[Chimera-users] Docking

[Muhammad ALi]

Hi How are you.....Sir I am doing docking with autodock vina in Chimera.. but sir i successfully did it, but with Opal server, and found the required binding sites of ligand binding and checked theier bonds,, but kindly sir tell me  how can i do it without using opal server.. which file will be required???? and how it is estimated that which binding between ligand and protein is best and how???
 
--- On Tue, 4/9/13, Elaine Meng <meng at cgl.ucsf.edu> wrote:

From: Elaine Meng <meng at cgl.ucsf.edu>
Subject: Re: [Chimera-users] 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, 8:25 PM

You're welcome!  Wow, you really did a lot!

Elaine

On Apr 9, 2013, at 12:32 PM, Muhammad ALi wrote:

> 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 following
> 1- Introduction to chimera
> 2-How to load a structure into chimera
>    open  and  fetch
> 3- 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 animations
> 6-How to use commands
> 7-How to save animation in movie file and in accession file
> 8- How to align and superimpose two or more model structures and then their sequences and how to check RMSD
> 9-How to make or built a structure from peptide or amino acid sequence , and how to get or show the sequnce from protein model
> 10-How to make Ramachandran Plot
> 11-How to save high defination image
> 12-How adjust bonding
> 13-How to make solvate model 
> 14-How to make userinterface of our own choice
> 15-How to select tow different atoms and then how to make bond between them
> 16-How to merg two different model into one
> 17-How to two find a conserved region in the structure by giving the conserved sequence as input
> 19-How to select and activate a specific model
> 20-How to move different objects by mouse 
> 21-How to split a model into its chains
> 22-How to close a specific model
> 23-commands
> 24-How to show the ligand surface
> 25-ViewDock check the binding between the ligand and receptor
> 26-How to check the resolution of PDB structure
> 27-How to measure volume and area
> 28-How to save selected part of model into another separate as a PDB file
> 29-analyzing metal ion coordination geometries
> 30-viewing controls (side view, camera, lighting, shining)
> 31-Find clashes and contacts
> 32-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???
> 
> Hello,
> 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:
> <http://structure.usc.edu/make-na/>
> <http://w3dna.rutgers.edu/index.php/rebuild>
> 
> Elaine
> ----------
> 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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