From: kanika s. <ksh...@gm...> - 2011-04-25 08:42:36
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i used 1a8y protein and used the following commands create 1a8y_a, 1a8y alter_state 1, 1a8y_a, 1a8y,(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 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? Regards, Kanika |
From: Tsjerk W. <ts...@gm...> - 2011-04-25 10:21:46
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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 |
From: Tsjerk W. <ts...@gm...> - 2011-04-25 10:39:40
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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 <ksh...@gm...> 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 |
From: kanika s. <ksh...@gm...> - 2011-04-25 11:01:49
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in the y-z coordinate the 8.3% format is not there.. On Mon, Apr 25, 2011 at 4:09 PM, Tsjerk Wassenaar <ts...@gm...> 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 <ksh...@gm...> > 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 > |
From: Abhinav V. <abh...@gm...> - 2011-04-25 11:08:32
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As Tsjerk pointed out!!.. it is exactly 8.3 ATOM 604 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 <ksh...@gm...>wrote: > in the y-z coordinate the 8.3% format is not there.. > > > On Mon, Apr 25, 2011 at 4:09 PM, Tsjerk Wassenaar <ts...@gm...>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 <ksh...@gm...> >> 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |