[PyMOL] Contact map visualizer
Dear Pymol users! I am in charge with the analysis of protein-protein association during long molecular dynamic simulation. In particularly I am interesting to find residues on one of the protein which are crustal for the binding interface established during Md. For that purpose I am trying to use Contact map visualizer plugin to map contact maps produced by gromacs onto the 3D structure via Pymol. The problem that on the stage of loading of the contact map Pymol proposed me to load only png or jpg files (not xpm produced by g_mdmat). How it's possible to solve the issue? Any other suggestions regarding my topic? Thanks! James -- Mobile security can be enabling, not merely restricting. Employees who bring their own devices (BYOD) to work are irked by the imposition of MDM restrictions. Mobile Device Manager Plus allows you to control only the apps on BYO-devices by containerizing them, leaving personal data untouched! https://ad.doubleclick.net/ddm/clk/304595813;131938128;j ___ 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
[PyMOL] Slow ray trace
Hello, Apologies for the somewhat naive and general question but I have tried anything I could think of and I'm running out of options. I was using pymol to ray some high quality images. The scene was quite complex. The settings used were: antialias 2 ray_trace_mode 1 stick_quality, 50 fancy_helices, on with these settings I would ray 3600 and take approx 10mins to complete. Two days later, after restoring the session from a saved .pse file, I was trying to render the same images at a different orientation, exactly the same settings. This time it took approximately 2 hours per image with a rate of 1 frame/hour. At first I though it was the complexity of the scene that had somehow changed in the new orientation but when I tried rendering a simple cartoon protein structure, which would otherwise take seconds, it now takes around 20 mins, same rate. I'm on ubunutu 14.04, nothing else is running on my workstation and nothing else is using the cpu. Interestingly, i tried using a different machine and I'm getting the same slow rate. Any ideas on what could cause this behaviour? I'm happy to provide further info if necessary. Cheers, Nick -- Mobile security can be enabling, not merely restricting. Employees who bring their own devices (BYOD) to work are irked by the imposition of MDM restrictions. Mobile Device Manager Plus allows you to control only the apps on BYO-devices by containerizing them, leaving personal data untouched! https://ad.doubleclick.net/ddm/clk/304595813;131938128;j___ 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] Contact map visualizer
Hi James, You can convert the .xpm file to .png/.jpg using tools like convert (imagemagick) and Gimp. Convert doesn't always get the Gromacs .xpm right, but it's an easy one to try. Cheers, Tsjerk On May 11, 2016 2:40 PM, "James Starlight" wrote: > Dear Pymol users! > > I am in charge with the analysis of protein-protein association during > long molecular dynamic simulation. In particularly I am interesting to > find residues on one of the protein which are crustal for the binding > interface established during Md. > For that purpose I am trying to use Contact map visualizer plugin to > map contact maps produced by gromacs onto the 3D structure via Pymol. > The problem that on the stage of loading of the contact map Pymol > proposed me to load only png or jpg files (not xpm produced by > g_mdmat). How it's possible to solve the issue? Any other suggestions > regarding my topic? > > Thanks! > > James > > > -- > Mobile security can be enabling, not merely restricting. Employees who > bring their own devices (BYOD) to work are irked by the imposition of MDM > restrictions. Mobile Device Manager Plus allows you to control only the > apps on BYO-devices by containerizing them, leaving personal data > untouched! > https://ad.doubleclick.net/ddm/clk/304595813;131938128;j > ___ > 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 > -- Mobile security can be enabling, not merely restricting. Employees who bring their own devices (BYOD) to work are irked by the imposition of MDM restrictions. Mobile Device Manager Plus allows you to control only the apps on BYO-devices by containerizing them, leaving personal data untouched! https://ad.doubleclick.net/ddm/clk/304595813;131938128;j___ 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
