Hi Boris,
PBC have not yet found their way to the main pymol code. What kind of stuff
do you need? lattice.py is quite convenient for shifting. For (a)symmetry
mates, you can use the scripts suggested by Thomas. If you need something
else, pbc operations are not very hard to script.
Cheers,
Tsje
Hi Sajeewa,
have you tried one of the alignment commands (align, super, cealign)?
http://pymolwiki.org/index.php/Align
You can't align "files", only "objects". So if your session files
contain only one object each, this is trivial. If they contain multiple
objects which need to be aligned in c
Hi John,
On 05/14/2012 08:35 AM, John Ladasky wrote:
> Hello everyone,
>
> I have two issues on which I would seek your advice. I am using PyMol 1.4.1.
>
> The first concerns creating protein structures from scratch. I select
> Build > Residue from the menu, and then I select my desired secondary
Hi Thomas,
Thanks for input - the 'bug' was because the
misbehaving PDB had ACs for residues in the
helices that were not being drawn correctly.
Stripping out the alternative conformations fixed
problem, and dss forces cylinder to match dssp
header, so I'm good.
Mark
>Hi Mark,
>
>cylindri
Hi Boris,
if you want to visualize neighboring cells, have a look at one of these
script from the PyMOLWiki:
http://pymolwiki.org/index.php/Supercell
http://pymolwiki.org/index.php/SuperSym
Or for symmetry mates within a given radius:
http://pymolwiki.org/index.php/Symexp
Hope that helps.
Chee
Hi Mark,
cylindrical helices just connect start and end of continous helix
annotations. Could it be that those "misplaced" helices just have a
strong bend to one or both ends, pulling the cylinder from the major
axis of the helix? Same with the fused helices, are you sure there is at
least one
I've run into a problem not encountered before: drawing a cartoon with
cylindrical helices does not accurately follow secondary structure (a couple of
helices are badly misplace and another 2 helices fused into 1) even though pdb
has secondary structure defined by dssp in header.
A cartoon with
Hello PyMOL users!
I was wondering if there's a way to enable periodic boundary
conditions in PyMOL?
I found a script called lattice.py in the mail archive, but the
message is 3 years old - so I thought may there have appeared a
built-in solution? Search on pymolwiki reveals nothing.
With great
I've reported this last week.
http://sourceforge.net/tracker/?func=detail&aid=3523770&group_id=4546&atid=104546
For the moment is not assigned.
Marius
On Mon, May 14, 2012 at 10:22 AM, Boris Kheyfets wrote:
> I use PyMOL 1.4.1 which I have compiled myself. Now I'd like to switch
> to the latest
I use PyMOL 1.4.1 which I have compiled myself. Now I'd like to switch
to the latest version, so I checked out the latest svn, have enabled
VMD plugins (and have also increased the fonts). I get the following
error during compilation:
contrib/uiuc/plugins/molfile_plugin/src/basissetplugin.c: In fu
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