Thanks for the reply, here are some additional points... > 2)Pymol has a "mutation" wizard (actually so does a Package > called KiNG), where you can select a residue, mutate it, and rotate > through all the rotamers, in addition it will show collisions as red > circles
>That's hard stuff, as it requires molecular mechanics computation. >Unlikely in Jmol, at least in the present incarnation. Actually, I don't think the other tools that do this really do any molecular mechanics. That would be great, but I just want to do quick check to see a particular amino acid will fit without disturbing the structure much. One could use the SCRL (I think) rotamer library for this. 4) In PyMol it puts the sequence at top with a slider and allows you to select from that. That's really what I'm looking for. -----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Angel Herraez Sent: Tuesday, March 04, 2008 10:29 AM To: [email protected] Subject: Re: [Jmol-users] Pymol, DSV, and Jmol Hi Robin Here's my two pence: > 1)PyMol has that great object/selection/etc list on the right > hand side, where the user can quickly change the color, style, etc of > everything displayed Not in Jmol. There might be something in Jmol-including suites like Bioclipse. > 2)Pymol has a "mutation" wizard (actually so does a Package > called KiNG), where you can select a residue, mutate it, and rotate > through all the rotamers, in addition it will show collisions as red > circles That's hard stuff, as it requires molecular mechanics computation. Unlikely in Jmol, at least in the present incarnation. > 3)DSV has a "Hierchy" window, a simple tree browser showing > the chains, amino acids, atoms. Which allows selections I think there is enough code base in Jmol for this to be easily achived by a programmer. It could be a plugin or complement to Jmol. > 4)PyMol and DSV both have a "sequence" view There is some code support in Jmol to recognize sequences ("within" command). I'd bet this is already in place in Bioclipse, but haven't checked it out. Others will surely follow with more specific details. ------------------------------------------------------------------------ - This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
