[Jmol-users] SMILES

Bob, A while back you modified Jmol SMILES and COMPARE so that coordination compounds involving square planar and octahedral would generate SMILES that could me distinguished by Jmol compare. This all works quite well, there is an interesting exception. If you use our square planar template

Re: [Jmol-users] SMILES

Same thing with CH2Cl2. I think there's a special exception for H. I could look into that. Sent from my stupid iphone On May 20, 2012, at 3:52 PM, Otis Rothenberger osrot...@chemagic.com wrote: Bob, A while back you modified Jmol SMILES and COMPARE so that coordination compounds

[Jmol-users] write broken in 12.0, 12.2, 12.3?

Dear Bob, I cannot write PDB files from 12.3.25, 12.2.25, or 12.0.31. I can write from 11.8.24 but there I cannot compare. $ write x.pdb script ERROR: write x.pdb Thanks, -Eric -- Live Security

[Jmol-users] compare broken in 12.2, 12.3?

Dear Bob, I cannot get compare to work in 12.3.25 or 12.2.25. Compare works in 12.0.31, but then I cannot write out the aligned PDB result! script ERROR: invalid argument line 19 command 20 of something.spt: compare { 2.1 } { 1.1 } subset { *.ca } rotate translate Thanks,

[Jmol-users] java in Safari in OS X Leopard 10.5

Apple has just (belatedly) released, for OS X 10.5 Leopard, the fix for most variants of the Flashback virus. Fixes for 10.6 and 10.7 were released some time ago. These fixes are part of regular Apple Software Updates. Luckily I read the fine print: The fix for 10.5 disables java in Safari,

Re: [Jmol-users] write broken in 12.0, 12.2, 12.3?

$ write x.pdb OK 2778 bytes C:/jmol-dev/bobtest/x.pdb Maybe it's something special with that particular PDB file? On Sun, May 20, 2012 at 8:47 PM, Eric Martz ema...@microbio.umass.eduwrote: Dear Bob, I cannot write PDB files from 12.3.25, 12.2.25, or 12.0.31. I can write from 11.8.24 but

Re: [Jmol-users] compare broken in 12.2, 12.3?

what in the world happened to your version, Eric? Try that same thing at http://chemapps.stolaf.edu/jmol/docs/examples-12/simple.htm and see if there's the same problem. You can drag/drop PDB or JMOL files into that if you want. On Sun, May 20, 2012 at 8:48 PM, Eric Martz

[Jmol-users] invitation to talk

You're invited. I don't know exactly when on Thursday or where, but sometime Thursday. My guess is 4 PM. Visualization of periodic crystalline structure and wave functions using Jmol This presentation, by the current principal developer of Jmol ( http://jmol.sourceforge.net), will focus on

Re: [Jmol-users] compare broken in 12.2, 12.3?

Dear Bob, The following is in a fresh start of 12.0.31: $ load 1a4f.pdb $ cartoon only $ color chain $ compare {:a} {:b} subset {*.ca} rotate translate RMSD 8.78 -- 2.32 Angstroms $ zap $ load 1a4f.pdb $ load append 1a4f.pdb 2 models $ cartoon only $ color chain $ compare {2.1} {1.1} subset

Re: [Jmol-users] write broken in 12.0, 12.2, 12.3?

Dear Bob, If I simply start Jmol 12.2.25 and then drag in a script containing the following single command cd $SCRIPT_PATH$ afterwards the write command no longer works. On the other hand if I execute cd /full_path (to the same path) write still works, whether I paste the command