Yes, there definitely was an error in the quotes... And thank you for the
insight in the parenthesis, actually it works without, I was not able to
figure it out....
So the script
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,y,z=x-a,y-b,z-c")
cmd.alter_state ("1",("%s-h" %(i)),"x,y,z=x-a,y-b,z-c")
now works fine...
But I still have the strange thing with the y displacement. If I run the
script and I check the fe position (set as the reference one):
PyMOL>iterate_state 1,1AW3 and name fe,(x,y,z)
(0.0, 9.5340003967285156, 0.0)
So the y position has not change while the x and z have shifted....
Strange, no?
Hi,
Firstly, I can see why there is a syntax error for the alter_state command:
cmd.alter_state ("1",("1AW3 and name fe"),((x,y,z)=(x-a,y-b,z-c))")
has the quotes in the wrong place. I guess it should be:
cmd.alter_state("1","(1AW3 and name fe)","((x,y,z)=(x-a,y-b,z-c))")
I can make every atom move by saying:
cmd.alter_state("1", "my_structure", "x, y, z = x + 1, y + 1, z + 1")
So, the "x,y,z=x-a,y-b,z-c" would probably work, too. I hadn't
realised that variables in the current scope were accessible from the
alter_state scope, too.
gilleain
On 6/19/07, Gilles Truan <gtr...@cg...> wrote:
> Sorry for my first post, I just relaized it was kind of hard to read
> with all the funny tags.... I am reposting for clarity!!!
> 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 ;)
