Re: [PyMOL] representing ferrocene in pymol
That's pretty slick. Alternatively you can delete the "drawn bonds" using the builder module. Then show nb_sphere for the Fe atom. If you have access to the CSD I would grab one from there Hope this helps From: Troels Emtekær Linnet [mailto:tlin...@gmail.com] Sent: Tuesday, 12 February 2013 3:17 a.m. To: Edward Deira Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] representing ferrocene in pymol How about. import select_sites sites 1a3l set_bond stick_radius, 0.1, resi 213 extract Fe_atom, resi 213 and name Fe Wiki http://www.pymolwiki.org/index.php/Select_sites http://www.pymolwiki.org/index.php/Set_bond Best Troels Troels Emtekær Linnet Ved kløvermarken 9, 1.th<http://1.th/> 2300 København S Mobil: +45 60210234 2013/2/11 Edward Deira mailto:edward.de...@gmail.com>> Dear all, How can I "accurately" represent ferrocene in pymol, without using CONECT lines in the pdb file ? By "accurately" I mean at least including the C-C bonds; I'd rather not have any Fe-C bonds, but if they are present I can live. I've been trying to figure out how to do this using atom selections, or trying to get gonds between the nonbonded... Any hints are welcome, all the best Ed. -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb ___ 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 -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb___ 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] representing ferrocene in pymol
How about. import select_sites sites 1a3l set_bond stick_radius, 0.1, resi 213 extract Fe_atom, resi 213 and name Fe Wiki http://www.pymolwiki.org/index.php/Select_sites http://www.pymolwiki.org/index.php/Set_bond Best Troels Troels Emtekær Linnet Ved kløvermarken 9, 1.th 2300 København S Mobil: +45 60210234 2013/2/11 Edward Deira > Dear all, > > How can I "accurately" represent ferrocene in pymol, without using CONECT > lines in the pdb file ? > By "accurately" I mean at least including the C-C bonds; I'd rather not > have any Fe-C bonds, but if they are present I can live. > > I've been trying to figure out how to do this using atom selections, or > trying to get gonds between the nonbonded... > > Any hints are welcome, > > all the best > Ed. > > > -- > Free Next-Gen Firewall Hardware Offer > Buy your Sophos next-gen firewall before the end March 2013 > and get the hardware for free! Learn more. > http://p.sf.net/sfu/sophos-d2d-feb > ___ > 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 > -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb___ 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] representing ferrocene in pymol
Dear all, How can I "accurately" represent ferrocene in pymol, without using CONECT lines in the pdb file ? By "accurately" I mean at least including the C-C bonds; I'd rather not have any Fe-C bonds, but if they are present I can live. I've been trying to figure out how to do this using atom selections, or trying to get gonds between the nonbonded... Any hints are welcome, all the best Ed. -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb___ 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
