From: William R. P. <wr...@vi...> - 2006-08-29 18:20:53
|
Though it seems clear that jmol will display h-bonds, I am not having much luck doing it. For example, there is a jmol structure down the page in: http://www.people.virginia.edu/~wrp/bioch503_l3.html that uses the script shown adjacent to it. But, no h-bonds for that piece of structure. Indeed, I have not had any luck showing h-bonds when I run that script in the jmol application, despite my best efforts to turn on hbonds. Help!! Bill Pearson |
From: Bob H. <ha...@st...> - 2006-08-29 18:29:26
|
must be a different URL An Error Has Occurred! URL Not Found The requested URL */~wrp/bioch503_l3.html * was not found on *www.people.virginia.edu * (Error 404-NOT_FOUND). The document may have been moved to a new location, there may be an error in the file name, it may no longer exist, or it may have been deleted. Please double-check your URL or contact the maintainer of the referring page, *(none)*, so they may update their link. William R. Pearson wrote: >Though it seems clear that jmol will display h-bonds, I am not having >much luck doing it. > >For example, there is a jmol structure down the page in: > >http://www.people.virginia.edu/~wrp/bioch503_l3.html > >that uses the script shown adjacent to it. > >But, no h-bonds for that piece of structure. Indeed, I have not had >any luck showing h-bonds when I run that script in the jmol >application, despite my best efforts to turn on hbonds. > >Help!! > >Bill Pearson > > >------------------------------------------------------------------------- >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=lnk&kid=120709&bid=263057&dat=121642 >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > |
From: <rg...@el...> - 2006-08-29 18:38:02
|
On Tue, August 29, 2006 2:29 pm, Bob Hanson wrote: > must be a different URL Yep, Bull forgot the enclosing directory. See: http://www.people.virginia.edu/~wrp/bioch503/bioch503_l3.html Rich |
From: Angel H. <ang...@ua...> - 2006-08-29 18:34:51
|
Hello, William 1.- Which version of Jmol are you using? There are some differences between 10.0 and 10.2 with respect to Hbonds. 2.- Your link does not work http://www.people.virginia.edu/~wrp/bioch503_l3.html The requested URL /~wrp/bioch503_l3.html was not found on www.people.virginia.edu (Error 404-NOT_FOUND). 3.- In 10.2 and later, you may need to give hbonds calculate before hbonds on (unless the Hbonds are specified in the PDB content, Jmol will not show any) 4.- Jmol will only show Hbonds between base pairs in nucleic acids and "backbone Hbonds" in proteins, i.e. between peptide CO and peptide NH |
From: William R. P. <wr...@vi...> - 2006-08-29 19:58:33
|
Sorry for the bad URL: Fixed below. > http://www.people.virginia.edu/~wrp/bioch503/bioch503_l3.html Begin forwarded message: > From: "William R. Pearson" <wr...@vi...> > Date: August 29, 2006 2:20:55 PM EDT > To: jmo...@li... > Subject: [Jmol-users] showing h-bonds with jmol > Reply-To: jmo...@li... > > > Though it seems clear that jmol will display h-bonds, I am not having > much luck doing it. > > For example, there is a jmol structure down the page in: > > http://www.people.virginia.edu/~wrp/bioch503/bioch503_l3.html > > that uses the script shown adjacent to it. > > But, no h-bonds for that piece of structure. Indeed, I have not had > any luck showing h-bonds when I run that script in the jmol > application, despite my best efforts to turn on hbonds. > > Help!! > > Bill Pearson > > > ---------------------------------------------------------------------- > --- > 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=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > |
From: William R. P. <wr...@vi...> - 2006-08-29 20:02:41
|
Adding "hbonds calculate" gets the job done. Thanks for the suggestion. Bill Pearson Begin forwarded message: >> From: "William R. Pearson" <wr...@vi...> >> Date: August 29, 2006 2:20:55 PM EDT >> To: jmo...@li... >> Subject: [Jmol-users] showing h-bonds with jmol >> Reply-To: jmo...@li... >> >> >> Though it seems clear that jmol will display h-bonds, I am not having >> much luck doing it. >> >> For example, there is a jmol structure down the page in: >> >> http://www.people.virginia.edu/~wrp/bioch503/bioch503_l3.html >> >> that uses the script shown adjacent to it. >> >> But, no h-bonds for that piece of structure. Indeed, I have not had >> any luck showing h-bonds when I run that script in the jmol >> application, despite my best efforts to turn on hbonds. >> >> Help!! >> >> Bill Pearson > |
From: Bob H. <ha...@st...> - 2006-08-29 20:39:08
|
Right. "hbonds on" now allows for just the hydrogen bonds originally displayed in the PDB file to be displayed. Most PDB files do not indicate hydrogen bonds, so this is a significant difference from 10.0, where "hbonds on" did the calculation as well. "hbonds calculate" was added so that one could, if one wanted, see just those hydrogen bonds that are explicitly given in a CONECT record of PDB files without doing any calculation. This also allows selective calculation of hydrogen bonds in selected regions of the molecule, as "hbonds calculate" only calculates hydrogen bonds within the currently selected set of atoms. William R. Pearson wrote: >Adding "hbonds calculate" gets the job done. Thanks for the suggestion. > >Bill Pearson > >Begin forwarded message: > > > >>>From: "William R. Pearson" <wr...@vi...> >>>Date: August 29, 2006 2:20:55 PM EDT >>>To: jmo...@li... >>>Subject: [Jmol-users] showing h-bonds with jmol >>>Reply-To: jmo...@li... >>> >>> >>>Though it seems clear that jmol will display h-bonds, I am not having >>>much luck doing it. >>> >>>For example, there is a jmol structure down the page in: >>> >>>http://www.people.virginia.edu/~wrp/bioch503/bioch503_l3.html >>> >>>that uses the script shown adjacent to it. >>> >>>But, no h-bonds for that piece of structure. Indeed, I have not had >>>any luck showing h-bonds when I run that script in the jmol >>>application, despite my best efforts to turn on hbonds. >>> >>>Help!! >>> >>>Bill Pearson >>> >>> > >------------------------------------------------------------------------- >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=lnk&kid=120709&bid=263057&dat=121642 >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > > |