Entering edit mode
7.0 years ago
underoath006
▴
10
I get msms.exe has stopped working from windows, and "AssertionError: Failed to generate surface file using command:msms -probe_radius 1.5 -" in python console.
I tried it with a different pdb, same result.
from Bio.PDB import PDBParser, ResidueDepth
p = PDBParser()
s = p.get_structure("X", '1crn.pdb')
model = s[0]
rd = ResidueDepth(model, '1crn.pdb')
print(rd[(chain_id, res_id)])
I'm stuck here, any help would be highly appreciated!
It's not clear what are you trying to do. A little bit of explanation of your problem background and context would attract better response.
I want to measure residue depth using biopython and MSMS.
What happens if you run msms on your XYZR file directly?
runs fine, it's a bug with biopython! https://github.com/biopython/biopython/issues/1140 I would appreciate though if you tell me how to install msms on ubuntu, I need to run my analysis!
You can download MGLTools here: http://mgltools.scripps.edu/downloads There's a GUI installer you can use for Linux.
not interested in the gui, I just want msms, there are amny linux/unix versions, I need to know which one to download, and how to install it
It depends on your system. It's very likely that this will work: Go to the page I referenced, scroll down to "MSMS 2.6.1 - Current Release" and download the one called "Unix/Linux i86". Run "tar xf msms_i86Linux2_2.6.1.tar.gz", cd to the directory and run "./msms.x86_64Linux2.2.6.1.staticgcc"