Re: [Jmol-users] PDB and SCOP

2004-09-30 Thread Jaime Prilusky
According to Miguel: > If the data is not in the input file then Jmol probably cannot do > anything. (Unless the algorithms are published and the techniques are > generally agreed-upon) As I understand, the SCOP classification is been constructed manually, so no automatic procedure is available.

Re: [Jmol-users] PDB and SCOP

2004-09-30 Thread Miguel
> I developed a small solution for displaying PDB Entries in a comfort > way with the applet that is great (With Ball and Stick what you > recommended me and a very useful cartoon visualisation). I must say > that the v10 beta works really great... I am glad that it was useful. > Apart from that

Re: [Jmol-users] coloring peptide chains

2004-09-30 Thread Miguel
> Apparently some old pdb files I had been using > with Chime are incompatible with Jmol. If you have a .pdb file that is incompatible with Jmol then I would like to see it. Please send it offlist to [EMAIL PROTECTED] Miguel --- This SF.net

Re: [Jmol-users] Jmol Applet

2004-09-30 Thread Miguel
Ujjwal wrote: > ... So the question is > whether Jmol can be made to open its own (Java) window (resizable) with > all the buttons and options. > > Any suggestions from anyone please, Jmol does not currently support this functionality. (Longer-term, it may be something worth investigating ... bu

Re: [Jmol-users] PDB and SCOP

2004-09-30 Thread Raphael A. Bauer
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 timothy driscoll wrote: | is this a public page? I'm always interested to see how people use | Jmol... I'll post our project's url when it's available publicly for testing... (roughly mid next week). Thanks for your interest, regards, Raphael - -- // p

Re: [Jmol-users] Jmol Applet

2004-09-30 Thread Raphael A. Bauer
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Ujjwal Das wrote: | Thank you for your reply. Your framing is absolutely apt. So the question is | whether Jmol can be made to open its own (Java) window (resizable) with all the buttons and | options. I don't think so... (Miguel?), you have to make yo

Re: [Jmol-users] coloring peptide chains

2004-09-30 Thread William Reusch
Miguel and Tim, Thanks for your advice. Apparently some old pdb files I had been using with Chime are incompatible with Jmol. The 1A3N.pdb hemoglobin structure from the data base works fine in both environments. In response to Miguel's question, I am using the latest version of Jmol for all my

Re: [Jmol-users] Jmol Applet

2004-09-30 Thread Ujjwal Das
Hi Sebastian, Thank you for your reply. Your framing is absolutely apt. So the question is whether Jmol can be made to open its own (Java) window (resizable) with all the buttons and options. Any suggestions from anyone please, cheers ujjwal > Could the original poster have asked something el

Re: [Jmol-users] Jmol Applet

2004-09-30 Thread timothy driscoll
On 2004-09-30 (14:32) Sebastian Lisken wrote: >>or for a non-javascript solution: >> >>My Jmol Page > >That target should be "_blank", not "_new". If you use "_new", the >browser will open a window called "_new" and reuse that whenever >links with that target are clicked. Useful feature, but it's

Re: [Jmol-users] Jmol Applet

2004-09-30 Thread Sebastian Lisken
or for a non-javascript solution: My Jmol Page That target should be "_blank", not "_new". If you use "_new", the browser will open a window called "_new" and reuse that whenever links with that target are clicked. Useful feature, but it's not what "_new" suggests (basically "_new" is not a spec

Re: [Jmol-users] Rx,Ry,Rz from T (was show Center)

2004-09-30 Thread Bob Hanson
[this is not really something for the Jmol-users list, but since it started that way, I feel I should continue] OK, not QUITE that easy. What I showed initially works only for -90 Define pure rotation 3x3 tansform: T= R_x*R_y*R_z such that ActualCoord * T = ViewCoord (rotate cw first x, then

Re: [Jmol-users] PDB and SCOP

2004-09-30 Thread Ujjwal Das
Hi All, Thanks a lot for the replies. Please have a look at http://www.ebi.ac.uk/interpro/3DViewer/view3D?domain=1pcn00&type=cath We use Astex viewer to show SCOP/CATH structural domain on PDB chain/chains. It is a public page. We want to introduce similar viewer specially with cartoon option for

Re: [Jmol-users] PDB and SCOP

2004-09-30 Thread timothy driscoll
On 2004-09-30 (10:51) Raphael A. Bauer wrote: >-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 > >Hi Jmol List, > >I developed a small solution for displaying PDB Entries in a comfort >way with the applet that is great (With Ball and Stick what you >recommended me and a very useful cartoon visualisa

Re: [Jmol-users] Jmol Applet

2004-09-30 Thread timothy driscoll
On 2004-09-30 (13:46) Raphael A. Bauer wrote: >Ujjwal Das wrote: >>Is there a way to make the applet appear in a separate window ? >> >>any help will be much appreciated. >Try this code snipplet: > >onclick='javascript:window.open("YOURPAGE.html","tile","width=800, >height =800,left=0,top=0")'>3D

Re: [Jmol-users] Jmol Applet

2004-09-30 Thread Raphael A. Bauer
Ujjwal Das wrote: Is there a way to make the applet appear in a separate window ? any help will be much appreciated. Try this code snipplet: 3D View of this molecule Then your html page will be loaded as pop-up window... Hope it helps... Raphael -

[Jmol-users] Jmol Applet

2004-09-30 Thread Ujjwal Das
Hi Jmol list, Is there a way to make the applet appear in a separate window ? any help will be much appreciated. cheers ujjwal Ujjwal K Das, PhD EMBL Outstation - The EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK Phone: +44 1223 494 428 Fax: +44 1223 494 468 -

[Jmol-users] PDB and SCOP

2004-09-30 Thread Raphael A. Bauer
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Jmol List, I developed a small solution for displaying PDB Entries in a comfort way with the applet that is great (With Ball and Stick what you recommended me and a very useful cartoon visualisation). I must say that the v10 beta works really great..