Hi Pymolers.
How would you get a list of surface residues the fastest way?
Like:
[3-10], [14-18]
I have a rough structure from crystallography, and have made
a trypsin digest and mass spec analysis.
And I see fragments which have been post-trans modified.
Now I am interested in matching if
Hi Troels,
I've been using
http://www.pymolwiki.org/index.php/FindSurfaceResidues
at some point. Seems to work well enough.
Otherwise you could go through the PISA server at
http://www.ebi.ac.uk/msd-srv/prot_int/pistart.html
But I don't remember how exactly I would get the surface residues
Dear Troels,
Personally I don't use PyMol for this problem. Rather I use the application
NACCESS (http://www.bioinf.manchester.ac.uk/naccess/) and choose a total
relative solvent accessibility of at least 5% (Miller, S. et al, 1987, J Mol
Biol 196, 641–656) to assess whether a residue is at
Hi Krisztina,
check the attached script (strongly modified). It doesn't use a regex
anymore, but uses a split function which takes parentheses into account.
Also it doesn't parse name and resi, but passes the selection string
directly to PyMOL (which understands most of CNS selection
Thanks!
Troels Emtekær Linnet
Ved kløvermarken 9, 1.th
2300 København S
Mobil: +45 60210234
2012/10/31 Abdullah Kahraman abdul...@imsb.biol.ethz.ch
Dear Troels,
Personally I don't use PyMol for this problem. Rather I use the
application NACCESS
Dear user
Can you please help me in finding the angle between
two structure upon alingment. I have aligned two structure and one
structure is not perfectly aligned on other. There is domain of two
structure tilting outward upon alignment. IS there any way to find the
angle
