Re: [Jmol-users] selecting atom IDs such as 1h47

On Oct 14, 2005, at 8:02 , Angel Herraez wrote: Hello all I have a PDB file in which some atoms have 4-character ID starting with a number; Jmol does not allow me to select them Example: ATOM 1 N50 LIP 1 -22.659 21.125 -23.903 .00 . ATOM 2 C47 LIP 1 -21.38

Re: [Jmol-users] selecting atom IDs such as 1h47

Angel & Miguel wrote: > >> Hello all >> I have a PDB file in which some atoms have 4-character ID starting with >> a number; Jmol does not allow me to select them [snip] > > This looks like a fundamental problem with the Jmol atom expression > parser. > > Having the integer first is causing problem

[Jmol-users] DOCUMENTATION: centerAt

> On 17 Aug 2005 at 8:59, Miguel > announced Jmol prerelease 10.00.32 > >> - default center of rotation is now the center of the bounding box >> instead of the average point >> - centerAt provides additional flexibility for defining the center of >> rotation > > This "centerAt" is not documented

Re: [Jmol-users] pmesh questions

>>Q: How would one decide where it would be displayed? >> > The default reference point could be the first coordinate in the pmesh > file. Optionally the number of the reference point coordinates in the > pmesh file could be specified in the pmesh definition line (e.g.: pmesh > example1 "example1.p

Re: [Jmol-users] pmesh questions

On Oct 19, 2005, at 12:37 , Rolf Huehne wrote: Maybe I should tell what we want to do. We want to highlight exon boundaries in protein structures. In order to be able to highlight for example PROSITE motifs at the same time the best way would be to show something between the two amino acids at

Re: [Jmol-users] pmesh questions

Miguel wrote: >>Hi all, >> >>I tried the "pmesh" functions of Jmol (10.00.36) and have a few questions. >> >>Currently there seems to be no labelling possibility for pmesh objects. >> >>Q: Would you consider adding a pmesh labelling command? >> > >It is not clear to me what kind of label yo

Re: [Jmol-users] PFAAT uses Jmol

On Oct 19, 2005, at 11:01 , [EMAIL PROTECTED] wrote: De: Timothy Driscoll <[EMAIL PROTECTED]> hi all, in case anyone is interested: I just came across a protein sequence alignment tool called PFAAT (). this software uses Jmol as an inline structure visualizati

Re: [Jmol-users] PFAAT uses Jmol

De: Timothy Driscoll <[EMAIL PROTECTED]> > >hi all, > >in case anyone is interested: > >I just came across a protein sequence alignment tool called PFAAT >(). this software uses Jmol as an >inline structure visualization module. it looks pretty cool, and I

Re: [Jmol-users] PFAAT uses Jmol

> hi all, > > in case anyone is interested: > > I just came across a protein sequence alignment tool called PFAAT > (). this software uses Jmol as an > inline structure visualization module. it looks pretty cool, and I > can see great possibilities in the combinati

[Jmol-users] PFAAT uses Jmol

hi all, in case anyone is interested: I just came across a protein sequence alignment tool called PFAAT (). this software uses Jmol as an inline structure visualization module. it looks pretty cool, and I can see great possibilities in the combination. (dis

Re: [Jmol-users] Update Request for 'Monitor / Measure' command

> In the category of wish lists, may I propose the following? > > Currently "monitor" ("measure") uses AtomNo for each of its parameters. > > As I develop a single page to service an Applet that > can dynamically load different, related structures, > the monitor command, of course, is less useful.

Re: [Jmol-users] pmesh questions

> Hi all, > > I tried the "pmesh" functions of Jmol (10.00.36) and have a few questions. > > Currently there seems to be no labelling possibility for pmesh objects. > > Q: Would you consider adding a pmesh labelling command? It is not clear to me what kind of label you want. Q: Do you want a

[Jmol-users] Update Request for "Monitor / Measure" command

In the category of wish lists, may I propose the following? Currently "monitor" ("measure") uses AtomNo for each of its parameters. As I develop a single page to service an Applet that can dynamically load different, related structures, the monitor command, of course, is less useful. The

[Jmol-users] pmesh questions

Hi all, I tried the "pmesh" functions of Jmol (10.00.36) and have a few questions. Currently there seems to be no labelling possibility for pmesh objects. Q: Would you consider adding a pmesh labelling command? In order to address pmesh objects individually it is necessary to put them into

Re: [Jmol-users] default zoom has changed along versions

El 16 Oct 2005 a las 19:45, Miguel escribió: > This is an intentional change. Great! I think this change is better. I will have to revise the versions in my website. · · · · · · · · · · · · · · · · · · · · · · · · · · · · · Dr. Angel Herraez Dep. Bioquimica y Biologia Molecular, Universidad de