Re: [PyMOL] Advice on plugin creation
Hi Ed, The tutorial doesn't consider that the "dialog" variable must not go out of scope. It needs an additional reference to keep it alive, e.g. a global will work: dialog = None def run_plugin_gui(): from pymol.Qt import QtWidgets global dialog if dialog is None: dialog = QtWidgets.QDialog() # TODO: FILL DIALOG WITH WIDGETS HERE dialog.show() The full example plugin on github doesn't suffer from this problem, it's kept alive by circular references - at least until you run the Python garbage collector (ouch!). Cheers, Thomas On Wed, Jun 12, 2019 at 7:02 PM Edward Lowe wrote: > > Hello, > > I'm trying to create what I think should be a fairly simple plugin to > use pymol to showcase structures for a University Open day - all it > needs to do is load up coordinate files and maps and present a very > simple GUI that visitors can use to move between pre-defined scenes. > > I've constructed a PyQt plugin following the tutorial on pymolwiki > which works up to a point... > If I display the window using dialog.show() as in the tutorial example, > the window disappears immediately on opening. > If I change this to using dialog.exec() my widget opens correctly and > everything works - but since this is now a modal window it is not > possible to return to the main pymol gui and interact with the > structure. This was the point of the exercise an why I'm not just > making a movie! > > Does anyone have any advice on what could be done to fix this > behaviour? It probably goes without saying that I am very much a > novice at this! > > Thanks, > Ed. > -- > Dr. E.D. Lowe edward.l...@bioch.ox.ac.uk > Department of Biochemistry Tel: ++44 (0)1865 (2)75392 > University of Oxford > Oxford UK, OX1 3QU > > > ___ > PyMOL-users mailing list > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] possible bug mouse coordinates
Hi Arnaud, This should be fixed now, see https://github.com/schrodinger/pymol-open-source/commit/af28e453c6 Cheers, Thomas > On Jun 13, 2019, at 5:46 PM, Thomas Holder > wrote: > > Hi Arnaud, > > I can reproduce both issues, at least with "sticks" representation. > Apparently PyMOL is missing pick color invalidation somewhere. > > As a workaround, click the "Rebuild" button (upper right button box), or type > the "rebuild" command. After that, picking should be correct again. > > Cheers, > Thomas > >> On Jun 13, 2019, at 4:21 PM, Arnaud Basle wrote: >> >> Dear All, >> >> We found that our home compiled version has the problem just even doing: >> >> load a pdb >> >> change the colour >> >> and then the mouse coordinates are wrong... Anyone else? >> >> Cheers, >> >> Arnaud >> >> >> On 13/06/2019 14:33, Arnaud Basle wrote: >>> Dear All, >>> >>> We may have found a bug where pymol does not get the correct mouse location >>> on the screen. >>> >>> We are using Version 2.3.0a0 on linux Mint 19 (~ubuntu). >>> >>> Maybe people can try to reproduce the bug: >>> >>> open a pdb file >>> >>> display sticks >>> >>> try to select residues or recenter and it should work fine. >>> >>> Now, reduce the top part window of pymol with the log output, movie buttons >>> and command line (the mouse pointer will change then click and drag). >>> >>> repeat selecting/centering and it should work. >>> >>> Then use a menu entry, for example Display>Background>White >>> >>> And if not only us now it seems we click on a residue but another one is >>> selected. It looks like there is a bug where pymol cannot determine the >>> correct mouse co-ordinates? >>> >>> Cheers, >>> >>> Arnaud >>> >>> >> -- >> Dr Arnaud Basle X-ray facilities manager >> Newcastle Structural Biology Laboratory >> University of Newcastle >> Medical School >> ICAMB >> Framlington place >> NE2 4HH Newcastle upon tyne >> Phone 0191 208 8931 >> >> >> >> ___ >> PyMOL-users mailing list >> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net >> Unsubscribe: >> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > > -- > Thomas Holder > PyMOL Principal Developer > Schrödinger, Inc. > -- Thomas Holder PyMOL Principal Developer Schrödinger, Inc. ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
[PyMOL] "Qt not available, using GLUT/Tk interface" error
Dear all, I installed pymol according to guide at https://pymolwiki.org/index.php/Linux_Install. When I launched pymol, and get the "Qt not available, using GLUT/Tk interface" error and no pymol GUI appeared. How could I deal with this problem? Best regards___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
Re: [PyMOL] Question about Pymol method / ESP rendering
Hi Thomas, Thank you for your reply. I made the cube file by using psi4 which is one of quantum chemistry package. I will check the file. Kind regards, Taka 2019年6月11日(火) 19:40 Thomas Holder : > Hi Taka, > > Your ESP.cube file doesn't look like an electrostatic potential map, it > looks like electron density. You need two map files, one for the density, > and one for the ESP. > > Cheers, > Thomas > > > On Jun 8, 2019, at 12:39 AM, Taka Seri wrote: > > > > Dear Pymol users, > > I am newbie of Pymol. > > I have a question of coloring method. I would like to draw isosurface > with ESP and would like to set color with ramp_new function. > > Attached files are example. > > When I load ESP file and type following command, I could get isosurface. > > But I could get only blue colored surface after setting color with > ramp_new function. > > > > > isosurface esp_surf, ESP, 0.2 > > > ramp_new color_map, ESP, [-0.1, 0.1] > > > > I read following url and it worked well. > > https://pymolwiki.org/index.php/Ramp_New > > > > Is something wrong in my ESP file or approach? Any advice or suggestions > will be greatly appreciated. > > > > Kind regards, > > > > Taka > > ___ > > PyMOL-users mailing list > > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > > Unsubscribe: > https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe > > -- > Thomas Holder > PyMOL Principal Developer > Schrödinger, Inc. > > ___ PyMOL-users mailing list Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
