Compatibility Problem Between Pymol And Python App'S Version

Question

[Thaman]

Currently I'm working with PyMol application and practicing to write some Python scripts which will run in Pymol terminal.

What I am trying to do is generate pairwise combination of structure for example

str1=['1bcd','3acz','cdsa', 'se1a']

str2=['dacd','qacz','acda', 'e2ac']

Generate pairwise comparision of str1, str2 and between str1 and str2. I loaded all structures in Pymol then I tried to run Python script in Pymol terminal which will calculate all pairwise combination and return RMS value.

But, problem I am facing is Pymol doesn't recognize intertools.combination module which I have used in python script.

Is there any Python latest plugin that I can download for Pymol to make it compatible? I am using python 2.7 but according to Pymol terminal I can see sys.version =2.4.2

How can I solve my problem?

Thank you

Answer 1

[Michael Schubert]

You have two options here.

• Write your own combination routine.

For combining the elements of str1, this would look something like:

combinations = []
for i in range(0, len(str1)):
    for j in range(i+1, len(str1)):
        combinations.append([str1[i], str1[j])

• Install PyMOL with a newer python version

Compile PyMOL yourself with a newer python version (cf. this post) or get a already built version, eg. here (HINT: you will most likely want pymol-1.3r1.win32-py2.7.exe as this is the by far easiest solution). Maybe there is a way to tell your already installed PyMOL to use the newer python version installed on your system, but I do not know if and how this is possible.