Warwick, You have inquired about selecting groups (or the LeadAtom of a group) when the atoms are off but the shapes are turned on.
This functionality was not available in RasMol 2.6b2, but is available in Chime. As I have said, solving this problem correctly and in the general way is very computationally expensive. Therefore, I assumed that Chime was doing some approximation. I have been able to get access to a machine with chime and play with a website that allows me to enter arbitrary commands. Here are some of my observations: 1. there is no general mechanism for picking the shapes themselves 2. the implementation of selecting is based upon the atoms themselves 3. when a shape is turned on, one is able to pick either alpha carbons or carbonyl oxygens, even though the atoms themselves are not turned on 4. it is not clear to me what they are using as the selection radius from the center of the CA or O. I believe that it is a fixed number of pixels 5. depending upon your zoom level, there can be a lot of space within the cartoon/ribbon/etc. where one can pick and not successfully pick an atom 6. when trace is on, or in cartoon random turn, it can be difficult to pick the group. this is because the shape does not pass through the alpha carbon. So the center of the alpha carbon is outside of the shape. So, picking outside the shape results in selecting the group. 7. when they are in this shape-selection mode, it is possible to pick any alpha carbon or carbonyl oxygen, even if its segment is not visible. load 1B07.pdb; cpk off; wireframe off; select 178-183; center selected; zoom 400 one can now click around and pick alpha carbons/carbonyl oxygens from groups other than 178-183 Based upon these observations, I can say the following: a) we can do a better job than Chime, but it won't be perfect. b) the initial implementation will probably be based upon selecting atoms, as in #2 c) there will be some space within a shape where clicking will have no effect ... as in #5 d) there will be space outside the shape but near the edges where clicking will result in selecting the group ... as in #6 e) Jmol will not pick groups unless the group is visible ... unlike #7 f) in the case of amino acid residues, we will never return the carbonyl oxygen, but will always return the alpha carbon. For nucleotide groups, we will return the LeadAtom. In priority order this is P, H5T, O5T, O5' g) this will be a good start. over time we can improve it if necessary. Warwick, I understand that you have an important milestone coming up in your project. I will make an effort to get something running within the next few days. Miguel ------------------------------------------------------- This SF.Net email is sponsored by the new InstallShield X. >From Windows to Linux, servers to mobile, InstallShield X is the one installation-authoring solution that does it all. Learn more and evaluate today! http://www.installshield.com/Dev2Dev/0504 _______________________________________________ Jmol-developers mailing list [EMAIL PROTECTED] https://lists.sourceforge.net/lists/listinfo/jmol-developers
