Dear MfG, formerly known as Holfelder, here's an expanded script:
load x_1.pdb
zoom
#orient molecule at this point as you desire
ray
png x_00001
disable x_1
for i in range (2,10001): \
cmd.load("x_%d.pdb" %i) \
cmd.super("x_%d" %i, "x_1") \
cmd.ray() \
cmd.png("x_%05d" %i) \
cmd.disable("x_%d" %i) # or cmd.delete("x_%d" %i)
If you put the script into a file and load the orientation of the first
molecule before the first ray-tracing, you can execute it remotely
without the interface on the fastest machine (pymol -qc script.py).
This will be much quicker. Assemble the png files into a movie with
Quicktime Pro or Adobe Premier or mencoder (see PyMOL Wiki).
Andreas
On 10/07/2011 6:18, Babban Mia wrote:
> Thanks a lot Andrea and Michael
>
> So this would align/super impose all the other pdbs wrt the first PDB.
> How Do I make a movie of that ?
>
> Please advise
> I want to be able to show this "blob" of structures(obtained after
> aligning) from different angles and by rotation.
>
> I guess I would use the mset command,Would it work ?
>
> Please also show me how to incorporate the zoom command in the python
> script so that the structures look well small and not enlarged and extended.
>
>
> Danke!
>
> MfG
>
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