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 bet
Thanks!
Troels Emtekær Linnet
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2012/10/31 Abdullah Kahraman
> 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
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 syntax!).
Dear All
thanks to Thomas for the modfication on the plot_noe.py. It turns out that the
CNS .tbl file can have different formats, the one I used only includes residue
ID and atom name, but soemtimes it also inlcudes segment ID as well, see on the
attached file. How do I have to modify the noe_r
Dear all,
I recently upgraded to Ubuntu 12.04 (pymol version 1.4.1-3). Since I did
the upgrade, mutations done with the mutagenesis wizard lead to
incorrect atom numbering in the saved pdb file. Before, the problem
definitely did not exist. I read the recent post in this forum
concerning this, but
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 the
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 out
