read file by python script and color pdb file with script
I am having 2 coordinates in check file. I want to take/read them and paint my pdb file loaded in chimera. I have chimera in my ~/bin/ System specs: ubuntu 64 bit, 13.10, 4gb ram
Below is the command I have used for script-chimera communication
$ chimera64-1.8.1 --script "y.py check" -- Q6UXT6.pdb
I am storing values in listu and want to use them for coloring my file loaded.
rc("color blue :"+listu[0]+"-"+listu[1])
This works well, if hard coded rc ("color red :55-86")
I do not get any error. The particular protein length is not colored.
attached 3 files. Kindly suggest, how do I proceed.
-- Regards
Sariya
Hi Sariya, Your "check" file contains this (one) line:
67 23
which means that the residue range you generate is ":67-23" which contains nothing. You want "check" to contain "23 67" so that your residue range becomes ":23-67".
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Apr 21, 2014, at 8:33 PM, Sanjeev Sariya s.sariya_work@ymail.com wrote:
I am having 2 coordinates in check file. I want to take/read them and paint my pdb file loaded in chimera. I have chimera in my ~/bin/ System specs: ubuntu 64 bit, 13.10, 4gb ram
Below is the command I have used for script-chimera communication
$ chimera64-1.8.1 --script "y.py check" -- Q6UXT6.pdb
I am storing values in listu and want to use them for coloring my file loaded.
rc("color blue :"+listu[0]+"-"+listu[1])
This works well, if hard coded rc ("color red :55-86")
I do not get any error. The particular protein length is not colored.
attached 3 files. Kindly suggest, how do I proceed.
-- Regards Sariya
<Q6UXT6.pdb><y.py><check>_______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev
Eric, Oops. my bad, corrected the script.
Thank you very much for attention and prompt reply to query. -- Regards
Sariya
On Tuesday, April 22, 2014 2:04 PM, Eric Pettersen pett@cgl.ucsf.edu wrote:
Hi Sariya, Your "check" file contains this (one) line:
67 23
which means that the residue range you generate is ":67-23" which contains nothing. You want "check" to contain "23 67" so that your residue range becomes ":23-67".
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
On Apr 21, 2014, at 8:33 PM, Sanjeev Sariya s.sariya_work@ymail.com wrote:
I am having 2 coordinates in check file. I want to take/read them and paint my pdb file loaded in chimera. I have chimera in my ~/bin/ System specs: ubuntu 64 bit, 13.10, 4gb ram
Below is the command I have used for script-chimera communication
$ chimera64-1.8.1 --script "y.py check" -- Q6UXT6.pdb
I am storing values in listu and want to use them for coloring my file loaded.
rc("color blue :"+listu[0]+"-"+listu[1])
This works well, if hard coded rc
("color red :55-86")
I do not get any error. The particular protein length is not colored.
attached 3 files. Kindly suggest, how do I proceed.
Regards
Sariya
<Q6UXT6.pdb><y.py><check>_______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev
participants (2)
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Eric Pettersen
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Sanjeev Sariya