When creating a movie usually I make a Chimera session file with all the models and markers, and I make a command script that carries out the action in the movie. To record I open the session and then open the script. It is much easier to set things up in a session then using commands. To refer to an individual marker in a command you can use the residue number of the marker. Each marker is in its own “residue”. display :5 Tom

On Aug 5, 2015, at 10:58 AM, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Dear Ana-Lucia, There isn’t a command to do the same thing as manually creating and placing markers. However, you already have the markers, so the work is done! Just open the markers in Chimera and undisplay them before starting to record, and then only display them at the time you want them to be shown in your movie. A marker set is implemented as a molecule model, and the markers as atoms, so you could just use “display” and “~display” commands to show and hide them, just like for atomic structures. <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/display.html>

For example, if your marker set is open as model 3, the commands to hide and show the whole set could be: ~disp #3 disp #3 To display them individually instead of a whole set at a time is tricker. Normally I would use atom name or serial number, but the example marker file I’m using doesn’t have either of these assigned. Maybe my coworkers can suggest how to specify the individual markers.

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 Aug 5, 2015, at 9:04 AM, Ana Lucia Alvarez Cabrera <anlualca@yahoo.com> wrote:

...

Dear colleagues,

I would like to know how can I place markers in specific points within an EM map, using commands (and not the Volume Tracer option in the graphic interface).

I am doing a movie and I need to place markers in different regions of a map. By placing the markers first manually with the mouse (using the Volume Tracer option in the graphic interface) into the map and saving the respective marker set I can know the specific coordinates for each marker by reading the output marker file "suffix.cmm" (for example: <marker id="1" x="22.28" y="24.608" z="17.976" r="1" g="0.49804" b="0" radius="2"/> ), but I still don't know how to use this information when writing the command for placing the marker in that position.

Thanks in advance,

Ana-Lucia

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Hi Ana-Lucia, You can use the command “combine” to make a copy of the marker set as a new model and “mcopy” to transfer all of its settings that weren’t already copied. For example to copy marker set model 0 to model 8 and remove the original: combine #0 model 8 name 'marker set 1' mcopy #0 #8 close 0 <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mcopy.html> You must manually specify the name (in the example above, 'marker set 1') because the other commands won’t transfer it automatically. You can combine all the commands into one line separated by semicolons if you don’t want to see the intermediate states. For example (this should all be one line, even if the mail program decides to split it up): combine #0 model 8 name 'marker set 1'; mcopy #0 #8; close 0 (My first idea was to save the marker set to file, close the marker set model, then open as the new model with something like “open 8 ~/Desktop/test.cmm” but when I try that the new model number is ignored. It may be a bug for marker sets, as I know if works correctly for pdb files. The slightly longer method above worked correctly in my marker set tests, however.) 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 Aug 7, 2015, at 2:46 AM, Ana Lucia Alvarez Cabrera <anlualca@yahoo.com> wrote:

Hi, I am writing a (long) command script to make king of fancy (complicated) movie. In order to make the things a little bit less complicated in my script, I need to change the model number of some marker sets that I have created previously. How can I change the identifier number of models/marker sets?. Thanks. Ana-Lucia

As Tom Goddard mentioned earlier, it is usually more convenient or efficient to have all this setup already done in a Chimera session. Then you just open the session, then run the script with the movie content (instead of re-running all this setup every time you use your script). Elaine On Aug 7, 2015, at 9:27 AM, Ana Lucia Alvarez Cabrera <anlualca@yahoo.com> wrote:

Thanks for the explanation, Elaine. I will try to make it as you said...hoppefully it will work properly in my script :)

Regards,

Ana-Lucia

-------------------------------------------- On Fri, 8/7/15, Elaine Meng <meng@cgl.ucsf.edu> wrote:

Subject: Re: [Chimera-users] Changue the identifier model number of a structure or marker set To: "Ana Lucia Alvarez Cabrera" <anlualca@yahoo.com> Cc: "chimera-users@cgl.ucsf.edu" <chimera-users@cgl.ucsf.edu> Date: Friday, August 7, 2015, 6:06 PM

Hi Ana-Lucia, You can use the command “combine” to make a copy of the marker set as a new model and “mcopy” to transfer all of its settings that weren’t already copied. For example to copy marker set model 0 to model 8 and remove the original:

combine #0 model 8 name 'marker set 1' mcopy #0 #8 close 0

<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mcopy.html>

You must manually specify the name (in the example above, 'marker set 1') because the other commands won’t transfer it automatically. You can combine all the commands into one line separated by semicolons if you don’t want to see the intermediate states. For example (this should all be one line, even if the mail program decides to split it up):

combine #0 model 8 name 'marker set 1'; mcopy #0 #8; close 0

(My first idea was to save the marker set to file, close the marker set model, then open as the new model with something like “open 8 ~/Desktop/test.cmm” but when I try that the new model number is ignored. It may be a bug for marker sets, as I know if works correctly for pdb files. The slightly longer method above worked correctly in my marker set tests, however.)

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 Aug 7, 2015, at 2:46 AM, Ana Lucia Alvarez Cabrera <anlualca@yahoo.com> wrote:

...

Hi, I am writing a (long) command script to make king of fancy (complicated) movie. In order to make the things a little bit less complicated in my script, I need to change the model number of some marker sets that I have created previously. How can I change the identifier number of models/marker sets?. Thanks. Ana-Lucia

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