Hi Yingjie, Yes, on this list one can really learn a lot about JmolScripting and combining this with other web techniques.
On Fri, Mar 25, 2011 at 15:18, Yingjie Lin <[email protected]> wrote: > 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? Please don't leave the Subject as "Re: Jmol-users Digest ..." but rather change it to "Re: jmolEvaluate problem" or "Re: [Jmol-users] one label per residue". In this way most Email-Clients are able to sort these emails together as a Thread and it gives the others an idea what's inside. > 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? =) I believe it is very useful for those who tried to help and later on those who search the list-archive to give a feedback if a solution worked out well for you. In this case when someone has a similar problem he/she can find a solution on the archive without waiting for other jmol-users to reply. Oliver >> 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 > ------------------------------------------------------------------------------ Create and publish websites with WebMatrix Use the most popular FREE web apps or write code yourself; WebMatrix provides all the features you need to develop and publish your website. http://p.sf.net/sfu/ms-webmatrix-sf _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
