Re: [PyMOL] problem with pymol on FC6

2008-08-21 Thread DeLano Scientific
 
Jhon,
 
This sounds like a typo in your bashrc file, wherein code is being
accidentally run instead of being used to define a path or alias, etc.
Another possibility could be that the Terminal application has somehow
stored some kind of state that is being restored on launch (this used to
happen on early versions of Mac OS X).
 
Cheers,
Warren

--
DeLano Scientific LLC
Subscriber Support Services
mailto:supp...@delsci.com



From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Jhon Thomas
Sent: Wednesday, August 20, 2008 7:45 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] problem with pymol on FC6


Hi all

I have recently downloaded the pymol on my FC6. Normally when i install a
program, i give a pathname of my program excutable in my .bashrc and then i
could launch the program by running pymol in a terminal application
launcher. But, this time whta happened that after installation i have
defined the path for pymol but, before launching with terminal whenever i
opens up the terminal for any purpose. pymol opensup automatically even
without envoking the launcher pymol.
kindly can anyone help me...

thanks in advance

jhon






[PyMOL] how to outline as in ray_trace_mode=2

2008-08-21 Thread O. J. Ganesh

Hey once again everyone,

   This is along the lines as my previous questions...   When I do:
set ray_trace_mode, 2;
It produces a 'black and white image', however this really is of the outlines 
of the objects in the model.   Is there a way I can manually make certain 
objects into this outline representation?   That is, not filled in with color, 
but outlined instead?   Or just control the thickness of the edges of objects 
in the picture?   This is outline view is fairly different than the other 
representations...

Thanks.



[PyMOL] hydrogen naming

2008-08-21 Thread David A. Horita
Hi,
How do I get proper (HN,HA, HE1, etc) hydrogen naming when using h_add
(instead of H01, H02, ...)?  
 
Worst case I can build them in Xplor/CNS; second worst would be if there
is a uniform rule per residue that I could write a script to convert on
a residue type basis.
 
Thanks,
Dave
- 
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016 
Tel: 336 713-4194
Fax: 336 716-7671 
email:  dhor...@wfubmc.edu
web:  http://www1.wfubmc.edu/biochem/faculty/Horita.htm
http://www1.wfubmc.edu/biochem/faculty/Horita.htm/ 
 


[PyMOL] Selecting Negative Residues

2008-08-21 Thread Buz Barstow

Dear All,

Does anyone know how to select residues with negative sequence numbers  
in Pymol?


I have a protein molecule with two residues with negative sequence  
numbers (-2 and -1). When I issue the command:


cmd.select('temp', 'resi -2 and name CA')

Pymol selects the alpha carbons of residues -2 to +2.

How can I tell Pymol that I don't want to select a range?

Thanks, and all the best,

--Buz



Re: [PyMOL] hydrogen naming

2008-08-21 Thread Schubert, Carsten [PRDUS]
phenix.reduce is an option

-Original Message-
From: pymol-users-boun...@lists.sourceforge.net 
[mailto:pymol-users-boun...@lists.sourceforge.net]on Behalf Of David A. Horita
Sent: Thursday, August 21, 2008 3:32 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] hydrogen naming


Hi,
How do I get proper (HN,HA, HE1, etc) hydrogen naming when using h_add (instead 
of H01, H02, ...)?  
 
Worst case I can build them in Xplor/CNS; second worst would be if there is a 
uniform rule per residue that I could write a script to convert on a residue 
type basis.
 
Thanks,
Dave
- 
David A. Horita, Ph.D.
Department of Biochemistry
Wake Forest University School of Medicine
Winston-Salem, NC 27157-1016 
Tel: 336 713-4194
Fax: 336 716-7671 
email:  dhor...@wfubmc.edu
web:  http://www1.wfubmc.edu/biochem/faculty/Horita.htm 
http://www1.wfubmc.edu/biochem/faculty/Horita.htm/ 
 



Re: [PyMOL] Selecting Negative Residues

2008-08-21 Thread Buz Barstow

Hi  Warren,

Thanks! That did the trick.

All the best,

--Buz


On Aug 21, 2008, at 4:25 PM, DeLano Scientific wrote:


Buz,

This is something PyMOL didn't handle well until recently, but I  
think you
can now prefix the minus sign with a backslash in order to force  
PyMOL to

interpret the value numerically instead of as a range.

# create some negative residue identifiers

load $TUT/1hpv.pdb
alter chain A, resi=int(resi)-200
set seq_view

# test selections

indicate resi \-127

indicate resi \-136-\-129

A bit ugly, but it works!

Cheers,
Warren


--
DeLano Scientific LLC
Subscriber Support Services
mailto:supp...@delsci.com


-Original Message-
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Buz  
Barstow

Sent: Thursday, August 21, 2008 12:32 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Selecting Negative Residues

Dear All,

Does anyone know how to select residues with negative sequence  
numbers in

Pymol?

I have a protein molecule with two residues with negative sequence  
numbers

(-2 and -1). When I issue the command:

cmd.select('temp', 'resi -2 and name CA')

Pymol selects the alpha carbons of residues -2 to +2.

How can I tell Pymol that I don't want to select a range?

Thanks, and all the best,

--Buz

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