[Chimera-users] Changue the identifier model number of a structure or marker set

Elaine Meng meng at cgl.ucsf.edu
Fri Aug 7 09:34:41 PDT 2015


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 at 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 at 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 at yahoo.com>
> Cc: "chimera-users at cgl.ucsf.edu" <chimera-users at 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 at 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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