Re: [Jmol-users] Drawing Bonds Between Different symops in Unit Cell
Well, this web site http://macxray.chem.upenn.edu/gam/9129b.html is
still using 11.0.2, so that won't help. You need to download 11.1.39.
I think what the problem is is that you are trying to use "symop=3555"
and it is not what you think it is. Your page suggests that what you
want to do is show the base atoms and then a set of symmetry-related
atoms, possibly shifted. That sound about right?
Then what you need to do is
a) load "" {555 555 0}
This loads the base atoms and the symmetry operation-related atoms. No
normalization is done, so many of these atoms will be outside cell 555.
b) do something like this:
function getOperation() {
var sym = "1";
for (i = 0; i < document.myForm.myRadio.length; i++) {
if (document.myForm.myRadio[i].checked) {
sym = document.myForm.myRadio[i].value;
}
}
var a = document.myForm.mySelect1.value // -1, 0, or 1 -- not 4, 5, or 6
var b = document.myForm.mySelect2.value // -1, 0, or 1 -- not 4, 5, or 6
var c = document.myForm.mySelect3.value // -1, 0, or 1 -- not 4, 5, or 6
var cmd = 'save orientation;load "" {555 555 0};selectionHalos
on;select symop='+sym+';translateselected {'+a+'/1 '+b+'/1
'+c+'/1};display not symmetry or selected;restore orientation'
return cmd
}
and
So what we are doing is loading one unit cell, without normalization.
then we are selecting a symmetry operation, moving those atoms as
desired, and displaying just the original atoms and the selected ones.
The save/restore orientation hides the reload.
I'm pretty sure that's what you are really after.
The other thing that I think is confusing you here is that the symmetry
operations you define are not expressed the way they are in the file.
You have:
x, y, z
x,½ - y, ½ + z
-x, -y, -z
-x, ½ + y, ½ - z
but from
show symmetry
we get:
Spacegroup: P 21/c
Number of symmetry operations: 4
Symmetry Operations:
x,y,z
-x, y+1/2, -z+1/2
-x, -y, -z
x, -y-1/2, z-1/2
Now, I know, these are the same, but if you really want to talk about
them and translate them and such, I think you should show the correct ones.
I would recommend just getting the operator straight from the file.
Something like this (which requires the latest Jmol.js):
var isdone = false
function getRadios() {
if (isdone)return;
isdone = true;
var Operations = jmolEvaluate('script("show
symmetry")').split("Symmetry Operations:")[1].split("\n")
var s = ""
for (var i = 0;i < Operations.length - 1;i++)
if (Operations[i].length > 0)
s+=''+Operations[i]+ ''
document.getElementById("radios").innerHTML = s
}
with:
Get Symmetry Operations
and, just to top it off, and a loadStructCallback to put those radio
buttons in automatically:
jmolApplet(500, "zap; set loadstructcallback = \"getRadios\";
set echo middle center; font echo 18 sanserif bold; color echo yellow;" +
"echo Loading cell|It could take a while||Please wait...; delay
0.5; load 9129b_files/9129.cif {444 666 0};" +
"zoom 150; restrict symop=1555;" +
"cpk 15%; wireframe 0.10; unitcell 0.05; color unitcell
lightblue; color boron SkyBlue;" +
"color carbon LightGrey; set perspectiveDepth OFF;
selectionHalos on; set measurements ANGSTROMS;" +
"select none; center{1/2,1/2,1/2}; set axesUnitCell; set axes
0.05; color axes red;" +
"set displayCellParameters OFF");
Bob
P.J. Carroll wrote:
>Bob,
> I'm also getting some similar weird behavior - if I
>explicitly select 3555 it appears where 3666 should be AND 3444
>appears where 3555 should be.
>
>
That's the shifting business I just fixed.
> BUT now I can't seem to get the same behavior with the
>buttons on my webpage! I'm confused??
>
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Re: [Jmol-users] animation questions
On May 14, 2007, at May 14, 6:56 PM, Bob Hanson wrote: This works perfectly when I do not have my state script between the load and the animation commands. But I have a state script to load and set up all the file display options, then the anim is triggered with a button. Any idea where to start looking for the problem? what's the problem, again? OK, before we go further I will do some additional checking. I will post again if need be. Thanks. Frieda /// Frieda Reichsman Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /// - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Drawing Bonds Between Different symops in Unit Cell
Bob, I'm also getting some similar weird behavior - if I explicitly select 3555 it appears where 3666 should be AND 3444 appears where 3555 should be. BUT now I can't seem to get the same behavior with the buttons on my webpage! I'm confused?? - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] animation questions
Frieda Reichsman wrote: > Hi Bob, Documentation for set backgroundmodel needs to be corrected, > it currently specifies (integer >= 1) > We need to take a good look at the documentation in relation to multiple files. > On May 14, 2007, at May 14, 5:52 PM, Bob Hanson wrote: > >> Ah, Frieda, you MUST use file.model notation with multiple files >> anywhere you would like to say "model n". Especially with PDB files, >> "set backgroundModel 1" would be too ambiguous. >> For example: >> >> load files "=1crn.pdb" "=1blu.pdb" "=1hje.pdb" >> animation mode palindrome >> animation fps 1 >> set backgroundmodel 1.1 >> frame range 1.1 3.1 >> frame play >> >> So I think it's just that one command. > > > This works perfectly when I do not have my state script between the > load and the animation commands. But I have a state script to load and > set up all the file display options, then the anim is triggered > with a button. Any idea where to start looking for the problem? > what's the problem, again? > BTW, what's with the "=" before the file names? Just curious. > that was SUPPOSED to read: load files "=1crn" "=1blu" "=1hje" It means "Go get these files from RCSB directly; I don't have them on my computer" I'm starting to use this so that anyone can run the script and it should work for them same as for me. No files required! > I am not sure what you mean here, in your following post: > >> hmm, a state save bug on that. Will fix > > 11.1.40 will fix a bug that prevents saving a state when there is a background model. > Frieda > > /// > > > Frieda Reichsman > > Molecules in Motion > > Interactive Molecular Structures > > http://www.moleculesinmotion.com > > > /// > > > > > >- >This SF.net email is sponsored by DB2 Express >Download DB2 Express C - the FREE version of DB2 express and take >control of your XML. No limits. Just data. Click to get it now. >http://sourceforge.net/powerbar/db2/ > > > >___ >Jmol-users mailing list >Jmol-users@lists.sourceforge.net >https://lists.sourceforge.net/lists/listinfo/jmol-users > > - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] animation questions
Hi Bob, Documentation for set backgroundmodel needs to be corrected, it currently specifies (integer >= 1) I *knew* there was a reason I had not tried file.model notation! :^) - should have tried it anyway!! On May 14, 2007, at May 14, 5:52 PM, Bob Hanson wrote: Ah, Frieda, you MUST use file.model notation with multiple files anywhere you would like to say "model n". Especially with PDB files, "set backgroundModel 1" would be too ambiguous. For example: load files "=1crn.pdb" "=1blu.pdb" "=1hje.pdb" animation mode palindrome animation fps 1 set backgroundmodel 1.1 frame range 1.1 3.1 frame play So I think it's just that one command. Bob Frieda Reichsman wrote: I'm looking for some scripting help. Using Jmol 11.1.38_dev, I am attempting an animation with four files. Each has one model. FIle 1 has an isosurface. Bob just wrote a nice post the other day re: frames and multiple files, but I am stuck nonetheless. I need to make file 1 stay visible throughout the animation, but set backgroundModel 1 has no effect. This is my script: file 0 display all animation mode PALINDROME 2.0 2.0 animation fps 1 set backgroundModel 1 frame RANGE 1.1 4.1 frame PLAY The result is that all the frames are looped through, and file 1 (frame 1) does not remain visible throughout. Changing from frame RANGE 1.1 4.1 to frame RANGE 2.1 4.1 just makes it so that frame 1 (file 1) never appears. Maybe it has something to do with this: Bob wrote: frame range 3.0 #all models in file 3 [there is a bug in 11.1.38 in this regard when the file only contains one model that I just fixed for 11.2] which caught my eye since I do only have one model in each file. But I am not following what the bug is. Also, once the animation is stopped, my buttons that allow the user to add a file to the current view are broken. If I say display displayed or file =3 file 3 does not appear. If I say file 0; display displayed or file =3 all the files appear. Frieda /// Frieda Reichsman Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /// - --- - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ - --- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- --- This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users /// Frieda Reichsman Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /// - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] animation questions
On May 14, 2007, at May 14, 5:52 PM, Bob Hanson wrote: Ah, Frieda, you MUST use file.model notation with multiple files anywhere you would like to say "model n". Especially with PDB files, "set backgroundModel 1" would be too ambiguous. For example: load files "=1crn.pdb" "=1blu.pdb" "=1hje.pdb" animation mode palindrome animation fps 1 set backgroundmodel 1.1 frame range 1.1 3.1 frame play So I think it's just that one command. This works perfectly when I do not have my state script between the load and the animation commands. But I have a state script to load and set up all the file display options, then the anim is triggered with a button. Any idea where to start looking for the problem? BTW, what's with the "=" before the file names? Just curious. I am not sure what you mean here, in your following post: hmm, a state save bug on that. Will fix Frieda /// Frieda Reichsman Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /// - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] animation questions
hmm, a state save bug on that. Will fix Bob Frieda Reichsman wrote: > I'm looking for some scripting help. Using Jmol 11.1.38_dev, > I am attempting an animation with four files. Each has one model. FIle > 1 has an isosurface. Bob just wrote a nice post the other day re: > frames and multiple files, but I am stuck nonetheless. > > I need to make file 1 stay visible throughout the animation, but > set backgroundModel 1 > has no effect. > > This is my script: > > file 0 > display all > animation mode PALINDROME 2.0 2.0 > animation fps 1 > set backgroundModel 1 > frame RANGE 1.1 4.1 > frame PLAY > > > The result is that all the frames are looped through, and file 1 > (frame 1) does not remain visible throughout. Changing from > frame RANGE 1.1 4.1 > to > frame RANGE 2.1 4.1 > just makes it so that frame 1 (file 1) never appears. > > Maybe it has something to do with this: > Bob wrote: > >> frame range 3.0 #all models in file 3 >> >> [there is a bug in 11.1.38 in this regard when the file only contains >> one model that I just fixed for 11.2] > > > which caught my eye since I do only have one model in each file. But I > am not following what the bug is. > > Also, once the animation is stopped, my buttons that allow the user to > add a file to the current view are broken. If I say > display displayed or file =3 > file 3 does not appear. > > If I say > file 0; display displayed or file =3 > all the files appear. > > Frieda > > > /// > > > Frieda Reichsman > > Molecules in Motion > > Interactive Molecular Structures > > http://www.moleculesinmotion.com > > > /// > > > > > >- >This SF.net email is sponsored by DB2 Express >Download DB2 Express C - the FREE version of DB2 express and take >control of your XML. No limits. Just data. Click to get it now. >http://sourceforge.net/powerbar/db2/ > > > >___ >Jmol-users mailing list >Jmol-users@lists.sourceforge.net >https://lists.sourceforge.net/lists/listinfo/jmol-users > > - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] animation questions
Ah, Frieda, you MUST use file.model notation with multiple files anywhere you would like to say "model n". Especially with PDB files, "set backgroundModel 1" would be too ambiguous. For example: load files "=1crn.pdb" "=1blu.pdb" "=1hje.pdb" animation mode palindrome animation fps 1 set backgroundmodel 1.1 frame range 1.1 3.1 frame play So I think it's just that one command. Bob Frieda Reichsman wrote: > I'm looking for some scripting help. Using Jmol 11.1.38_dev, > I am attempting an animation with four files. Each has one model. FIle > 1 has an isosurface. Bob just wrote a nice post the other day re: > frames and multiple files, but I am stuck nonetheless. > > I need to make file 1 stay visible throughout the animation, but > set backgroundModel 1 > has no effect. > > This is my script: > > file 0 > display all > animation mode PALINDROME 2.0 2.0 > animation fps 1 > set backgroundModel 1 > frame RANGE 1.1 4.1 > frame PLAY > > > The result is that all the frames are looped through, and file 1 > (frame 1) does not remain visible throughout. Changing from > frame RANGE 1.1 4.1 > to > frame RANGE 2.1 4.1 > just makes it so that frame 1 (file 1) never appears. > > Maybe it has something to do with this: > Bob wrote: > >> frame range 3.0 #all models in file 3 >> >> [there is a bug in 11.1.38 in this regard when the file only contains >> one model that I just fixed for 11.2] > > > which caught my eye since I do only have one model in each file. But I > am not following what the bug is. > > Also, once the animation is stopped, my buttons that allow the user to > add a file to the current view are broken. If I say > display displayed or file =3 > file 3 does not appear. > > If I say > file 0; display displayed or file =3 > all the files appear. > > Frieda > > > /// > > > Frieda Reichsman > > Molecules in Motion > > Interactive Molecular Structures > > http://www.moleculesinmotion.com > > > /// > > > > > >- >This SF.net email is sponsored by DB2 Express >Download DB2 Express C - the FREE version of DB2 express and take >control of your XML. No limits. Just data. Click to get it now. >http://sourceforge.net/powerbar/db2/ > > > >___ >Jmol-users mailing list >Jmol-users@lists.sourceforge.net >https://lists.sourceforge.net/lists/listinfo/jmol-users > > - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] animation questions
I'm looking for some scripting help. Using Jmol 11.1.38_dev, I am attempting an animation with four files. Each has one model. FIle 1 has an isosurface. Bob just wrote a nice post the other day re: frames and multiple files, but I am stuck nonetheless. I need to make file 1 stay visible throughout the animation, but set backgroundModel 1 has no effect. This is my script: file 0 display all animation mode PALINDROME 2.0 2.0 animation fps 1 set backgroundModel 1 frame RANGE 1.1 4.1 frame PLAY The result is that all the frames are looped through, and file 1 (frame 1) does not remain visible throughout. Changing from frame RANGE 1.1 4.1 to frame RANGE 2.1 4.1 just makes it so that frame 1 (file 1) never appears. Maybe it has something to do with this: Bob wrote: frame range 3.0 #all models in file 3 [there is a bug in 11.1.38 in this regard when the file only contains one model that I just fixed for 11.2] which caught my eye since I do only have one model in each file. But I am not following what the bug is. Also, once the animation is stopped, my buttons that allow the user to add a file to the current view are broken. If I say display displayed or file =3 file 3 does not appear. If I say file 0; display displayed or file =3 all the files appear. Frieda /// Frieda Reichsman Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /// - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JmolViewer.getGroupsPresentBitSet()
Thanks Bob for your quick and helful reply. > 2) I add a note to this effect in JmolViewer.java and explain how to get > around it. This sounds good to me, that fulfills my needs (better than the old method) Thank you, Amy - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] bug fixes in 11.1.38
Nico has released 11.1.39, which fixes bugs brought to my attention by
Nick Greeves, Pat Carroll, and Amy Wilson.
Keep up the good work!
Bob
# bug fix for mo data misreading in smol files
# bug fix for lcaoCartoon "s" giving incomplete spheres
# bug fix for select symop=3555 not giving proper atoms when load ""
{444 666 0}
# bug fix for PDB files not supplying information about residues for
the popup menu.
# bug fix in frame range 1.0 when file 1 has only one model.
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Re: [Jmol-users] Motivated Proteins incorporates Jmol 11
Bob wrote: >Say, David, I really like this feature: > >Protein 1blu not found in the Protein Motif database. >This protein is catagorized as: ELECTRON TRANSPORT >Proteins in the database of type ?ELECTRON TRANSPORT? are listed below: We needed to do that because our db is representative, rather than anywhere near comprehensive. We pull the header information off EBI Cambridge using one of their publicly assessable cgis (with their knowledge and permission of course). I'm not sure whether RCSB PDB provide similar hooks. David -- ___ David P.Leader, Biochemistry and Molecular Biology Davidson Building, University of Glasgow, Glasgow G12 8QQ, UK Phone: +44 41 330-5905 http://doolittle.ibls.gla.ac.uk/leader ___ - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Drawing Bonds Between Different symops in Unit Cell
Patrick J. Carroll wrote:
>Bob,
> I'm trying to work through your suggestions about using "display",
>but meanwhile, I've noticed some other strange behavior. On that same page,
>
> http://macxray.chem.upenn.edu/gam/9129b.html
>
>when I try to add a molecule by using symmetry operation no. 3 (center of
>symmetry), when I try to select symop = 3555, the green Ni atom in symop =
>1555 is instead selected. This is the atom that lies on the symmetry
>element (at .5, .5,.5).
>
That Ni atom is in both 1555 and 3555. Everything on that page looks to
me to be working right after a "fill cell" operation.
fill cell, then...
console
selectionHalos on
select symop=1555 # looks right
select symop=3555 # looks right
select symop=1555 and symop=3555 # just that Ni atom
I think 3555 is not working properly, but not for the reasons you think.
That Ni should be present, but the other selected atoms should also be
in cell 555, and they are not.
Is that the problem, perhaps? If so, I'll look into that. I think it
probably has something to do with how the symmetry gets defined using
load cifs/9129.cif {444 666 0}
I think what's happening is that 3555 for atoms other than the base set
is getting shifted over by one unit cell and really pulling in 3444.
Yes, that's it.
select symop=3666
gets you what you expect for symop=3555, I think, from that load.
So I will fix that.
Thanks.
Bob
Bob
>I have seen this behavior in other cells whenever
>an atom lies directly on a symmetry operation and I select a symop that
>should be the symmetry-related molecule, the atoms in the central molecule
>(1555) that lie directly on the symmetry element are selected, instead.
>See, for example
>
> http://macxray.chem.upenn.edu/lgs/3160b.html
>
>In this case, several of the atoms in 1555 lie on a mirror plane at y=.25.
>When I try to select symop = 4555, these atoms in 1555 that lie on the
>mirror plane are selected instead.
>
>
>
>Pat Carroll
>UPenn X-ray Facility
>
>
>
>
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Re: [Jmol-users] Drawing Bonds Between Different symops in Unit Cell
Bob, I'm trying to work through your suggestions about using "display", but meanwhile, I've noticed some other strange behavior. On that same page, http://macxray.chem.upenn.edu/gam/9129b.html when I try to add a molecule by using symmetry operation no. 3 (center of symmetry), when I try to select symop = 3555, the green Ni atom in symop = 1555 is instead selected. This is the atom that lies on the symmetry element (at .5, .5,.5). I have seen this behavior in other cells whenever an atom lies directly on a symmetry operation and I select a symop that should be the symmetry-related molecule, the atoms in the central molecule (1555) that lie directly on the symmetry element are selected, instead. See, for example http://macxray.chem.upenn.edu/lgs/3160b.html In this case, several of the atoms in 1555 lie on a mirror plane at y=.25. When I try to select symop = 4555, these atoms in 1555 that lie on the mirror plane are selected instead. Pat Carroll UPenn X-ray Facility - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] [Jmol-developers] JmolViewer.getGroupsPresentBitSet()
Bob Hanson wrote:
>Bug in Jmol 11.1.38 found and fixed: PDB files load but do not populate
>popup menu select submenu with group lists.
>
>[users who are not developers need not read further]
>
>
>
Actually, come to think of it, perhaps some users might be interested in
knowing that on a web page you can have full access to all the
information used in the popup menu identifying PDB groups and how many
of each are present in each model and in the full set of models. This
information is returned using the Jmol.js function:
jmolGetPropertyAsArray("auxiliaryInfo").group3Lists
and
jmolGetPropertyAsArray("auxiliaryInfo").group3Counts
(not working for PDB files in 11.1.38, though; works for mmCIF files;
will be fixed for 11.1.39 and 11.2)
Bob
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Re: [Jmol-users] JmolViewer.getGroupsPresentBitSet()
Bug in Jmol 11.1.38 found and fixed: PDB files load but do not populate
popup menu select submenu with group lists.
[users who are not developers need not read further]
Amy, I'd checked carefully against 10.2, and in fact you found the one
and only one method that was removed from JmolViewer. The reason it was
removed is coming back to me now. What this method did was return a
BitSet indicating the groups that are present in a model set. There is
an internal "predefined" list of groups that this would be referring to,
plus a set of additional groups that are added on the fly as a model is
read. In going to a multifile/multimodel format I abandoned this method
as "unusable" for the following reasons:
(1) It was exposing pointers to a core Jmol list that was not itself
exposed and was not protected against people like me rearranging it.
(2) In a multimodel/multiframe environment it wasn't clear how this
could be of any utility.
(3) It didn't really give enough information to be _generally_ useful.
So there are two possibilities, which I think you can decide for me:
1) I add back this rudamentary method, for you. (Which I'd be happy to
do if that's important...)
2) I add a note to this effect in JmolViewer.java and explain how to get
around it. That would look something like this:
/*
Jmol 11 greatly expands the capability for a program utilizing the
JmolViewer interface to determine information relating to any model
loaded. This information is maintained in the Hashtable returned by
getModelSetAuxiliaryInfo() for the overall set of models and
getModelSetAuxiliaryInfo(int modelIndex) for an individual model.
In the case of group information such as is used in the Jmol popup menu
to identify and count the PDB groups present in a model, the two
Hashtable elements of interest are String[] group3Lists and int[][]
group3Counts. To access these for a JmolViewer viewer, use:
JmolViewer viewer;
...
modelSetInfo = viewer.getModelSetAuxiliaryInfo();
int[][] counts = (int[][]) modelSetInfo.get("group3Counts");
String[] lists = (String[]) modelSetInfo.get("group3Lists");
These two lists (which may be null) can then be used to determine the
full set of groups present in each model in the model set, including how
many of each group is present in each case.
counts[0] counts the groups for the first model, counts[1] counts the
groups for the second model, etc. In addition,
counts[viewer.getModelCount()] counts the groups for all models and
lists[viewer.getModelCount()] lists those groups.
lists[modelIndex] is a coded string of 3-letter group codes ininitially
in the following format (line returns added only for this presentation):
,[ALA],[ARG],[ASN],[ASP],[CYS],[GLN],[GLU],[GLY],[HIS]
,[ILE],[LEU],[LYS],[MET],[PHE],[PRO],[SER],[THR],[TRP]
,[TYR],[VAL],[ASX],[GLX],[UNK]
,[G ],[C ],[A ],[T ],[I ],[U ],[+G ],[+C ],[+A ],[+T ],[+I ],[+U ]
,[AFL],[AGC],[AHR],[ARA],[ARB],[BDF],[BDR],[BGC],[BMA]
,[FCA],[FCB],[FRU],[FUC],[FUL],[GAL],[GLA],[GLB],[GLC]
,[GUP],[LXC],[MAN],[RAA],[RAM],[RIB],[RIP],[XYP],[XYS]
,[CBI],[CT3],[CTR],[CTT],[LAT],[MAB],[MAL],[MLR],[MTT]
,[SUC],[TRE],[ASF],[GCU],[MTL],[NAG],[NAM],[RHA],[SOR],[XYL]
This list includes all amino acids, nucleic acids, and carbohydrates
Jmol by default identifies. JmolConstants.java identifies the number of
amino acids on this list as:
public final static short GROUPID_AMINO_MAX = 23;
and the number of amino acids + nucleic acids as:
public final static short GROUPID_SHAPELY_MAX = 36;
In this way, one can know if any given group is an amino acid (id <23),
a nucleic acid (id >= 23 and id < 36), or a carbohydrate (id >= 36).
If additional groups are present, they are appended to this list as they
are identified in the file loading process, and that process
automatically identifies the group as to its type (see below).
In this string, each group is allocated 6 characters, starting with a
comma and ending with a right bracket. If a group is NOT present, it
appears as above.
If a group IS present, then the comma is changed to a character that
indicates what kind of group this is (p protein, n nucleic acid, c
carbohydrate, o other), and the left bracket is changed to a
greater-than sign. For example, for 1blu we have:
p>ALA]p>ARG]p>ASN]p>ASP]p>CYS]p>GLN]p>GLU]p>GLY]p>HIS]
p>ILE]p>LEU]p>LYS]p>MET],[PHE]p>PRO]p>SER]p>THR],[TRP]
p>TYR]p>VAL],[ASX],[GLX],[UNK]
,[G ],[C ],[A ],[T ],[I ],[U ],[+G ],[+C ],[+A ],[+T ],[+I ],[+U ]
,[AFL],[AGC],[AHR],[ARA],[ARB],[BDF],[BDR],[BGC],[BMA],
[FCA],[FCB],[FRU],[FUC],[FUL],[GAL],[GLA],[GLB],[GLC],
[GUP],[LXC],[MAN],[RAA],[RAM],[RIB],[RIP],[XYP],[XYS]
,[CBI],[CT3],[CTR],[CTT],[LAT],[MAB],[MAL],[MLR],[MTT]
,[SUC],[TRE],[ASF],[GCU],[MTL],[NAG],[NAM],[RHA],[SOR],[XYL]
o>FS4]o>HOH]
*/
Bob
group3List = (lists == null ? null : lists[n]);
group3Counts = (lists == null ? null : ((int[][])
modelSetInfo.get("group3Counts"))[n]);
Amy Wilson wrote:
>Hi there
Re: [Jmol-users] JmolViewer.getGroupsPresentBitSet()
Ah, that's why we need everyone involved to take a look. Thank you, Amy. I will look back at the JmolViewer interface for 10.2 and make sure that everything that was there is there in 11. I do see that note also says "unusable", so I definitely misunderstood something there. Amy, can you tell me quickly what you use that for, so I can make sure it still does what you think it does? Bob Amy Wilson wrote: >Hi there, just upgrading from version 10 to version 11 and I notice that >JmolViewer.getGroupsPresentBitSet() is gone. The commit it's deleted in >(5956) describes it as "unnecessary", so I'm hoping there's some other way >to get the same information. Can anyone help me out? > >Thanks, >Amy > > >- >This SF.net email is sponsored by DB2 Express >Download DB2 Express C - the FREE version of DB2 express and take >control of your XML. No limits. Just data. Click to get it now. >http://sourceforge.net/powerbar/db2/ >___ >Jmol-users mailing list >Jmol-users@lists.sourceforge.net >https://lists.sourceforge.net/lists/listinfo/jmol-users > > - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] help requested - summary of additions in Jmol 11
Angel Herraez wrote: > Dear Jmol users, > I want to update the History page on Jmol's web, to include the improvements > made in > Jmol since 10.2. I'm entitling that "Jmol outgrows Chime". > Bob recently posted a message summarizing some of the new features, and there > is an > extensive detailed list of changes in his website, but I would like something > brief, simple > and meaningful for the novice users reading the web, not for a technical > document. > So, I would appreciate that any of you provide a brief account of even a > single feature > that has fulfilled your dreams in molecular viewing thanks to work on the > 11.x series. > > This is Bob's summary: > - > Perhaps hard to believe that last year at this time Jmol... > ...was already an amazing applet, but it... > ...couldn't load multiple files > ...had only CUBE file support for isosurfaces > ...only included pmesh support for planes > ...couldn't do a thing with molecular orbitals > ...didn't include the concept of crystallographic symmetry > ...had essentially no variables or arithmetic operations > ...oh, I'm too tired to list any more! > - > > - saving and restoring the state (very compact, fast and incredibly well human-readable) - almost unlimited zoom - drawing planes, arrows etc. - exporting images from the applet - highly expanded information retrieval functions (Jmol -> javascript) - really good translucency - zoom automatically to the selected atoms There are certainly some more, but currently they don't come into my mind. Regards, Rolf - This SF.net email is sponsored by DB2 Express Download DB2 Express C - the FREE version of DB2 express and take control of your XML. No limits. Just data. Click to get it now. http://sourceforge.net/powerbar/db2/ ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
