> Hi Chris > > I am not sure, but I recall that there may be a difference between internal > model number and sequential model number in Jmol "frame" or "model" > commands. > Check the docs and, in any case, try using number 3 (27 could be 1, first > model, so 29 is 3)
Hola Angel, you seem to be correct. This makes sense if one thinks in terms of animation but it is getting quite cumbersome if one would like to stick to the model numbers as given in the PDB file. It also seems to be inconsistent since the 'load' command asks for consecutive integers starting with 1 whereas the 'frame'/'model' command requires the PDB model number. May I ask the Jmol developers to extend the 'load' command such that it can cope with model numbers contained in the PDB file? To assist you, I have included pathologic cases I found when scanning our database for this problem. The following PDB files have non-sequential model numbers, some containing the model number '0': 1nh5, 1j6y, 2fce, 1sm7, 1ljz The worst case example, 1nh5, has only models 1, 2, 6, 7, 9, 11, 18, 19, 25, 26, 28, 32, 34, 38, 39, 41, 42, 46, 49, 50. And here is a list of PDB codes of files where the model number does not start with 1. The minimum and maximum model numbers are printed next to the PDB code column. +------+------+------+ | code | min | max + +------+------+------+ | 2ezq | 11 | 20 | | 3ezc | 15 | 27 | | 1ezc | 18 | 34 | | 1kld | 18 | 33 | | 1gdy | 18 | 34 | | 2new | 19 | 35 | | 2axx | 20 | 40 | | 1crr | 21 | 40 | | 2ezr | 21 | 30 | | 1vve | 22 | 42 | | 1sag | 27 | 52 | | 1sah | 27 | 52 | | 3ezd | 28 | 40 | | 2ezs | 31 | 40 | | 1ezd | 35 | 50 | | 1gdz | 35 | 50 | | 1saj | 53 | 76 | | 1sai | 53 | 77 | +------+------+------+ Thanks for your consideration. Chris ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Jmol-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-users
