[Jmol-users] Jmol 14.3.12_2015.02.22

http://chemapps.stolaf.edu/jmol/zip/jmol-14.3.12_2015.02.22.zip Jmol.___JmolVersion=14.3.12_2015.02.22 bug fix: minimizer treats hydrogen bonds as covalent single bonds new feature: Windows BMP image reading -- reads 24-bit (full color) as well as 16-, 8-, 4-, 2-, and 1-bit color palette modes

Re: [Jmol-users] bugs(?) in Jmol Feb18

The design was to not allow SMILES of biomolecules because of how huge they are. But it seems reasonable to relax that. On Sat, Feb 21, 2015 at 4:07 PM, Eric Martz ema...@microbio.umass.edu wrote: Dear Bob, Tested in Jmol application 14.3.12_2015.02.18 # item 1-- load

[Jmol-users] defined groups

There is a very nice list of defined groups: http://chemapps.stolaf.edu/jmol/docs/misc/groups.txt. My question is about the ether group specifically: define ~etherO oxygen and connected(2,carbon) and not ~carbonylO define ~ROR ~etherO Is it possible to make the definition more specific?

Re: [Jmol-users] defined groups

This is exactly what SMARTS is for: select within(SMARTS,O1CC1) #or for just the O: select within(SMARTS,[Or3]) #or use { } to select specific atoms: select within(SMARTS,{O}1CC1) #specifically select ether O next to a CH2: select within(SMARTS,C{O}[CH2]) #or the C of the CH2 (not the Hs):

Re: [Jmol-users] defined groups

ps - there is information about Jmol and SMARTS here: [1] http://chemapps.stolaf.edu/jmol/docs/?search=SMARTS#jmolsmarts/smiles A full discussion of Jmol SMARTS notation is at [2] sourceforge.net/p/jmol/code/HEAD/tree/trunk/Jmol/src/org/jmol/smiles/package.html?format=raw The key is that