Re: [chimerax-users] Set up to take pictures of structure with a specific angle
Hi Emilie, How to use the command is shown in the "view matrix" help: http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#matrix
There is no colon, you would want a command something like the following, all on one line (the Mail app may show it as broken into multiple lines but it should all be one line):
view matrix camera -0.97114,-0.2031,0.12509,57.651,-0.030537,0.62598,0.77924,221.24,-0.23657,0.75293,-0.61412,-21.353
I hope this helps, Elaine
On Nov 24, 2020, at 10:31 AM, EMILIE MONTELLIER emilie.montellier@univ-grenoble-alpes.fr wrote:
Dear Elaine,
Thanks for your answers, it really helps me to understand how to use ChimeraX.
For the question 2 I manage to get the camera matrix by using view matrix in the command. Then I moved my structure and tried to apply the camera matrix I had, but I did not suceed. I did view matrix :the number obtained in camera position Here is a picture of the log :
Please do you know what I did wrong?
Thanks by advance for your help, Best regards,
Emilie
De: "Elaine Meng" meng@cgl.ucsf.edu À: "EMILIE MONTELLIER" emilie.montellier@univ-grenoble-alpes.fr Cc: "chimerax-users" chimerax-users@cgl.ucsf.edu Envoyé: Mardi 24 Novembre 2020 17:09:33 Objet: Re: [chimerax-users] Set up to take pictures of structure with a specific angle
Hi Emilie, (1) Cartoon thickness. You would use the "cartoon style" command to change the ribbon dimensions and shape. It can be done separately for helix, strand, and coil. For example:
cartoon style coil thickness 1.0
There are many options, see: http://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style
(2) Multiple images from different sessions with same orientation.
(A) If all your different sessions were made with either the same starting structure (same PDB file) or structures that were already fit on each other when they were opened, you could get matrix from the view that you want and apply the matrix to all the others. You would use "view matrix" without arguments in the session that already has the view you want, to report the camera matrix in the Log. Then you would use "view matrix" specifying that camera matrix in your other sessions to put them into the same view.
(B) If all your different sessions were made with different PDBs that weren't already fit on each other, then I believe the only way is to include a reference structure in each one, make sure the reference structure is in the position you want as in (A) above, and match the structure for the image onto the reference structure (e.g. with matchmaker or align), and then hide the reference structure.
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 24, 2020, at 12:45 AM, EMILIE MONTELLIER emilie.montellier@univ-grenoble-alpes.fr wrote:
Dear ChimeraX users,
I have worked on p53 structure, and the goal was to highlight certain residues on the structure. I have about 10 files of the same p53 structure (same PDB) with different groups of residues highlighted and now I would like to take pictures of them with the same display of the protein (same angle, rotation) in order to compare the 10 pictures together on a same figure. Is there a way to copy the angle/rotation of one p53 structure, and to apply it to another p53 structure?
Also, is there a way to increase specifically the thickness of what is not alpha helix or beta sheet (the kind "spaghetti" structure)?
Thanks by advance for your help, Regards, Emilie
Thanks Elaine, this is very helpful! Regards, Emilie
------------------------------- Emilie Montellier, PhD
MSCA Post-doctoral Researcher Institute for Advanced Biosciences - Grenoble, France Prof. Pierre Hainaut's laboratory Tel: +33 (0)4 76 54 95 76 Email: emilie.montellier@univ-grenoble-alpes.fr
De: "meng" meng@cgl.ucsf.edu À: "EMILIE MONTELLIER" emilie.montellier@univ-grenoble-alpes.fr Cc: "chimerax-users" chimerax-users@cgl.ucsf.edu Envoyé: Mardi 24 Novembre 2020 20:19:22 Objet: Re: [chimerax-users] Set up to take pictures of structure with a specific angle
Hi Emilie, How to use the command is shown in the "view matrix" help: < [ http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#matrix | http://rbvi.ucsf.edu/chimerax/docs/user/commands/view.html#matrix ] >
There is no colon, you would want a command something like the following, all on one line (the Mail app may show it as broken into multiple lines but it should all be one line):
view matrix camera -0.97114,-0.2031,0.12509,57.651,-0.030537,0.62598,0.77924,221.24,-0.23657,0.75293,-0.61412,-21.353
I hope this helps, Elaine
BQ_BEGIN On Nov 24, 2020, at 10:31 AM, EMILIE MONTELLIER <emilie.montellier@univ-grenoble- [ http://alpes.fr/ | alpes.fr ] > wrote:
Dear Elaine,
Thanks for your answers, it really helps me to understand how to use ChimeraX.
For the question 2 I manage to get the camera matrix by using view matrix in the command. Then I moved my structure and tried to apply the camera matrix I had, but I did not suceed. I did view matrix :the number obtained in camera position Here is a picture of the log :
BQ_END
BQ_BEGIN Please do you know what I did wrong?
Thanks by advance for your help, Best regards,
Emilie
De: "Elaine Meng" < [ mailto:meng@cgl.ucsf.edu | meng@cgl.ucsf.edu ] > À: "EMILIE MONTELLIER" < [ mailto:emilie.montellier@univ-grenoble-alpes.fr | emilie.montellier@univ-grenoble-alpes.fr ] > Cc: "chimerax-users" < [ mailto:chimerax-users@cgl.ucsf.edu | chimerax-users@cgl.ucsf.edu ] > Envoyé: Mardi 24 Novembre 2020 17:09:33 Objet: Re: [chimerax-users] Set up to take pictures of structure with a specific angle
Hi Emilie, (1) Cartoon thickness. You would use the "cartoon style" command to change the ribbon dimensions and shape. It can be done separately for helix, strand, and coil. For example:
cartoon style coil thickness 1.0
There are many options, see: < [ http://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style | http://rbvi.ucsf.edu/chimerax/docs/user/commands/cartoon.html#style ] >
(2) Multiple images from different sessions with same orientation.
(A) If all your different sessions were made with either the same starting structure (same PDB file) or structures that were already fit on each other when they were opened, you could get matrix from the view that you want and apply the matrix to all the others. You would use "view matrix" without arguments in the session that already has the view you want, to report the camera matrix in the Log. Then you would use "view matrix" specifying that camera matrix in your other sessions to put them into the same view.
(B) If all your different sessions were made with different PDBs that weren't already fit on each other, then I believe the only way is to include a reference structure in each one, make sure the reference structure is in the position you want as in (A) above, and match the structure for the image onto the reference structure (e.g. with matchmaker or align), and then hide the reference structure.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Nov 24, 2020, at 12:45 AM, EMILIE MONTELLIER < [ mailto:emilie.montellier@univ-grenoble-alpes.fr | emilie.montellier@univ-grenoble-alpes.fr ] > wrote:
Dear ChimeraX users,
I have worked on p53 structure, and the goal was to highlight certain residues on the structure. I have about 10 files of the same p53 structure (same PDB) with different groups of residues highlighted and now I would like to take pictures of them with the same display of the protein (same angle, rotation) in order to compare the 10 pictures together on a same figure. Is there a way to copy the angle/rotation of one p53 structure, and to apply it to another p53 structure?
Also, is there a way to increase specifically the thickness of what is not alpha helix or beta sheet (the kind "spaghetti" structure)?
Thanks by advance for your help, Regards, Emilie
BQ_END
participants (2)
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Elaine Meng -
EMILIE MONTELLIER