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
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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Mahendra B Thapa