[Chimera-users] Python Script to Find Contact Area Between 2 Proteins

[Eric Pettersen]

Hi Kevin,
	Those arguments are “surface pieces”.  Each molecular surface has only one “piece” (despite possibly looking like multiple disjoint pieces).  Once you run the “surface” command (generating two molecular surfaces) you can get the p1/p2 arguments with this code fragment:

	p1, p2 = [s.surface_piece for s in openModels.list(modelTypes=[MSMSModel])]

Both openModels and MSMSModel are in the “chimera” module, but since your code does a “from chimera import *” you can get away with just the above.

—Eric

	Eric Pettersen
	UCSF Computer Graphics Lab

> On Aug 27, 2019, at 1:03 PM, Kevin Wang <kevinkw.wang at mail.utoronto.ca> wrote:
> 
> Hi,
> 
> I am writing a python script to find the area between 2 proteins using the contact_area python command below.
> 
> def contact_area(p1, p2, d, color = None, offset = None, slab = None,
>                  smooth = False, optimize = True):
> 
> Is there a specific object for p1 and p2 and if so how do I get it?
> 
> My current code is as follows:
> 
> import os
> import chimera
> from Measure import contactarea
> from chimera import *
> 
> Path = "/Users/kevinwang/desktop/VEGFR_NO_LIGAND/results/clustering/pdbfit/split"
> 
> filelist = os.listdir(Path)
> for x in filelist:
>     #if x.startswith("trp.pdb."):
>     if (x == "trp.pdb.00001"):
>         print x
>         opened = chimera.openModels.open(x, type ="PDB")
>         runCommand('surface')
>         y = contactarea.contact_area('0.1', '0.2', 2.5)
>         text_file = open("buriedArea.txt", "w")
>         text_file.write(y)
>         text_file.close()
> 
> The error message I am getting is as follows:
> 
> AttributeError: 'str' object has no attribute 'geometry'
> 
>   File "/Applications/Chimera.app/Contents/Resources/share/Measure/contactarea.py", line 8, in contact_area
>     v1, t1 = p1.geometry
> 
> How should I be passing in my arguments?
> 
> Best,
> Kevin
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