From: Daniel A. <aio...@gm...> - 2012-06-30 18:29:06
Attachments:
drgfin_GMX.pqr
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I'm creating the sasurface of a set of atoms of the attached molecule like this: load 'drgfin_GMX.pqr'; select 1.OAF, 1.HAH, 1.OAA, 1.HAA, 1.OAB, 1.HAB; isosurface sasurface 1.4 map 'map.dx' translucent .3; zoom 40; Analysing the created isosurface I noticed that vertex number 2659 (indexed from zero) is not used by any of the triangles. I'm extracting the data via the Java API: viewer.getProperty("java", "isosurfaceInfo", null); Is it expected to get unused vertices from time to time from the calculated surface, or is it possibly indicative of a potential problem in the surface calculation routine? |
From: Robert H. <ha...@st...> - 2012-07-02 19:06:57
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I would check the bounds of map.dx to make sure it really spans the entire molecule. If a surface point is outside the range of mapped data, then this could happen because the value will be introduced as "NaN" Q: What does it look like at that vertex? You can use DRAW to show a dot at that point in order to find it. Is there a hole there as well? Q: What is the value at that vertex point? On Sat, Jun 30, 2012 at 1:28 PM, Daniel Aioanei <aio...@gm...> wrote: > I'm creating the sasurface of a set of atoms of the attached molecule like > this: > > load 'drgfin_GMX.pqr'; select 1.OAF, 1.HAH, 1.OAA, 1.HAA, 1.OAB, > 1.HAB; isosurface sasurface 1.4 map 'map.dx' translucent .3; zoom 40; > > Analysing the created isosurface I noticed that vertex number 2659 > (indexed from zero) is not used by any of the triangles. I'm > extracting the data via the Java API: viewer.getProperty("java", > "isosurfaceInfo", null); > > Is it expected to get unused vertices from time to time from the > calculated surface, or is it possibly indicative of a potential > problem in the surface calculation routine? > > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Jmol-users mailing list > Jmo...@li... > https://lists.sourceforge.net/lists/listinfo/jmol-users > > -- Robert M. Hanson Larson-Anderson Professor of Chemistry Chair, Chemistry Department 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 |