Hi Mahendra,
Oops, yep my code was missing a triple quote.  Anyway, maybe you should send me your code and a test PDB file offline.  Clearly the code you included below is not the code that produced the output you provided.  In your code, j takes values in range(3429,3450), which does not include the value 3450 itself, yet in your output clearly j does have the value 3450.  So you either provided the wrong script or the wrong output.  I don't think anyone else on the list is interested in the details of what went wrong, so you should just mail me directly.

--Eric

On Jun 3, 2015, at 11:04 AM, Mahendra B Thapa <thapamb@mail.uc.edu> wrote:

Dear Eric

I had not realized that not every amino acid consisted of CB atom. Thank you for the code which worked; just want to add a very minor addition ( """ ) to the left of the code, i.e.
sel = OSLSelection("""#0.1:%d.B@CB""" %i) instead of sel = OSLSelection(#0.1:%d.B@CB""" %i)

I tried another code as
import string
rc("open " + 'test.pdb')   # 60 models, each model has chains A,B,C
for i in [2196,2197]:
            for j in range(3429,3450):
                     for k in ['A','B','C']:
                               sel = OSLSelection("""#0.3:%d.%s@CA""" %(j,k))
                               sol = OSLSelection("""#0.2:%d.B@CA""" %i)
                               if ((len(sel.residues()) != 1) or (len(sel.residues()) != 1)):
                                            continue
                               if ((len(sol.residues()) != 1) and (len(sol.residues()) != 1)):
                                             continue
                              rc("""distance #0.2:%d.B@CA #0.3:%d.%s@CA""" %(i,j,k))

I got the output as (without any error message)
Distance between #0.2:2196.B@CA and #0.3:3450.C@CA: 104.315

The 'for' loop did not work for k (above) and only gave results for C only but not for A and B.

Thank you for help,
Mahendra Thapa
University of Cincinnati,OH


On Fri, May 29, 2015 at 1:55 PM, Thapa, Mahendra (thapamb) <thapamb@mail.uc.edu> wrote:
 
From: Eric Pettersen
Sent: Friday, May 29, 2015 11:55:18 AM (UTC-06:00) Central America
To: Thapa, Mahendra (thapamb)
Cc: chimera-users@cgl.ucsf.edu
Subject: Re: [Chimera-users] Python code problem

Hi Mahendra,
In the first case, as you saw, it tries exactly two distances; the first involving :2011.B and the second involving :2420.B.  In the second case it will try every distance from :2011.B through :2419.B (note that the range command does not include the ending number in the range).  This means if the structure is missing any of those residues then the distance command will fail with the error you got, since the atom spec will only select one atom.
So you either need to explicitly use just the residue numbers that exist, or you need to test if the residue you are about to try to use exists.  So code to do that might be:

from chimera.selection import OSLSelection
sel = OSLSelection(#0.1:%d.B@CB""" %i)
if len(sel.residues()) != 1:
continue

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On May 29, 2015, at 6:37 AM, Mahendra B Thapa <thapamb@mail.uc.edu> wrote:

Dear Chimera users,

                        The command I used was
                         chimera --nogui test.py
I tried two codes (following previous posts and tutorials in chimera) in 'test.py' as follows

(i)
import os
from chimera import runCommand as rc
from chimera import replyobj
rc("open " + 'test.pdb')
for i in [2011,2420]:
rc("""distance #0.2:2010.B@CB #0.1:%d.B@CB""" %i)

This code gave the result as expected:
Executing test.py...
Opening test.pdb...
60 models opened
Distance between #0.2:2010.B@CB and #0.1:2011.B@CB: 72.346
Distance between #0.2:2010.B@CB and #0.1:2420.B@CB: 92.979
Executed test.py

(ii)
import os
from chimera import runCommand as rc
from chimera import replyobj
rc("open " + 'test.pdb')
for i in range(2011,2420):
rc("""distance #0.2:2010.B@CB #0.1:%d.B@CB""" %i)

This code gave the result as
'  You selected %d.' % numSelected)
MidasError: Exactly two atoms/axes/planes must be selected.  You selected 1.
Error while processing test.py:
MidasError: Exactly two atoms/axes/planes must be selected.  You selected 1.

  File "/opt/UCSF/Chimera64-1.5.3/share/Midas/__init__.py", line 1266, in distance
    '  You selected %d.' % numSelected)

What could be the error this code? Only difference between two codes is:  "for i in [2011,2420]:"  &  "for i in range(2011,2420):"
That is, I am interested to use range operator in 2nd case instead of two values as in the 1st case.

Thank you for help,
Mahendra Thapa
University of Cincinnati,OH


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