Add mcopy command

[olibclarke@…]

The mcopy command is useful for replacing a model in a figure and getting the same coloring, styles, parts shown.

Begin forwarded message:

From: Oliver Clarke
Subject: Re: [chimerax-users] Recreating views
Date: May 21, 2020 at 10:18:18 AM PDT
To: goddard@…, tic20@…
Cc: chimerax-users@…

Hi Tom - for coloring it the same as the old - is there an equivalent of the “mcopy” command in chimeraX yet? Absent support for scenes that would be the next best thing

Cheers
Oli

On May 21, 2020 at 17:15 GMT, Tom Goddard wrote:

Hi Tristan,

It gets really hard to restore all the settings used to make a figure using commands like "view matrix" and "camera" to find field of view, and trying to match the colors and styles and lighting.... A better approach is always save a ChimeraX session used to make the figure, I usually give it the same file name as the figure image file. Then when the model is revised, open the original session, load the new model, color and style it the same as the old, close the old model, and save the revised figure session. It is also useful to use "view name figure" to name the camera view and model positions used for the image so you can rotate the view around and still easily get back to the figure view point with "view figure". The named views are saved in sessions.

Tom

On May 21, 2020, at 10:05 AM, Tristan Croll wrote:

One good reason for using "view matrix" and applying a script to regenerate the scene rather than simply saving a session is that for experimentalists the model itself might change - that is, the figure is made, then an error is picked up in the model and it's re-refined, so the figure needs to be regenerated from a new file.

[Tom Goddard]

Done.

I added the mcopy command to copy colors, styles, visibility... from one atomic structure to another. The syntax is like the Chimera mcopy command.

mcopy #1 toAtoms #2 settings csv

I made a few minor changes compared to Chimera. I added a separate "h" settings value to copy secondary structure (helix/strand/turn) info. In Chimera it copied secondary structure when you used "s" (style) which seemed wrong. I made "c" (colors) not copy label colors. Use "l" to copy labels including their colors. Also "l" (labels) does not delete labels already on the target atoms that are not present in the source atoms. The mcopy command does not effect molecular surfaces.