From: Bob H. <ha...@st...> - 2006-05-25 06:30:32
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Are these going in as t Aidan Heerdegen wrote: > > [I am resending this message as it hasn't appeared on the list yet, > apologies if you get two copies] > > Re: Unable to make bonds between models (frames) > >> This is a feature. You cannot connect two atoms in different frames. >> Each frame is a separate model, and bonds are part of models, so it >> gets way too >> messy to consider bonds between models. > > > As I thought. I use this feature, I just wasn't sure if it was possible > to *force* Jmol to make bonds between frames. It's not. I'm fine with that. > >> Solution #1: >> >> You can set up measurements between frames, and if you turn off the >> numbers, then it looks a lot like what you are asking for. > > > Sounds fine. I might even want the numbers, but I can't get it to work > with 10.2.0, the trunk version via subversion or your branches/bob200603 > version. I can make a measurement between atoms in the same frame, but > different frames, no dice. > > I use syntax like this: > > measure 1.0 20.0 (atomno=1 and model=1) (atomono=30 and model=1) > #worked in bob200603 > measure 1.0 20.0 (atomno=1 and model=1) (atomono=30 and model=2) > #didn't work in bob200603 > OK, I consider that a bug, since you can do it by clicking on atoms. It is fixed now. In the latest version at http://www.stolaf.edu/people/hansonr/jmol/test/proto that works. Just be sure in each set you are selecting ONE specific atom -- as you are. If you were to do measure all (atomno=1) (atomno=2) then it will only draw lines between atom 1 and atom 2 in each model independently. But if you do measure (atomno=1 and */1) (atomno=2 and */2) then you will get a line, because each of these specifies a SINGLE atom -- thus not ambiguous and clearly what someone wants. > And yes, there are four frames. I can do this: > > select (atomno=1 and model=1), (atomono=30 and model=2) > color yellow > > and see the two atoms coloured appropriately. So no problems with my > selection syntax. > >> Solution #2: >> >> In addition, you can (in 10.x) draw lines that look a lot like bonds >> between any >> two atoms, regardless of their frame. But I don't think that's the >> best solution. > > > I don't know, that sounds pretty good to me. I'd like to colour them for > identification, turn them on and off etc. What is this new feature > called? Is this in the bob200603 branch? I'm wrong. You can't do that right now with draw objects -- they are model specific. draw [idname] [magnitude_percent] [starting point] [ending point] e.g. draw myline 100 (atomno=1) (atomno=30) color $myline translucent red > >> Solution #3: >> >> Put them all in one file, turn autobonding off, load the file, use >> connect, perhaps: >> >> connect 1.0 1.5 (atomno<=30) (atomno<=30) >> connect 1.0 1.5 (atomno>30) (atomno>30) >> >> (that will take some experimentation) >> >> and whatever additional connections you want between the sets. > > > Yes, I am sure that would work. I'm not sure I want to do it that way if > there is an alternative. > > This sort of brings me back to the mol2 format question. I have all my > molecules in mol2 format, with all the bonding already sorted out. If I > (or someone else) wrote a mol2 format parser, is the default behavour in > Jmol to respect the bonding information contained in a file, or would > autobonding be turned on by default? > > Thanks for your suggestions by the way, and for all the work by yourself > and the Jmol developers. > > Cheerio > > Aidan > > > > ------------------------------------------------------- > All the advantages of Linux Managed Hosting--Without the Cost and Risk! > Fully trained technicians. The highest number of Red Hat certifications in > the hosting industry. Fanatical Support. Click to learn more > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=107521&bid=248729&dat=121642 > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users -- -- Robert M. Hanson, ha...@st..., 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:ha...@st... http://www.stolaf.edu/people/hansonr "Imagination is more important than knowledge." - Albert Einstein |