Hello to everybody,
I am trying to run a script to translate all pdb structures so that an atom
of the protein gets the coordinate (0,0,0)
I have written a small script for that:
for i in pdb_names:
stored.xyz = []
cmd.iterate_state(1,("%s and name fe" %(i)),"stored.xyz.append([x,y,z])")
a=stored.xyz[0][0]
b=stored.xyz[0][1]
c=stored.xyz[0][2]
cmd.alter_state ("1",("%s" %(i)),"x=x-a")
cmd.alter_state ("1",("%s" %(i)),"y=y-b")
cmd.alter_state ("1",("%s" %(i)),"z=z-c")
First, I have not been able to translate all the coordinates at once in the
script with something like
cmd.alter_state ("1",("%s" %(i)),"((x,y,z)=(x-a,y-b,z-c))")
I get this error message
cmd.alter_state ("1",("1AW3 and name fe"),((x,y,z)=(x-a,y-b,z-c))")
^
SyntaxError: invalid syntax
This was overcome by affecting each value separately. But then, when I check
the coordinates of the fe atom that should be (0,0,0) all of them have zero
values for x and z, but ot for y!!!!!!
All the y values are unaffected!!!
Is there something I am missing in the number format? When I check
coordinates via the cmd.iterate_state, I can see that most of them are
numbers with around 15 to 16 significative figures... where the pdb file has
only three figures!! Is there something that is added by the iterate_state
command, and might this could affect the calculation of the translation?
Thanks in advance for your answers ;)
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Dr. Gilles Truan
Centre de Génétique Moléculaire, CNRS
1 Av. de la Terrasse, 91198 Gif-sur-Yvette, France
Phone: 33-1-69 82 36 65, Fax: 33-1-69 82 36 82,
<http://www.cgm.cnrs-gif.fr/pompon/index.html> Lab Web Site
<mailto:gtr...@cgm.cnrs-gif.fr> Email
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