ensemble match; ensemble cluster; plotting RMSD
Dear ChimeraX users, After a hole evening trying everything, reading every possible page, I can not do what I want that is superposing models of an NMR PDB (ej 20 models) all by all and compare their RMSD (a matrix if possible). And also compare this ensemble (NMR with 20 models) with another (let's say another NMR with 30-50 models). My chimeraX has not the option "Structure comparison" in the tools bars. The web manual doesn't give the commands needed to do so.
Below is what is written in the manual but, as I said, structure comparison is not in my tools bar. " Ensemble Match, a tool in the Structure Comparison and MD/Ensemble Analysis categories". I know that there are tools to work with MD simulations (several conformers), but also can not find in the version install in my windows 10 computer. I know this is passible from chimeraX. Could you please help me find the solution? has anybody try this? Is very important for me to do it. Thank you very much in advanced, Cristina
Cristina Marino Buslje MS, PhD Researcher, National Research Council (CONICET) Head of Bioinformatics Unit Fundación Instituto Leloir Av. Patricias Argentinas 435. Buenos Aires, Argentina Tel: +54(11)5238-7500 | Fax: +54(11)5238-7501 http://www.leloir.org.arhttp://www.leloir.org.ar/
Dear Cristina, You are looking at the manual for Chimera.
ChimeraX is a different program than Chimera and does not have the Ensemble Match tool.
If you want to use Ensemble Match, get Chimera! http://www.rbvi.ucsf.edu/chimera/index.html
Besides the manual page you were looking at, there is also a Chimera tutorial with an example of using Ensemble Match. http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/ensembletut.html
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 25, 2020, at 1:58 PM, Cristina Marino Buslje cmb@leloir.org.ar wrote:
Dear ChimeraX users, After a hole evening trying everything, reading every possible page, I can not do what I want that is superposing models of an NMR PDB (ej 20 models) all by all and compare their RMSD (a matrix if possible). And also compare this ensemble (NMR with 20 models) with another (let's say another NMR with 30-50 models). My chimeraX has not the option "Structure comparison" in the tools bars. The web manual doesn't give the commands needed to do so.
Below is what is written in the manual but, as I said, structure comparison is not in my tools bar. " Ensemble Match, a tool in the Structure Comparison and MD/Ensemble Analysis categories". I know that there are tools to work with MD simulations (several conformers), but also can not find in the version install in my windows 10 computer. I know this is passible from chimeraX. Could you please help me find the solution? has anybody try this? Is very important for me to do it. Thank you very much in advanced, Cristina
participants (2)
-
Cristina Marino Buslje -
Elaine Meng