Hi Bob, Your answer is very thorough. My problem is solved. More importantly, I learned a lot from your solutions. Thank you!
Two side questions: 1. when replying to a thread, does the title of my email matter? For example, should I use "Re: Jmol-users Digest, Vol 58, Issue 33" or "Re: jmolEvaluate problem" as my title? 2. if at the end of a thread, I just want to say thank you to the people who have offered help, should I reply to [email protected] or just reply to those people? =) Yingjie > If you label the alpha carbons, then some of those labels won't appear, > because they are not visible. > > Well, first question, I guess, is: How did you make them visible or not? > > Also, where do you want the labels to appear? > > This worked reasonably well: > > load =1crn > > # establish the box > boundbox {0 0 0} {10 10 10} > > # just to see what I'm working with > boundbox on > > # select all alpha carbons for groups with any atoms in the box > select *.ca and within(group, within(boundbox)) > label %r > > # display only these groups > display within(group, selected) > > # "hide" all atoms outside the box. The labels will > # still be there, because I'm not turning those off > select not within(boundbox) > spacefill off;wireframe off > > > I guess the only question is whether you think the labels are in the right > place. > > Let's see if I can label JUST the atoms in the box. This time I'll define > some variables so we can make sense of the logic: > > load 1crn.pdb > boundbox {0 0 0} {10 10 10} > boundbox on > inBox = within(boundbox) > display inBox > select *;labels off > allGroupsIntersectingBox = {within(group, inBox)} > allGroupsInBox = {allGroupsIntersectingBox and not within(group, not inBox)} > allGroupsPartiallyInBox = {allGroupsIntersectingBox and not allGroupsInBox} > allAlphaInBox = {*.ca and allGroupsInBox} > allTerminatingAtoms = {allGroupsPartiallyInBox and connected(not inBox)} > selectedAtoms = allAlphaInBox or allTerminatingAtoms > select selectedAtoms > label %r > > # That comes close, but includes two labels for some groups that have two > # connections into the box. I guess if you want only one label per group you > still > # have to use a for loop: > > finalSelection = ({}) > var nAtoms = selectedAtoms.size > for (var i = 1; i <= nAtoms; i++) { > var a = selectedAtoms[i] > if ({finalSelection and within(group, a)}.size == 0) { > finalSelection |= a > } > } > select *;labels off > select finalSelection > label %r > > ------------------------------------------------------------------------------ Enable your software for Intel(R) Active Management Technology to meet the growing manageability and security demands of your customers. Businesses are taking advantage of Intel(R) vPro (TM) technology - will your software be a part of the solution? Download the Intel(R) Manageability Checker today! http://p.sf.net/sfu/intel-dev2devmar _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
