From: Amanda C <pit...@ya...> - 2011-06-24 05:56:08
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Hello All, I am attempting to write a script that take a single residue of interest in a protein and then creates a selection that is all residues within 4 Angstroms of that residue. Then I would like to find the polar contacts within that new expanded selection and print out the pair of residue names, residue numbers, the atom names involved in the contact and the distance to a text file. #select interest, resi 463 cmd.select ("interest","(resi 463)") #Action, modify, expand, by 4 A, residues cmd.select("exp_interest","(byres (interest expand 4))",enable=1) # show lines for all within 4 Ang cmd.show("lines" ,"exp_interest") #show sticks for residue of interest cmd.show("sticks" ,"interest") #Action, find, polar contact, within selection #distance exp_interest_polar, exp_interest, exp_interest, 3.6, 2 cmd.dist("interest_polar_conts","exp_interest","exp_interest",quiet=1,mode=2,label=1,reset=1);cmd.enable("interest_polar_conts") I am using the command: cmd.dist("interest_polar_conts","exp_interest","exp_interest",quiet=1,mode=2,label=1,reset=1);cmd.enable("interest_polar_conts") to find the polar contacts. This command creates an object in the panel but I cannot figure out how to print the information I am seeing, like the distance and the atoms involved, in the viewer to a file. Thanks for the help, Amanda |
From: Thomas H. <sp...@us...> - 2011-06-24 08:20:12
Attachments:
pairs.py
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Hi Amanda, > I am using the command: > cmd.dist("interest_polar_conts","exp_interest","exp_interest",quiet=1,mode=2,label=1,reset=1);cmd.enable("interest_polar_conts") > >to find the polar contacts. > > This command creates an object in the panel but I cannot figure out > how to print the information I am seeing, like the distance and the > atoms involved, in the viewer to a file. as far as I know the "raw data" of distance objects cannot be accessed. Have a look at the attached script, it does a very similar job to the distance command but returns atom pairs with (model,index) keys. pairlist = polarpairs("exp_interest", "exp_interest", cutoff=3.6, \ name="interest_polar_conts") You can drop the 'name' argument if you don't need the object for visual inspection but only the pair list. Cheers, Thomas -- Thomas Holder MPI for Developmental Biology |