RE: [PyMOL] drawing hydrogen bonds or dashes

2004-02-20 Thread John Berrisford
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=1356alloc_id=3438op=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

2004-02-20 Thread Warren DeLano
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=1356alloc_id=3438op=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=1356alloc_id=3438op=click
 ___
 PyMOL-users mailing list
 PyMOL-users@lists.sourceforge.net
 https://lists.sourceforge.net/lists/listinfo/pymol-users
 





[PyMOL] drawing hydrogen bonds or dashes

2004-02-19 Thread John Berrisford
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