Hi,
On Fri, Oct 20, 2017 at 11:37:56AM -0700, mathog wrote:
> Pymol 2.0 was recently announced
That announcement was misleading, while the subject indeed said that,
what was actually announced was the proprietary Pymol *incentive* 2.0
release.
The open source 2.0 release is apparently pushed bac
Hi,
on Debian, we got a bug report which looks like the bug reported here as
well: http://sourceforge.net/p/pymol/bugs/130/
Unfortunately, there has been no discussion of this bug so far.
There seems to be some race condition for scripts, does anybody a
work-around, and/or fix for this? Or is t
Hi,
On Sat, Jun 13, 2015 at 09:38:40PM +1000, Brenton Horne wrote:
> set ray_opaque_background, 1
> png Trimethoprim_img0003.png, dpi=500, ray=1, width = 4000, height = 2325
>
> to render a structure of Trimethoprim I had loaded. While the rendering was
> somewhat better than that generated on 1.
Hi,
Debian/Ubuntu are trying to build packages with some hardening flags by
default, and PyMOL fails to build with -Werror=format-security on in one
place:
|contrib/uiuc/plugins/molfile_plugin/src/maeffplugin.cpp: In function
|'int {anonymous}::write_timestep(void*, const molfile_timestep_t*)':
|
Hi,
I noticed that the mutagenesis wizard uses PYMOL_PATH/data to locate the
chempy sidechains, however, PYMOL_DATA would be more appropriate if the
data is not installed alongside the pymol modules.
The attached patch fixes this.
Michael
--- ./modules/pymol/wizard/mutagenesis.py.orig 2014-01-2
Hi,
On Tue, Jan 14, 2014 at 05:11:51PM -0600, Jason Vertrees wrote:
> We are happy to announce the release of PyMOL v1.7.0.0!
Congrats!
One thing though: the open-source splash image has not been updated for
1.7 and still says "1.6.x".
Michael
Hi Stephen,
On Mon, Mar 25, 2013 at 01:33:16PM -0400, Stephen P. Molnar wrote:
> On Sun, 24 Mar 2013 11:02:08 +0100
> Thomas Holder wrote:
> > The pre-release version of PyMOL 1.6 has been pushed to the open
> > source repository on SourceForge. Besides several minor fixes and
> > improvements, t
Hi,
On Sun, Mar 24, 2013 at 11:02:08AM +0100, Thomas Holder wrote:
> The pre-release version of PyMOL 1.6 has been pushed to the open
> source repository on SourceForge. Besides several minor fixes and
> improvements, this version should complete the transition to
> shader-based rendering for all
Hi,
On Sun, Mar 24, 2013 at 11:02:08AM +0100, Thomas Holder wrote:
> The pre-release version of PyMOL 1.6 has been pushed to the open
> source repository on SourceForge. Besides several minor fixes and
> improvements, this version should complete the transition to
> shader-based rendering for all
Hi,
On Mon, Apr 09, 2012 at 11:01:35AM -0400, Jason Vertrees wrote:
> The latest commit (3995) should fix this for the Intel card. Try
> pulling the latest (3996) from the open source branch.
That worked splendidly, I am uploading pymol-1.5.0.1 with some
subversion changesets to Debian now.
Are
Hi,
On Wed, May 02, 2012 at 09:39:59AM -0400, Jason Vertrees wrote:
> Thanks for this feedback. Since the inception the Script Library on
> the PyMOLWiki the policy is that all deposited scripts are
> open-source:
> http://pymolwiki.org/index.php/Category_talk:Script_Library#Policy.
> This link i
On Mon, Apr 30, 2012 at 01:14:39PM -0400, Jason Vertrees wrote:
> This is just a quick note to let you know that as of revision 3997
> PyMOL has an improved plugin/script manager. This system was written
> by Thomas Holder as part of his PyMOL Open Source Fellowship. Some new
> features include:
>
Hi,
On Thu, Apr 05, 2012 at 08:01:11AM -0400, Jason Vertrees wrote:
> Due to the number of problems that arise when rendering on Intel video
> cards, we're going to automatically disable new rendering features if
> an Intel video card is detected. You will be able to use PyMOL, but
> with the olde
Hi,
On Fri, Apr 01, 2011 at 05:34:47PM -0400, Jason Vertrees wrote:
> I got back from my trip last night and immediately started putting the
> new features into the open source branch as promised. I've finished
> the merge, pushed the changes to SourceForge (revision 3938), and
> uploaded a tar f
Hi,
On Tue, Feb 16, 2010 at 08:26:00PM +0100, Daniel Seeliger wrote:
> take a look into
> ~/.ADplugin/pymol_autodock_plugin.conf
> and set the path to the autodocktools scripts correctly. Then the plugin
> should find them.
Speaking of which, I was just taking a look about including your autodo
On Thu, Apr 15, 2010 at 11:53:06AM -0600, Maia Cherney wrote:
> I downloaded apbs and pdb2pqr, but I don't know how to install them on
> my ubuntu 9.04. Is it possible to make an easy to install release?
> For now, could you please send me the instruction.
apbs is available in Ubuntu (via Debian
Hi,
we are looking into integrating freemol/pymol into Debian/Ubuntu now,
this looks very promising.
On Thu, Sep 18, 2008 at 12:32:07PM -0700, DeLano Scientific wrote:
> > This might be a good reason to start moving towards distribution of
> > APBS and PDB2PQR with PyMOL! :)
>
> Indeed, along th
Hi,
maybe I missed it in the announcement, but what is the subversion
revision for 1.2?
I can't find a tag in the repo, nor any obvious commit message.
Thanks,
Michael
--
__
On Mon, May 04, 2009 at 11:09:06PM +0200, Justin Lecher wrote:
> Waren points me to the fact, that it might be good to explain how to
> work with the github. I wrote a little howto, but there are alot more
> in the web, which can be easily be found via google. I think
> nonetheless it is a good sta
On Thu, Mar 19, 2009 at 05:24:41PM +0100, Justin Lecher wrote:
> some time ago I asked for the script you used for the image on
> pymol.org and I lost it somewhere. Could you post it again, please?
If you mean the main image at the top, you can probably get the effect
using the "QuteMol Like" sect
On Tue, Jul 22, 2008 at 03:38:53PM +0100, Daniel Rigden wrote:
> First let me confess that my problem does not just involved pymol.
> However, it is hampering my use of pymol amongst other things and there
> must be many python experts who read this list.
>
> My problem, on a completely fresh Ubun
On Mon, Nov 20, 2006 at 10:27:48AM -0800, DeLano Scientific wrote:
> My preference would be for a fast, clean, back-end cheminformatics library
> with a simple C API that could be exposed to and interporate with Python,
> Java, C, C++, SQL, and .NET. Several proprietary examples of this design
> e
On Fri, Jun 09, 2006 at 12:30:01PM +0530, Arvind Marathe wrote:
> Error: unable to initialize plugin 'apbs_tools'.
I don't think this is the default, did you install over a local version
or something?
Michael
On Fri, Mar 03, 2006 at 06:00:03PM -0800, Warren DeLano wrote:
> These may be infamous last words, but I do believe that the latest PyMOL
> v0.99 release candidate has reached a level of stability, performance,
> and bug containment such that most everyone should feel comfortable
> downloading and
On Wed, Oct 13, 2004 at 06:12:11PM +0200, peter.du...@cellbio.unige.ch wrote:
> According to a thread on PyKDE, "The tls (thread local storage) stuff only
> works if you are running a tls-enabled glibc on a 2.6 kernel, and when
> installing nvidia-glx, you are normally asked by debconf on what to u
On Fri, Aug 20, 2004 at 09:37:00AM -0700, chuit...@interchange.ubc.ca wrote:
> >In any case, you ask a useful question: I too would like to know
> >what license, if any, is granted by the tutorial's authors. If
> >released under an appropriate license, it could be modified for
> >Linux/Unix/MacOS
On Fri, Aug 13, 2004 at 08:34:17AM -0500, D. Joe Anderson wrote:
> > I have a small tutorial for getting started with PyMOL and I have no idea
> > if people actually use it...
> > Anyway, our server has changed and the webpage has been moved to:
> >
> > http://www.microbiology.ubc.ca/eltis/pymol/
On Thu, Jul 29, 2004 at 04:44:32PM +0200, Vladimir Daric wrote:
> Hello I made a Debian package for Pymol (only for x86 arch). Here are
> instructions for how to get it and how to use it.
>
> There are two ways to install pymol from a Debian package :
>
> The automatic way:
> add this line in yo
On Wed, May 12, 2004 at 09:04:11AM -0700, Ezequiel Panepucci wrote:
> Because some people prefer to answer mailing list questions directly
> to the poster of the question it would be great if the poster would
> take a few minutes to compile a summary quoting all the unique answers
> he or she recei
On Tue, May 11, 2004 at 05:18:37PM -0500, rbax...@uchicago.edu wrote:
> I am running Pymol 0.95 on Mandrake Linux 10.0, or at least I was until today.
> Yesterday I performed a standard update on the system, and today pymol crashes
> with the following error:
>
> GLUT: Fatal Error in pymol.exe: Op
On Thu, Apr 15, 2004 at 10:27:32AM -0400, Shu-Hsien Sheu wrote:
> [mfitz...@man local]$ sudo rpm -V pymol-0.95-1 package pymol-0.95-1 is
> not installed
Just a shot in the dark, but are you sure the package is called
pymol-0.95-1 and not just pymol?
Michael
On Thu, Feb 19, 2004 at 12:24:53PM +0100, Michael Banck wrote:
> On Thu, Feb 19, 2004 at 08:22:14AM +0100, Thomas Siegmund wrote:
> > For me PyMol on SuSE 8.2 crashed always when raytracing a line element.
>
> That seems to be identical to Debian Bug #229080
> (http://bugs
On Mon, Mar 08, 2004 at 10:55:15AM -0800, Warren DeLano wrote:
> It has been a while since anyone's tried to build/run PyMOL on a
> 64-bit system...it may not currently be 64-bit clean.
For the record, 64 bit Debian packages are built on alpha and ia64 (I
believe the other architectures are
On Thu, Feb 19, 2004 at 08:22:14AM +0100, Thomas Siegmund wrote:
> For me PyMol on SuSE 8.2 crashed always when raytracing a line element.
That seems to be identical to Debian Bug #229080
(http://bugs.debian.org/229080)
> The stock compiler on SuSE 8.2 is gcc 3.3 20030226 (prerelease). I
> got
Package: pymol
Version: 0.93-2
On Thu, Jan 22, 2004 at 08:53:37AM -0800, Morri Feldman wrote:
> On Thu, 22 Jan 2004 11:02:25 +0100 Michael Banck wrote:
>
> > On Wed, Jan 21, 2004 at 09:11:01PM -0800, Morri Feldman wrote:
> > > Regarding my problems raytracing on my d
On Wed, Jan 21, 2004 at 09:11:01PM -0800, Morri Feldman wrote:
> Regarding my problems raytracing on my debian/testing machine.
What is the exact version of the pymol .deb you're using? 0.93-2?
What architecture are you running on? i386 or something else?
Do you use pymol's internal raytracer, or
On Tue, Jan 20, 2004 at 10:52:17PM -0800, Morri Feldman wrote:
> My debian/testing system at home also has trouble ray
> tracing, especially with sticks. When it fails I get a
> segmentation fault.
What architecture are you running on? i386 or something else?
Do you use pymol's internal raytra
undefined
> symbol:
> glTexGeniv
>
>
> I don't know whether I have not installed something, or it is a bug in
> the debianized pymol-0.90, or this error come from the NVIDIA opengl
> driver.
> I'm really happy, if you can help me resolving this discrepa
On Mon, Jan 05, 2004 at 11:11:15AM -0800, Mark Wilke wrote:
> Is there a searchable archive of this newsgroup?
There's a browsable archive at
http://sourceforge.net/mailarchive/forum.php?forum_id=60
Dunno whether one can search it, too.
Michael
On Thu, Dec 18, 2003 at 12:26:48AM +0100, Michael Banck wrote:
> On Wed, Dec 17, 2003 at 06:00:44PM -0500, Michael George Lerner wrote:
> > I've gotten the code much closer to working. Also, I think it's factored
> > well enough that most of it should be non-G
On Wed, Dec 17, 2003 at 06:00:44PM -0500, Michael George Lerner wrote:
> I've gotten the code much closer to working. Also, I think it's factored
> well enough that most of it should be non-GPL-contaminated. After I
> actually get it working completely, I'll email the APBS folks to see if
> they
On Sun, Dec 14, 2003 at 10:27:35PM +, Ramanan Selvaratnam wrote:
> On Sun, 2003-12-14 at 19:49, Ben Cornett wrote:
> > I'm not much of a graphic artist, so I will probably stay away from
> > creating any custom button pixmaps.
>
> I will be happy to look into this although it is not clear wha
On Sun, Dec 14, 2003 at 03:58:00AM -0500, Ben Cornett wrote:
> I've put together a preliminary Gtk2 replacement for PyMol's usual Tk
> interface. Those interested can find screenshots, patches, and
> installation instructions at http://www.tuxbox.us
Swt. Do you plan to make it more GTK/GNOMEi
Hi,
I've got a bug on pyopengl (http://bugs.debian.org/214026). Seems the
immeadiate fix is
--- pymol-0.90.orig/setup.py
+++ pymol-0.90/setup.py
@@ -32,7 +32,7 @@
else:
inc_dirs=["layer0","layer1","layer2","layer3","layer4","layer5"]
libs=["GL","GLU","glut","png"]
- pyogl_libs = []
+
On Thu, Sep 18, 2003 at 05:48:56PM +0100, Paulo Martel wrote:
> On Thu, 2003-09-18 at 14:36, Alan Wilter Sousa da Silva wrote:
> >
> > And about Ghemical project?
> >
>
> Ghemical is not a Python project, it is a GNU GPL package written in C
FWIW, ghemical is written in C++.
> using the Gtk to
On Tue, Sep 09, 2003 at 06:40:37AM -0700, Warren L. DeLano wrote:
> RPM doesn't look at the file system (AFAIK), it looks in the RPM
> database for the names of (Redhat-specific) known dependency packages.
AFAIK, rpms can also declare file-dependencies. Whether this is a good
thing or not, I
Hi,
On Unix-like systems, stock pymol installs all images/data files/demo
stuff under /usr/lib/python2.x/site-packages/pymol/. I believe this is a
violation of the File Hierachy Standard (FHS) (well, at least its
spirit, I'm not sure about the letter), as only architecture-dependent
files should b
On Thu, Jun 05, 2003 at 02:35:24PM +0100, Andy Calder wrote:
> Well I'm fairly new to the fink / X11 way of using PyMOL on a Mac but
> I self updated fink to version: 0.13.0 (Distribution version:
> 0.5.2.cvs) Without a hitch and did an update-all but fink reports
> pymol remains at 0.86-3.
Just
On Tue, Jun 03, 2003 at 04:52:34PM -0700, Warren L. DeLano wrote:
> My advice is not to try to figure out all this stuff by yourself, but
> rather to try the new demos and then ask questions via the mailing list.
> Or, simply wait until I get some time later this month or next to update
> the docum
Hi,
On Sat, Apr 19, 2003 at 12:11:12PM -0800, Warren L. DeLano wrote:
> Mac, Linux, and Windows will remain the primary PyMOL platforms, but I
> welcome your feedback on the following question: How important is it
> that PyMOL run well (be tested and released for use) under traditional
> Unix ope
Hi again,
Ok, so the license is available at
http://www.bio.cam.ac.uk/nmr/ccp/project/about_ccpn/licensing/licensing.html
Unfortunately, this looks quite incompatible to the GPL:
(2) Conditions for DISTRIBUTION of SOFTWARE to MEMBERS
(2.1) An individual or ORGANISATION must be a MEMBER of
On Thu, Dec 12, 2002 at 10:33:47AM +, Jules Jacobsen wrote:
> I completely agree here, an integrated total platform would be immensely
> useful.
> I think that the problem is not necessarily all that far from a solution-
> currently there is a collaborative computing project for NMR (CCPN)
>
>
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