From: SourceForge.net <no...@so...> - 2007-11-13 11:42:06
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Feature Requests item #1830586, was opened at 2007-11-12 18:21 Message generated for change (Comment added) made by rhuehne You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1830586&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: Open Priority: 5 Private: No Submitted By: Rolf Huehne (rhuehne) Assigned to: Nobody/Anonymous (nobody) Summary: show boundbox on structure part Initial Comment: The "show boundbox" command is quite useful for scripting purposes. But there are many PDB files, especially of biological units from the PDB that contain a lot of rather uninteresting water molecules (e.g. 4otb.pdb1; in the case of a reduction compared to the asymmetric unit usually all water molecules remain in the first biological unit file) that disturb the boundbox information. Therefore it would be very useful to be able to provide an atom expression to restrict the boundbox: show boundbox (atom_expression) ---------------------------------------------------------------------- >Comment By: Rolf Huehne (rhuehne) Date: 2007-11-13 11:42 Message: Logged In: YES user_id=1344570 Originator: YES Hi Bob, thanks for implementing this immediately. But unfortunately you also changed the output of "show boundbox". What I am really interested in are only vectorX, vectorY and vectorZ which are not available any more. Although it seems possible to obtain it from the corner coordinates it is far more complicated with Jmol scripting (my script has to work in the application and the applet). Besides the "center point + vectorX/Y/Z" information immediately revealed the geometry of the boundbox while now you have to do several calculations to obtain this information. And others might also use the "show boundbox" output for scripting and won't like this (unnecessary) change. So why do you want to change the output (besides adding the volume)? ---------------------------------------------------------------------- Comment By: Bob Hanson (hansonr) Date: 2007-11-13 03:50 Message: Logged In: YES user_id=1082841 Originator: NO Fabulous idea. version=11.3.44_dev # new feature: boundbox {atomExpression} [on|off] # sets the bound box around the specified atom expression # default ON/OFF is to NOT change current setting # new feature: boundbox {centerExpression} {centerExpression} [on|off] # sets the bound box to encompass the two center points # strangely enough this allows setting the boundbox to a 2D or 1D box # new feature: show boundbox gives two corner points and volume ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=379136&aid=1830586&group_id=23629 |