Feature Requests item #1115290, was opened at 2005-02-03 04:00 Message generated for change (Comment added) made by hansonr You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1115290&group_id=23629
Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: None Group: None >Status: Closed Priority: 5 Submitted By: Nobody/Anonymous (nobody) Assigned to: Bob Hanson (hansonr) Summary: distance/angle measurement in movies Initial Comment: up to version 4, the measurement of an angle or distance etc. was visible in all fromes of an animation. this was enormous useful, because one could track a certain distance during a configuration change. in all new versions, this no more possible (the measurement semms to be connected to a single frame) ---------------------------------------------------------------------- >Comment By: Bob Hanson (hansonr) Date: 2006-03-07 00:58 Message: Logged In: YES user_id=1082841 you've got it. monitor ALL (atom expr) (atom expr) ..... see http://www.stolaf.edu/people/hansonr/jmol/test/json/measure.htm ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2006-03-06 07:45 Message: Logged In: YES user_id=1082841 There seems merit in this request. With the newly introduced capability to designate atom selection sets for monitor, one could definitely imagine: monitor (atomno=1) (atomno=2) which would apply the monitor bitsets to ANY displayed model, since these designations, without "and */1", do in fact designate ALL such comparisons. The current prototype at http://www.stolaf.edu/people/hansonr/jmol/test/json/ interprets: monitor (atomno=1) (atomno=2) as "monitor the distance between the FIRST occurance of "(atomno=1)" and the FIRST occurance of "(atomno=2)" so that would be in the first model. But it wouldn't have to.... The question becomes how to distinguish this from cross-model measurements, which is also possible now and potentially very useful: monitor (atomno=1 and */1) (atomno=1 and */2) but I think this is doable. We could, for example, create the option ALL: monitor ALL (atomno=1) (atomno=2) which would imply first occurance "in all models". One question, then, would be if the full generalization would not be restricted to only one measurement per model: monitor ALL (carbon and within(1.5, oxygen) (oxygen and within(1.5, carbon) might throw up a measurement for all such sets. Of course, doing something silly like monitor ALL (all) (all) would give quite a mess, but that's not a real problem. I think we'd need the implied condition with ALL that the monitored atoms are in the SAME model, but beyond that, I see no serious difficulty implementing this. Is there a hard limit on the number of displayed measurements? Bob Hanson ---------------------------------------------------------------------- Comment By: Rene Kanters (rkanters) Date: 2005-02-26 07:54 Message: Logged In: YES user_id=905185 I only got involved with Jmol after version 4, so I don't know what was possible then. I believe that currently that is indeed not possible (so you aren't overlooking anything). The reason may be the following (I don't know, maybe Miguel can elaborate). There is no reason to assume (nor inform Jmol) that the models in each frame are representations of the same molecules or even the same sets of atoms. Thus the distance between atoms 1 and 2 in one frame could be that between Fe and Cl, while in another one between C and H. I agree that probably in a lot of cases of output from calculations or simulations each frame contains the same atoms in the same order. I have come across cases where I wished I could do exactly what you are asking for. Rene ---------------------------------------------------------------------- Comment By: Alexander Poddey (alexxy) Date: 2005-02-26 05:25 Message: Logged In: YES user_id=337746 I miss the same - or do we overlook something? ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1115290&group_id=23629 ------------------------------------------------------- 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&kid=110944&bid=241720&dat=121642 _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
