[Chimera-users] Copy a pdb display configuration to another pdb model
goddard at cgl.ucsf.edu
Tue Mar 10 12:56:36 PDT 2009
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:
> 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.
> 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.
> Xiangan Liu wrote:
> 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?
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