John, It is simply a matter of restricting your atom selections to lie within that single object:
dist my_line, e4_final//A/97/OE1, e4_final//M/200/MN hide labels See http://pymol.sourceforge.net/newman/user/S0220commands.html#7 for more information on atom selections. Cheers, Warren > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > John Berrisford > Sent: Friday, February 20, 2004 3:27 AM > To: Warren DeLano; pymol-users@lists.sourceforge.net > Subject: RE: [PyMOL] drawing hydrogen bonds or dashes > > Thanks that works fine apart from one thing: > I wish to display lines between 97AOE1 and MN in two > overlapped structures, with identical chain identification, > in two different colours. Using the below command draws two > lines in the same colour. Is there a way a specifying a line > between the two below atoms only within a specific pdb file > (defined as an object). > > eg line between A97OE1 and MN only within object e4_final. > > I hope this is clear > > thanks > > John > > Quoting Warren DeLano <war...@delanoscientific.com>: > > > John, > > > > Welcome to PyMOL! > > > > > I wish to do the equivalent to the following molscript > command "line > > > position res-atom A97 OE1 to position res-atom M200 MN;" > > > > dist my_line, a/97/OE1, M/200/MN > > hide labels > > > > Also note that PyMOL can draw hydrogen-bonds automatically > using its > > limited chemical intuition according to the global "h_bond_..." > > settings. (Sorry guys, that isn't documented -- I am thinking about > > creating a new command for it since "dist" isn't the right > place for this). > > > > dist hbnd, all, all, mode=2 > > hide labels > > > > (But I don't think that will help with MN.) > > > > If you don't want dashes, then > > > > set dash_length, 3 > > set dash_gap, 0 > > > > Seems to work for me... > > > > Cheers, > > Warren > > > > > > > -----Original Message----- > > > From: pymol-users-ad...@lists.sourceforge.net > > > [mailto:pymol-users-ad...@lists.sourceforge.net] On > Behalf Of John > > > Berrisford > > > Sent: Thursday, February 19, 2004 10:09 AM > > > To: pymol-users@lists.sourceforge.net > > > Subject: [PyMOL] drawing hydrogen bonds or dashes > > > > > > I have searched the manual and forum and cannot find how > to draw a > > > hydrogen bond between two specific atoms. > > > > > > I wish to do the equivalent to the following molscript > command "line > > > position res-atom A97 OE1 to position res-atom M200 MN;" > > > > > > which draws a line between two atoms A97 OE1 and Mn200. So not a > > > hydrogen bond but a specific line. > > > > > > Is this possible in pymol? > > > > > > I have read posts on changing the thickness of a dash and > the number > > > of dashes in a line. But none on how to draw the line. > > > > > > Can anyone help me, i'm a new user by the way! > > > > > > thanks > > > > > > John > > > > > > > > > > > > ------------------------------------------------------- > > > SF.Net is sponsored by: Speed Start Your Linux Apps Now. > > > Build and deploy apps & Web services for Linux with a free DVD > > > software kit from IBM. Click Now! > > > http://ads.osdn.com/?ad_id=1356&alloc_id=3438&op=click > > > _______________________________________________ > > > PyMOL-users mailing list > > > PyMOL-users@lists.sourceforge.net > > > https://lists.sourceforge.net/lists/listinfo/pymol-users > > > > > > > > > > > > -- > John Berrisford > Department of Molecular Biology and Biotechnology University > of Sheffield > > email: j.berrisf...@sheffield.ac.uk > > > ------------------------------------------------------- > SF.Net is sponsored by: Speed Start Your Linux Apps Now. > Build and deploy apps & Web services for Linux with a free > DVD software kit from IBM. Click Now! > http://ads.osdn.com/?ad_id=1356&alloc_id=3438&op=click > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
