From: Roni G. <ron...@ut...> - 2010-06-01 11:12:01
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Hello, I'm trying to show the "shrink-wrapped" surface of a ligand in Jmol -- but it appears that "isosurface" will simply render the portion of the complete (i.e. all loaded models) solvent-accessible surface. For a partially buried ligand, this breaks the surface noticeably. "geoSurface" seems to be a close approximation, but it renders as "spacefill", and turns into "dots" during rotation. Is there an option to only consider the requested {atom-expression} when calculating the surface -- that is, as though no other atoms are present? Thanks, Roni |
From: Robert H. <ha...@st...> - 2010-06-01 11:33:52
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Check the documentation regarding the isosurface command and the options SELECT and IGNORE. Some combination of those two will do exactly what you want. If you use SASURFACE and you want the same scale as geosurface or dots or spacefill, be sure to use SASURFACE 0. Some reason not to just use spacefill? Or are you already using that within a translucent surface? I should probably remove the geosurface-dots motion business. It's not a much-used shape, and I'm not sure it makes any real difference in rendering speed. Bob On Tue, Jun 1, 2010 at 5:45 AM, Roni Gordon <ron...@ut...> wrote: > Hello, > > I'm trying to show the "shrink-wrapped" surface of a ligand in Jmol > -- but it appears that "isosurface" will simply render the portion of > the complete (i.e. all loaded models) solvent-accessible > surface. For a partially buried ligand, this breaks the surface > noticeably. "geoSurface" seems to be a close approximation, but it > renders as "spacefill", and turns into "dots" during rotation. > > Is there an option to only consider the requested {atom-expression} > when calculating the surface -- that is, as though no other atoms are > present? > > Thanks, > > Roni > > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > 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 |
From: Aya <ae...@ii...> - 2011-01-17 01:59:53
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Hello there! I am having a hard time making solvent/molecular/sasurface generate closed surfaces for the molecules I'm working with. I have even tried the following: isoSurface surf1 select(selectedAtoms) ignore(not selectedAtoms) molecular /solvent/sasurface; Which is better, but still pretty 'holy'. Geosurface is Perfect! Closed surfaces and fast rendering. However, there is no ID set for the geosurface, and when I add a new surface, the color of the previously generated geosurface defaults to the color of the atoms. I'd like to add and remove these surfaces as the user pleases. Do you think there is a way around this? A way I could write a script to define a unique identifier for a geosurface? Or a new way to use the isosurface? Or perhaps something else? Thank you kindly! Aya |
From: Robert H. <ha...@st...> - 2011-01-17 04:05:18
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Aya, what version of Jmol are you using? The equivalent of geosurface would be isosurface vanderwaals (with the desired select/ignore) Those should be closed surfaces.... Send an example, please. Bob On Sun, Jan 16, 2011 at 7:59 PM, Aya <ae...@ii...> wrote: > Hello there! > > I am having a hard time making solvent/molecular/sasurface generate closed > surfaces for the molecules I'm working with. I have even tried the > following: > > isoSurface surf1 select(selectedAtoms) ignore(not selectedAtoms) molecular > /solvent/sasurface; > > Which is better, but still pretty 'holy'. Geosurface is Perfect! Closed > surfaces and fast rendering. However, there is no ID set for the > geosurface, and when I add a new surface, the color of the previously > generated geosurface defaults to the color of the atoms. I'd like to add > and remove these surfaces as the user pleases. > > Do you think there is a way around this? A way I could write a script to > define a unique identifier for a geosurface? Or a new way to use the > isosurface? Or perhaps something else? > > Thank you kindly! > Aya > > > ------------------------------------------------------------------------------ > Protect Your Site and Customers from Malware Attacks > Learn about various malware tactics and how to avoid them. Understand > malware threats, the impact they can have on your business, and how you > can protect your company and customers by using code signing. > http://p.sf.net/sfu/oracle-sfdevnl > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > 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 |
From: Robert H. <ha...@st...> - 2011-01-17 03:50:49
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If the molecule is big, you may be just running into the problem that the resolution is low, because it is adjusted by default for 80x80x80 points. You could try RESOLUTION 1.0 as a parameter. On Sun, Jan 16, 2011 at 9:40 PM, Robert Hanson <ha...@st...> wrote: > Aya, what version of Jmol are you using? The equivalent of > > geosurface > > would be > > isosurface vanderwaals > > (with the desired select/ignore) > > Those should be closed surfaces.... Send an example, please. > > Bob > > On Sun, Jan 16, 2011 at 7:59 PM, Aya <ae...@ii...> wrote: > >> Hello there! >> >> I am having a hard time making solvent/molecular/sasurface generate closed >> surfaces for the molecules I'm working with. I have even tried the >> following: >> >> isoSurface surf1 select(selectedAtoms) ignore(not selectedAtoms) >> molecular/solvent/sasurface; >> >> Which is better, but still pretty 'holy'. Geosurface is Perfect! Closed >> surfaces and fast rendering. However, there is no ID set for the >> geosurface, and when I add a new surface, the color of the previously >> generated geosurface defaults to the color of the atoms. I'd like to add >> and remove these surfaces as the user pleases. >> >> Do you think there is a way around this? A way I could write a script to >> define a unique identifier for a geosurface? Or a new way to use the >> isosurface? Or perhaps something else? >> >> Thank you kindly! >> Aya >> >> >> ------------------------------------------------------------------------------ >> Protect Your Site and Customers from Malware Attacks >> Learn about various malware tactics and how to avoid them. Understand >> malware threats, the impact they can have on your business, and how you >> can protect your company and customers by using code signing. >> http://p.sf.net/sfu/oracle-sfdevnl >> >> _______________________________________________ >> Jmol-users mailing list >> Jmo...@li... >> 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 |