RE: [PyMOL] drawing hydrogen bonds or dashes

[Warren D. <wa...@de...>]

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: pym...@li... 
> [mailto:pym...@li...] On Behalf Of 
> John Berrisford
> Sent: Friday, February 20, 2004 3:27 AM
> To: Warren DeLano; pym...@li...
> 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 <wa...@de...>:
> 
> > 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: pym...@li...
> > > [mailto:pym...@li...] On 
> Behalf Of John 
> > > Berrisford
> > > Sent: Thursday, February 19, 2004 10:09 AM
> > > To: pym...@li...
> > > 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
> > > 
> > > 
> > > 
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> > 
> > 
> 
> 
> --
> John Berrisford
> Department of Molecular Biology and Biotechnology University 
> of Sheffield
> 
> email: j.b...@sh...
> 
> 
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