Hens Borkent just pointed out to me that it should be 'chemapps' in the url, that's all. How slow I am.
Dave 2009/9/4 N David Brown <[email protected]>: >> see also http://cehmapps.stolaf.edu/jmol/docs/examples-11/new.htm > > Bob, just so you know: as far as I'm aware, that URL hasn't worked > since you emailed it to us. > > Could you possibly let me know where in the code the new stuff is? I'm > interested to look at the code. > > Many thanks again for such a fast implementation :) > > Dave > > >> On Wed, Sep 2, 2009 at 7:10 PM, Robert Hanson <[email protected]> wrote: >>> >>> Dave, attached is a final script for you. Just run it, and after that you >>> can run >>> >>> print calcVolume() >>> >>> for any structure you load. Needs testing. >>> >>> Bob >>> >>> >>> On Wed, Sep 2, 2009 at 3:09 PM, Robert Hanson <[email protected]> wrote: >>>> >>>> Sorry, I shouldn't have been so critical. Table 3 has some pretty major >>>> differences for aromatics. In the paper they describe multiple >>>> approximation >>>> methods and then point out that different programs that do the actual >>>> molecular volume calculation (as Jmol is doing) produce different results. >>>> They hypothesize that these different results are due to different settings >>>> for VDW radii without really checking it out. When they reparameterize they >>>> get better results, but as far as I can tell it is totally ad hoc. >>>> >>>> I would say that Jmol, when loaded with the same VDW radii using, for >>>> example: >>>> >>>> load xxxxx.mol >>>> {carbon}.vdw = 1.7 >>>> {oxygen}.vdw = 1.52 >>>> >>>> gives the same result as their MacroModel values (Tran). I don't see any >>>> point in comparing values to "TSAR" program without first asking for what >>>> they use for VDW radii -- if any program is giving different values, that's >>>> almost certainly all there is to it. >>>> >>>> I only have a few of these models on hand, but here is what I get: >>>> >>>> >>>> compound Bindi Abraham Jmol (isosurface >>>> volume resolution 20 sasurface 0) >>>> >>>> benzene 80.3 95.9 82.7 >>>> chloromethane 42.0 41.1 42.3 >>>> cyclohexane 102.0 103.8 101.7 >>>> testosterone 292.7 309.4 293.6 >>>> (resolution 15) >>>> >>>> So, except for the aromatics, that's pretty good. I apologize! >>>> >>>> OK, so the benefit of the calculation they do is that you don't need a >>>> structure. Just a molecular formula and some knowledge about the number of >>>> aromatic rings. With Jmol, we have structures. So the first thing I would >>>> say is that there's little point in approximating this way; we can do >>>> better. Obviously it shouldn't take an isosurface calculation to do this. I >>>> think you could get an exact value using a simple Jmol script. It's just a >>>> simple analytical calculation. >>>> >>>> Let me see if I can write that.... >>>> >>>> >>>> Bob >>>> >>>> >>>> >>>> On Wed, Sep 2, 2009 at 2:25 PM, N David Brown <[email protected]> >>>> wrote: >>>>> >>>>> 10-20%? Where's that from, Bob? >>>>> >>>>> Egon, there are two sets of values compared; one is TSAR, a QSAR >>>>> package (I'm just quoting here). The other is values from MacroModel. >>>>> Example values are methanol is approximated to 35 instead of 37, while >>>>> N((CH2)3CH3)4BPh4 is 592 vs 609. That latter value is the max >>>>> difference listed for the MacroModel program. >>>>> >>>>> David >>>>> >>>>> >>>>> >>>>> 2009/9/2 Robert Hanson <[email protected]>: >>>>> > Sorry, it just seems to me that 10-20% error is not very good for such >>>>> > a >>>>> > simple calculation. (Just comparing their two methods.) I think these >>>>> > people back in 2003 just didn't have suitable resources. It's not like >>>>> > it's >>>>> > that difficult a calculation, but it is true that without the right >>>>> > tools, >>>>> > you do have a problem. But I realize now that I didn't match my VDW >>>>> > radii >>>>> > with theirs. (I'll reply to Angel in a minute.) Maybe you can check >>>>> > some of >>>>> > this out and get back to us?. >>>>> > >>>>> > Wed, Sep 2, 2009 at 1:11 PM, N David Brown <[email protected]> >>>>> > wrote: >>>>> >> >>>>> >> Given the 677 compounds tested and the proximity to the TSAR values, >>>>> >> I >>>>> >> think that's an odd comment. It's an approximation, true, but for the >>>>> >> drop in computational cost I find the accuracy astounding. >>>>> >> >>>>> >> Thanks for the isosurface command I requested. >>>>> >> >>>>> >> >>>>> >> 2009/9/2 Robert Hanson <[email protected]>: >>>>> >> > So I read that JOC article... I think both their methods are crap. >>>>> >> > Jmol >>>>> >> > should be doing a much better job because it is the ACTUAL area, >>>>> >> > not >>>>> >> > some >>>>> >> > (gross) approximation. >>>>> >> > >>>>> >> > Bob >>>>> >> > >>>>> >> > >>>>> >> > On Wed, Sep 2, 2009 at 10:58 AM, Robert Hanson <[email protected]> >>>>> >> > wrote: >>>>> >> >> >>>>> >> >> Using Jmol 11.8: >>>>> >> >> >>>>> >> >> isosurface volume sasurface 0 >>>>> >> >> >>>>> >> >> should do it. You might have to increase the resolution for good >>>>> >> >> results: >>>>> >> >> >>>>> >> >> isosurface resolution 10 volume sasurface 0 >>>>> >> >> >>>>> >> >> keep increasing the number until you are satisfied. >>>>> >> >> >>>>> >> >> I'll also check that reference. Maybe we can implement that. >>>>> >> >> >>>>> >> >> Bob >>>>> >> >> >>>>> >> >> >>>>> >> >> On Wed, Sep 2, 2009 at 10:10 AM, N David Brown >>>>> >> >> <[email protected]> >>>>> >> >> wrote: >>>>> >> >>> >>>>> >> >>> Ok, thanks for the info, Angel :o) >>>>> >> >>> >>>>> >> >>> Bob, clarification please? >>>>> >> >>> >>>>> >> >>> I've just found an intriguing paper indeed, "Fast calculation of >>>>> >> >>> van >>>>> >> >>> der Waals volume as a sum of atomic bond contributions and its >>>>> >> >>> application to drug compounds" by Zhao, Abraham and Zissimos (J. >>>>> >> >>> Org. >>>>> >> >>> Chem. 2003, 68, 7368-7373). They describe a method of calculating >>>>> >> >>> the >>>>> >> >>> vdW volume using utterly trivial maths - so simple they actually >>>>> >> >>> test >>>>> >> >>> it in an Excel spreadsheet! Incredibly it seems to work to a high >>>>> >> >>> accuracy; examples they provide show deviation from the >>>>> >> >>> MacroModel >>>>> >> >>> calc'd value (the long but accurate calculation method) of at >>>>> >> >>> most ~19 >>>>> >> >>> Angstroms. Very happy they've discovered this! >>>>> >> >>> >>>>> >> >>> David >>>>> >> >>> >>>>> >> >>> >>>>> >> >>> >>>>> >> >>> 2009/9/2 Angel Herráez <[email protected]>: >>>>> >> >>> > David, I remebmer reading of a recent feature in Jmol that >>>>> >> >>> > offers >>>>> >> >>> > the >>>>> >> >>> > volume inside an isosurface. Maybe that can be extended or >>>>> >> >>> > matched >>>>> >> >>> > to >>>>> >> >>> > a vdW surface (there are many options in the isosurface >>>>> >> >>> > command) >>>>> >> >>> > >>>>> >> >>> > Surely Bob will tell you, but you can follow that line --and >>>>> >> >>> > let us >>>>> >> >>> > know :-) >>>>> >> >>> > >>>>> >> >>> > >>>>> >> >>> >>>>> >> >>> >>>>> >> >>> >>>>> >> >>> >>>>> >> >>> ------------------------------------------------------------------------------ >>>>> >> >>> Let Crystal Reports handle the reporting - Free Crystal Reports >>>>> >> >>> 2008 >>>>> >> >>> 30-Day >>>>> >> >>> trial. Simplify your report design, integration and deployment - >>>>> >> >>> and >>>>> >> >>> focus on >>>>> >> >>> what you do best, core application coding. Discover what's new >>>>> >> >>> with >>>>> >> >>> Crystal Reports now. http://p.sf.net/sfu/bobj-july >>>>> >> >>> _______________________________________________ >>>>> >> >>> Jmol-users mailing list >>>>> >> >>> [email protected] >>>>> >> >>> https://lists.sourceforge.net/lists/listinfo/jmol-users >>>>> >> >> >>>>> >> >> >>>>> >> >> >>>>> >> >> -- >>>>> >> >> Robert M. Hanson >>>>> >> >> Professor of Chemistry >>>>> >> >> St. Olaf College >>>>> >> >> 1520 St. Olaf Ave. >>>>> >> >> Northfield, MN 55057 >>>>> >> >> http://www.stolaf.edu/people/hansonr >>>>> >> >> phone: 507-786-3107 >>>>> >> >> >>>>> >> >> >>>>> >> >> If nature does not answer first what we want, >>>>> >> >> it is better to take what answer we get. >>>>> >> >> >>>>> >> >> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >>>>> >> > >>>>> >> > >>>>> >> > >>>>> >> > -- >>>>> >> > Robert M. Hanson >>>>> >> > Professor of Chemistry >>>>> >> > St. Olaf College >>>>> >> > 1520 St. Olaf Ave. >>>>> >> > Northfield, MN 55057 >>>>> >> > http://www.stolaf.edu/people/hansonr >>>>> >> > phone: 507-786-3107 >>>>> >> > >>>>> >> > >>>>> >> > If nature does not answer first what we want, >>>>> >> > it is better to take what answer we get. >>>>> >> > >>>>> >> > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >>>>> >> > >>>>> > >>>>> > >>>>> > >>>>> > -- >>>>> > Robert M. Hanson >>>>> > Professor of Chemistry >>>>> > St. Olaf College >>>>> > 1520 St. Olaf Ave. >>>>> > Northfield, MN 55057 >>>>> > http://www.stolaf.edu/people/hansonr >>>>> > phone: 507-786-3107 >>>>> > >>>>> > >>>>> > If nature does not answer first what we want, >>>>> > it is better to take what answer we get. >>>>> > >>>>> > -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >>>>> > >>>> >>>> >>>> >>>> -- >>>> Robert M. Hanson >>>> Professor of Chemistry >>>> St. Olaf College >>>> 1520 St. Olaf Ave. >>>> Northfield, MN 55057 >>>> http://www.stolaf.edu/people/hansonr >>>> phone: 507-786-3107 >>>> >>>> >>>> If nature does not answer first what we want, >>>> it is better to take what answer we get. >>>> >>>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >>> >>> >>> >>> -- >>> Robert M. Hanson >>> Professor of Chemistry >>> St. Olaf College >>> 1520 St. Olaf Ave. >>> Northfield, MN 55057 >>> http://www.stolaf.edu/people/hansonr >>> phone: 507-786-3107 >>> >>> >>> If nature does not answer first what we want, >>> it is better to take what answer we get. >>> >>> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >> >> >> >> -- >> Robert M. Hanson >> Professor of Chemistry >> St. Olaf College >> 1520 St. Olaf Ave. >> Northfield, MN 55057 >> http://www.stolaf.edu/people/hansonr >> phone: 507-786-3107 >> >> >> If nature does not answer first what we want, >> it is better to take what answer we get. >> >> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 >> > ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
