From: Patrick J. C. <car...@sa...> - 2008-02-29 15:02:50
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I remember a discussion a couple years ago about the van der Waal's radii used in Jmol. There was a feeling that the values in Jmol are somewhat "over-estimated". Is there a way that a user can input his own radii? (other than using the explcit "spacefill 1.70" every time he wants to draw a van der Waals carbon atom). Or, alternatively, can the values in JmolConstants.jave be changed to those in, e.g., A. Bondi, J. Phys. Chem, vol.68, p.441 (1964) - which, I think, are widely accepted. Pat Carroll U of Penn Phila, PA |
From: Angel H. <ang...@ua...> - 2008-02-29 15:41:29
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As far as I remember, when Bob added support to read PQR files, I saw that the radii values in the file were used by Jmol instead of the default ones, so there surely is a way. I bet there is a radius propperty for each atom that can be changed via script. |
From: Bob H. <ha...@st...> - 2008-02-29 18:18:56
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Angel Herraez wrote: >As far as I remember, when Bob added support to read PQR files, I saw >that the radii values in the file were used by Jmol instead of the >default ones, so there surely is a way. >I bet there is a radius propperty for each atom that can be changed >via script. > > > But these are not the values used by the SPACEFILL command. That command uses the original values. (That could be changed.) >------------------------------------------------------------------------- >This SF.net email is sponsored by: Microsoft >Defy all challenges. Microsoft(R) Visual Studio 2008. >http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 |
From: P.J. C. <car...@sa...> - 2008-03-02 22:37:48
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Bob, That new feature in 11.5.12 that allows different default VDW radii does the trick! Thank you, Pat |
From: Bob H. <ha...@st...> - 2008-02-29 17:59:22
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Pat, VDW radii are used for many things, not just spacefill. So I'm reticent to do any global change to any of these numbers. But, yes, that's an issue. Let's discuss it again. The Jmol code comments state that the values used are from OpenBabel. However, when I look at openbabel-2.1.1/data/element.txt, that's not what I see. So I don't know what that is about. First, Jmol is not using the VDW radii from OpenBabel. Second, some are larger, some smaller; they aren't "generally larger" or "generally smaller". I've also compared Jmol's values to openRasmol. Here's the comparison of these three packages: http://jmol.svn.sourceforge.net/viewvc/*checkout*/jmol/trunk/Jmol/src/org/jmol/_documents/vdw_comparison.xls Options include: a) include one or more optional sets of VDW radii b) include the option for the user to set individual VDW radii c) leave as is -- just defining the spacefill as you suggest, one element at a time Bob Patrick J. Carroll wrote: >I remember a discussion a couple years ago about the van der Waal's radii used >in Jmol. There was a feeling that the values in Jmol are somewhat >"over-estimated". Is there a way that a user can input his own radii? (other >than using the explcit "spacefill 1.70" every time he wants to draw a van der >Waals carbon atom). Or, alternatively, can the values in JmolConstants.jave be >changed to those in, e.g., A. Bondi, J. Phys. Chem, vol.68, p.441 (1964) - >which, I think, are widely accepted. > > >Pat Carroll >U of Penn >Phila, PA > > >------------------------------------------------------------------------- >This SF.net email is sponsored by: Microsoft >Defy all challenges. Microsoft(R) Visual Studio 2008. >http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 |
From: Rich <rg...@el...> - 2008-03-01 13:29:37
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On 29-2-2008 12:59, Bob Hanson wrote: > Pat, > > VDW radii are used for many things, not just spacefill. So I'm reticent > to do any global change to any of these numbers. But, yes, that's an > issue. Let's discuss it again. > > [snip] > Options include: > a) include one or more optional sets of VDW radii > b) include the option for the user to set individual VDW radii > c) leave as is -- just defining the spacefill as you suggest, one > element at a time > > > >> I vote for a, b and part of c. >> Put the openbabel and the Bondi values in as available sets. Allow the user to specify a set either as a complete replacement for the defaults or just a partial overwrite of one of them. Still permit element by element definition. Rich >> > > > |
From: Bob H. <ha...@st...> - 2008-03-01 19:18:08
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Jmol development versions 11.5.8, 11.5.9, and 11.5.10 cannot save/restore states and should be considered nonfunctional. This is all fixed in 11.5.11, just released, takes care of this bug as well as a few others and also adds preliminary support for customizable VDW radii. Jmol 11.5.11 includes: # bug fix: save/restore of atom data incorrect when user has set propertyAtomNumberField or propertyDataField # bug fix: functions, save/restore state were disabled by bug in 1.5.8 # bug fix: command "test()" where test() is a user-defined function causes array-out-of-bounds error # bug fix: undocumented .vdw atom property was equivalent to .valence # bug fix: GAMESS reading of F orbital order incorrect new feature: user-settable Van der Waals radius -------------------------------------------------- Long ago, Jmol 11.2 introduced the capability of defining custom Van der Waals radii for atoms, but those only affected the production of isosurfaces. Jmol 11.5.11 adds "SPACEFILL ON" to this list of affected properties. So, for example, you can use: {carbon}.vanderwaals = 1.7 spacefill ON or you can use the DATA statement for multiple atoms at once: select *; DATA "property_vanderwaals" 1.7 1.7 1.6 1.3 1.3 1.5 END "property_vanderwaals" Jmol 11.5.12 will include:: # new feature: three optional defaults for default Van der Waals radii: # # set defaultVDW "jmol" # set defaultVDW "rasmol" # set defaultVDW "babel" # # These settings persist past file loading. # # For full state compatibility, these commands should be given prior to # model loading, as they affect all calculations involving Van der Waals # radii -- including default zoom. # # see src/_documents/vdw_comparison.xls Bob |
From: Bob H. <ha...@st...> - 2008-02-29 22:27:34
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Pat, I think the absurdly large spacefill radius for carbon was designed to mimic Rasmol (which in the version I have here puts it at about 1.85 A). The idea there, I think, is to account at least somewhat for the missing H atoms in PDB files. I could be wrong about that.... Patrick J. Carroll wrote: >I remember a discussion a couple years ago about the van der Waal's radii used >in Jmol. There was a feeling that the values in Jmol are somewhat >"over-estimated". Is there a way that a user can input his own radii? (other >than using the explcit "spacefill 1.70" every time he wants to draw a van der >Waals carbon atom). Or, alternatively, can the values in JmolConstants.jave be >changed to those in, e.g., A. Bondi, J. Phys. Chem, vol.68, p.441 (1964) - >which, I think, are widely accepted. > > >Pat Carroll >U of Penn >Phila, PA > > >------------------------------------------------------------------------- >This SF.net email is sponsored by: Microsoft >Defy all challenges. Microsoft(R) Visual Studio 2008. >http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 |
From: Bob H. <ha...@st...> - 2008-03-02 19:39:10
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Pat, Here's my initial solution, ready for testing in 11.5.12. It's a compromise between not changing Jmol enough to cause problems with compatibility and wanting to make it possible to have better control over Van der Waals radii. It involves several new capabilities: --Three internal lists: Jmol, Babel, and Rasmol. Any one of these three lists can be designated as the one for defining default vdw radii. These settings persist through file loading, like element colors. (They do not get reset with ZAP.) set defaultVDW Jmol set defaultVDW Babel set defaultVDW Rasmol --Users can also load their own list or modify these lists with selected values using the DATA command. The basis is always whatever list is currently set, then DATA "element_vdw" the following is user-defined data note that only numeric data are parsed so all these lines are ignored just don't put any numbers here! 1 1.0 //H 6 1.7 //C 7 1.6 //N END "element_vdw" set defaultVDW User or, more compactly, with semicolons: DATA "element_vdw" 1 1.0; 6 1.7; 7 1.6 END "element_vdw" set defaultVDW User --You can show these using show vdw # the current defaults show vdw Jmol show vdw Babel show vdw Rasmol show vdw User --Saving the state also saves user vdw information; you can check that to see just the specific values you have changed. --You can show individual atom vdw settings using LABEL %V --You can also directly set the vdw radius of any selected atom(s) to anything you want. This information is also saved in the state and can be displayed using "show state" {carbon}.vdw = 1.7 {atomno=2}.vdw = 1.8 --Note that {carbon}.vdw=1.7 is NOT persistent, because that just says, "select all the carbons and set their radius to 1.7", not "set elemental carbon vdw to always be 1.7" -- to do that you must use the DATA statement: DATA "element_vdw" 6 1.7 END "element_vdw" --If you do change values, you must do a SPACEFILL command again to incorporate these changes in the actual displayed model. In general, it is recommended that element-based settings be done prior to file loading. --The SPACEFILL, HALO and STAR commands now all have the same format. (They mostly did before, but this is better.) This format includes a way of indicating percentage of the vdw radius based on any of the four lists. star 100%Babel halo 50%Jmol spacefill 40% # of the current settings or specified atom radius stars 1.7 # 1.7 anstroms spacefill +1.2 # 1.2 angstroms larger than the current vdw defaults or specific atom settings stars @x%Babel # math is fully implemented (make sure x is an integer) stars @{x + 10}%Jmol # x must be an integer --Initial program defaults for file loading display atoms as spacefill 20%Jmol, as before. This is independent of what is the current defaultVDW setting. Initial zoom is based on the Jmol vdw list, again, regardless of the settings. --The DOTS, GEOSURFACE, and ISOSURFACE commands use whatever is the current default setting or whatever specific atom settings have been made. Seems to me that should be enough to at least get us started. Pat, it's amazing how bloated the Jmol setting for spacefill looks when you can switch back and forth. Hmm. Sure appreciate your pointing that out. Bob Patrick J. Carroll wrote: >I remember a discussion a couple years ago about the van der Waal's radii used >in Jmol. There was a feeling that the values in Jmol are somewhat >"over-estimated". Is there a way that a user can input his own radii? (other >than using the explcit "spacefill 1.70" every time he wants to draw a van der >Waals carbon atom). Or, alternatively, can the values in JmolConstants.jave be >changed to those in, e.g., A. Bondi, J. Phys. Chem, vol.68, p.441 (1964) - >which, I think, are widely accepted. > > >Pat Carroll >U of Penn >Phila, PA > > >------------------------------------------------------------------------- >This SF.net email is sponsored by: Microsoft >Defy all challenges. Microsoft(R) Visual Studio 2008. >http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >_______________________________________________ >Jmol-users mailing list >Jmo...@li... >https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 |