Hi,

Why can't you use set_name tun1, ..., etc? The attempt trying to change names is quite odd, and won't do what you want anyway.
You could use

basename="your_tag"
cmd.set_name(cmd.get_object_list()[0], basename+"_subtag")
... and so on.

Cheers,

Tsjerk

On Mar 21, 2012 6:56 AM, "Sajeewa Pemasinghe" <sajeewasp@gmail.com> wrote:

Hi everyone,

I have a pml script by which I am trying to change 6 object names. These are on molecular tunnels. The 6 object names are

Total_protein 
start (starting point of the tunnels)
crisscross
tun1 (tunnel1)
tun2 (tunnel2)
tun3 (tunnel3)

Objects 1,4,5 and 6 can be accessed as (cmd.get_object_list())[0], (cmd.get_object_list())[1], (cmd.get_object_list())[2], (cmd.get_object_list())[3]

My script is

set_name crisscross,E125Dch113nscris
set_name start,E125Dch113nsst
(cmd.get_object_list())[0]=E125Dch113ns
(cmd.get_object_list())[1]=E125Dch113nstn1
(cmd.get_object_list())[2]=E125Dch113nstn2
(cmd.get_object_list())[3]=E125Dch113nstn3

Although the first two lines work the other lines give errors as

(cmd.get_object_list())[0]=E125Dch113ns
Traceback (most recent call last):
  File "C:\Program Files (x86)\PyMOL\PyMOL/modules\pymol\parser.py", line 464, in parse
    exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
  File "<string>", line 1, in <module>
NameError: name 'E125Dch113ns' is not defined
PyMOL>(cmd.get_object_list())[1]=E125Dch113nstn1
Traceback (most recent call last):
  File "C:\Program Files (x86)\PyMOL\PyMOL/modules\pymol\parser.py", line 464, in parse
    exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
  File "<string>", line 1, in <module>
NameError: name 'E125Dch113nstn1' is not defined
PyMOL>(cmd.get_object_list())[2]=E125Dch113nstn2
Traceback (most recent call last):
  File "C:\Program Files (x86)\PyMOL\PyMOL/modules\pymol\parser.py", line 464, in parse
    exec(layer.com2+"\n",self.pymol_names,self.pymol_names)
  File "<string>", line 1, in <module>
NameError: name 'E125Dch113nstn2' is not defined

changing the names in this iterative fashion is really needed for me coz I am creating the pml script iteratively using a java program for 240 files. Could you please give me suggestions for modifications to iteratively change the object names. This would help my work really big.

Thank you 

Sajeewa


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