Hello,
I have recently prepared a script for Pymol that works well in
evaluating RMSD values for a list of residues from proteins of interest
(targetted residues are generated by script embedded commands). However,
I wished to implement the script to allow the user to select what
residues to analyse. I have tried to use the INPUT function, but it
fails to work. Since the code is a bit long, I simplified progressively
the scripts to find out the problem. In that way, I ended up with the
following two scripts:
"test.py":
```
import Bio.PDB
import numpy as
np
from pymol import cmd
import os,glob
from LFGA_functions import
user_entered
List_tot = user_entered()
print (List_tot)
```
which calls
the simple "user_entered" function that is inside the "My_function.py"
script, which generates the residue numbers for the same residue in a
hexameric protein:
```
def user_entered():
List_res = []
List_tot = []
a = input("Please indicate the number of residues to
analyze/per monomer:")
numberRes =int(a)
for i in
range(numberRes):
Res = input("Please provide each residue
NUMBER and hit ENTER:")
Res1 = int(Res)
Res2 =
Res1+2000
Res3 = Res1+3000
Res4 = Res1+4000
Res5
= Res1+5000
Res6 = Res1+6000
List_res =
(str(Res1),str(Res2),str(Res3),str(Res4),str(Res5),str(Res6))
List_tot.append(List_res)
return List_tot
```
The script "test.py"
works well when directly executed by Python (3.7.5, which is installed
with Pymol 2.3.4,under Windows 7 Prof) from a windows command line. This
is an example of what I get:
[first input "3" indicates that 3 cases
will be treated, followed by the identification number for each residue]
However, when the script is run from Pymol GUI, I get the following
error message:
INPUT():LOST SYS.STDIN
Here the error in more detail:
File "C:\Program Files\PyMOL\lib\site-packages\pymol\parsing.py", line
527, in execfile
exec(co, global_ns, local_ns)
File "C:/Program
Files/PyMOL/Lib/test.py", line 7, in <module>
List_tot =
user_entered()
File "C:\Program Files\PyMOL\lib\LFGA_functions.py",
line 18, in user_entered
a = input("Please indicate the number of
residues to analyze/per monomer:")
Does anybody know what is the
problem. Please, take into account that I am a very basic Python user...
I profit also to ask something related to this problem... in the
original script that works well when run from Pymol (before trying to
implement the "input" option), I stored transiently some data (residue
name, type and chain) in the form of a Python "set". I need a set, and
not a list, because it removes automatically data repeatitions. However,
when I try to run the script from Python (with intention to overcome the
abovementioned problem with INPUT from Pymol), it stops with a message:
name 'close_to_A' not defined.
This name corresponds to the set
name, which is defined as follows within the
script:
```
cmd.select("in_A", "Average and chain A near_to 5 of chain
B+C")
close_to_A =
set()
cmd.iterate("(around_A)","close_to_A.add((chain,resi,resn))")
```
How
shall I define a set in Python 3 ? Why does it work when run from Pymol
?
I would really appreciate if you could help me to solve these two
problems. Thank you in advance,
Best regards,
Luis
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