From: S. F. Y. <SY...@gn...> - 2006-06-01 18:10:25
|
Hi, I was wondering if there's a way in PyMOL to separate different objects. That is, different objects don't move together. When an object (molecule) is hidden it doesn't change the orientation no matter how the others move. This would be useful if you want to visualize a set of related targets but not conformationally connected. =20 Thanks a lot, Frank |
From: Cartailler, Jean-P. <jp.cartailler@Vanderbilt.Edu> - 2007-01-23 21:19:30
|
Greetings, Does anyone know if the camera commands (turn & move) can be constrained to the reference (global) axes? I would imagine that the turn command (http://pymol.sourceforge.net/newman/ref/S1000comref.html#2_166) would cause a camera of 45 degrees about the reference axis: PyMOL> turn x, 45 However, it appears to turn the camera about the viewport "orientation", i.e. about the (horizonal) x-axis axis of the viewport. Note - this is pretty clear if you use Robert Campbell's axes_cyl.py to visualize the reference axis. According to the manual, it is also supposed to be constrained to the origin as well but doesn't appear to do so, at least not in my hands Are its constraints possibly overridden by such commands as center, orient, origin? Reason for asking this is that it would be very nice (at least for me) to be able to perform "local" transformations (i.e. about local object axes, be it the camera or other) that are bound to locally-defined axes - that are independent of the "global" or viewport orientation. Using winXP/Pymol 0.98. Thanks! JP Cartailler |
From: DeLano S. <de...@de...> - 2007-01-23 22:17:54
|
JP, > According to the manual, it is also supposed to be > constrained to the origin as well but doesn't appear to do > so, at least not in my hands Are its constraints possibly > overridden by such commands as center, orient, origin? origin position=[0,0,0] turn axis,angle can change the origin, but x,y,z are always in the camera frame of reference with the turn and move commmands. > Reason for asking this is that it would be very nice (at > least for me) to be able to perform "local" transformations > (i.e. about local object axes, be it the camera or other) > that are bound to locally-defined axes > - that are independent of the "global" or viewport orientation. For this, use the rotate command. # atomic coordinate based (geometry must be recomputed) rotate x,90, # object matrix based (geometry remains valid, but causes other problems) rotate x,90,object=object-name Note that the optional "camera" option (0,1) can control whether global or camera frame of reference applies, and that the current global origin is always the center. origin object-name-or-selection to change it Don't mix the two types of rotations or PyMOL will get confused. Cheers, Warren > -----Original Message----- > From: pym...@li... > [mailto:pym...@li...] On Behalf > Of Cartailler, Jean-Philippe > Sent: Tuesday, January 23, 2007 1:19 PM > To: pym...@li... > Subject: [PyMOL] Command:turn > > Greetings, > > Does anyone know if the camera commands (turn & move) can be > constrained to the reference (global) axes? I would imagine > that the turn command > (http://pymol.sourceforge.net/newman/ref/S1000comref.html#2_16 > 6) would cause a camera of 45 degrees about the reference axis: > > PyMOL> turn x, 45 > > However, it appears to turn the camera about the viewport > "orientation", i.e. about the (horizonal) x-axis axis of the > viewport. Note - this is pretty clear if you use Robert > Campbell's axes_cyl.py to visualize the reference axis. > > According to the manual, it is also supposed to be > constrained to the origin as well but doesn't appear to do > so, at least not in my hands Are its constraints possibly > overridden by such commands as center, orient, origin? > > Reason for asking this is that it would be very nice (at > least for me) to be able to perform "local" transformations > (i.e. about local object axes, be it the camera or other) > that are bound to locally-defined axes > - that are independent of the "global" or viewport orientation. > > Using winXP/Pymol 0.98. > > Thanks! > > JP Cartailler > > -------------------------------------------------------------- > ----------- > Take Surveys. Earn Cash. Influence the Future of IT Join > SourceForge.net's Techsay panel and you'll get the chance to > share your opinions on IT & business topics through brief > surveys - and earn cash > http://www.techsay.com/default.php?page=join.php&p=sourceforge > &CID=DEVDEV > _______________________________________________ > PyMOL-users mailing list > PyM...@li... > https://lists.sourceforge.net/lists/listinfo/pymol-users |