> if I only display meshribbon and hbonds > load pdb file > cpk off > wireframe off > meshribbon > connect auto hbond > hbonds 50 > spin > while rotation the mesh changes color (bug or feature?)
bug :-) > the property > ribbonedge on > which restores the original Jmol cartoon style had had only a short stay > during past Jmol versions, was this intended? That was intended to stay. I will investigate. > if bonds are added to a partial wireframe representation, they are > created invisible+ > load pdb file > cpk off > wireframe off > select [PRO] > wireframe 70 > # not 50 > select protein and *.O > connect modify double (*.C and within(group, selected)) > neither the visible bonds alter their style nor the invisible bonds get > visible. I think that every newly created/modified bond should be > visible as it gets created. I think I disagre. You are modifying bonds that already exist. You are modifying the order. They retain their color and size. If you create new bonds then they are displayed by default. Q: What do others think? > ... >> * exposure of 'bondcount' as an atom property: >> >> select bondcount=2 >> > how are double bounds counted? At the moment this a > connected atoms count (rename to boundedcount ?) Correct. It is the connected atoms count. It is not the sum of the bond orders. If the names 'bondcount' and 'hbondcount' are going to be confusing then should change them. Q: Please recommend other names ... connectedAtomsCount ? > and only selects *.OG and *.SG (which > is correct, if not >C=O) I do not understand this. > select bondcount=3 and carbon > connect modify aromatic > the graph is a bit stochastic. I would prefer if either inner and outer > bonds regularly change in showing hbond style bond or only the inner > bonds are hbond style. You are referring to the positioning of the dotted and solid lines in 'aromatic' bonds. I wrote this code several years ago, to support aromatic rings. The code was designed to find the inside of the ring. I was not aware of other applications where 'aromatic' would be used outside of a 'ring'. If there are specific rules for placement of 'aromatic' bonds outside of a ring context then we can investigate that after the 10.1 release. While the 'aromatic' code is old, most people have never seen it ... so it has not been subject to much review. So it is possible/likely that it will make 'incorrect' decisions in ring or multi-ring contexts. > rotating such a graph often results in > Exception in thread "AWT-EventQueue-0" > java.lang.ArrayIndexOutOfBoundsException: 188856 > at org.jmol.g3d.Graphics3D.plotPixelsClipped(Graphics3D.java:1260) > at > org.jmol.g3d.Circle3D.plot8FilledCircleCenteredClipped(Circle3D.java:133) > at > org.jmol.g3d.Circle3D.plotFilledCircleCenteredClipped(Circle3D.java:163) > at > org.jmol.g3d.Graphics3D.fillScreenedCircleCentered(Graphics3D.java:365) This is somewhat disturbing. This code has not changed in a long time. I cannot reproduce this problem. Please try to produce a script with a specific molecule that causes the problem. Q: If anyone else has seen this type of problem please speak up. Miguel ------------------------------------------------------- This SF.Net email is sponsored by xPML, a groundbreaking scripting language that extends applications into web and mobile media. Attend the live webcast and join the prime developer group breaking into this new coding territory! http://sel.as-us.falkag.net/sel?cmd=lnk&kid0944&bid$1720&dat1642 _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
