RE: [PyMOL] drawing hydrogen bonds or dashes
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 : > > > 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 >
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 : > 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
RE: [PyMOL] drawing hydrogen bonds or dashes
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 >
