Spencer's example was in PyMOL command syntax (.pml script). To use it in a
Python script, it would look like this:
from pymol import cmd, stored
stored.f = open("ss.txt", "w")
cmd.iterate("n. CA", "stored.f.write(resi + ':' + ss+'\n')")
stored.f.close()
Cheers,
Thomas
On 13 Jan 2017, at 18:44, Academic Research <[email protected]> wrote:
> Thank you for your replay.
>
> Running the command from a python code is much better for me. But can you
> elaborate more about the code? it still gives me a syntax error:
>
> file.py
> import pymol
> f=open("ss.txt","w")
> iterate n. CA, f.write(resi + ':' + ss+"\n")
> f.close()
>
> Result:
> File "1.py", line 3
> iterate n. CA, print ss #f.write(resi + ':' + ss+"\n")
> ^
> SyntaxError: invalid syntax
>
>
> How can I fix it?
> Where do I call the .pdb file?
>
> On Jan 13, 2017, at 02:59 pm, Spencer Bliven <[email protected]> wrote:
>
>> This can be done using normal python file i/o:
>>
>> f=open("ss.txt","w")
>> iterate n. CA, f.write(resi + ':' + ss+"\n")
>> f.close()
>>
>> On Fri, Jan 13, 2017 at 10:38 AM, Academic Research <[email protected]>
>> wrote:
>> That would be good as well, How?
>>
>> keep in mind, my protein is synthetic, it is not from the PDB database, and
>> the .pdb file only contains ATOMS, no header or anything else.
>>
>> On Jan 13, 2017, at 12:37 pm, Albert <[email protected]> wrote:
>>
>>> I think you can obtain it from your Linux terminal
>>>
>>>
>>>
>>> On 01/13/2017 10:34 AM, Academic Research wrote:
>>>> Pymol Professionals I need your help,
>>>>
>>>> I have the following command:
>>>>
>>>> iterate n. CA, print resi + ':'
>>>> + ss
>>>>
>>>> I use this command in pymol to print out each residue number and its
>>>> corresponding secondary structure. The command prints out the result in
>>>> pymol itself.
>>>>
>>>> My question is: How can I save the output from this command into a file?
>>>>
>>>> AC Research
--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.
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