Hello, Is it possible, in Chimera, to select only the internal water molecules of a protein structure? I need to find out how many water molecules enter the protein structure from the outside during a molecular dynamics simulation. Thanks! John John M. Beale, Jr., Ph.D. Professor of Medicinal Chemistry and Pharmacognosy Saint Louis College of Pharmacy 4588 Parkview Place Saint Louis, Missouri 63110 314-446-8461 Cell: 314-315-0409 FAX: 314-446-8460 jbeale@stlcop.edu<mailto:jbeale@stlcop.edu>
On Feb 28, 2011, at 11:44 AM, Beale, John wrote:
Hello,
Is it possible, in Chimera, to select only the internal water molecules of a protein structure? I need to find out how many water molecules enter the protein structure from the outside during a molecular dynamics simulation.
Hi John, I pretty sure this requires some (possibly simple) Python scripting. No script can really be written though without the answer to this question: what is your definition of "internal"? --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
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Beale, John -
Eric Pettersen