[Chimera-users] Copy a pdb display configuration to another pdb model

Tom Goddard goddard at cgl.ucsf.edu
Tue Mar 10 12:56:36 PDT 2009

Hi Xiangan,

  The mcopy command can copy attributes from one molecule to several 
molecules, for example,

    mcopy #0 #1-419

copies the color, style, visibility of molecule #0 to molecules 1 
through 419.  It does not allow you to specify more than one molecule 
for the first argument -- it does not match molecule names.

  If all your 420 pdb files have different coloring / display style / 
visibility settings then to apply these to your second set of 420 pdb 
files you'll need 420 mcopy commands.  That can be done with a Python 
script.  If you run out of memory then the script would have to open a 
new pdb, copy settings, then close the original pdb before moving on to 
the next pdb.  Or you need to work with a 64-bit Chimera (currently 
available only on Linux).


Xiangan Liu wrote:
> Tom,
> Thank for your quick response. 
> I have 420 pdb files for icosahedron T=7 virus capsid. All the file 
> names is the same as the ones in previous session file. Is it possible 
> to do it with one command? If I load all the 840 pdb files into 
> chimera, it will be very slow and even crash my computer.
> Is it possible to do it without loading into Chimera? 
> Again, thank you for implementing these commands.
> Xiangan
> On Tue, Mar 10, 2009 at 1:51 PM, Tom Goddard <goddard at cgl.ucsf.edu 
> <mailto:goddard at cgl.ucsf.edu>> wrote:
>     Hi Xiangan,
>      I've added a new Chimera command "mcopy" to copy colors, display
>     styles, coordinates and other settings from one molecule to another.
>       mcopy #0 #1
>     will copy the colors, display styles (ribbon, stick, sphere, ...),
>     and visibility (which atoms/residues shown) from molecule #0 to
>     molecule #1.   To copy other attributes such as atom coordinates,
>     molecule placement (transform), or labels use the "settings" option:
>       mcopy #0 #1 settings lxp
>     copies just atom/residue labels, atomic coordinates and placement.
>      The recognized settings are: c = color, s = style, v = visibilty,
>     l = labels, x = coords, p = placement, a = all.  The default is "csv".
>      This command will be in tonight's Chimera builds.
>       http://www.cgl.ucsf.edu/chimera/alpha-downloads.html
>      Tom
>     Xiangan Liu wrote:
>         Tom,
>         I asked you a question in BPS meeting regarding the
>         implementation of copying a display configuration of a pdb
>         file to anoth pdb with the same sequences. Did you get chance
>         to implement it into chimera daily release? If yes, what is
>         the command. If not, can you send me the corresponding python
>         codes to me?
>         Thanks,
>         Xiangan

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