Thanks Tsjerk! now the map is accepted fine by the Pymol- however there is an problem due to the mismatching of atoms in ref structure and the map (although I use ref.pdf from which contact map has been produced). Probably the source of the error is Martini's atom representation used in my system - I've had the same issue in case of some VMD script which do the same task. Do any alternativeties are exist which can identify residues (even on one of the protein) crucial for the formation of the complex during md run with the possibility to map it to the structure for the visualization?
J. 2016-05-12 12:52 GMT+02:00 Tsjerk Wassenaar <tsje...@gmail.com>: > Hey :) > > That's been a choice of the author. You can contact him and ask. > > Cheers, > > Tsjerk > > On May 12, 2016 12:25, "James Starlight" <jmsstarli...@gmail.com> wrote: >> >> Ok, thanks! >> >> however it's normal that pymol ask me for the contact map in the png >> and not for the original xpm produced by gromacs? It seems for the >> that to operate directly with Pymol outputs is more trivial :-) >> >> J. >> >> 2016-05-12 6:51 GMT+02:00 Tsjerk Wassenaar <tsje...@gmail.com>: >> > 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" <jmsstarli...@gmail.com> >> > 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
