[PyMOL] CONECT card and STATES / damien
Hello PyMOL users, I am currently puzzled by the CONECT card and the display of multi-states. After, many trials I cannot end up with a correct representation of my work. I loaded 9 states to PyMOL made of 2 different PDB files. The second files of each states contains specific CONECT cards according to the index number of each atoms (inter residue connection). When I run my script, Pymol is working nicely except for the CONECT cards... Basically, PyMOL only put in memory the CONECT card of the second files of the first state and apply it to the rest of the states. In addition, I tried pdb_ignore_connect and connect_mode... Despites their fancy names those commands were useless. Does someone knows how to force PyMol to read stricly PDB files when loading multi-states? Many thanks. -- *Damien CLAVEL* PhD student at Laboratoire Chimie Physique (UP Sud) and Institut de Biologie Structurale (EPN Campus) -- Laboratoire de Chimie Physique <http://www.lcp.u-psud.fr/rubrique.php3?id_rubrique=266/> Institut de Biologie Structurale <http://www.ibs.fr/spip.php?lang=en> Bul. 350 Campus Orsay EPN Campus 15, Av. Jean Perrin 6, rue Jules Horowitz F-91405 ORSAY Cedex F-38000 GRENOBLE Image and video hosting by TinyPic <http://tinypic.com?ref=28s7yvd> -- Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server from Actuate! Instantly Supercharge Your Business Reports and Dashboards with Interactivity, Sharing, Native Excel Exports, App Integration & more Get technology previously reserved for billion-dollar corporations, FREE http://pubads.g.doubleclick.net/gampad/clk?id=157005751&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
[PyMOL] Using cartoon putty-like command
Hello everyone, I would like to create my own command within the pymol environement. I have currently a set of points in a pdb files with b-factors that i would like to represent as the /cartoon putty/ command is doing.(ie pdb file) The main problem is that I don't precisely know what /cartoon putty/ is doing. So I would like to know where the code of cartoon putty is hidden in pymol and how the code could be modify in order to work on all atoms rather than CA. Many thanks, -- *Damien CLAVEL* Cellphone +33 7 81 66 61 70 Landline +33 4 57 42 87 35 PhD student at Laboratoire Chimie Physique (UP Sud) and Institut de Biologie Structurale (EPN Campus) -- Laboratoire de Chimie Physique <http://www.lcp.u-psud.fr/rubrique.php3?id_rubrique=266/> Institut de Biologie Structurale <http://www.ibs.fr/spip.php?lang=en> Bul. 350 Campus Orsay EPN Campus 15, Av. Jean Perrin 6, rue Jules Horowitz F-91405 ORSAY Cedex F-38000 GRENOBLE Image and video hosting by TinyPic <http://tinypic.com?ref=28s7yvd> UPW_sim2_06_00559.pdb Description: Protein Databank data -- ___ 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] Drawing grid of cubes
Good evening pymol users, I would like to represent a protein with a superimposed 3D grid of cubes. I tried the applet cubes.py but it is not appropriate for me... So my goal is to control the size of the cubes that will be part of such grid. In addition, it will be really great if I could even control the color (shaded) of each cubes. Does anyone could help me? -- *Damien CLAVEL* Cellphone +33 7 81 66 61 70 Landline +33 4 57 42 87 35 PhD student at Laboratoire Chimie Physique (UP Sud) and Institut de Biologie Structurale (EPN Campus) -- Laboratoire de Chimie Physique <http://www.lcp.u-psud.fr/rubrique.php3?id_rubrique=266/> Institut de Biologie Structurale <http://www.ibs.fr/spip.php?lang=en> Bul. 350 Campus Orsay EPN Campus 15, Av. Jean Perrin 6, rue Jules Horowitz F-91405 ORSAY Cedex F-38000 GRENOBLE Image and video hosting by TinyPic <http://tinypic.com?ref=28s7yvd> -- ___ 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] Drawing grid of cubes
Hi Tsjerk, As a matter of fact the replacement of atoms by cubes is possible with cubes.py. However, this applet doesn't suit my project. Indeed, I would like to get a script that describe your second guess! D Le 11/12/15 17:12, Tsjerk Wassenaar a écrit : Hi Damien, Do you mean replacing the atoms by cubes, or by binning the atoms on a 3D grid and show these cubes if filled? Cheers, Tsjerk On Fri, Dec 11, 2015 at 4:51 PM, Damien Clavel <mailto:dcla...@ibs.fr>> wrote: Good evening pymol users, I would like to represent a protein with a superimposed 3D grid of cubes. I tried the applet cubes.py but it is not appropriate for me... So my goal is to control the size of the cubes that will be part of such grid. In addition, it will be really great if I could even control the color (shaded) of each cubes. Does anyone could help me? -- *Damien CLAVEL* Cellphone +33 7 81 66 61 70 Landline +33 4 57 42 87 35 PhD student at Laboratoire Chimie Physique (UP Sud) and Institut de Biologie Structurale (EPN Campus) -- Laboratoire de Chimie Physique <http://www.lcp.u-psud.fr/rubrique.php3?id_rubrique=266/> Institut de Biologie Structurale <http://www.ibs.fr/spip.php?lang=en> Bul. 350 Campus Orsay EPN Campus 15, Av. Jean Perrin 6, rue Jules Horowitz F-91405 ORSAY Cedex F-38000 GRENOBLE Image and video hosting by TinyPic <http://tinypic.com?ref=28s7yvd> -- ___ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net <mailto: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 -- Tsjerk A. Wassenaar, Ph.D. -- *Damien CLAVEL* Cellphone +33 7 81 66 61 70 Landline +33 4 57 42 87 35 PhD student at Laboratoire Chimie Physique (UP Sud) and Institut de Biologie Structurale (EPN Campus) -- Laboratoire de Chimie Physique <http://www.lcp.u-psud.fr/rubrique.php3?id_rubrique=266/> Institut de Biologie Structurale <http://www.ibs.fr/spip.php?lang=en> Bul. 350 Campus Orsay EPN Campus 15, Av. Jean Perrin 6, rue Jules Horowitz F-91405 ORSAY Cedex F-38000 GRENOBLE Image and video hosting by TinyPic <http://tinypic.com?ref=28s7yvd> -- ___ 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
