Structural Allignment in Chimera
Hello I want to know how chimera does Structural allignment. I am writing a python script to allign protein structures(from MD simulations) and eventually calculate RMSD. Please can anyone provide me a source code or a helping material.Thanx in advance. Hira Batool Student of BS-Bioinformatics Biosciences Department COMSATS Institute of Information Technology Islamabad, PAKISTAN
Hello, The source is included in the Chimera download, and the methods are described in the documentation; see here and follow the links from this page for further details: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html> If the methods are suitable for your work, you could just use Chimera to do the alignments and RMSD calculations. <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html> However, maybe you are supposed to write your own code for some homework project. In that case, there may be more direct, basic information available on the Web (rather than digging into Chimera code). 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 Oct 4, 2013, at 2:26 AM, Syeda Hira Batool wrote:
Hello I want to know how chimera does Structural allignment. I am writing a python script to allign protein structures(from MD simulations) and eventually calculate RMSD. Please can anyone provide me a source code or a helping material.Thanx in advance. Hira Batool Student of BS-Bioinformatics Biosciences Department COMSATS Institute of Information Technology Islamabad, PAKISTAN
Specifically, the matching code is in <your Chimera>/share/chimera/match.py. (On a Mac, "<your Chimera>" would be Chimera.app/Contents/Resources.) --Eric Eric Pettersen UCSF Computer Graphics Lab On Oct 4, 2013, at 9:17 AM, Elaine Meng wrote:
Hello, The source is included in the Chimera download, and the methods are described in the documentation; see here and follow the links from this page for further details: <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>
If the methods are suitable for your work, you could just use Chimera to do the alignments and RMSD calculations. <http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>
However, maybe you are supposed to write your own code for some homework project. In that case, there may be more direct, basic information available on the Web (rather than digging into Chimera code). 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 Oct 4, 2013, at 2:26 AM, Syeda Hira Batool wrote:
Hello I want to know how chimera does Structural allignment. I am writing a python script to allign protein structures(from MD simulations) and eventually calculate RMSD. Please can anyone provide me a source code or a helping material.Thanx in advance. Hira Batool Student of BS-Bioinformatics Biosciences Department COMSATS Institute of Information Technology Islamabad, PAKISTAN
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participants (3)
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Elaine Meng -
Eric Pettersen -
Syeda Hira Batool