Excellent, many thanks Bob! Dave
2009/9/3 Robert Hanson <[email protected]>: > Jmol 11.9.2 (http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip) > introduces a calculation for molecular volume. This calculation depends > upon what set of Van Der Waals radii one uses. "type" can be one of "Jmol", > "Babel", "Rasmol" or "User". If not provided, "type" defaults to the default > type specified by the command <b>set defaultVanDerWaal</b>. The calculation > is a simple one that just adds up all the Van Der Waals volumes and > subtracts off the overlap of spheres associated with bonds as described by > A. Bondi (<b>J. Phys. Chem. 68, 1964, 441-451.</b>). The built-in Van der > Waals set "Babel" most closely represents this setting. > > load c6h6.smol;set defaultVDW babel; > print "" + {1.1}.volume() > print "" + {1.1}.volume("Babel") > print "" + {1.1}.volume("Jmol")' > print "" + {1.1}.volume("Rasmol") > > see also http://cehmapps.stolaf.edu/jmol/docs/examples-11/new.htm > > > Bob > > > > 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
