Re: [Jmol-users] adding hydrogens (Was: loading jmol file from open babel)
Here is Bob Hanson's reply, from late October, to my inquiry regarding Jmol's ability to sprout hydrogens as was possible within Chime. (My knowledge is not sophisticated enough to know whether this line of pursuit might meet your needs, but here it is.) There was little feedback from others so I believe it was dropped or back-burnered. Byrne I've been looking into sprouting hydrogens, and it's no problem. The only thing is what do people really want. Please start discussing what you want. 1) Only PDB models (like Chime)? 2) Only the 20 common amino acids (like Chime)? 3) Just carbons or all atoms? 4) If not just PDB residues, suggestions for resolving oxidation state ambiguities like -CCCO, which could be CH2CH2CH2OH or several other possibilities. 5) If not just carbons, suggestions for resolving pKa issues. 6) If not just carbons, suggestions for resolving dihedral selection. 7) full model or selected subsets? Bob On 1/29/07 3:16 PM, Francesco Pietra [EMAIL PROTECTED] wrote: Let me say that a package dealing with molecules that does not place hydrogens correctly is of no use professionally. I must add that I am strongly disappointed, and back to my old MM package, which places the hydrogens correctly, like the nonvolatiles. How do you start a quantum mechanical computation with hydrogens not at their due place? Cheers francesco pietra --- Angel Herraez [EMAIL PROTECTED] wrote: I am opening two new threads for Paul questions in his last post to loading jmol file from open babel On 29 Jan 2007 at 10:44, H. Paul Benton wrote: To all the other uses I have one more question to ask If a file was loaded with no Hydrogens how can I get Jmol to put them on?. Jmol cannot add hydrogens right now. Remebre it is a viewer, not a molecule builder. I can recommend two programs that allow you to do so. One is Discovery Studio Visualizer, from Accelrys (formerly known by several names such as WebLab Viewer, Accelrys Viewer, DS Viewer, etc.) The other is ChemSketch, from ACDLabs. This is actually a 2D chemical drawing package, but imports and exports MOL files and has a 3D module. If you haven't used any of them, go for DS Visualizer. It will open your pdb, mol, xyz etc files, then go to menu Tools Hydrgens Add and save again. - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users __ __ Want to start your own business? Learn how on Yahoo! Small Business. http://smallbusiness.yahoo.com/r-index - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - Take Surveys. Earn Cash. Influence the Future of IT Join SourceForge.net's Techsay panel and you'll get the chance to share your opinions on IT business topics through brief surveys - and earn cash http://www.techsay.com/default.php?page=join.phpp=sourceforgeCID=DEVDEV ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] sprout hydrogens
Bob, Thanks for looking into this. I am not a sophisticated user so I can;t comment on 4, 5, 6. I mostly am making tutorials for my AP Biology students which also are used by other teachers for general Biology students at the high school level. That said, here's what would work for me. I've only used PBD models. I'm trying to emphasize the fit between substrate and active site as well as hydrogen bonding. So it would be nice to extend the sprouted hydrogen set from carbons to at least include those involved in hbonding. The ideal would also include hydrogens involved between residues in the specificity pocket and those on the non-residue substrate. I extensively searched the archives and found no mention of sprouted hydrogens. If I the only one asking, please don't go out of your way on this. Thanks, Byrne On 10/26/06 7:24 AM, [EMAIL PROTECTED] [EMAIL PROTECTED] wrote: I've been looking into sprouting hydrogens, and it's no problem. The only thing is what do people really want. Please start discussing what you want. 1) Only PDB models (like Chime)? 2) Only the 20 common amino acids (like Chime)? 3) Just carbons or all atoms? 4) If not just PDB residues, suggestions for resolving oxidation state ambiguities like -CCCO, which could be CH2CH2CH2OH or several other possibilities. 5) If not just carbons, suggestions for resolving pKa issues. 6) If not just carbons, suggestions for resolving dihedral selection. 7) full model or selected subsets? Bob ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] sprouting Hydrogens, coloring isosurfaces
I am resurrecting some RasMol/Chime scripts and have a couple commands I can't duplicate. I have extensively searched the archives, documentation and experimented to no avail. The sprout hydrogen command (Chime?) would calculate positions for hydrogen atoms not resident in a pdb file so they could be displayed. I see Jmol seems capable of such calculations for producing isosurfaces but I can't find how to display them in simple spacefill mode. (I am trying to emphasize the substrate-active site fit in a protein structure tutorial.) I also cannot get the isosurface command to generate any other than a uniformly colored surface. I previously generated, and colored, surfaces with the molesurface command with such ancillary commands as: surface molsurface white 0.45; set mep distance 99.0; set charge function gasteiger; calculate charges refresh; list molsurface color potential; (I probably copied and tweaked this from others so don't think I'm ready for too erudite a response on this!) The purpose here was to paint a picture of the protein as this unique electromagnetic landscape ready to interact with its environment in unique ways. The other purpose was, of course, because it looks cool. I have tried the colorscheme parameter (again on a pdb file) without luck. The Jmol interactive scripting documentation seems a bit short on how some of these parameters should be specifically coded. For instance, it shows the argument of COLORSCHEME in quotes which certainly doesn't work within a jmolRadio call. Thanks for any help on this. Byrne Pedit [EMAIL PROTECTED] - Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
