From: Bob H. <ha...@st...> - 2007-03-01 04:48:38
|
Frieda Reichsman wrote: > Say I have 3 files loaded but my set of labels should appear on only > one of them. I also want to be able to turn on and off the display of > the three proteins at will. > > Is there an easy way to select a series of single atoms for labeling > and have the label apply only to one file? > > Or is the only way to do this to repeat "select file=1 and ..." over > and over, like so: > > select file=1 and 263.n > label helix 1 > If it's one model per file, you can just use the old syntax: select 263.n/1; label helix1 Certainly you need only the number of select/label combinations as you have distinct labels, but other than that, yes, you need to specify the atom and model number to get the label on just that atom. > In other words is there some way to say, "the following selections > apply ONLY to file =1" (and then also end it in some way)? > Well, you could do: select 263.n; label helix1 select 283.n; label helix2 ... select file != 1 labels off That is, just put all the labels in, but then in the end turn the unwanted ones off. Bob > > /////////////////////////////////////////// > > > Frieda Reichsman, PhD > > Molecules in Motion > > Interactive Molecular Structures > > http://www.moleculesinmotion.com > > > /////////////////////////////////////////// > > > |
From: Harris P. <ha...@vt...> - 2007-03-01 12:15:28
|
I try to load multiple files but i can't... I 'm working with perl : print " <form> <script> jmolInitialize("Jmol.js"); jmolApplet(300, "load "fileset" "1BZ8.pdb" "1C26.pdb"; select */2; color red;"); </script> </form>"; The problem is quotes... how can i do this ? I tried : print " <form> <script> jmolInitialize("Jmol.js"); jmolApplet(300, "load 'fileset' '1BZ8.pdb' '1C26.pdb'; select */2; color red;"); </script> </form>"; But it does not work too. And : print " <form> <script> jmolInitialize("Jmol.js"); jmolApplet(300, load "fileset" "1BZ8.pdb" "1C26.pdb"; select */2; color red;); </script> </form>"; The same.. Thanx Bob Hanson a écrit : > Frieda Reichsman wrote: > > >> Say I have 3 files loaded but my set of labels should appear on only >> one of them. I also want to be able to turn on and off the display of >> the three proteins at will. >> >> Is there an easy way to select a series of single atoms for labeling >> and have the label apply only to one file? >> >> Or is the only way to do this to repeat "select file=1 and ..." over >> and over, like so: >> >> select file=1 and 263.n >> label helix 1 >> >> > If it's one model per file, you can just use the old syntax: > > select 263.n/1; label helix1 > > Certainly you need only the number of select/label combinations as you > have distinct labels, but other than that, yes, you need to specify the > atom and model number to get the label on just that atom. > > >> In other words is there some way to say, "the following selections >> apply ONLY to file =1" (and then also end it in some way)? >> >> > Well, you could do: > > select 263.n; label helix1 > select 283.n; label helix2 > ... > select file != 1 > labels off > > That is, just put all the labels in, but then in the end turn the > unwanted ones off. > > Bob > > >> /////////////////////////////////////////// >> >> >> Frieda Reichsman, PhD >> >> Molecules in Motion >> >> Interactive Molecular Structures >> >> http://www.moleculesinmotion.com >> >> >> /////////////////////////////////////////// >> >> >> >> > > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > |
From: Frieda R. <fr...@ns...> - 2007-03-01 12:50:47
|
Hi Harris, > jmolInitialize("Jmol.js"); is incorrect - in the parenthesis should be the path to the Jmol =20 applet. If the applet is in the same directory, use simple a single =20 dot (.). Jmol.js must be referred to in the header, like this: <script language=3D"javascript" type=3D"text/javascript" = src=3D"Jmol.js"></=20 script> Frieda On Mar 1, 2007, at 7:15 AM, Harris Procopiou wrote: > I try to load multiple files but i can't... I 'm working with perl : > > print " > <form> > <script> > jmolInitialize("Jmol.js"); > jmolApplet(300, "load "fileset" "1BZ8.pdb" > "1C26.pdb"; select */2; color red;"); > </script> > </form>"; > > The problem is quotes... how can i do this ? > > I tried : > > print " > <form> > <script> > jmolInitialize("Jmol.js"); > jmolApplet(300, "load 'fileset' '1BZ8.pdb' > '1C26.pdb'; select */2; color red;"); > </script> > </form>"; > > But it does not work too. And : > > print " > <form> > <script> > jmolInitialize("Jmol.js"); > jmolApplet(300, load "fileset" "1BZ8.pdb" > "1C26.pdb"; select */2; color red;); > </script> > </form>"; > > The same.. > > Thanx > > Bob Hanson a =E9crit : >> Frieda Reichsman wrote: >> >> >>> Say I have 3 files loaded but my set of labels should appear on only >>> one of them. I also want to be able to turn on and off the =20 >>> display of >>> the three proteins at will. >>> >>> Is there an easy way to select a series of single atoms for labeling >>> and have the label apply only to one file? >>> >>> Or is the only way to do this to repeat "select file=3D1 and ..." = over >>> and over, like so: >>> >>> select file=3D1 and 263.n >>> label helix 1 >>> >>> >> If it's one model per file, you can just use the old syntax: >> >> select 263.n/1; label helix1 >> >> Certainly you need only the number of select/label combinations as =20= >> you >> have distinct labels, but other than that, yes, you need to =20 >> specify the >> atom and model number to get the label on just that atom. >> >> >>> In other words is there some way to say, "the following selections >>> apply ONLY to file =3D1" (and then also end it in some way)? >>> >>> >> Well, you could do: >> >> select 263.n; label helix1 >> select 283.n; label helix2 >> ... >> select file !=3D 1 >> labels off >> >> That is, just put all the labels in, but then in the end turn the >> unwanted ones off. >> >> Bob >> >> >>> /////////////////////////////////////////// >>> >>> >>> Frieda Reichsman, PhD >>> >>> Molecules in Motion >>> >>> Interactive Molecular Structures >>> >>> http://www.moleculesinmotion.com >>> >>> >>> /////////////////////////////////////////// >>> >>> >>> >>> >> >> >> ---------------------------------------------------------------------=20= >> ---- >> Take Surveys. Earn Cash. Influence the Future of IT >> Join SourceForge.net's Techsay panel and you'll get the chance to =20 >> share your >> opinions on IT & business topics through brief surveys-and earn cash >> http://www.techsay.com/default.php?=20 >> page=3Djoin.php&p=3Dsourceforge&CID=3DDEVDEV >> _______________________________________________ >> Jmol-users mailing list >> Jmo...@li... >> https://lists.sourceforge.net/lists/listinfo/jmol-users >> >> > > ----------------------------------------------------------------------=20= > --- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to =20 > share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?=20 > page=3Djoin.php&p=3Dsourceforge&CID=3DDEVDEV > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users /////////////////////////////////////////// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /////////////////////////////////////////// |
From: Egon W. <ewi...@un...> - 2007-03-01 13:34:53
|
Hi Harris, On Thursday 01 March 2007 13:15:16 Harris Procopiou wrote: > I try to load multiple files but i can't... I 'm working with perl : > > print " > <form> > <script> > jmolInitialize("Jmol.js"); > jmolApplet(300, "load "fileset" "1BZ8.pdb" > "1C26.pdb"; select */2; color red;"); > </script> > </form>"; In Perl you can escape the quotes with \"... so try this: print " <form> <script> jmolInitialize(\"Jmol.js\"); jmolApplet(300, 'load \"fileset\" \"1BZ8.pdb\" \"1C26.pdb\"; select */2; color red;'); </script> </form>"; Egon -- CUBIC blog: http://chem-bla-ics.blogspot.com/ |
From: Rolf H. <rh...@fl...> - 2007-03-01 13:49:44
|
Harris Procopiou wrote: > I try to load multiple files but i can't... I 'm working with perl : > > print " > <form> > <script> > jmolInitialize("Jmol.js"); > jmolApplet(300, "load "fileset" "1BZ8.pdb" > "1C26.pdb"; select */2; color red;"); > </script> > </form>"; > > The problem is quotes... how can i do this ? > > I tried : > > print " > <form> > <script> > jmolInitialize("Jmol.js"); > jmolApplet(300, "load 'fileset' '1BZ8.pdb' > '1C26.pdb'; select */2; color red;"); > </script> > </form>"; > > But it does not work too. And : > > print " > <form> > <script> > jmolInitialize("Jmol.js"); > jmolApplet(300, load "fileset" "1BZ8.pdb" > "1C26.pdb"; select */2; color red;); > </script> > </form>"; > > The same.. > > Hi Harris, since you mentioned perl as the script language you are using to create the HTML code I guess your question refers to the syntax errors you will get in perl if you try the above 'print' commands. There are two methods in perl to solve this problem. The first one is to 'escape' the double quotes inside the 'print' statement with a backslash,e.g.: print "jmolApplet(300, \"load 'fileset' '1BZ8.pdb' '1C26.pdb'\");"; The disadvantage of this method is that the text is less good readable and that you have to change the HTML code you might have tested in a plain HTML text before you started to integrate it into your perl script. Therefore I prefer the second method: using the general quoting operator 'qq'. The above example could look like this: print qq{jmolApplet(300, "load 'fileset' '1BZ8.pdb' '1C26.pdb");}; You can replace the brace ('{') behind the 'qq' by any other non-alphanumeric character. Then the end brace ('}') must also be replaced by the same character (or the corresponding closing bracket character if you use '(' or '['). In my work the brace has proven to work in most cases for HTML code. Regards, Rolf |
From: Frieda R. <fr...@ns...> - 2007-03-01 12:53:12
|
Thanks, Bob, I never seem to remember the /model syntax, and the last solution is great - so simple. Frieda On Feb 28, 2007, at 11:48 PM, Bob Hanson wrote: > Frieda Reichsman wrote: > >> Say I have 3 files loaded but my set of labels should appear on only >> one of them. I also want to be able to turn on and off the display of >> the three proteins at will. >> >> Is there an easy way to select a series of single atoms for labeling >> and have the label apply only to one file? >> >> Or is the only way to do this to repeat "select file=1 and ..." over >> and over, like so: >> >> select file=1 and 263.n >> label helix 1 >> > If it's one model per file, you can just use the old syntax: > > select 263.n/1; label helix1 > > Certainly you need only the number of select/label combinations as you > have distinct labels, but other than that, yes, you need to specify > the > atom and model number to get the label on just that atom. > >> In other words is there some way to say, "the following selections >> apply ONLY to file =1" (and then also end it in some way)? >> > Well, you could do: > > select 263.n; label helix1 > select 283.n; label helix2 > ... > select file != 1 > labels off > > That is, just put all the labels in, but then in the end turn the > unwanted ones off. > > Bob > >> >> /////////////////////////////////////////// >> >> >> Frieda Reichsman, PhD >> >> Molecules in Motion >> >> Interactive Molecular Structures >> >> http://www.moleculesinmotion.com >> >> >> /////////////////////////////////////////// >> >> >> > > > ---------------------------------------------------------------------- > --- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to > share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php? > page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users /////////////////////////////////////////// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /////////////////////////////////////////// |
From: John T. <j.t...@ma...> - 2007-03-01 23:07:50
|
Hello I have a page with three applets (loaded columns in a table row , B- A- and Z DNA) with a set of radio buttons for each applet in the same table row. I want to have a single set of radio buttons that relate to all three applets at once. I can set up buttons outside the table and get them to apply to the one applet at a time using a "jmolSetTarget" and specifying the applet but cannot get them to work on all 3. Regards John Tweedie Associate Professor in Biochemistry Institute of Molecular BioSciences Massey University Private Bag 11-222 Palmerston North NEW ZEALAND e-mail (Massey): j.t...@ma... Phone (Massey):64 6 350 5515 Ext 2581 e-mail (Home): jtw...@ma... Phone (Home): 64 6 358 0150 Home Address: 15 Annandale Avenue Palmerston North NEW ZEALAND On Mar 1, 2007, at 05:48 PM, Bob Hanson wrote: > Frieda Reichsman wrote: > >> Say I have 3 files loaded but my set of labels should appear on only >> one of them. I also want to be able to turn on and off the display of >> the three proteins at will. >> >> Is there an easy way to select a series of single atoms for labeling >> and have the label apply only to one file? >> >> Or is the only way to do this to repeat "select file=1 and ..." over >> and over, like so: >> >> select file=1 and 263.n >> label helix 1 >> > If it's one model per file, you can just use the old syntax: > > select 263.n/1; label helix1 > > Certainly you need only the number of select/label combinations as you > have distinct labels, but other than that, yes, you need to specify > the > atom and model number to get the label on just that atom. > >> In other words is there some way to say, "the following selections >> apply ONLY to file =1" (and then also end it in some way)? >> > Well, you could do: > > select 263.n; label helix1 > select 283.n; label helix2 > ... > select file != 1 > labels off > > That is, just put all the labels in, but then in the end turn the > unwanted ones off. > > Bob > >> >> /////////////////////////////////////////// >> >> >> Frieda Reichsman, PhD >> >> Molecules in Motion >> >> Interactive Molecular Structures >> >> http://www.moleculesinmotion.com >> >> >> /////////////////////////////////////////// >> >> >> > > > ---------------------------------------------------------------------- > --- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to > share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php? > page=join.php&p=sourceforge&CID=DEVDEV > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > |
From: Angel H. <ang...@ua...> - 2007-03-01 13:31:07
|
Hello Harris Yes, it seems a quotes problem. First, try this: Jmol requires double quotes for load, so you should use single quotes for the javascript: <form> <script> jmolInitialize('.'); jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select */2; color red;'); </script> </form> However, since you have a more external set of double quotes for your "print", it may not work. I think I read about the use of ", but right now I canot find it. If I do, I will post again. If you want to try, it could be (I haven't checked): <form> <script> jmolInitialize('.'); jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select */2; color red;'); </script> </form> |
From: Angel H. <ang...@ua...> - 2007-03-01 23:53:36
|
Hi John How about setting a javascript function that will do the job three times, one for each applet? |
From: <ha...@vt...> - 2007-03-01 14:28:46
|
<br />thanx all for your help but I tried all the possibilities and it does= not work...<br /><br />The last method i tried is :<br /><br />print qq{<b= r />  = ; <for= m><br /> &nbs= p; = <script><br /> &= nbsp; &nbs= p; jmolInitialize("../softs/= jmol-10.2.0");<br /> &n= bsp;  = ; jmolApplet(300, "load 'fileset' = '../pdb_structures/1BZ8.pdb' '../pdb_structures/1C26.pdb'; select */1;"= ;);<br /> = &l= t;/script><br /> &n= bsp;  = ; </form><br /> };<br= /><br />Is this command correct ? jmolApplet(300, "load 'fileset' '1B= Z8.pdb' '1C26.pdb'; select */2;");<br /><br />Should the applet show a= nything or not ?<br /><br />Thanx<br /><br />Harris =0D <BR> |
From: Egon W. <ewi...@un...> - 2007-03-01 14:32:16
|
On Thursday 01 March 2007 15:28:35 ha...@vt... wrote: > The last method i tried is : > > print qq{ > =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 <fo= rm> > =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 <sc= ript> > =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0=A0=A0 jmolInitialize("../softs/jmol-10.2.0"); > =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0= =A0=A0=A0 jmolApplet(300, "load 'fileset' > '../pdb_structures/1BZ8.pdb' '../pdb_structures/1C26.pdb'; select */1;"); > </script> > =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0 </f= orm> > =A0=A0=A0=A0=A0=A0=A0 }; > > Is this command correct ? jmolApplet(300, "load 'fileset' '1BZ8.pdb' > '1C26.pdb'; select */2;"); You still need to apply what Angel mentioned: switch the " and ' in the loa= d=20 command. So: print qq{ <form> <script> jmolInitialize("../softs/jmol-10.2.0"); jmolApplet(300, 'load "fileset" "../pdb_structures/1BZ8.pdb" "../pdb_structures/1C26.pdb"; select */1;'); </script> </form> }; E. =2D-=20 CUBIC blog: http://chem-bla-ics.blogspot.com/ |
From: <ha...@vt...> - 2007-03-01 14:40:44
|
<p><br />ok thank you...</p><p> </p><p>Now when I do : </p><p> </= p><pre><p>jmolApplet(300, 'load "fileset" "1BZ8.pdb" &q= uot;1C26.pdb"; select */1;');</p><p>It shows 1BZ8 structure. But if i = do : </p><pre><p>jmolApplet(300, 'load "fileset" "1BZ8.pdb&q= uot; "1C26.pdb"; select */2;');</p><p> </p><p>It shows nothi= ng.. .is it normal ? </p></pre><br />Egon Willighagen a =C3=A9crit&nbs= p;:</pre><p><blockquote>=0D <pre>On Thursday 01 March 2007 15:28:35 ha...@vt... wrote:<br /></pr= e>=0D <blockquote><pre>The last method i tried is :<br /><br />print qq{<br />&= nbsp; &nbs= p; <form>= <br /> &nb= sp; <s= cript><br /> = &nb= sp; jmolInitialize("../softs/jmol-= 10.2.0");<br /> &= nbsp; &nbs= p; jmolApplet(300, "load 'fileset'<br />= '../pdb_structures/1BZ8.pdb' '../pdb_structures/1C26.pdb'; select */1;"= ;);<br /></script><br /> &nb= sp; = </form><br /> &= nbsp; };<br /><br />Is this command correct ? jmolApplet(300, "load 'f= ileset' '1BZ8.pdb'<br />'1C26.pdb'; select */2;");<br /></pre></blockq= uote>=0D <pre><!----><br />You still need to apply what Angel mentioned: switch th= e " and ' in the load <br />command. So:<br /><br />print qq{<br /> = <form><br /> <script&g= t;<br /> jmolInitialize("../softs/jmol-10= .2.0");<br /> jmolApplet(300, 'load "f= ileset"<br />"../pdb_structures/1BZ8.pdb" "../pdb_struc= tures/1C26.pdb"; select */1;');<br /></script><br /> = </form><br /> };<br /><br />E.<br /><br /></pre>= =0D </blockquote>=0D =0D </p><BR> |
From: Frieda R. <fr...@ns...> - 2007-03-01 15:44:43
|
you need to insert the command file 0 which makes all the files you loaded "displayable" (but not displayed) so say jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; file 0; select =20= */2; spacefill on;'); the last command is just to actually render the structure in a style, =20= choose whatever rendering you like. Also, the reason that select */1 worked was simply that when you load multiple files, only the first =20 one shows up by default. Frieda On Mar 1, 2007, at 9:40 AM, <ha...@vt...> <ha...@vt...> wrote: > > ok thank you... > > > Now when I do : > > > jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select */1;'); > > It shows 1BZ8 structure. But if i do : > > jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select */2;'); > > > It shows nothing.. .is it normal ? > > > Egon Willighagen a =E9crit : > > On Thursday 01 March 2007 15:28:35 ha...@vt... wrote: > The last method i tried is : > > print qq{ > > > > }; > > Is this command correct ? jmolApplet(300, "load 'fileset' '1BZ8.pdb' > '1C26.pdb'; select */2;"); > > You still need to apply what Angel mentioned: switch the " and ' in =20= > the load > command. So: > > print qq{ > > > > }; > > E. > > > > ----------------------------------------------------------------------=20= > --- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to =20 > share your > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?=20 > page=3Djoin.php&p=3Dsourceforge&CID=3DDEVDEV____________________________= ____=20 > _______________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users /////////////////////////////////////////// Frieda Reichsman, PhD Molecules in Motion Interactive Molecular Structures http://www.moleculesinmotion.com /////////////////////////////////////////// |
From: Frieda R. <fr...@ns...> - 2007-03-01 15:56:31
|
oops - I misspoke -- I said: > > you need to insert the command > file 0 > which makes all the files you loaded "displayable" (but not displayed) > BUT I was incorrect. "file 0" actually does display all the files loaded. So instead say so say: jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; file 0; display file=2;'); the command display file=2 is what displays ONLY file 2. Below is a "reprint" of a complete explanation that Bob H wrote to the list yesterday (in response to my questions). Frieda ------------------------ reprint ------------------------ Bob said: > The logic is supposed to be: > > "display x" hides all atoms except x. > "hide x" displays all atoms except x. > > To this we add: > > display xxx # display ONLY x > hide not xxx # same thing! > > display not xxx # display everything but x > hide xxx # same thing! > > display hidden # toggle shown for unshown > hide displayed # same thing! > > display displayed and not xxx # remove xxx from the display --- what > you want here > hide hidden or xxx # same thing! > > display displayed or xxx # add x to the display --- also what you > want > hide hidden and not xxx # add x to the display > > So just don't use "hide" if it confuses you. It is never necessary. > Thinking in terms of what is displayed gets you anything you want. The > key for this situation is to use "displayed" as part of that > checkbox item. > > [x] file 1: [x]"display displayed or file=1" [ ] "display > displayed > and not file=1" > [x] file 2 : [x]"display displayed or file=2" [ ] "display > displayed > and not file=2" > [x] file 3 : [x]"display displayed or file=3" [ ] "display > displayed > and not file=3" > |
From: Angel H. <ang...@ua...> - 2007-03-02 13:57:53
|
Hi Harris Although others had posted more detailed solutions to your question, I think the problem you had with > jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select */1;'); > It shows 1BZ8 structure. But if i do : > > > jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select */2;'); > It shows nothing.. .is it normal ? is that, when several files are loaded, they are assigned frame/model numbers 1001, 2001, not 1, 2. So, in your examples: jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select */1001;'); # first model in 1BZ8.pdb jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select */2001;'); # first model in 1C26.pdb The new syntax in Jmol 11.1.x allows to use the more clear "file 1", "file 2" and "1.1", "1.2", "2.1" identifiers, which have already been recommended by others. HTH |
From: Bob H. <ha...@st...> - 2007-03-02 22:47:19
|
In 11.1.x we are recommending going to a simpler method of naming models in multiple file mode: Files have each one model: 1.1, 2.1, 3.1, .... Files have more than one model: 1.1, 1.2, 1.3, ... 2.1, 2.2, 2.3.... etc. Then, in analogy to model 0 for displaying all models, now we have: model 1.0 # all models in File 1 The original idea of 1001 2001 3001 still is implemented, but this is better. Also, in 11.1.x I fixed it so that model 1 model 2 etc. works as well, as long as the files really only have one model each. That's because "model 1" is the same as "model 1.0" -- "all models in file 1". So if you say model 1 or model 1.0 that's the same -- all models in file 1. I think this works reasonably intuitively. Bob Bob Angel Herraez wrote: >Hi Harris > >Although others had posted more detailed solutions to your question, >I think the problem you had with > > > >>jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select */1;'); >>It shows 1BZ8 structure. But if i do : >> >> >>jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select */2;'); >>It shows nothing.. .is it normal ? >> >> > > >is that, when several files are loaded, they are assigned frame/model >numbers 1001, 2001, not 1, 2. So, in your examples: >jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select >*/1001;'); # first model in 1BZ8.pdb >jmolApplet(300, 'load "fileset" "1BZ8.pdb" "1C26.pdb"; select >*/2001;'); # first model in 1C26.pdb > >The new syntax in Jmol 11.1.x allows to use the more clear "file 1", >"file 2" and "1.1", "1.2", "2.1" identifiers, which have already >been recommended by others. > >HTH > > >------------------------------------------------------------------------- >Take Surveys. Earn Cash. Influence the Future of IT >Join SourceForge.net's Techsay panel and you'll get the chance to share your >opinions on IT & business topics through brief surveys-and earn cash >http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > |
From: Craig T M. <cm...@ch...> - 2007-05-03 12:49:53
|
> Message: 3 > Date: Wed, 02 May 2007 19:14:11 -0500 > From: Bob Hanson <ha...@st...> > Subject: [Jmol-users] signed applets > To: jmo...@li... > Message-ID: <463...@st...> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > I looking for someone who is using the signed applet. Dear Bob, I use it all the time, though only for local file access, not from one server to another. In my usage, i have a javascript that figures out if the access is local or to a server. If the former, then it uses the signed applet. Thus all of my local development is with the signed applet. However, I've had a hard time keeping up with the (fantastic) pace of your development. The most recent version I've used is 10.9.98. The signed applet works great with that (on a Mac, usually Safari). Did you have a specific question? Craig Craig Martin cm...@ch... |
From: Craig T M. <cm...@ch...> - 2007-05-03 17:28:38
|
Bob, As someone else pointed out, i think, when you access the signed applet, it will ask you for permission to run. A dialog will pop up before Jmol fully loads. If you get that dialog, and then everything after that goes smoothly, then the signed applet is working. It will only ask you once per session. To see the request again, you'll have to quit your browser and then reopen. You can pull down a test that when run locally should automatically run the trusted applet at: <http://people.chem.umass.edu/cmartin/Jmol/JmolTest.zip> Craig Craig Martin cm...@ch... On May 3, 2007, at 11:31 AM, Bob Hanson wrote: > Craig T Martin wrote: > >>> Message: 3 >>> Date: Wed, 02 May 2007 19:14:11 -0500 >>> From: Bob Hanson <ha...@st... <mailto:ha...@st...>> >>> Subject: [Jmol-users] signed applets >>> To: jmo...@li... <mailto:jmol- >>> us...@li...> >>> Message-ID: <463...@st... <mailto: >>> 463...@st...>> >>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>> >>> I looking for someone who is using the signed applet. >> >> >> Dear Bob, >> >> I use it all the time, though only for local file access, not >> from one server to another. >> >> In my usage, i have a javascript that figures out if the access >> is local or to a server. If the former, then it uses the signed >> applet. Thus all of my local development is with the signed applet. >> >> However, I've had a hard time keeping up with the (fantastic) >> pace of your development. The most recent version I've used is >> 10.9.98. The signed applet works great with that (on a Mac, >> usually Safari). >> >> Did you have a specific question? >> > Yes. What should I do to test that I have the signed applet working? > >> Craig >> >> Craig Martin >> cm...@ch... <mailto:cm...@ch...> >> >> >> > |
From: Bob H. <ha...@st...> - 2007-05-03 21:06:57
|
Jmol 11.1.30 is ready for release, Nico. Signed applet tests successful and, for example, loads files directly from RCSB's depository simply with load =xxxx where =xxxx is an equal sign followed by a four-digit ID. I recommend that if you want to use the signed applet you use the single-file format of initialization: jmolInitialize(".", "JmolAppletSigned.jar") rather than jmolInitialize(".", true) becaue "true" gives you a download of all the separate jar files, starting with JmolAppletSigned0.jar, and at least Opera asks for an OK on the certificate for every one of them individually. That's a bit of a pain. OK, features. Not too many: full support for switching languages, including a new "language" menu item --------------------------------------------------------------------------- Now you can switch languages anytime you want. Just pop up the menu and select the new "language" item near the bottom. WE NEED PEOPLE TO VOLUNTEER TO DO MORE TRANSLATIONS, even in just the set of languages we are supporting. It would be nice just to get that menu put translation done. Someone want to work on this? # # Jmol.js: # # jmolSetCallback("language", "de") # # Jmol scripting: # # language = "de" # # Menu: # # new language submenu with checkboxes. # # allows for efficient specific file reader options for the applet (particularly) # _spinning variable ------------------ You can now check in IF commands for whether spinning is on or off and script accordingly. For example: wasSpinning = _spinning load myfile.pdb if(wasSpinning);spin on;endif better handling of spin in relation to zoomTo and moveTo -------------------------------------------------------- If the model is spinning when a zoomTo or moveTo command is executed, or if the user uses the mouse to rotate the model, then spinning is halted and only resumes one full second after the manipulation is complete. zoomTo and moveTo the same location changed to no time delay -------------------------------------------------------------------------------- Previously if you did two of the same zoomTo or moveTo operations in a row, Jmol would appear to stall while just counting seconds. That is no longer the case. The second zoomTo or moveTo is simply skipped. hover now is turned off during spinning or user manipulation of the model -------------------------------------------------------------------------- I noticed that hover was picking up atom labels under the mouse when the model was rotating by and considered that a bug. Now when the model is spinning, moving the mouse over atoms (or moving atoms under the mouse) does not show the hover tag. If spinning is stopped, the hover action returns. Pqr reader ---------- Jmol now reads Pqr data files created using PDB2PQR file type forcing ----------------- This feature is of no current use; Jmol correctly assigns file type based on file contents to all file types it reads. But in the future two "flavors" of a format may be difficult to distinguish. load xxx::myfile.whatever xxx:: is a file type, such as MOL; followed by two colons. faster loading (maybe) ---------------------- Jmol 11.1.30 uses a much more efficient mechanism for file loading. Let us know if it works. As part of this work the JAR files were realigned and have new names: *JmolApplet0.jar *JmolAppletCore.jar *JmolAppletJars.jar *JmolAppletJvxl.jar *JmolAppletMain.jar *JmolAppletPopup.jar *JmolAppletViewer.jar JmolAppletQuantum.jar JmolAppletReadersCifPdb.jar JmolAppletReadersMolXyz.jar JmolAppletReadersMore.jar JmolAppletReadersXml.jar JmolAppletShapeBio.jar JmolAppletShapeSpecial.jar JmolAppletSmiles.jar JmolApplet_i18n.jar (translations) *required (650 Kb) JmolApplet0.jar is still there, but the other six are replaced by the above list, which are loaded only as needed and can even be left off a site (though that is not recommended) if not used. So, for example, if you never use molecular orbitals, they will never be there; if you never use biomolecular cartoons, your user will never have them downloaded. The required download is now about 650 Kb, only about 80% of the size of Jmol 10.2. The first time you use "cartoon on", for example, the ShapeBio package is delivered. This means that there could be noticeable delays later in the loading process. If this does not suit you, just use JmolApplet.jar; it's size (1M) is still only about 75% of the size of 11.1.29 and only 22% larger than Jmol 10.2. ----------------------------------- That's all for 11.1.30 Bob Hanson |
From: Nicolas V. <nve...@nu...> - 2007-05-03 21:17:38
|
Bob Hanson wrote: > Jmol 11.1.30 is ready for release, Nico. > See my other mail, there's a bug somewhere when running monster_script.spt. Can you fix it before I release 11.1.30 ? Nico |
From: Bob H. <ha...@st...> - 2007-05-04 06:23:05
|
Thanks, Craig. That's just what I needed. Craig T Martin wrote: > Bob, > > As someone else pointed out, i think, when you access the signed > applet, it will ask you for permission to run. A dialog will pop up > before Jmol fully loads. If you get that dialog, and then everything > after that goes smoothly, then the signed applet is working. > > It will only ask you once per session. To see the request again, > you'll have to quit your browser and then reopen. > > You can pull down a test that when run locally should automatically > run the trusted applet at: > > <http://people.chem.umass.edu/cmartin/Jmol/JmolTest.zip> > > Craig > > Craig Martin > cm...@ch... <mailto:cm...@ch...> > > > > On May 3, 2007, at 11:31 AM, Bob Hanson wrote: > >> Craig T Martin wrote: >> >>>> Message: 3 >>>> Date: Wed, 02 May 2007 19:14:11 -0500 >>>> From: Bob Hanson <ha...@st... <mailto:ha...@st...> >>>> <mailto:ha...@st...>> >>>> Subject: [Jmol-users] signed applets >>>> To: jmo...@li... >>>> <mailto:jmo...@li...> >>>> <mailto:jmo...@li...> >>>> Message-ID: <463...@st... >>>> <mailto:463...@st...> >>>> <mailto:463...@st...>> >>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >>>> >>>> I looking for someone who is using the signed applet. >>> >>> >>> >>> Dear Bob, >>> >>> I use it all the time, though only for local file access, not >>> from one server to another. >>> >>> In my usage, i have a javascript that figures out if the access is >>> local or to a server. If the former, then it uses the signed applet. >>> Thus all of my local development is with the signed applet. >>> >>> However, I've had a hard time keeping up with the (fantastic) pace >>> of your development. The most recent version I've used is 10.9.98. >>> The signed applet works great with that (on a Mac, usually Safari). >>> >>> Did you have a specific question? >>> >> Yes. What should I do to test that I have the signed applet working? >> >>> Craig >>> >>> Craig Martin >>> cm...@ch... <mailto:cm...@ch...> >>> <mailto:cm...@ch...> >>> >>> >>> >> > >------------------------------------------------------------------------ > >------------------------------------------------------------------------- >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 >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > |
From: Angel H. <ang...@ua...> - 2007-05-03 23:41:02
|
Bob Hanson wrote: > Jmol 11.1.30 is ready for release, Nico. > load =3Dxxxx Impressive! > OK, features. Not too many: Not too many? You MUST be kidding! > full support for switching languages, including a new "language" menu it= em > ------------------------------------------------------------------------= --- > Now you can switch languages anytime you want. Just pop up the menu and > select > the new "language" item near the bottom. This is heaven! > WE NEED PEOPLE TO VOLUNTEER TO DO MORE TRANSLATIONS, even in just the > set of languages we are supporting. It would be nice just to get that > menu put translation done. Someone want to work on this? Not sure what you mean: translating the new "language" menu entry itself? Oh, I see. We have all names of available languages as sub-entries in that= menu. I am about to translate them all into Spanish for es.po, but not sure it is a good id= ea. Shouldn't we have each one fixed in its own language, independently of the locale? I mean, If I am French and the menu opens in English, I'd rather recognize= "Fran=E7ais" than "French". Or, if Bob opens Jmol in a Spanish computer, and wants his Engli= sh menus, will he prefer seeing "English" or "Ingl=E9s" --well, Bob is not a good example, h= e can recongize Spanish words ;-) What are your views? > Pqr reader > ---------- > Jmol now reads Pqr data files created using PDB2PQR No need to use the file type forcing ? |
From: Benny C. <b....@uc...> - 2007-09-02 08:48:24
|
Does anyone know if it is possible to define a file name (for example to save an image) as a variable , so that one can automatically move from file to file in a looping script ? Or is there any other way to save repeated images not in the same file during script execution ? Benny Chain Benjamin Chain Department of Immunology and Molecular Pathology Windeyer Institute of Medical Sciences UCL, 46 Cleveland St. London W1T 4JF Fax 00 44 20 7679 9301 |
From: Angel H. <ang...@ua...> - 2007-09-02 10:27:56
|
Hello Benny I'm quite sure it can be done using Jmol math, but I have no experience wth that. I would say there have been posts regarding this; do a search in the list archive, possibly for "animated images" which was a frequent discussion topic. > Does anyone know if it is possible to define a file name (for example to save an image) as > a variable , so that one can automatically move from file to file in a looping script ? Or is > there any other way to save repeated images not in the same file during script execution ? > > Benny Chain |
From: Bob H. <ha...@st...> - 2007-09-02 14:21:50
|
Jmol math: x = "myfile.xyz" load @x Angel Herraez wrote: >Hello Benny > >I'm quite sure it can be done using Jmol math, but I have no experience wth that. >I would say there have been posts regarding this; do a search in the list archive, possibly for >"animated images" which was a frequent discussion topic. > > > >>Does anyone know if it is possible to define a file name (for example to save an image) as >>a variable , so that one can automatically move from file to file in a looping script ? Or is >>there any other way to save repeated images not in the same file during script execution ? >> >>Benny Chain >> >> > > >------------------------------------------------------------------------- >This SF.net email is sponsored by: Splunk Inc. >Still grepping through log files to find problems? Stop. >Now Search log events and configuration files using AJAX and a browser. >Download your FREE copy of Splunk now >> http://get.splunk.com/ >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 |