Hi Troels,
your idea sounds good, indeed! We are working on a improved plugin
system for PyMOL that supports fetching from repositories, versioning
and metadata for plugins. It will handle "scripts" and "plugins" the
same way. It will rather not include the subversion <> wiki interface as
you
I started this some time ago and also announced it on the mailing list. But it
didn't caught much interest.
https://github.com/jlec/Pymol-script-repo
So if there is interest, please feel free to check in your scripts.
Justin
- Reply message -
Von: "Thomas Holder"
Datum: Do., Nov. 10,
Hi Justin,
> I started this some time ago and also announced it on the mailing list. But
> it didn't caught much interest.
The idea didn't get much traction because it was ahead of its time. I
think now is its time.
The plugin manager that Thomas is creating will be able to aggregate
scripts fro
I personally think git hub is a good suggestion.
And we need you wikiguys (Jason etc. ) to catch the idea and implement it.
:-)
Security is an issue, and I also believe that you need to control this.
I don't know if github is able to make securities in groups of a owner of a
script and some "supe
Hi folks,
on OS10.5, and 10.6 Macs running MacPymol 1.2r1, we are trying to
export movies as Quicktime with H.264 which results in a one-frame
movie only, despite every frame being displayed on screen during the
write. Looking online led me to bug #1545548 back in 2006
http://sourceforge.ne
Hi,
A fragment of my protein is predicted by I-TASSER to be similar to a
homodimer module. But the predicted pdb file (named copy) is only a
monomer. Can I generate a dimer using pymol? I tried symexp sym, copy,
copy, 2.5, which would work for other known pdb file, but got the error
message "no s
Hello Karen,
Predicting protein complexes structures is "docking". Pymol should not be
used for this. I would advise you to look at docking software that allows
for symmetrical molecules, such as HADDOCK (http://haddocking.org/) or
SymmDock (http://bioinfo3d.cs.tau.ac.il/SymmDock/).
Best,
João [
Hi all
I'm looking for a way to get filled rings for cyclic molecules. An example is
the tetrapyrrole rings in heme. It's very similar in representation to the
nucleic acid ring mode (filled bases), but I'd like it for an arbitrary ring .
Any approaches would be appreciated!
F
--
Hi Francis,
> I'm looking for a way to get filled rings for cyclic molecules. An
> example is the tetrapyrrole rings in heme. It's very similar in
> representation to the nucleic acid ring mode (filled bases), but I'd
> like it for an arbitrary ring .
try this:
set cartoon_ring_finder, 4
set car
Hi James,
> Recently I've opened such topic but I didnt obtain answer on this
> question so I try to paraphrase my task. Also I want to specify this
> topic on questions lincked with the processing of pdbs.
>
> 1) I need to remove some elements fron my structure described as the
> individual r
Hi,
That days I simply copied the scripts from the wiki into the repo. After
that many scripts got updated in the wiki, so we need to synchronize it
again. I am sorry but I lost the interest because I wanted it to be
community based not as my own project.
Currently the repo is set to be open for
Hi Andrey,
We plan on releasing Incentive PyMOL v1.5.0 before the end of the
year. Current Incentive subscribers can already download Incentive
PyMOL betas builds from http://pymol.org/dsc and review the new
features here http://pymol.org/dsc/dokuwiki/doku.php?id=media:new15.
As has always been th
Hi Gals and Gils.
I have struggled with making a movie easy and fast. The MPEG way is just
snappy snappy fast.
I was pleased to see that installation instructions has been updated for
the pymol open source.
I added installation instructions (Ubuntu/Mint) with MPEG support for the
opensource pymo
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