PyMOLers,
Just a quick note: if you're on the list and see a feature you like,
please reply to that email with a quick "yea" vote. It's even better
if you let us know why you like it. Silence regarding a feature only
down-weights its perceived importance.
Thanks,
-- Jason
--
Jason Vertrees,
For the sale of PyMOL, we had to take down FreeMOL temporarily. I
will put it back up soon. I think you can still get access to the
code from bioinformatics.org.
I'll update the list when I've posted the FreeMOL code.
Thanks,
-- Jason
On Wed, Jan 20, 2010 at 10:27 PM, David Hall wrote:
> In
In my incentive build, freemol is present with the following readme:
This is a binary distribution of the FreeMOL Open-Source Compilation.
The FreeMOL project home page can be found at:
http://bioinformatics.org/freemol
Complete source code for building FreeMOL and its various components
c
David,
Some good suggestions, but I think too localized to you, specifically.
My comments follow.
> 1) I would love it if the PDB Loader Service Plugin would clean up what it
> left in /tmp on pymol exit. I have a feeling this might be complicated
> though. I just have a bad memory when I fi
Thanks,
But I could not find the download site for FreeMol.
Could somebody send me a link to FreeMol?
Maia
Jason Vertrees wrote:
> Maia,
>
> You can already move structures independently. If you install
> PyMOL+FreeMOL you can have access to the MMFF-enabled PyMOL that will
> allow you to do s
1) I would love it if the PDB Loader Service Plugin would clean up what it left
in /tmp on pymol exit. I have a feeling this might be complicated though. I
just have a bad memory when I first entered this world and I had pymol open and
I was trying to load a pdb and the plugin just would not w
That seems like a modification that makes it less flexible. Now I can't do:
ray 2.5in, 20cm, dpi=300
Don't ask me why I might want to use two different units, I just don't see a
reason to make it so I cannot. I'm frequently surprised by my desires.
And resolution is inconsistent with the png
Several more votes for one of these from lots of people in my lab.
On Wed, Jan 20, 2010 at 3:54 PM, Tsjerk Wassenaar wrote:
> Hi,
>
> > ray 10cm, 20cm, dpi=300?
> > ray 2.5in, 5in, dpi=300?
>
> I'd slightly modify that to read:
>
> ray 10,10,units=cm,resolution=300
>
> where units can be pixels
PyMOLers,
I just want to quickly reiterate: PyMOL will still be supported on the
Mac--no need to worry. Even though other Schrodinger software doesn't
run on the Mac, PyMOL will.
MacPyMOL will live on.
Best,
-- Jason
--
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC
(e) jason.ve
Maia,
You can already move structures independently. If you install
PyMOL+FreeMOL you can have access to the MMFF-enabled PyMOL that will
allow you to do small molecule cleanup and editing.
Try putting your mouse into "Editing Mode" and moving atoms around.
It's not hard. Check this out:
http:/
Roger,
Both of these features are available to PyMOL subscribers already.
You can get AxPyMOL which has the ActiveX plugin for PowerPoint.
There is no need to "tab out" of your presentation. Also in the
incentive version is "RigiMOL" the molecular morpher. We could
probably clean up the interfac
Hi,
> ray 10cm, 20cm, dpi=300?
> ray 2.5in, 5in, dpi=300?
I'd slightly modify that to read:
ray 10,10,units=cm,resolution=300
where units can be pixels (default), cm, inches, meters, yards, lightyears...
Cheers,
Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.
Computational Chemist
Medicinal Chemist
Adrian,
My comments follow.
> 1) set pdb_mirror option to be able to use a European (EBI) mirror for
> example. The RCSB mirror is rather slow from Europe.
This is a good idea; allowing people to set their own server.
> 2) uppercase support for fetch_path; currently only lowercase file
> names
Georg,
Thanks for the reply. My comments are below.
> 1) Ever since I have used the ray function in PyMOL i ran into problems
> creating the right resolution/size of the ray trace images for
> posters/papers. I know its just a matter of x/y pixel settings, but
> every time i had to look it up a
Hi there,
Please, did someone check that? It would be very appreciated.
Thanks
Alan
On Mon, Jan 4, 2010 at 16:49, Alan wrote:
> Hi there,
>
> I use both pymol via Fink (on MBP 10.6.2) all in 64 bits and MacPymol 1.2r3
> (licensed to PDBe).
>
> Both work fine but I tried
> http://pymolwiki.org/
Phil,
The answers to your questions lie in the "iterate," "iterate_state,"
"alter," and "alter_state" commands. The PyMOLWiki has extensive
documentation on these commands
(http://pymolwiki.org/index.php/Iterate). Once you select something
with the mouse you can get information using iterate/alt
Hi Jason
I need such features. I open two different pdbs and I want to manually
move one structure relative to another. I want to dock one structure
into another or superpose 2 structures manually. Is it possible?
Or I want to move a fragment of the molecule relative to the rest of the
molecu
Two items come to mind:
1. A Powerpoint plugin for live Pymol viewing in presentations.
2. A simpler method of doing structure morphs in Pymol. Intelligent
morphing is incredibly powerful for visualizing protein conformational
changes based on "endpoint" protein structures, or just
evaluating/
- Original Message
> From: Adrian Schreyer
> To: jason.vertr...@schrodinger.com; PyMOL-users@lists.sourceforge.net
> Sent: Wed, January 20, 2010 10:00:03 AM
> Subject: [PyMOL] New Feature Ideas
>
> Something more challenging:
>
> 3) Export scenes as webGL.This is a bit more ambitious t
Hi Jason,
here are two minor improvements:
1) set pdb_mirror option to be able to use a European (EBI) mirror for
example. The RCSB mirror is rather slow from Europe.
2) uppercase support for fetch_path; currently only lowercase file
names are loaded.
Something more challenging:
3) Export scene
I am writing a Pymol plugin, in which I need to extract, manipulate, and
replace the coordinates of selected atoms. Are there examples out there
I could use as a prototype?
For starters, what command(s) do I use to get the name strings of
residues that I've selected with mouse clicks. I would li
Matthias,
Good thinking. Nice workaround.
-- Jason
On Wed, Jan 20, 2010 at 2:54 AM, Matthias Haffke
wrote:
> Thanks for your help Jason and David!
>
> I'll have a look at your suggestions, although I solved my problem in a
> different way. I just copied the coordinates of the important symmetr
Hi!
1) Ever since I have used the ray function in PyMOL i ran into problems
creating the right resolution/size of the ray trace images for
posters/papers. I know its just a matter of x/y pixel settings, but
every time i had to look it up again. However i wrote a little script
embedded in the B
Hi Jason,
I think the number one feature I would like to see is eMovie
incorporated into the standard build of PyMOL. The built in movie
making facilities in PyMOL may be powerful but the scripting is a bit
beyond those of us "biologists who use computers" especially if one is
trying to ma
Hi Marius
Marius Retegan wrote:
> No according to this
> http://www.nvidia.com/object/3D_Vision_Requirements.html and an old
> post from the list http://bit.ly/61Lwbn.
I thought this question was about getting pymol to run in 3D on win7.
Not get your directX games to run in 3D.
Pymol run Open
On Wed, Jan 20, 2010 at 9:35 AM, Jesper Lykkegaard Karlsen <
je...@bioxray.au.dk> wrote:
> Hi Deepangi,
>
> > 1. OS: Windows 7
> >
> > 2. Monitor:Samsung Syncmaster 2233RZ 22in 3D Gaming LCD
> >
> > 3. Card: EVGA GeForce 9800 GTX+ 512MB PCIe w/Dual Link DVI
> >
> > 4. Glasses: NVIDIA 3D Vision Gla
Hi Deepangi,
> 1. OS: Windows 7
>
> 2. Monitor:Samsung Syncmaster 2233RZ 22in 3D Gaming LCD
>
> 3. Card: EVGA GeForce 9800 GTX+ 512MB PCIe w/Dual Link DVI
>
> 4. Glasses: NVIDIA 3D Vision Glasses
>
Wrong graphics card:
http://www.nvidia.com/object/quadro_pro_graphics_boards.html
/Jesper
---
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