Hi Tom,
It is always good to have an interactive and a scripted way to do things. You point to interesting use cases for both, some I had not considered before. Thank you.
I think it it also good to have no executable code in session files. I don't normally share session files because I mostly use ChimeraX to inspect cryoEM maps and, like you point out, the maps are not saved in the session file by default (and the file gets very large if you add them).
When I share command files, I don't see exposing more people to the command language as a drawback. It is actually a great way to learn about available features. For this reason, I love that everything one does interactively gets printed to the Log in command form. This is most often how I use ChimeraX: I play interactively to get what I want quickly, knowing that most of the script I intend to put together is now right there in the Log and ready after some (often straightforward) edits. That there is no strict separation between interactive and command use is extremely convenient.
Cheers,
Guillaume
________________________________ From: Tom Goddard goddard@sonic.net Sent: Wednesday, August 30, 2023 9:31:47 PM To: Hunkeler, Moritz; Guillaume Gaullier Cc: ChimeraX Users Help Subject: Command scripts and session files
Hi Guillaume, Moritz,
It is good to think about when ChimeraX command scripts are useful and when session files are useful.
Of course session files can be large, they contain the atomic model data whereas a script does not. The size of a ChimeraX session file after opening 30,000 atom PDB 3cf0 is 1.5 Mbytes, while the 3cf0 mmCIF files is 3 Mbytes. The session is a bit smaller because it is compressed (LZ4 compression). Some common things make session files very large, for instance including molecular surfaces. The 3cf0 session with molecular surfaces is 122 Mbytes. Also if you create volume models those will make session files large, although if you open an EM map or other volume the session just contains the path of the map file unless you use the "includeMaps true" option when saving the session.
In ChimeraX the session files contain only the data, no commands. This is different from old Chimera session files which used Python code. We changed to just including the data to make it safe to share these files on the internet. If you are sharing executable code the concern about malicious code in such files becomes an issue when you don't know who created the file. Since ChimeraX sessions have no executable code embedded we think they are safe to share widely on the internet.
When you have to process lots of files in the same way, scripts are a good way to go. But even in that case saving a single session and then having the script just replace a model in that session with another one can simplify the scripting. The "foreach" option of the open command allows running a script on each data file in a directory.
https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#foreachfile
A common case where both command scripts and session files are useful is in making a movie. I always do this by making a session file that has all the data and most of the styles, colors, positions all setup. Then I have a short movie command script that animates some things starting from that session (e.g. hiding and showing models, zooming in, ...).
The main drawback I see with using command scripts where sessions could do as well, is that the command scripts requires more knowledge of the ChimeraX command language than most users have. But for advanced users who know they command language well and are accustomed to using command scripts that is a reasonable approach.
Tom
On Aug 30, 2023, at 10:56 AM, Hunkeler, Moritz via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
I don’t really like relying on sessions for figures. I think it’s much faster to have a script, e.g. in case you want to replace a pdb (let’s say you have a new version of the pdb from a more recent refinement) or a map (maybe you repeated a refinement with a different mask?). Just replace the path in the script and rerun and you get the same figure but with an updated model. Somebody asked exactly this a couple of days ago on this mailing list (how to ‘port’ settings from one model to another); they would not have had that problem if they had used a script, I would argue. Or, other example: Let’s say you need to open 60 maps, color 7 of them according to an underlying model, then save PNGs of all of them in two different views at two different threshold levels. How would you do that efficiently with a single session file? And then later you realize that you want to turn all of them 180º (just an example), super easy to fix with a script (add turn y 180 and rerun), but very tedious with session files. In addition, you can copy and reuse a lot of script blocks (let’s say coloring of a large pdb that it the same in many different figures/pdbs) across projects. And yes, all the other things you mentioned (aspect ratio, how to display the model, etc etc) are of course all part of a figure script. What I gave in my last message was just an example snippet. Knowing the commands to reproduce a certain display style and then going from there is definitely my preferred way over sessions and is also better to teach people the chimera syntax. Anyways, everybody has different ways of doing things. I don’t know how people use pyMOL nowadays, but that’s how we did it years ago.
Moritz
From: Tom Goddard <goddard@sonic.netmailto:goddard@sonic.net> Date: Wednesday, August 30, 2023 at 11:57 AM To: Hunkeler, Moritz <Moritz_Hunkeler@DFCI.HARVARD.EDUmailto:Moritz_Hunkeler@DFCI.HARVARD.EDU> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] save "side view" settings
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Hi Moritz,
The way to create figures and later change them in ChimeraX is to save a session "save figure1.cxs", then later when you decide you want to change it "open figure1.cxs". This works very well. Usually I name the session file the same as the image name "save figure1.png". In theory you could record all the info with commands, including lots you left out like which atoms are shown, what ribbons, what surfaces, their colors, what text labels are shown, the window aspect ratio, ..., but I don't see the advantage of figuring out all the commands to reproduce the scene. Is that how it is done in PyMol?
Regarding using the center of the box for the clip plane reference point, it is not great, because if you decide to hide one chain then the center is now in a different position and the clip plane positions are different.
Tom
On Aug 30, 2023, at 7:27 AM, Hunkeler, Moritz via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Tom,
I understand that it can get complicated without a defined point of reference. And again, it’s possible to get around it by just ‘clip off’ in figure scripts, so this discussion is just about details. I guess it is just confusing sometimes, as I have seen people struggling with this before.
For me it’s more a matter of ease-of-use. As in I would like to have a command that writes out all necessary settings to recreate a view of a model/map. For example, why can the point of reference not be (and stay) the center of the surrounding box for the displayed model(s), irrespective of already applied clipping planes? And then write out the position of the clipping planes plus the depth cue values when using e.g. ‘view matrix’ (or some other command). Like this all the important information for recreating a certain view (of these model(s)) could be written out from a single command and could then be copied into a script . Again, that would be similar to ‘get_view’ in pyMOL (https://pymolwiki.org/index.php/Get_Viewhttps://secure-web.cisco.com/1ouVm-O14_62oyQsqJE-tA4UMyJ52bNNv_ZJWsfp-9IAL8WPQrSWtNHsFBi72VrxlvY-KY1E193VvPJ3LR3ZaF22hXNkNf6d_QaCtTTwtA6QlxoL2JxGxP1rDUrZcGRAqc2XThVwzG-fsAnsXTwkJnaZdo-D52rb_s0GWcHAwZPAuHx12YT6EFjHyPApodC_Ui5-QY0JySQERtLwJPqpYPuS0LHvztKF39FtRBQhqJoEEYJ0ia6oKxzcUZNGLvklLq-FuSI4lpevTJ1zBN3RVty7mVJVr_7KZveKHKQB0VUAaQvJAb66g7QwGC8pyP-JVvo5Y7AbHoW2lmvXgt2_byQ/https%3A%2F%2Fpymolwiki.org%2Findex.php%2FGet_View). Right now, to recreate a view reproducibly looks something like this:
1. ‘view matrix’ -> copy paste the camera values into the script 2. ‘clip list’ -> copy paste the clip values into the script after a clip off command 3. Decide what lighting and depth cue values -> copy paste into script 4. Then the script will look somewhat like this
view matrix camera -0.18203,-0.11049,-0.97707,-138.8,-0.96294,-0.1811,0.19988,197.66,-0.19904,0.97724,-0.073424,107.97 clip off clip near -3 clip far 30 lighting soft depthCueStart 0.5 depthCueEnd 0.7 save "PNG/example.png"
Which is completely fine, but it would save some copy-pasting if everything was accessible from a single command.
Best, Moritz
From: Tom Goddard <goddard@sonic.netmailto:goddard@sonic.net> Date: Tuesday, August 29, 2023 at 9:35 PM To: Hunkeler, Moritz <Moritz_Hunkeler@DFCI.HARVARD.EDUmailto:Moritz_Hunkeler@DFCI.HARVARD.EDU> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu>, vincent Chaptal <vincent.chaptal@ibcp.frmailto:vincent.chaptal@ibcp.fr> Subject: Re: [chimerax-users] save "side view" settings
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Hi Moritz,
I agree that absolute clip plane positions can be useful. The question is what are the absolute positions measure relative to? For example if I say "clip near 8" that is supposed to be 8 Angstroms in front of what point? The rules the ChimeraX clip command uses are a bit complicated because what reference point to measure distances from is not obvious. So if no clip planes are shown then the 0 position is the center of the bounding box of the displayed models. If the clip plane is shown then 0 means the current plane position. And if you want to define your own reference point then use the position option "clip near 8 position /B:123@CA" means the 0 point is at the C-alpha atom of residue 123 in chain B.
To get reproducible clip plane positions you need a reproducible reference point that the distances are measured relative to.
Tom
On Aug 28, 2023, at 10:25 AM, Hunkeler, Moritz via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Not 100% sure I understand the question correctly, but maybe the confusing part is the following: The clip numbers are not absolute, but are additive. As in every time you use the following command:
clip far 35
the far clipping plane would be moved by 35. This can lead to some inconsistencies, for example when one uses ‘clip list’ and gets a value of 210, and then puts that value into a script that changes the clipping plane several times for different views. Safest way to not have that problem is: put a ‘clip off’ in front of all clipping commands in a script. This way the exact view will be reproduced every time. E.g.
. . . #set view 1 view matrix camera -0.20791,2.5127e-09,-0.97815,-250.33,-0.97815,-4.5356e-09,0.20791,309.25,-9.8669e-09,1,4.8527e-09,229.38 clip off clip near -1 clip far 134 save "PNG/view_1.png"
#set view 2 view matrix camera -0.96824,-0.21649,0.12504,-223.03,-0.075286,-0.22447,-0.97157,-549.26,0.2384,-0.95013,0.20104,356.85 clip off clip near -16 clip far 35 save "PNG/view_2.png" . . .
In this example, the first view will be at clipping near/far of -1/134, and the second view will be at -16/35. If one omits the ‘clip off’, the second view would be at clip near=-17 and clip far=169 (instead of the intended -16, 35)
For me personally absolute values would be more intuitive (I guess similar to pymol (which many people might be used to), where ‘get_view’ would give you a matrix that reproduces both view and also clipping/fogging every time, no matter whether there is already fog/clipping present.)
Best, Moritz
From: Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> Date: Monday, August 28, 2023 at 11:59 AM To: vincent Chaptal <vincent.chaptal@ibcp.frmailto:vincent.chaptal@ibcp.fr> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> Subject: [chimerax-users] Re: save "side view" settings External Email - Use Caution
Hi Vincent, I always save a session file with the view for each publication image. Trying to do it this other way is much harder, in my opinion, and I have never tried it myself. As far as I know, the "view matrix" command should report (and restore) the camera and model positions, and "clip list" report (and "clip" restore) the clipping plane position(s):
https://secure-web.cisco.com/1MVnhhzN19WBilS9gDO4_Q4yCh88PWvZfX-39fwyPLIlx6y4Vz3erktHutC1_lKG0kNF5i7X1vpZ7EWpHymhI9own4UCYQDyy245qU8KiJfSeI282n3t0Lt4kYQGx7NLjSiWQYIRlp84o6PVH6X9EUHJBZzTt2SRhRejzqbrEhvgPa64B1kDYW8xNta0vRQDIBmq8mjNAC3NY5px5EfwuoG0iTlnewXuEifYJRWHp6ACyMas0YrxHVwJfshSUq8ank_K2DLemsI1f6ECTd8K7bZCVQ4RFPwUkWmX8Tr41j_tEfbkruTRSi5UoMb6FcMAsNnE9QFKwhNLqfOFG2hXo_w/https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fview.html%23matrix https://secure-web.cisco.com/1rH6UOFHJhkT9dijsnzAEc3Hc8ARJKTd5xv5ALjfH1y-k5g4IK3l8co6LiNk9qjkgrwKk9eMLlyWjhtYrdPqg4Siy0MRjcp9fZngrYrOFiTM8kjV3bxH7udnPoeNhGW3st_N9PH9-pYscgbTW9E508Wf4-U5IkR2tVGRqGOimTv68XGSjgm5QqZMsIdGZUJS0Ahkn2CPJYnNE450ekgoCE5nUnXSenyXxRNbUq8__qZTIas3sBteUOb1Enmo05OXaswwSZLia_YEYuK6XbH5Ewb13Fht0YRaay0qjzUobh05clvM-qA550zp_NjZAUGpXKviIAWGEh5Io-IFqO0pUvQ/https%3A%2F%2Frbvi.ucsf.edu%2Fchimerax%2Fdocs%2Fuser%2Fcommands%2Fclip.html
What you showed for results from "clip list" does not make sense: the near and far planes do not have a tilt axis, so their axis will only be 0,0,1 or 0,0,-1. But you said "modified" so maybe you edited it? It is impossible for me to tell what is really in your session if you don't include the whole results for clip list.
Then if you want it to look the same you should set exactly the same clip plane(s) as reported by clip list. If you have a front or back plane, you should also set the reported axis ("axis" option of "clip", see help above) and point cordinates ("position" option of "clip").
If it is not working and you feel it is a bug, please use Help... Report a Bug and attach the session, and the details of how you tried to reproduce it; however, that would put your data in a publicly available repository. If you have a simpler example you could attach that to the bug report instead.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 28, 2023, at 7:48 AM, vincent Chaptal via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi Elaine,
I've been playing around with it but I can't get to what I want. The second option of saving views works within a session, but it is lost if I restart ChimeraX or changes session, so what I'm looking for is really some numbers to place in a script so I can touch up my figure for publication multiple times.
Using "clip list" does list me an offset for the "far", as I modified it: Using 1 clip planes: far offset -1.5964, axis 0.032,-0.040,0.999, point 106.7,107.9,112.8)
I am trying to reproduce the view with: view matrix camera 0.051145,-0.99818,0.03201,113.43,0.99794,0.049838,-0.040387,99.325,0.038719,0.034009,0.99867,323.92 clip front 0 far -1.5964
(and varying flavors) but it doesn't recreate the same view. The clipping offset is much more drastic with my command line compared to the manual twicking of the far plane. Could you please point me in the right direction? Thank you Vincent
Le 22/08/2023 à 17:08, Elaine Meng a écrit :
Hi Vincent, You can report current clip settings in the Log with command:
clip list
More to your point, however, you can save the current view (which includes the clipping plane positions) with command:
view name myviewname
....of course you can name it something else, and you can have multiple saved views with different names. Then later in the same session, either not quitting ChimeraX between, or from saving a session file after you saved the view(s) and later restoring the session from the file, you can get back to that view with command:
view myviewname
...there are various command options, like gradually moving to the view over a number of frames as is often done for recording a movie, see the help:
I hope this helps, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Aug 22, 2023, at 3:34 AM, vincent Chaptal via ChimeraX-users <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> wrote:
Hi,
I opened the side view dialog window and adjusted the view planes for a nice figure. I would like to save the parameters so I can go back and modify the figure at a later stage, but the setting are not stored in the "view matrix" command. Could you tell me which command can save these settings? (I'm using chimeraX 1.5).
Thank you. Best Vincent
-- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab
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