[Chimera-users] building DNA

Muhammad ALi muh.ali741 at yahoo.com
Tue Apr 9 12:32:02 PDT 2013

thank you sir actually I am student of BS(Hons.) Bionfo & Biotech and Chimera was my presentation topic , Today was my presention and I do alot ..I presented the following1- Introduction to chimera2-How to load a structure into chimera   open  and  fetch3- How to edit, select(chains, residues, atoms, also atom specifier), delete, 4- Actions, zoom and drag , coloring and change the view of model (bonds, atoms, surface, ribbon, residues etc...) 5-How to make animations6-How to use commands7-How to save animation in movie file and in accession file8- How to align and superimpose two or more model structures and then their sequences and how to check RMSD9-How to make or built a structure from peptide or amino acid sequence , and how to get or show the sequnce from protein model10-How to make Ramachandran Plot11-How to save high defination image12-How adjust bonding13-How to make solvate model 14-How to make userinterface of our own choice15-How to
 select tow different atoms and then how to make bond between them16-How to merg two different model into one17-How to two find a conserved region in the structure by giving the conserved sequence as input19-How to select and activate a specific model20-How to move different objects by mouse 21-How to split a model into its chains22-How to close a specific model23-commands24-How to show the ligand surface25-ViewDock check the binding between the ligand and receptor26-How to check the resolution of PDB structure27-How to measure volume and area28-How to save selected part of model into another separate as a PDB file29-analyzing metal ion coordination geometries30-viewing controls (side view, camera, lighting, shining)31-Find clashes and contacts32-Docking with autodock vina ( ligand-receptor binding )
 thank you so much sir for helping......
--- On Tue, 4/9/13, Elaine Meng <meng at cgl.ucsf.edu> wrote:

From: Elaine Meng <meng at cgl.ucsf.edu>
Subject: building DNA
To: "Muhammad ALi" <muh.ali741 at yahoo.com>
Cc: "chimera-users at cgl.ucsf.edu Mailing List" <chimera-users at cgl.ucsf.edu>
Date: Tuesday, April 9, 2013, 4:15 PM

On Apr 8, 2013, at 6:42 AM, Muhammad ALi wrote:

> hi 
> can we make a DNA model with chimera???

Although you can build very approximate DNA in Chimera with the "rna" command <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rna.html>, the result is rough and mainly just for viewing.  If you are planning to do detailed modeling or further calculations with the DNA, I would recommend not using Chimera, but instead some other program.

For example, here are some web servers that I believe will build DNA:

Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

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