Dear PyMol developers,
PyMol is an awesome program, but I'm a casual user. Please remove my
email address from your bulletin board.
Thanks
Dave Stout
4-22-10
d...@scripps.edu
--
Thank, Robert, Jason.
Finally I figured this out with your help.
Maia
Robert Campbell wrote:
> Hi Maia,
>
> Just to add to what Jason said:
>
> On Thu, 22 Apr 2010 17:16:41 -0400, Jason Vertrees
> wrote:
>
>
>>> 2. Which plugin allows me to move one structure relative to another. (I
>>> want
Hi Maia,
Just to add to what Jason said:
On Thu, 22 Apr 2010 17:16:41 -0400, Jason Vertrees
wrote:
> > 2. Which plugin allows me to move one structure relative to another. (I
> > want to do manual docking of one structure into another).
>
> You don't need a plugin to move objects. Just use SH
Maia,
> 1. How can I undo a plugin. By mistake I tried to plugin a program using a
> wrong file and now I get an error message every time I open pymol.
Newer versions of PyMOL have a menu option to remove plugins: Plugin >
Manage Plugins > Remove. You can also remove a plugin by simply
removing
Hi Jason,
1. How can I undo a plugin. By mistake I tried to plugin a program using
a wrong file and now I get an error message every time I open pymol.
2. Which plugin allows me to move one structure relative to another. (I
want to do manual docking of one structure into another).
Maia
Jason
(s/benchmark/bookmark/)
On Thu, Apr 22, 2010 at 4:12 PM, David Hall wrote:
> I started a pymolwiki page for this at
> http://www.pymolwiki.org/index.php/Connect_mode so I had something to
> benchmark. If someone knows what connect_mode=3 does, please fill it
> in. The code in layer2/ObjectMolec
I started a pymolwiki page for this at
http://www.pymolwiki.org/index.php/Connect_mode so I had something to
benchmark. If someone knows what connect_mode=3 does, please fill it
in. The code in layer2/ObjectMolecule2.c is probably where to start
if you want to take a stab at figuring it out.
-Da
Hi David,
Check out the "connect_mode" setting:
set connect_mode, 1
# no bonds
fetch 1cll
Cheers,
-- Jason
On Thu, Apr 22, 2010 at 2:14 PM, David Hall wrote:
> Is it possible to load a pdb file and have pymol skip making bonds?
> There's a bunch of undocumented options to load, but I don't
actually, you can ignore this email, it seems pymol was having issues
because there were a bunch of CONECT records, if I delete those, pymol
actually loads it really fast. Kind of odd behavior, but interesting.
-David
On Thu, Apr 22, 2010 at 2:14 PM, David Hall wrote:
> Is it possible to load a
Is it possible to load a pdb file and have pymol skip making bonds?
There's a bunch of undocumented options to load, but I don't think any
of them do what I want. I have a file where there's a bunch of
jumbled atoms and there's no relation between them, just thousands in
the same place and pymol s
Renuka,
In this case the 'fit' command is detecting the residues that are common
between your two sequences and fitting those. The operator in question here
is "in". You can select atoms from one chain that are "in" another. For
example,
# load your two proteins p and q, then select the
# resi
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