[PyMOL] Segmentation fault with pymol2
Dear all,
I have implemented a software in python/pyQT to draw chemical structure.
For the visualisation it uses a pymol widget (using the pymol2 package). I
haven't used it for a while (it was part of an old project), but today I
noticed that it is no longer working.
When I run the following code:
def paintGL(self):
print("Paint")
glViewport(0, 0, self.width(), self.height())
self._pymol.idle()
self._pymol.draw()
the last line returns me a "segmentation fault 11".
I am using Python 2.7, PyMOL 1.6 and Mac OS X Yosemite, but the problem is
present also with Mavericks. Both python and PyMOL have been installed
using homebrew.
Does anyone have any suggestion?
Thank you for your help,
Alessia
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[PyMOL] Select different set of atoms in different molecules
Dear pyMOL users, I'm puzzled about how to solve an apparently simple task. I loaded on PyMOL two molecules (e.g., m1 and m2) and I wanted to select two different sets of atoms from each of them. Let's say I want to select atoms [1,2,3] from m1 and and atoms [7,8,9] from m2. I tried several combinations of "load" and "select", but no option worked. The last selection is always applied to both molecules. I also Googled it, without any success. Does anyone know if its possible to make a selection in isolation over a given molecule? Any suggestion will be highly appreciated! Thanks in advance, Alessia -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58041391&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Select different set of atoms in different molecules
It helped a lot, thank you very much. Alessia On 5 September 2013 22:20, Bernhard Lechtenberg < blechtenb...@sanfordburnham.org> wrote: > Hi Allesia, > > I am not quite sure how to want to select the atoms, but if you want to > have the selected atoms of both m1 and m2 in the same selection (here s1), > then try this: > select s1, (m1 and id 1-3) or (m2 and id 7-9) > > if you want two different selections, just do > select s1, m1 and id 1-3 > select s2, m2 and id 7-9 > > Hope that helps, > Bernhard > > On Sep 5, 2013, at 12:40 PM, Alessia Visconti > wrote: > > > Dear pyMOL users, > > I'm puzzled about how to solve an apparently simple task. > > > > I loaded on PyMOL two molecules (e.g., m1 and m2) and I wanted to select > two different sets of atoms from each of them. > > Let's say I want to select atoms [1,2,3] from m1 and and atoms [7,8,9] > from m2. > > > > I tried several combinations of "load" and "select", but no option > worked. > > The last selection is always applied to both molecules. I also Googled > it, without any success. > > > > Does anyone know if its possible to make a selection in isolation over a > given molecule? > > Any suggestion will be highly appreciated! > > > > Thanks in advance, > > Alessia > > > -- > > Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! > > Discover the easy way to master current and previous Microsoft > technologies > > and advance your career. Get an incredible 1,500+ hours of step-by-step > > tutorial videos with LearnDevNow. Subscribe today and save! > > > http://pubads.g.doubleclick.net/gampad/clk?id=58041391&iu=/4140/ostg.clktrk___ > > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58041391&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Embedding PyMol in a custom designed GUI
This is a good news (and starting point), thanks for the tip! On the other hand I need to translate all my code in C++. Any thought of making a version for a Python Qt application? ;) Cheers, Alessia On 4 September 2013 13:18, Massimiliano Pippi wrote: > On Wed, Sep 4, 2013 at 12:48 PM, Alessia Visconti > > if you need to embed PyMol in a C++ Qt application you can take a look at > this: > > https://github.com/evonove/moply > > the only pre-requisite is having PyMol installed in your system, then > run qmake, make and try the "playground" executable. > > Cheers > > -- > Massimiliano Pippi > Evonove Srl > ma...@evonove.it :: https://evonove.it :: http://twitter.com/evonove > -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
Re: [PyMOL] Embedding PyMol in a custom designed GUI
Hi all, as Raj, I'm also wondering if there is any way to embed PyMOL in my PyQt4 GUI. Does anyone has any suggestion about where/how to start? Thanks in advance, Alessia > Hello all, > > I have recently been looking for tips or help on embedding PyMol into a GUI > built upon Qt4. I looked at this post from years ago: > > http://sourceforge.net/mailarchive/message.php?msg_id=27413273 > > However on newer versions of pymol I get the same GLUT error and on the > earlier version suggested in the thread I cannot get the example code to > work. > > I really actually have no clue where to start, but all I need is a simple > molecule viewer that I can embed in a GUI frame. PyMol seems like the right > choice but I for some reason cannot get it to work. > > Any tips? Prior experience? > > Thanks in advance! > > Regards, > > Raj Mirpuri > Research Assistant > Roberts Group > California Institute of Technology > *** > -- Learn the latest--Visual Studio 2012, SharePoint 2013, SQL 2012, more! Discover the easy way to master current and previous Microsoft technologies and advance your career. Get an incredible 1,500+ hours of step-by-step tutorial videos with LearnDevNow. Subscribe today and save! http://pubads.g.doubleclick.net/gampad/clk?id=58040911&iu=/4140/ostg.clktrk___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
