Miguel schrieb:
This was available in the more current RasMol2.7.2 versions you may useWarwick,
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.
set picking group
and click on the cartoon (shift click to add further groups) or
set picking atom
than you will get only *.CA for protein cartoon and only the corresponding *.P for nucleic cartoon (and you may use a lasso for selection)
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 think an approximation would be good enough
this is badI 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
but I'm glad that it is not the case with RasMol2.7.2, only what has visible representations (a backbone may be considered as representation of the whole group if picking is set to 'group') could be selected by picking
Based upon these observations, I can say the following:
a) we can do a better job than Chime, but it won't be perfect.
select by picking would be very useful for the end-user.
if the picking (mimic) is set to groups, groups should be selected on click on a backbone/ trace/ cartoonb) 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 carbonylOK if the picking (mimic) is set to atom.
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'
Yes, this - and the (re-)enabling of picking for (group, atom) selection - sounds good, regards, Jan
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
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