From: <ha...@us...> - 2010-11-12 14:15:20
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Revision: 14640 http://jmol.svn.sourceforge.net/jmol/?rev=14640&view=rev Author: hansonr Date: 2010-11-12 14:15:13 +0000 (Fri, 12 Nov 2010) Log Message: ----------- version=12.0.22_dev # bug fix: Ramachandran approximation of P straightness off by a few percent Modified Paths: -------------- branches/v12_0/Jmol/src/org/jmol/modelsetbio/AminoPolymer.java branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties Modified: branches/v12_0/Jmol/src/org/jmol/modelsetbio/AminoPolymer.java =================================================================== --- branches/v12_0/Jmol/src/org/jmol/modelsetbio/AminoPolymer.java 2010-11-12 14:11:09 UTC (rev 14639) +++ branches/v12_0/Jmol/src/org/jmol/modelsetbio/AminoPolymer.java 2010-11-12 14:15:13 UTC (rev 14640) @@ -157,7 +157,7 @@ * * where * - * cos(theta/2) = dq[i]\dq[i-1] = cos(dPsi/2)cos(dPhi/2) - sin(alpha)sin(dPsi/2)sin(dPhi/2) + * cos(theta/2) = dq[i]\dq[i-1] = cos(dPsi/2)cos(dPhi/2) - cos(alpha)sin(dPsi/2)sin(dPhi/2) * * and * @@ -168,8 +168,7 @@ float dPhi = (float) ((phiNext - phi) / 2 * Math.PI / 180); float dPsi = (float) ((psiNext - psi) / 2 * Math.PI / 180); return (float) (180 / Math.PI * 2 * Math.acos(Math.cos(dPsi) - * Math.cos(dPhi) - Math.cos(70 * Math.PI / 180) * Math.sin(dPsi) - * Math.sin(dPhi))); + * Math.cos(dPhi) - Math.sin(dPsi) * Math.sin(dPhi) / 3)); case 'c': case 'C': /* an approximation by Bob Hanson and Dan Kohler, 7/2008 Modified: branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties =================================================================== --- branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2010-11-12 14:11:09 UTC (rev 14639) +++ branches/v12_0/Jmol/src/org/jmol/viewer/Jmol.properties 2010-11-12 14:15:13 UTC (rev 14640) @@ -4,6 +4,7 @@ version=12.0.22_dev +# bug fix: Ramachandran approximation of P straightness off by a few percent # bug fix: SMILES matching string with ".[C@H]" reads stereochemistry incorrectly # bug fix: load SMILES with %nn fails # bug fix: Jmol creating possibly ambiguous aromatic amine SMILES This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |