[PyMOL] Model pdb section support
Have pdb file with pseudobeads: MODEL 2 HETATM1 O24.000 46.000 39.000 HETATM2 O24.000 47.000 39.000 HETATM3 O24.000 47.000 38.000 HETATM4 O25.000 47.000 38.000 HETATM5 O25.000 47.000 39.000 HETATM6 O25.000 46.000 39.000 HETATM7 O25.000 45.000 39.000 HETATM8 O25.000 45.000 40.000 HETATM9 O26.000 45.000 40.000 HETATM 10 O26.000 45.000 39.000 HETATM 11 O26.000 45.000 38.000 HETATM 12 O25.000 45.000 38.000 HETATM 13 N11.000 43.000 8.000 HETATM 14 C12.000 43.000 8.000 HETATM 15 C13.000 43.000 8.000 HETATM 16 C13.000 44.000 8.000 HETATM 17 N 0.000 5.000 29.000 HETATM 18 C49.000 5.000 29.000 HETATM 19 C48.000 5.000 29.000 HETATM 20 C47.000 5.000 29.000 HETATM 21 N23.000 30.000 17.000 HETATM 22 C22.000 30.000 17.000 HETATM 23 C21.000 30.000 17.000 HETATM 24 C20.000 30.000 17.000 ENDMDL MODEL 1 HETATM99985 Z 0.000 0.000 0.000 HETATM99986 Z50.000 0.000 0.000 HETATM99987 Z 0.000 50.000 0.000 HETATM99988 Z50.000 50.000 0.000 HETATM99989 Z 0.000 0.000 50.000 HETATM0 Z50.000 0.000 50.000 HETATM1 Z 0.000 50.000 50.000 HETATM2 Z50.000 50.000 50.000 CONECT9998599986 CONECT9998599987 CONECT9998599989 CONECT9998699988 CONECT999860 CONECT9998799988 CONECT999871 CONECT999882 CONECT999890 CONECT999891 CONECT02 CONECT12 ENDMDL Want to picture BOTH models, not second one only. How to do that WITHOUT splitting into one model? WITHOUT because it's just test data for real structures more than 10 beads. -- Kind regards, Sergey Ivanov -- Gaining the trust of online customers is vital for the success of any company that requires sensitive data to be transmitted over the Web. Learn how to best implement a security strategy that keeps consumers' information secure and instills the confidence they need to proceed with transactions. http://p.sf.net/sfu/oracle-sfdevnl ___ 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] Model pdb section support
Hi Sergey, If I understand you correctly, you want the following: set all_states then load your file. Cheers, -- Jason On Mon, Jan 10, 2011 at 10:38 AM, Sergey Ivanov icegood1...@gmail.com wrote: Have pdb file with pseudobeads: MODEL 2 HETATM 1 O 24.000 46.000 39.000 HETATM 2 O 24.000 47.000 39.000 HETATM 3 O 24.000 47.000 38.000 HETATM 4 O 25.000 47.000 38.000 HETATM 5 O 25.000 47.000 39.000 HETATM 6 O 25.000 46.000 39.000 HETATM 7 O 25.000 45.000 39.000 HETATM 8 O 25.000 45.000 40.000 HETATM 9 O 26.000 45.000 40.000 HETATM 10 O 26.000 45.000 39.000 HETATM 11 O 26.000 45.000 38.000 HETATM 12 O 25.000 45.000 38.000 HETATM 13 N 11.000 43.000 8.000 HETATM 14 C 12.000 43.000 8.000 HETATM 15 C 13.000 43.000 8.000 HETATM 16 C 13.000 44.000 8.000 HETATM 17 N 0.000 5.000 29.000 HETATM 18 C 49.000 5.000 29.000 HETATM 19 C 48.000 5.000 29.000 HETATM 20 C 47.000 5.000 29.000 HETATM 21 N 23.000 30.000 17.000 HETATM 22 C 22.000 30.000 17.000 HETATM 23 C 21.000 30.000 17.000 HETATM 24 C 20.000 30.000 17.000 ENDMDL MODEL 1 HETATM99985 Z 0.000 0.000 0.000 HETATM99986 Z 50.000 0.000 0.000 HETATM99987 Z 0.000 50.000 0.000 HETATM99988 Z 50.000 50.000 0.000 HETATM99989 Z 0.000 0.000 50.000 HETATM0 Z 50.000 0.000 50.000 HETATM1 Z 0.000 50.000 50.000 HETATM2 Z 50.000 50.000 50.000 CONECT9998599986 CONECT9998599987 CONECT9998599989 CONECT9998699988 CONECT999860 CONECT9998799988 CONECT999871 CONECT999882 CONECT999890 CONECT999891 CONECT02 CONECT12 ENDMDL Want to picture BOTH models, not second one only. How to do that WITHOUT splitting into one model? WITHOUT because it's just test data for real structures more than 10 beads. -- Kind regards, Sergey Ivanov -- Gaining the trust of online customers is vital for the success of any company that requires sensitive data to be transmitted over the Web. Learn how to best implement a security strategy that keeps consumers' information secure and instills the confidence they need to proceed with transactions. http://p.sf.net/sfu/oracle-sfdevnl ___ 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 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Gaining the trust of online customers is vital for the success of any company that requires sensitive data to be transmitted over the Web. Learn how to best implement a security strategy that keeps consumers' information secure and instills the confidence they need to proceed with transactions. http://p.sf.net/sfu/oracle-sfdevnl ___ 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] Model pdb section support
Dear Sergey, From looking at your PDB file, I don't think PyMOL supports exactly what you want. I believe that in order for all_states to show atoms properly, they have to be in all of the states (all MODELs). So, you could do something like the following, but it feels a little clunky to me. Also, I have found it difficult to show changing CONECT records in different states. I hope it's helpful in some way. I just put the atoms you don't want to see in each frame off camera (at 999). === PML file = load tmp2.pdb set_view (\ 0.0,0.0,1.0,\ 0.0,1.0,0.0,\ 1.0,0.0,0.0,\ 0.0,0.0, -160.0,\ 170.746078491, 17.884912491, 31.797996521,\ -322.770446777, 1235.630004883, -20.0 ) hide everything show sticks show spheres set sphere_scale, 0.5 color black, elem z show sticks === = PDB file == MODEL 1 HETATM1 O 999.000 999.000 999.000 HETATM2 O 999.000 999.000 999.000 HETATM3 O 999.000 999.000 999.000 HETATM4 O 999.000 999.000 999.000 HETATM5 O 999.000 999.000 999.000 HETATM 13 N 999.000 999.000 999.000 HETATM 14 C 999.000 999.000 999.000 HETATM 15 C 999.000 999.000 999.000 HETATM99985 Z 0.000 0.000 0.000 HETATM99986 Z50.000 0.000 0.000 HETATM99987 Z 0.000 50.000 0.000 HETATM99988 Z50.000 50.000 0.000 HETATM99989 Z 0.000 0.000 50.000 HETATM0 Z50.000 0.000 50.000 HETATM1 Z 0.000 50.000 50.000 HETATM2 Z50.000 50.000 50.000 CONECT9998599986 CONECT9998599987 CONECT9998599989 CONECT9998699988 CONECT999860 CONECT9998799988 CONECT999871 CONECT999882 CONECT999890 CONECT999891 CONECT02 CONECT12 ENDMDL MODEL 2 HETATM1 O24.000 46.000 39.000 HETATM2 O24.000 47.000 39.000 HETATM3 O24.000 47.000 38.000 HETATM4 O25.000 47.000 38.000 HETATM5 O25.000 47.000 39.000 HETATM 13 N11.000 43.000 8.000 HETATM 14 C12.000 43.000 8.000 HETATM 15 C13.000 43.000 8.000 HETATM99985 Z 999.000 999.000 999.000 HETATM99986 Z 999.000 999.000 999.000 HETATM99987 Z 999.000 999.000 999.000 HETATM99988 Z 999.000 999.000 999.000 HETATM99989 Z 999.000 999.000 999.000 HETATM0 Z 999.000 999.000 999.000 HETATM1 Z 999.000 999.000 999.000 HETATM2 Z 999.000 999.000 999.000 ENDMDL === On Mon, Jan 10, 2011 at 9:38 AM, Sergey Ivanov icegood1...@gmail.comwrote: Have pdb file with pseudobeads: MODEL 2 HETATM1 O24.000 46.000 39.000 HETATM2 O24.000 47.000 39.000 HETATM3 O24.000 47.000 38.000 HETATM4 O25.000 47.000 38.000 HETATM5 O25.000 47.000 39.000 HETATM6 O25.000 46.000 39.000 HETATM7 O25.000 45.000 39.000 HETATM8 O25.000 45.000 40.000 HETATM9 O26.000 45.000 40.000 HETATM 10 O26.000 45.000 39.000 HETATM 11 O26.000 45.000 38.000 HETATM 12 O25.000 45.000 38.000 HETATM 13 N11.000 43.000 8.000 HETATM 14 C12.000 43.000 8.000 HETATM 15 C13.000 43.000 8.000 HETATM 16 C13.000 44.000 8.000 HETATM 17 N 0.000 5.000 29.000 HETATM 18 C49.000 5.000 29.000 HETATM 19 C48.000 5.000 29.000 HETATM 20 C47.000 5.000 29.000 HETATM 21 N23.000 30.000 17.000 HETATM 22 C22.000 30.000 17.000 HETATM 23 C21.000 30.000 17.000 HETATM 24 C20.000 30.000 17.000 ENDMDL MODEL 1 HETATM99985 Z 0.000 0.000 0.000 HETATM99986 Z50.000 0.000 0.000 HETATM99987 Z 0.000 50.000 0.000 HETATM99988 Z50.000 50.000 0.000 HETATM99989 Z 0.000 0.000 50.000 HETATM0 Z50.000 0.000 50.000 HETATM1 Z 0.000 50.000 50.000 HETATM2 Z50.000 50.000 50.000 CONECT9998599986 CONECT9998599987
Re: [PyMOL] Model pdb section support
Hello Sergey, On Mon, 10 Jan 2011 16:38:52 +0100 Sergey Ivanov icegood1...@gmail.com wrote: Have pdb file with pseudobeads: MODEL 2 HETATM1 O24.000 46.000 39.000 HETATM2 O24.000 47.000 39.000 etc. I displayed this file using Nathan's suggestion to set all_states to 1. That appeared to work just fine. But then I noticed that your second model is simply a box. If that is what you always have in the second model, you could replace that with a CRYST1 line used to represent the unit cell of a crystal structure. Hence, your file could look like this: CRYST1 50.0050.000 50.000 90.00 90.00 90.00 P 1 HETATM1 O24.000 46.000 39.000 HETATM2 O24.000 47.000 39.000 HETATM3 O24.000 47.000 38.000 HETATM4 O25.000 47.000 38.000 HETATM5 O25.000 47.000 39.000 HETATM6 O25.000 46.000 39.000 HETATM7 O25.000 45.000 39.000 HETATM8 O25.000 45.000 40.000 HETATM9 O26.000 45.000 40.000 HETATM 10 O26.000 45.000 39.000 HETATM 11 O26.000 45.000 38.000 HETATM 12 O25.000 45.000 38.000 HETATM 13 N11.000 43.000 8.000 HETATM 14 C12.000 43.000 8.000 HETATM 15 C13.000 43.000 8.000 HETATM 16 C13.000 44.000 8.000 HETATM 17 N 0.000 5.000 29.000 HETATM 18 C49.000 5.000 29.000 HETATM 19 C48.000 5.000 29.000 HETATM 20 C47.000 5.000 29.000 HETATM 21 N23.000 30.000 17.000 HETATM 22 C22.000 30.000 17.000 HETATM 23 C21.000 30.000 17.000 HETATM 24 C20.000 30.000 17.000 END Then you can turn on the display of the box by showing the cell representation for the object (under the S menu or by typing show cell). Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821Fax: 613-533-2497 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc -- Gaining the trust of online customers is vital for the success of any company that requires sensitive data to be transmitted over the Web. Learn how to best implement a security strategy that keeps consumers' information secure and instills the confidence they need to proceed with transactions. http://p.sf.net/sfu/oracle-sfdevnl ___ 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
