[Jmol-users] Problem with JVXL data on Mac OSX - solution

[Nick Greeves]

Hi Frieda, You can drag and drop to and from the Console window as I've done here, or look in console.log using the Console.app application. You can copy from console.log. JVXL solvent-excluded surface range (-3.331551, -2.0765, -3.5629022) to (3.331551, 2.0765, 2.1107209) -10 -6.295719 -3.9240162 -6.7329097 42 0.3228574 0.0 0.0 27 0.0 0.3270014 0.0 37 0.0 0.0 0.315341 6 6.0 0.0 0.0 -1.2322642 8 8.0 0.0 0.0 -3.520375 6 6.0 2.416227 0.0 0.3037184 1 1.0 2.4853716 1.6563448 1.5109056 1 1.0 4.0280476 0.0 -0.94921017 1 1.0 2.4853716 -1.6563448 1.5109056 6 6.0 -2.416227 0.0 0.3037184 1 1.0 -2.4853716 1.6563448 1.5109056 1 1.0 -2.4853716 -1.6563448 1.5109056 1 1.0 -4.0280476 0.0 -0.94921017 -1 35 90 35 90 Jmol voxel format version 0.9f # # isosurface delete resolution 6 solvent map mep translucent 0.0 4263 4908 4908 -0.08689388 0.044563316 -0.08689388 0.044563316 snip mlnmmmllmnkllmopqrrqpkklnprsrsrrrqokkkllnprqqpnjkkkqqojkkqojkkqokkkklqqpnkkllnnpprrrqrqokllmopsqsrrrrqpllmnsssrmnprssssrkmoqstttsrqkmoqstttsrqkmoqstttsrqmnprssssrsssr #-------end of jvxl file data------- Script completed Jmol script terminated All the best Nick --  WWW Pages:     http://www.liv.ac.uk/Chemistrywww/Staff/greeves.html Tel:             +44 (0)151-794-3506 (3500 secretary) On 5 Oct 2006, at 16:03, [EMAIL PROTECTED] wrote: Message: 5 Date: Wed, 4 Oct 2006 10:51:29 -0400 From: Frieda Reichsman <[EMAIL PROTECTED]> Subject: Re: [Jmol-users] surfaces and JVXL files To: jmol-users@lists.sourceforge.net Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="us-ascii" Long delayed response on this thread... Frieda wrote: I am getting only very partial surfaces on e.g., 1mbo.pdb (myoglobin) and on other pdb files as well. Is there something more to it than just opening the file, selecting protein, and issuing the command? Bob Hanson wrote: The problem is those water molecules. Yes, we need a new option. This is to ignore a certain set of atoms, in this case the   water molecules. Here you go, just uploaded: isosurface ignore(solvent) sasurface This tells Jmol you don't want the surface around the water molecules. OK, I have now tested this on 10.9.70 and it works as advertised - I   get a complete surface on the protein instead of a fragmented one. Yay! Further question: on your test page when you issue this command, the   resulting surface has rounded "bumps". When I do it locally, the   surface is "pointy" instead of rounded. You are using a cif file on   the test site and I am using a pdb file. Is this a difference between   Jmol handling of cif and pdb files? Or ?? Problem with JVXL data on Mac OSX: I cannot copy the contents of the   Jmol script console to the clipboard. Therefore when I say show isosurface to get the JVXL data, I can see them but have no way to get them from   the Jmol console into a file for later use. This is true for the app   and the applet. I seem to recall that this is due to a problem with Apple's   implementation of Java, and that on a Win machine you can copy/paste   from/to the Jmol console. Any ideas on how to get around this problem   on a Mac? (Note that on Mac OSX you can copy from the Jmol Console and paste   into the Jmol Console - but not between apps). Bob Hanson wrote:  I'd be very interested in knowing how other programs handle this. The program I can comment on for handling of surfaces is Chime. I   recall that Chime ignored whatever was not selected when calculating   a surface. I find that more intuitive - "just put a surface around   whatever is selected" but perhaps there are reasons for using ignore  () instead. In any case I am very glad to have surfaces implemented! Frieda /////////////////////////////////////////// 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
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users