[PyMOL] opensource pymol with MPEG support

[Troels Emtekær Linnet]

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 pymol.

http://www.pymolwiki.org/index.php/Linux_Install#Ubuntu.2FMint_Compile_and_install_with_MPEG_support

Best
Troels
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Re: [PyMOL] PyMOL 1.5 release

[Jason Vertrees]

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 the case, some new features added to Incentive
PyMOL v1.5.0 will not be immediately added to the open-source project,
as Incentive subscribers pay to have priority access to these new
features.

Open-source PyMOL v1.4.2, should be updated, tagged, and released
later this year or early next year.

Cheers,

-- Jason

On Tue, Nov 8, 2011 at 5:04 AM, Андрей Гончар  wrote:
> Hi all
> Do anybody know about the PyMol 1.5 release date?
>
> --
>
> Andrey Gontchar
>
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-- 
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(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

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Re: [PyMOL] Antw.: Put scripts in a svn folder

[Justin Lecher]

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 any commit. Of course this has
know security implications but doesn't need selected commiters.
If we would select one or some trusted commiter we could do it on github
in a nice way. The main repo could be closed to commit access for the
trusted ones. If someone wants to add/modify something the main repo can
be forked, modified and request pull (http://help.github.com/fork-a-repo/).

justin



On 11/10/11 5:45 PM, Troels Emtekær Linnet wrote:
> 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 "super users". 
> So only a few users can change the script.
> Would it possible to have the same user credentials to the github as the
> wiki?
> 
> Host / mirror.
> As far as I know, one can find each file at a github webpage.
> So, maybe the pymolwiki could show that file in a window at the wiki?
> 
> People with github experience should throw in some experience. :-)
> 
> Best
> Troels
> 
> 
> 
> 
> Troels Emtekær Linnet
> Slotsvej 2
> 4300 Holbæk
> Mobil: +45 60210234
> 
> 
> 
> 2011/11/10 Jason Vertrees  >
> 
> 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 from various locations and install them on the fly without one
> needing to restart PyMOL. Do you mind working with Thomas to help
> integrate with the git-hub repo?
> 
> Downloading scripts and running them creates a security hazard. So, we
> need to be careful about that.
> 
> Some points to consider for the repository:
>  * it should mirror or host the code from the PyMOLWiki, not fork it
>  * be secure from misuse (can anyone commit or just you?)
> 
> What do you think?
> 
> Cheers,
> 
> -- Jason
> 
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
> 
> (e) jason.vertr...@schrodinger.com
> 
> (o) +1 (603) 374-7120 
> 
> 
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> )
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> 
> 




-- 
Justin Lecher
Institute of Complex Systems
ICS-6 Structural Biochemistry
Research Centre Juelich
52425 Juelich, Germany
phone: +49 2461 61 2117




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Re: [PyMOL] Editing of the pdb structure

[Thomas Holder]

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 residue and place another element of the same size on the 
> place of the first element.
> 
> In particular I have two  different peptides both of wich have small cap 
> groups on C and N termi. ( attached)
> 
> I need to remove all caps ( two caps FOR and ETA because there are two 
> identical chains in that structure) from the 1MAG structure and build  
> exactly on this place another cap groups wich I'd like to copy from the 
> second peptide ( KALP).

the "Mutagenesis Wizard" comes in handy for editing caps. However it
fails with non-standard amino acis as far as I know. Then you have to do
it manually.

These commands could be a good start for your task:
http://pymolwiki.org/index.php/Remove
http://pymolwiki.org/index.php/Fuse

> So I'd like to change FOR- > ACE and ETA-> NH2 
> twisely for the 1MAG dtructure

hm, shouldn't it be the other way round? FOR is N-terminus and ETA is 
C-terminus?

Cheers,
   Thomas

-- 
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MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen


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Re: [PyMOL] Filled rings for cyclic molecules?

[Thomas Holder]

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 cartoon_ring_mode, 3
as cartoon

It's a bit hidden in the PyMOLWiki:
http://pymolwiki.org/index.php/Examples_of_nucleic_acid_cartoons#Cartoon_ring_finder

Cheers,
   Thomas

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[PyMOL] Filled rings for cyclic molecules?

[Francis E Reyes]

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




-
Francis E. Reyes M.Sc.
215 UCB
University of Colorado at Boulder






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Re: [PyMOL] Create a dimer from predicted monomer

[João Rodrigues]

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 [...] Rodrigues



2011/11/8 Cell Cycle 

> 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 symmetry loaded". Can anyone tell me how to create a dimer from
> my predcited monomer? Thanks,
>
> Karen
>
>
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[PyMOL] Create a dimer from predicted monomer

[Cell Cycle]

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 symmetry loaded". Can anyone tell me how to create a dimer from
my predcited monomer? Thanks,

Karen
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[PyMOL] movie in H.264 yields one frame

[Martin Stoermer]

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.net/tracker/?func=detail&aid=1545548&group_id=4546&atid=104546

Is this bug due to the assumption that Quicktime Pro is installed? No  
errors arise on screen just that the output file is very small and has  
one frame.

thanks,
Martin

_
   Dr. Martin Stoermer
   Senior Research Officer
   INSTITUTE FOR MOLECULAR BIOSCIENCE
   University of Queensland 4072 AUSTRALIA
   Phone: +61-7-3346 2991   Fax: +61-7-3346 2101
   Email:martin.stoer...@uq.edu.au  http://www.imb.uq.edu.au
_





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Re: [PyMOL] Antw.: Put scripts in a svn folder

[Troels Emtekær Linnet]

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 "super users".
So only a few users can change the script.
Would it possible to have the same user credentials to the github as the
wiki?

Host / mirror.
As far as I know, one can find each file at a github webpage.
So, maybe the pymolwiki could show that file in a window at the wiki?

People with github experience should throw in some experience. :-)

Best
Troels




Troels Emtekær Linnet
Slotsvej 2
4300 Holbæk
Mobil: +45 60210234



2011/11/10 Jason Vertrees 

> 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 from various locations and install them on the fly without one
> needing to restart PyMOL. Do you mind working with Thomas to help
> integrate with the git-hub repo?
>
> Downloading scripts and running them creates a security hazard. So, we
> need to be careful about that.
>
> Some points to consider for the repository:
>  * it should mirror or host the code from the PyMOLWiki, not fork it
>  * be secure from misuse (can anyone commit or just you?)
>
> What do you think?
>
> Cheers,
>
> -- Jason
>
> --
> Jason Vertrees, PhD
> PyMOL Product Manager
> Schrodinger, LLC
>
> (e) jason.vertr...@schrodinger.com
> (o) +1 (603) 374-7120
>
>
> --
> RSA(R) Conference 2012
> Save $700 by Nov 18
> Register now
> http://p.sf.net/sfu/rsa-sfdev2dev1
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
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Re: [PyMOL] Antw.: Put scripts in a svn folder

[Jason Vertrees]

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 from various locations and install them on the fly without one
needing to restart PyMOL. Do you mind working with Thomas to help
integrate with the git-hub repo?

Downloading scripts and running them creates a security hazard. So, we
need to be careful about that.

Some points to consider for the repository:
  * it should mirror or host the code from the PyMOLWiki, not fork it
  * be secure from misuse (can anyone commit or just you?)

What do you think?

Cheers,

-- Jason

-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

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[PyMOL] Antw.: Put scripts in a svn folder

[Lecher, Justin]

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, 2011 10:47
Betreff: [PyMOL] Put scripts in a svn folder
An: "Troels Emtekær Linnet" 
Cc: "pymol-users@lists.sourceforge.net" 


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 suggested, but other functionality that will provide similar
convenience.

More news about that soon.

Cheers,
  Thomas

Troels Emtekær Linnet wrote, On 11/09/11 23:57:
> Hi Pymolers.
>
> I sometimes find small errors in my scripts, which I then correct.
> But then I get a little "sad", that now my "unfinished" script still
> lives "out there".
>
> So I think, why is the pymolwiki scripts not under subversion control?
>
> Then authors could push corrections to their scripts to the subversion
> directory, and users would get these corrections.
>
> I dont know if the pymol wiki could fetch and display the scripts from
> the subversion folder.
>
> How does this idea sounds?
>
> Bes
> Troels

--
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MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

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Re: [PyMOL] Put scripts in a svn folder

[Thomas Holder]

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 suggested, but other functionality that will provide similar 
convenience.

More news about that soon.

Cheers,
   Thomas

Troels Emtekær Linnet wrote, On 11/09/11 23:57:
> Hi Pymolers.
> 
> I sometimes find small errors in my scripts, which I then correct.
> But then I get a little "sad", that now my "unfinished" script still 
> lives "out there".
> 
> So I think, why is the pymolwiki scripts not under subversion control?
> 
> Then authors could push corrections to their scripts to the subversion 
> directory, and users would get these corrections.
> 
> I dont know if the pymol wiki could fetch and display the scripts from 
> the subversion folder.
> 
> How does this idea sounds?
> 
> Bes
> Troels

-- 
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen

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