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@cgl.ucsf.edu> wrote:
From: Elaine Meng <meng@cgl.ucsf.edu> Subject: building DNA To: "Muhammad ALi" <muh.ali741@yahoo.com> Cc: "chimera-users@cgl.ucsf.edu Mailing List" <chimera-users@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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