there a missing bond restraint - what happens when you display using colour-by-chain? 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] [EXTERNAL] Re: Bug in coot to change torsion angles?
Hi Paul, Thank you very much for your timely reply. There are still some puzzles for me. I would like to change some torsion angles of a ligand in coot but it did not work as what I expected. I was able to play with the torsion angles formed by C06 C07 N08 O10 but not C06 C07 N08 O09 (shown in the figure below). One implies the other, it seems to me. I do not agree. One changes the position of O10, while the other changes O9. What I would like to do is to manually make the O9 and O10 in the same plane with aromatic ring if possible. I was able to rotate O10 along the C07-N08 bond but not 09, which I shall be able to do in coot? By the way, I was able to make O9 and O10 in the same plane with the aromatic ring by adding planar restraint. I would like to know why I could not rotate O9 along the N08-C07 bond if possible. [cid:image001.png@01D8BCA9.3A780A30] The restraint file for the torsion angle (C06 C07 N08 O10) is defined quite well: LIG CONST_23 O09 N08 C07 C06 -5.58, which is close to zero. Therefore, O9, O10 N08 should be more or less in the same plane with the benzene ring. I agree. By default Coot does not refine torsion angles. Also torsions named "CONST" are not refined. You can turn on torsion angle refinement in the R/RC dialog I turned on the torsion angle refinement in the R/RC dialog and did real space refinement again, but O9 and O10 were still not in the same plane with the aromatic ring. I thought CONST means that this torsion angle is fixed (for example in the benzene ring), while Var means variable (flexible). This ligand has a cyclohexane ring also. The torsion angles for the carbons in the cyclohexane ring is labelled with Var_... because these angles are flexible. Could you please also help clarify this puzzle? My last question is what does esd mean? Estimated standard deviation? The esd is zero for all the torsion angles labelled with CONST. Perhaps this is why the restraint was not used during phenix.refine? I really appreciate your time and effort to help! Best regards, Zhen From: Paul Emsley Date: Tuesday, August 30, 2022 at 19:21 To: Gong, Zhen , COOT@JISCMAIL.AC.UK Subject: [EXTERNAL] Re: Bug in coot to change torsion angles? On 30/08/2022 22:26, Gong, Zhen wrote: Dear Coot developers and users, I would like to change some torsion angles of a ligand in coot but it did not work as what I expected. I was able to play with the torsion angles formed by C06 C07 N08 O10 but not C06 C07 N08 O09 (shown in the figure below). One implies the other, it seems to me. The restraint file for the torsion angle (C06 C07 N08 O10) is defined quite well: LIG CONST_23 O09 N08 C07 C06 -5.58, which is close to zero. Therefore, O9, O10 N08 should be more or less in the same plane with the benzene ring. I agree. By default Coot does not refine torsion angles. Also torsions named "CONST" are not refined. You can turn on torsion angle refinement in the R/RC dialog If I click on the ligand with “real space refinement”, it should make the O9, O10 N08 more or less in the same plane with the benzene ring. However, coot did not do it. If you don't have plane restraints for the nitro and ring atoms then coot doesn't know (hasn't been told) to keep them planar. All you've done is said to Coot "here's a torsion angle, don't use it.| The corollary of the above is to turn on torsion angle refinement and rename the torsion var_23. You could also add O09 to the ring plane restraint with perhaps double or triple the esd. 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] [EXTERNAL] Re: Bug in coot to change torsion angles?
On 31/08/2022 01:17, Gong, Zhen wrote: Hi Paul, Thank you very much for your timely reply. There are still some puzzles for me. I would like to change some torsion angles of a ligand in coot but it did not work as what I expected. I was able to play with the torsion angles formed by C06 C07 N08 O10 but not C06 C07 N08 O09 (shown in the figure below). One implies the other, it seems to me. I do not agree. One changes the position of O10, while the other changes O9. What I would like to do is to manually make the O9 and O10 in the same plane with aromatic ring if possible. I was able to rotate O10 along the C07-N08 bond but not 09, which I shall be able to do in coot? If I understand correctly what you are saying then that's a bug. C06-C07-N08-O09 defines a rotatable bond (C07-N08) about which one side of the fragment (the smaller side) is rotated - i.e. you cannot move O10 without moving O09 also. That's how it should work. It seems that you are saying that that is not how it's working for you. By the way, I was able to make O9 and O10 in the same plane with the aromatic ring by adding planar restraint. I would like to know why I could not rotate O9 along the N08-C07 bond if possible. Me too. It does seem very curious. Is there a missing bond restraint - what happens when you display using colour-by-chain? 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] Bug in coot to change torsion angles?
On 30/08/2022 22:26, Gong, Zhen wrote: Dear Coot developers and users, I would like to change some torsion angles of a ligand in coot but it did not work as what I expected. I was able to play with the torsion angles formed by C06 C07 N08 O10 but not C06 C07 N08 O09 (shown in the figure below). One implies the other, it seems to me. The restraint file for the torsion angle (C06 C07 N08 O10) is defined quite well: LIG CONST_23 O09 N08 C07 C06 -5.58, which is close to zero. Therefore, O9, O10 N08 should be more or less in the same plane with the benzene ring. I agree. By default Coot does not refine torsion angles. Also torsions named "CONST" are not refined. You can turn on torsion angle refinement in the R/RC dialog If I click on the ligand with “real space refinement”, it should make the O9, O10 N08 more or less in the same plane with the benzene ring. However, coot did not do it. If you don't have plane restraints for the nitro and ring atoms then coot doesn't know (hasn't been told) to keep them planar. All you've done is said to Coot "here's a torsion angle, don't use it.| The corollary of the above is to turn on torsion angle refinement and rename the torsion var_23. You could also add O09 to the ring plane restraint with perhaps double or triple the esd. 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/
[COOT] Bug in coot to change torsion angles?
Dear Coot developers and users, I would like to change some torsion angles of a ligand in coot but it did not work as what I expected. I was able to play with the torsion angles formed by C06 C07 N08 O10 but not C06 C07 N08 O09 (shown in the figure below). Is it a bug or some geometry knowledge that I do not know? The restraint file for the torsion angle (C06 C07 N08 O10) is defined quite well: LIG CONST_23 O09 N08 C07 C06 -5.58, which is close to zero. Therefore, O9, O10 N08 should be more or less in the same plane with the benzene ring. If I click on the ligand with “real space refinement”, it should make the O9, O10 N08 more or less in the same plane with the benzene ring. However, coot did not do it. Can anyone please help? Many thanks in advance! Best, Zhen [cid:image002.png@01D8BC94.06712650] 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/
