Re: [Jmol-users] Color maps for bonds

As I said, the version of jmol I am running is the 14.6.3 of 2016-09-18. I ran your script again using the cafeine molecule loaded directly from jmol (File -> Get MOL), and, in this case, all bonds are colored as expected. However, the same script has no effect when I run it over my xyz file. I

Re: [Jmol-users] Color maps for bonds

Hi Bob, The problem that still persist is how to use the values bond lengths to assign the colors for each bond. I included a new variable to get the bond length inside the for loop: y=x.bonds.length. However, I think the variable colors[ ] just accept integer values, right? So, one possibility

Re: [Jmol-users] Color maps for bonds

ps - I forgot to mention that this bond set syntax [{...}] makes it unnecessary to use BOND in the select command: select [{2}] selects the third bond in the model. On Tue, Jan 17, 2017 at 7:32 PM, Robert Hanson wrote: > If you know the ordering in the file, you can

Re: [Jmol-users] Color maps for bonds

Hi Bob, Thank for the tips. I tried to run your script right now, but something seems to be wrong with the color assignment. Jmol is returning the following error message: script ERROR: invalid argument color bonds "" for ( var i = { all } . bonds . count ; -- i

Re: [Jmol-users] Color maps for bonds

What version of Jmol are you running? Should be no problem running that exact script. Just did it again now. On Wed, Jan 18, 2017 at 11:44 AM, Max Pinheiro Jr wrote: > Hi Bob, > > Thank for the tips. I tried to run your script right now, but something > seems to be wrong