Thanks I know Jmol can calculate DSSP secondary structures, but I mainly use it to calculate solvent accessibilities (secondary structures are a side effect). I also use other programs like PSAIA or SPEEDFILL to calculate other things... (my main concern it's not just show secondary structures, solvent accessibilities or whatever on screen, but also provide the transformed pdb text files for further studies). So I just used secondary structures to illustrate the problem. I will try "set rangeSelected" on Monday (I cannot do it during the weekend), but what I need is not to specify a range of residues to color, but a range of temperatures to consider (I know it's from 1 to 8 in the secondary structure case, can't I just specify from 1 to 8, instead of specifying the residues?)
2011/4/1 Robert Hanson <hans...@stolaf.edu> > Daniel, > > First note that Jmol has DSSP included now -- an authorized and verified > implementation of "real" DSSP -- you should have no need to do this > separately. I have no idea what you mean by "DSSP might crash" -- that's > very odd. Why would DSSP crash? Anyway, if you just use > > calculate structure > > That gives you DSSP structure. These structure types include "helix310" > "helixAlpha" "helixPi", "sheet", and "turn". The DSSP output also indicates > isolated "bridge" residues, but although the hydrogen bonds are indicated > using > > calculate hbonds structure > > we don't right now have a specific selection option for that. We also do > not indicate "bend". > > But that really wasn't your question: > > > On Fri, Apr 1, 2011 at 10:49 AM, Daniel Carbajo > <daniel.carb...@gmail.com>wrote: > >> >> It works properly until I load the homology models. They are all in blue >> (the first color of the user color scheme). It seems like Jmol has taken the >> temperature range using the native structure temperature values. Since I >> have loaded the native structure with the temperature values unchanged, the >> range of these values do not go from 1 to 8, they go from 0 to around 100. >> Then I load the homology models and they are all in blue since their highest >> value is 8 and falls in the first category if we count from 0 to around >> 100.... >> >> > you need to > > set rangeSelected > > before you use > > color temperature > > > That indicates that you want to set the color range based just on the > selected residues. > > Bob > > > -- > Robert M. Hanson > Professor of Chemistry > St. Olaf College > 1520 St. Olaf Ave. > Northfield, MN 55057 > http://www.stolaf.edu/people/hansonr > phone: 507-786-3107 > > > If nature does not answer first what we want, > it is better to take what answer we get. > > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 > > > ------------------------------------------------------------------------------ > Create and publish websites with WebMatrix > Use the most popular FREE web apps or write code yourself; > WebMatrix provides all the features you need to develop and > publish your website. http://p.sf.net/sfu/ms-webmatrix-sf > > _______________________________________________ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > >
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