Re: [PyMOL] format problem
Hi Kanika, alter_state 1, 1a8y_a, 1a8y,(x,y,z)=(-0.5*x + 0.886025*y, 0.886025*x + 0.5*y, -z) This doesn't work like that. It should probably be alter_state 1, 1a8y_a,(x,y,z)=(-0.5*x + 0.886025*y, 0.886025*x + 0.5*y, -z) then i saved the molecule in pymol from file--save molecule--1a8y_a.pdb This worked for me as expected. The problem is that when i open the file as text file the format is improper since the space distribution is different from actual pdb files. I am saying this because i have to use this file to convert in tleap format and further use in a program. Is there any other way to save the molecule in pymol? Can you give an example of where the spacing is wrong, e.g., post a section from the original file and the corresponding section from the new file? Cheers, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- Fulfilling the Lean Software Promise Lean software platforms are now widely adopted and the benefits have been demonstrated beyond question. Learn why your peers are replacing JEE containers with lightweight application servers - and what you can gain from the move. http://p.sf.net/sfu/vmware-sfemails ___ 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] format problem
i have attached a small section of the file after applying the matrix.. the spacing between x,y and z axis is abnormal part.pdb Description: Protein Databank data -- Fulfilling the Lean Software Promise Lean software platforms are now widely adopted and the benefits have been demonstrated beyond question. Learn why your peers are replacing JEE containers with lightweight application servers - and what you can gain from the move. http://p.sf.net/sfu/vmware-sfemails___ 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] format problem
Hi Kanika, No, the spacing, or in this case the lack of it, is correct. The coordinate section of the pdb file is %8.3f%8.3f%8.3f, i.e. each coordinate eight characters wide with three decimal precision. Cheers, Tsjerk On Mon, Apr 25, 2011 at 12:28 PM, kanika sharma ksharma...@gmail.com wrote: i have attached a small section of the file after applying the matrix.. the spacing between x,y and z axis is abnormal -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- Fulfilling the Lean Software Promise Lean software platforms are now widely adopted and the benefits have been demonstrated beyond question. Learn why your peers are replacing JEE containers with lightweight application servers - and what you can gain from the move. http://p.sf.net/sfu/vmware-sfemails ___ 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] format problem
in the y-z coordinate the 8.3% format is not there.. On Mon, Apr 25, 2011 at 4:09 PM, Tsjerk Wassenaar tsje...@gmail.com wrote: Hi Kanika, No, the spacing, or in this case the lack of it, is correct. The coordinate section of the pdb file is %8.3f%8.3f%8.3f, i.e. each coordinate eight characters wide with three decimal precision. Cheers, Tsjerk On Mon, Apr 25, 2011 at 12:28 PM, kanika sharma ksharma...@gmail.com wrote: i have attached a small section of the file after applying the matrix.. the spacing between x,y and z axis is abnormal -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- Fulfilling the Lean Software Promise Lean software platforms are now widely adopted and the benefits have been demonstrated beyond question. Learn why your peers are replacing JEE containers with lightweight application servers - and what you can gain from the move. http://p.sf.net/sfu/vmware-sfemails___ 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] format problem
As Tsjerk pointed out!!.. it is exactly 8.3 ATOM604 OG SER A 77 37.493 60.526-103.507 1.00 26.47 O 123456781234567812345678 cheers, Abhi On Mon, Apr 25, 2011 at 12:59 PM, kanika sharma ksharma...@gmail.comwrote: in the y-z coordinate the 8.3% format is not there.. On Mon, Apr 25, 2011 at 4:09 PM, Tsjerk Wassenaar tsje...@gmail.comwrote: Hi Kanika, No, the spacing, or in this case the lack of it, is correct. The coordinate section of the pdb file is %8.3f%8.3f%8.3f, i.e. each coordinate eight characters wide with three decimal precision. Cheers, Tsjerk On Mon, Apr 25, 2011 at 12:28 PM, kanika sharma ksharma...@gmail.com wrote: i have attached a small section of the file after applying the matrix.. the spacing between x,y and z axis is abnormal -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- Fulfilling the Lean Software Promise Lean software platforms are now widely adopted and the benefits have been demonstrated beyond question. Learn why your peers are replacing JEE containers with lightweight application servers - and what you can gain from the move. http://p.sf.net/sfu/vmware-sfemails ___ 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 -- Fulfilling the Lean Software Promise Lean software platforms are now widely adopted and the benefits have been demonstrated beyond question. Learn why your peers are replacing JEE containers with lightweight application servers - and what you can gain from the move. http://p.sf.net/sfu/vmware-sfemails___ 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
