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
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John Berrisford
Department of Molecular Biology and Biotechnology University
of Sheffield
email: j.berrisf...@sheffield.ac.uk
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