Surfnet command line

Dear All, is there a command line equivalent for surfnet applied to atom selection (not interfase)? Best, JD Dr. Jean-Didier Maréchal Lecturer Computational Biotechnological Chemistry @ Transmet Unitat de Química Física Departament de Química Universitat Autònoma de Barcelona Edifici C.n. 08193 Cerdanyola (Barcelona) Tel: +34.935814936 e-mail: JeanDidier.Marechal@uab.es ----- Missatge original ----- De: chimera-users-request@cgl.ucsf.edu Data: Dilluns, Desembre 14, 2009 9:00 pm Assumpte: Chimera-users Digest, Vol 80, Issue 14
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Today's Topics:
1. help in installation of chimera-1.4-linux_x86_64.exe (Dr Muhammad Nadeem Kardar) 2. Re: help in installation of chimera-1.4-linux_x86_64.exe (Elaine Meng)
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Message: 1 Date: Mon, 14 Dec 2009 10:45:22 +0500 From: Dr Muhammad Nadeem Kardar <drmnkardar@ciitlahore.edu.pk> To: chimera-users@cgl.ucsf.edu Subject: [Chimera-users] help in installation of chimera-1.4-linux_x86_64.exe Message-ID: <38c1a890912132145o18302b67r6fc153793de8d76d@mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1"
chimera-1.4-linux(2).exe
chimera-1.4-linux.exe chimera-1.4-linux_x86_64.exe
I have three files of chimera but unable to execute chimera kindly help Kardar
-- M. Nadeem Kardar, PhD Assistant Professor Department of Chemical Engineering COMSATS Institute of Information Technology Defence Road Off Raiwind Road, Lahore, Pakistan Cell# +92-300-2414231 Email: drmnkardar@ciitlahore.edu.pk Website: http://www.ciitlahore.edu.pk/researchgroups/bcrg/page/kardar.html--- ----------- next part -------------- An HTML attachment was scrubbed... URL: <http://www.cgl.ucsf.edu/pipermail/chimera- users/attachments/20091214/5abbdcee/attachment-0001.html>
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Message: 2 Date: Mon, 14 Dec 2009 08:45:21 -0800 From: Elaine Meng <meng@cgl.ucsf.edu> To: Dr Muhammad Nadeem Kardar <drmnkardar@ciitlahore.edu.pk> Cc: chimera-users@cgl.ucsf.edu Subject: Re: [Chimera-users] help in installation of chimera-1.4-linux_x86_64.exe Message-ID: <92B97B1E-8164-4CC4-AD10-6161D911791F@cgl.ucsf.edu> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
Hi Kardar, The *exe file is not Chimera itself but an installer. Please click
the appropriate "Instructions" link on the download page to see how to install Chimera from the *exe file.
<http://www.cgl.ucsf.edu/chimera/download.html>
Elaine ----- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 13, 2009, at 9:45 PM, Dr Muhammad Nadeem Kardar wrote:
chimera-1.4-linux(2).exe
chimera-1.4-linux.exe chimera-1.4-linux_x86_64.exe
I have three files of chimera but unable to execute chimera kindly help
Kardar
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End of Chimera-users Digest, Vol 80, Issue 14 *********************************************

Hi JD, Sorry, there is no surfnet command. Perhaps it can be done with python, but one of the other developers would have to reply about that. Best, Elaine On Dec 15, 2009, at 12:26 AM, Jean Didier Pie Marechal wrote:
Dear All, is there a command line equivalent for surfnet applied to atom selection (not interfase)? Best, JD

Hi JD, If you resort to Python, the following script should do it: from SurfNet import atoms_surfnet atoms_surfnet("your atom spec here") There are other arguments you could provide to atoms_surfnet() if you wanted non-default behavior. Have a look in SurfNet/base.py to see what they are. --Eric On Dec 15, 2009, at 8:10 AM, Elaine Meng wrote:
Hi JD, Sorry, there is no surfnet command. Perhaps it can be done with python, but one of the other developers would have to reply about that. Best, Elaine
On Dec 15, 2009, at 12:26 AM, Jean Didier Pie Marechal wrote:
Dear All, is there a command line equivalent for surfnet applied to atom selection (not interfase)? Best, JD
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participants (3)
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Elaine Meng
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Eric Pettersen
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Jean Didier Pie Marechal