<table cellspacing="0" cellpadding="0" border="0" ><tr><td valign="top" style="font: inherit;"><br>Hi <div>How are you.....</div><div>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???</div><div><br></div><div> <br>--- On <b>Tue, 4/9/13, Elaine Meng <i><meng@cgl.ucsf.edu></i></b> wrote:<br><blockquote style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"><br>From: Elaine Meng <meng@cgl.ucsf.edu><br>Subject: Re: [Chimera-users] building DNA<br>To: "Muhammad ALi" <muh.ali741@yahoo.com><br>Cc: "chimera-users@cgl.ucsf.edu Mailing List"
<chimera-users@cgl.ucsf.edu><br>Date: Tuesday, April 9, 2013, 8:25 PM<br><br><div class="plainMail">You're welcome! Wow, you really did a lot!<br><br>Elaine<br><br>On Apr 9, 2013, at 12:32 PM, Muhammad ALi wrote:<br><br>> 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 ..<br>> I presented the following<br>> 1- Introduction to chimera<br>> 2-How to load a structure into chimera<br>> open and fetch<br>> 3- How to edit, select(chains, residues, atoms, also atom specifier), delete, <br>> 4- Actions, zoom and drag , coloring and change the view of model (bonds, atoms, surface, ribbon, residues etc...) <br>> 5-How to make animations<br>> 6-How to use commands<br>> 7-How to save animation in movie file and in accession file<br>> 8- How to align and superimpose two or more model structures and
then their sequences and how to check RMSD<br>> 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<br>> 10-How to make Ramachandran Plot<br>> 11-How to save high defination image<br>> 12-How adjust bonding<br>> 13-How to make solvate model <br>> 14-How to make userinterface of our own choice<br>> 15-How to select tow different atoms and then how to make bond between them<br>> 16-How to merg two different model into one<br>> 17-How to two find a conserved region in the structure by giving the conserved sequence as input<br>> 19-How to select and activate a specific model<br>> 20-How to move different objects by mouse <br>> 21-How to split a model into its chains<br>> 22-How to close a specific model<br>> 23-commands<br>> 24-How to show the ligand surface<br>> 25-ViewDock check the binding between the ligand and receptor<br>>
26-How to check the resolution of PDB structure<br>> 27-How to measure volume and area<br>> 28-How to save selected part of model into another separate as a PDB file<br>> 29-analyzing metal ion coordination geometries<br>> 30-viewing controls (side view, camera, lighting, shining)<br>> 31-Find clashes and contacts<br>> 32-Docking with autodock vina ( ligand-receptor binding )<br>> <br>> thank you so much sir for helping......<br>> <br>> --- On Tue, 4/9/13, Elaine Meng <<a ymailto="mailto:meng@cgl.ucsf.edu" href="/mc/compose?to=meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>> wrote:<br>> <br>> From: Elaine Meng <<a ymailto="mailto:meng@cgl.ucsf.edu" href="/mc/compose?to=meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>><br>> Subject: building DNA<br>> To: "Muhammad ALi" <<a ymailto="mailto:muh.ali741@yahoo.com" href="/mc/compose?to=muh.ali741@yahoo.com">muh.ali741@yahoo.com</a>><br>> Cc: "<a
ymailto="mailto:chimera-users@cgl.ucsf.edu" href="/mc/compose?to=chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a> Mailing List" <<a ymailto="mailto:chimera-users@cgl.ucsf.edu" href="/mc/compose?to=chimera-users@cgl.ucsf.edu">chimera-users@cgl.ucsf.edu</a>><br>> Date: Tuesday, April 9, 2013, 4:15 PM<br>> <br>> On Apr 8, 2013, at 6:42 AM, Muhammad ALi wrote:<br>> <br>> > hi <br>> > can we make a DNA model with chimera???<br>> <br>> Hello,<br>> Although you can build very approximate DNA in Chimera with the "rna" command <<a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rna.html" target="_blank">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/rna.html</a>>, 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.<br>> <br>> For
example, here are some web servers that I believe will build DNA:<br>> <<a href="http://structure.usc.edu/make-na/" target="_blank">http://structure.usc.edu/make-na/</a>><br>> <<a href="http://w3dna.rutgers.edu/index.php/rebuild" target="_blank">http://w3dna.rutgers.edu/index.php/rebuild</a>><br>> <br>> Elaine<br>> ----------<br>> Elaine C. Meng, Ph.D. <br>> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab<br>> Department of Pharmaceutical Chemistry<br>> University of California, San Francisco<br>> <br>> _______________________________________________<br>> Chimera-users mailing list<br>> <a ymailto="mailto:Chimera-users@cgl.ucsf.edu" href="/mc/compose?to=Chimera-users@cgl.ucsf.edu">Chimera-users@cgl.ucsf.edu</a><br>> <a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users"
target="_blank">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br><br></div></blockquote></div></td></tr></table>