Re: [Chimera-users] Request for axes measurements
Hi, You’re welcome, but I don’t have any further details than what is already given in the manual: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes> It’s recommended you send Chimera questions to chimera-users@cgl.ucsf.edu instead of me directly, in case others may be able to provide better answers! Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Mar 31, 2015, at 6:26 PM, Jayaraman T <jram@pusan.ac.kr> wrote:
Hi Elaine Meng, Yes i could figure now the axes as well as angle measurements between them and thanks for your timely help.
I would be happy if you could tell me the principle on which these axes are calculated. I have noticed that it's from Eigen vector values that are calculated for the coordinates of the set of atoms.
I'm really interested on the backend for this calculation particularly, might help a bit progressing more for my research.
Thanks again.
Hi .. Thats fine and i'll do that. Thank you. - - With warm regards Jram | 201493155 PhD Scholar jram@pusan.ac.kr Bio molecular Engineering Lab Dept of Chemical Engineering Pusan National University Busan, South Korea +8210 9906 3680
Hi all, I have calculated few helix axes angles and they are all in positives using defined axes in Chimera . Could you please explain me why they are all in positives ? It would be grateful. Thanks. - - With warm regards Jram | 201493155 PhD Scholar jram@pusan.ac.kr Bio molecular Engineering Lab Dept of Chemical Engineering Pusan National University Busan, South Korea +8210 9906 3680
Hi, For angle measurement, axes are treated as infinite lines (not vectors, so they don’t have a directionality). You could use any set of atoms to define an axis (or centroid or plane) and they would not necessarily have any relationship to directionality along a peptide backbone. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes> For example, the N->C direction of a helix axis is not used, so the order in which you specify two helix axes for angle measurement doesn’t matter, the result will be the same either way. A positive angle is reported, but by visual inspection of the helix N->C directionalities you can convert to an equivalent negative angle as needed. It is not automatic, however, so more work. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 8, 2015, at 11:35 PM, Jayaraman T <jram@pusan.ac.kr> wrote:
Hi all, I have calculated few helix axes angles and they are all in positives using defined axes in Chimera . Could you please explain me why they are all in positives ? It would be grateful. Thanks.
Dear Elaine, Thanks for the information. And further, we have got for most of the helix axes angles are in positives (like a pattern) So we need to confirm them whether it'd be in only positives or negatives and\or both. Is there any options to look after for changing them into negative angles ? If any please revert me. Please help me out in this. Thank you. Hi, For angle measurement, axes are treated as infinite lines (not vectors, so they don’t have a directionality). You could use any set of atoms to define an axis (or centroid or plane) and they would not necessarily have any relationship to directionality along a peptide backbone. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/structuremeas/structuremeas.html#axes> For example, the N->C direction of a helix axis is not used, so the order in which you specify two helix axes for angle measurement doesn’t matter, the result will be the same either way. A positive angle is reported, but by visual inspection of the helix N->C directionalities you can convert to an equivalent negative angle as needed. It is not automatic, however, so more work. I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 8, 2015, at 11:35 PM, Jayaraman T <jram@pusan.ac.kr> wrote:
Hi all, I have calculated few helix axes angles and they are all in positives using defined axes in Chimera . Could you please explain me why they are all in positives ? It would be grateful. Thanks.
- - With warm regards Jram | 201493155 PhD Scholar jram@pusan.ac.kr Bio molecular Engineering Lab Dept of Chemical Engineering Pusan National University Busan, South Korea +8210 9906 3680
Hi all, We defined axes for helices (user defined set of atoms) using axes module in Chimera and we found the angles between them are positives. If we do consider the axes are infinite lines and not as vector, then how could we normalize them for finding the eigenvectors/values for the selected set of atomic coordinates. We have been trying for a while but couldn't get them clearly, please help us and it'd be grateful. Thank you. - - With warm regards Jram | 201493155 PhD Scholar jram@pusan.ac.kr Bio molecular Engineering Lab Dept of Chemical Engineering Pusan National University Busan, South Korea +8210 9906 3680
Sorry, Chimera does not figure this out for you. In other words, it does not treat axes as vectors. After you get the positive value, you would have to look at the N->C directionality of the helices yourself to decide whether it should be converted to negative, or even kept positive but subtracted from 180. Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco On Jun 14, 2015, at 7:13 AM, Jayaraman T <jram@pusan.ac.kr> wrote:
Hi all,
We defined axes for helices (user defined set of atoms) using axes module in Chimera and we found the angles between them are positives.
If we do consider the axes are infinite lines and not as vector, then how could we normalize them for finding the eigenvectors/values for the selected set of atomic coordinates.
We have been trying for a while but couldn't get them clearly, please help us and it'd be grateful.
Thank you.
participants (2)
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Elaine Meng -
Jayaraman T