sure color property temperature absolute 0.0 8.0
On Fri, Apr 1, 2011 at 1:33 PM, Daniel Carbajo <daniel.carb...@gmail.com>wrote: > 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 >> >> > > > ------------------------------------------------------------------------------ > 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 > > -- 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
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