From: lina <lin...@gm...> - 2011-09-06 15:28:11
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Hi, such as the atom name as H01, H03 How can I change it to H1, H3, Thanks for any suggestions (except modifying the .pdb file). -- Best Regards, lina |
From: lina <lin...@gm...> - 2011-09-27 07:35:38
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Hi, how can I change the atom such as H01 to H22 in command Thanks ahead, -- Best Regards, lina |
From: Thomas H. <sp...@us...> - 2011-09-27 07:54:02
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Hi Lina, atom properties can be changed with the "alter" command. It takes a selection (the atoms that should be modified) and an assignment expression in python syntax. Example: alter name H01, name="H22" It's important to quote strings in the assignment expression! More details and examples: http://pymolwiki.org/index.php/Alter Cheers, Thomas On 09/27/2011 09:35 AM, lina wrote: > Hi, > > how can I change the atom such as > > H01 to H22 in command > > Thanks ahead, > > -- > Best Regards, > > lina -- Thomas Holder MPI for Developmental Biology |
From: Marius R. <mar...@gm...> - 2011-09-06 15:39:34
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Google search lead me to this http://www.pymolwiki.org/index.php/Atom_name_wildcard I think this should to the job in you case alter all, name=string.replace(name,"H0","H") Best regards, Marius ---------------------------------------------------------- Dr. Marius Retegan Postdoctoral Fellow Département de Chimie Moléculaire Université Joseph Fourier 301 Rue de la Chimie BP 53, 38041 Grenoble Cedex 9, France Tel: +33 (0) 4 76 63 44 03 GnuPG http://db.tt/rr7Hd0Y On Tue, Sep 6, 2011 at 5:28 PM, lina <lin...@gm...> wrote: > Hi, > > such as the atom name as > H01, H03 > > How can I change it to H1, H3, > > Thanks for any suggestions (except modifying the .pdb file). > -- > Best Regards, > > lina > > ------------------------------------------------------------------------------ > Special Offer -- Download ArcSight Logger for FREE! > Finally, a world-class log management solution at an even better > price-free! And you'll get a free "Love Thy Logs" t-shirt when you > download Logger. Secure your free ArcSight Logger TODAY! > http://p.sf.net/sfu/arcsisghtdev2dev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > |
From: lina <lin...@gm...> - 2011-09-06 15:46:56
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On Tue, Sep 6, 2011 at 11:39 PM, Marius Retegan <mar...@gm...> wrote: > Google search lead me to this > http://www.pymolwiki.org/index.php/Atom_name_wildcard > > I think this should to the job in you case > > alter all, name=string.replace(name,"H0","H") Thanks, it works. before I googled, might used poor keyword to search, so did not meet this page. Thanks again and best regards,. lina > > Best regards, > Marius > > ---------------------------------------------------------- > Dr. Marius Retegan > Postdoctoral Fellow > > Département de Chimie Moléculaire > Université Joseph Fourier > 301 Rue de la Chimie > BP 53, 38041 Grenoble Cedex 9, France > Tel: +33 (0) 4 76 63 44 03 > > GnuPG http://db.tt/rr7Hd0Y > > > > On Tue, Sep 6, 2011 at 5:28 PM, lina <lin...@gm...> wrote: >> Hi, >> >> such as the atom name as >> H01, H03 >> >> How can I change it to H1, H3, >> >> Thanks for any suggestions (except modifying the .pdb file). >> -- >> Best Regards, >> >> lina >> >> ------------------------------------------------------------------------------ >> Special Offer -- Download ArcSight Logger for FREE! >> Finally, a world-class log management solution at an even better >> price-free! And you'll get a free "Love Thy Logs" t-shirt when you >> download Logger. Secure your free ArcSight Logger TODAY! >> http://p.sf.net/sfu/arcsisghtdev2dev >> _______________________________________________ >> PyMOL-users mailing list (PyM...@li...) >> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users >> Archives: http://www.mail-archive.com/pym...@li... >> > |
From: H. A. S. <ad...@st...> - 2011-10-20 20:43:54
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Hi all, Does anyone know of a pdb that was created for the structure of water molecules in ice? I have not been able to find one and am not looking forward to creating one! :) H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 |
From: Joel T. <joe...@ot...> - 2011-10-21 01:31:27
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A quick google search found this: http://www.nyu.edu/pages/mathmol/library/water/ hope this helps _________________________________ Joel Tyndall, PhD Senior Lecturer in Medicinal Chemistry National School of Pharmacy University of Otago PO Box 56 Dunedin 9054 New Zealand Skype: jtyndall http://www.researcherid.com/rid/C-2803-2008 Pukeka Matua Te Kura Taiwhanga Putaiao Te Whare Wananga o Otago Pouaka Poutapeta 56 Otepoti 9054 Aotearoa Ph / Waea +64 3 4797293 Fax / Waeawhakaahua +64 3 4797034 -----Original Message----- From: H. Adam Steinberg [mailto:ad...@st...] Sent: Friday, 21 October 2011 9:31 a.m. To: pym...@li... Subject: [PyMOL] pdb of ice Hi all, Does anyone know of a pdb that was created for the structure of water molecules in ice? I have not been able to find one and am not looking forward to creating one! :) H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 ------------------------------------------------------------------------------ The demand for IT networking professionals continues to grow, and the demand for specialized networking skills is growing even more rapidly. Take a complimentary Learning@Cisco Self-Assessment and learn about Cisco certifications, training, and career opportunities. http://p.sf.net/sfu/cisco-dev2dev _______________________________________________ PyMOL-users mailing list (PyM...@li...) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pym...@li... |
From: H. A. S. <ad...@st...> - 2011-10-21 13:40:25
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Thank you Joel! DOH! let this be a lesson on keeping searches simple... if you want a pdb for ice simply search for "ice .pdb"! forget about using words like molecular, dynamics, structure, crystal, etc. :) Adam On Oct 20, 2011, at 8:31 PM, Joel Tyndall wrote: > A quick google search found this: > > http://www.nyu.edu/pages/mathmol/library/water/ > > hope this helps > > _________________________________ > Joel Tyndall, PhD > > Senior Lecturer in Medicinal Chemistry > National School of Pharmacy > University of Otago > PO Box 56 Dunedin 9054 > New Zealand > Skype: jtyndall > http://www.researcherid.com/rid/C-2803-2008 > Pukeka Matua > Te Kura Taiwhanga Putaiao > Te Whare Wananga o Otago > Pouaka Poutapeta 56 Otepoti 9054 > Aotearoa > > Ph / Waea +64 3 4797293 > Fax / Waeawhakaahua +64 3 4797034 > > > -----Original Message----- > From: H. Adam Steinberg [mailto:ad...@st...] > Sent: Friday, 21 October 2011 9:31 a.m. > To: pym...@li... > Subject: [PyMOL] pdb of ice > > Hi all, > > Does anyone know of a pdb that was created for the structure of water molecules in ice? I have not been able to find one and am not looking forward to creating one! :) > > H. Adam Steinberg > 7904 Bowman Rd > Lodi, WI 53555 > 608/592-2366 > > > ------------------------------------------------------------------------------ > The demand for IT networking professionals continues to grow, and the demand for specialized networking skills is growing even more rapidly. > Take a complimentary Learning@Cisco Self-Assessment and learn about Cisco certifications, training, and career opportunities. > http://p.sf.net/sfu/cisco-dev2dev > _______________________________________________ > PyMOL-users mailing list (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... H. Adam Steinberg 7904 Bowman Rd Lodi, WI 53555 608/592-2366 |