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

Ana Lucia Alvarez Cabrera anlualca at yahoo.com
Fri Aug 7 09:43:04 PDT 2015


Yeap, I already have everything in a Chimera session ;)
Thanks!
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 BB" <chimera-users at cgl.ucsf.edu>
 Date: Friday, August 7, 2015, 6:34 PM
 
 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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 > Chimera-users mailing list
 > Chimera-users at cgl.ucsf.edu
 > http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
 >
 
 



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