this works for me when testing using PDB ID code 4GRV (and others). Can you
test this PDB ID with your setup to see if it works? The unknown variable here
is your pdb file, possibly something is odd about it or something might be
wrong with PyMOL as Thomas has indicated. If PDB ID code 4GRV w
[ Nicholas Noinaj ]
the Buchanan Lab
Laboratory of Molecular Biology
LMB-NIDDK, NIH
50 South Drive, Room 4505
Bethesda, MD 20892-8030
1-301-594-9230 (lab)
1-859-893-4789 (cell)
noin...@niddk.nih.gov
[ the Buchanan Lab ]
http://www-mslmb.niddk.nih.gov/buchanan
07, 2013 2:38 PM
To: Noinaj, Nicholas (NIH/NIDDK) [F]
Cc: Gianluigi Caltabiano; James Starlight; pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Cartoon transparency
I must say, 'cartoon skip' does not do what I thought it would do.
fetch 1RV1
cartoon skip, i. 55
# now a helix
Not sure if u have solved this yet, but see 'cartoon skip', i think that is
what u r looking for.
Cheers
Nick
From: Gianluigi Caltabiano [chimic...@yahoo.it]
Sent: Thursday, June 06, 2013 7:50
To: James Starlight; pymol-users@lists.sourceforge.net
Subje
Hi,
I am getting an error when trying to use AxPymol within PPT. While i can open
my PSW file within PyMOL and it looks great, it just won't display when called
within the AxPymol plugin within PPT. I think i have narrowed the problem down
to the fact that i am using a mesh (SAXS envelope) t
using v1.3
(which agrees reasonably well with other programs), people currently using
v1.2r3 or the like might want to investigate further by comparing their results
to v1.3.
Thanks in advance for any feedback!
Cheers,
Nick
[ Nicholas Noinaj ]
the Bu
Madhavi,
Not sure if anyone has replied to your post. i think there are at least two
ways to scan the available rotamers (at least with Windows XP). Once you
have made the mutation...
1- use the arrow keys to change rotamers
2- use the forward (>) and back (<) arrows on the frame selection
nfo/pymol-users
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Nicholas Noinaj
University of Kentucky College of Medicine
Department of Molecular and Cellular Biochemistry
The Cente
ashutosh,
disclaimer: i am probably not the best person to give advice about this, but
you might check out the morph server.
http://www.molmovdb.org/molmovdb/morph/
i am assuming that you have two pdb files that differ only the helix/sheet that
you are interested in trying to create the mor
My vote is against animated-GIFs. I have experienced problems with animated
GIFs in the past where they seem to run fine on my computer, then not work
properly (very slow) on a laptop during a presentation, etc. Could be that
I am setting them up wrong, but for this reason, I avoid animated-GI
I follow the method outlined by Nick with one additional step, after
selecting the new residue you can run through a sidechain rotamer
library using the forward arrows at the bottom of the window. You
also have a choice to use backbone dependant or backbone independant
rotamers.
Andrew
On 4/18/06
orla,
If in fact you actually have to move molecules independently using the 'dirty'
method that I have suggested, you will probably need the rotate command too,
for more flexibility in setting things up.
rotate
DESCRIPTION
"rotate" can be used
orla,
not actually had to do this, but I think you can try the translate command.
--
translate
DESCRIPTION
"translate" can be used to translate the atomic coordinates of a
molecular object. Behavior differs depending on whether or not the
"
Orla,
This is simply, for the most part. Here is what I do.
Load your *.pdb file. Then under WIZARD in the menu bar, select MUTAGENESIS.
Then pretty much, follow directions. In the PyMOL VIEWER window, it will ask
you to ' pick a residue.' Once you pick a residue, select the type of resi
Tiger,
Unfortunately I don't have much experience with this procedure. But one
thing came to mind, you can manually assign secondary structure within
DEEPVIEW/SWISS PDB Viewer [EDIT]. Not sure how many pdb files you have
generated for the morph, but if nothing else works, you could try manua
create two objects and draw the trace for each of these.
Cheers,
Tsjerk
On 4/13/06, Noinaj wrote:
Tiger,
I am no expert by far, but can you select the linkage? If so, just select
and hide. Also, you might try just hiding the two residues that are linked,
this might get
Tiger,
I am no expert by far, but can you select the linkage? If so, just select
and hide. Also, you might try just hiding the two residues that are linked,
this might get rid of the link and you probably wouldn't notice the missing
residues unless it is a small protein. alternatively, and
this helps.
Cheers,
Nick
- Original Message -
From: "Noinaj"
To: "Chun Tang"
Sent: Wednesday, April 12, 2006 10:45 AM
Subject: Re: [PyMOL] pqr file
Chun,
You might check out the web site below, it probably contains all
information that you might need and cont
m the various vendors but that was also hit and
miss...
There didn't seem to be a consistent fix
Chris
On Apr 10, 2006, at 4:47 PM, Noinaj wrote:
Thanks Chris for your help. As you have noted and as I have read online,
there seems to be a problem with the graphics drivers, is this co
Hi PyWorld,
I have been trying to help a friend install PyMol on her laptop (Sony Vaio)
that has Windows XP Home Edition. The installation runs smooth with no problem
at all. But once we try to open the program, its seems to stall, then crashes,
and Windows XP asks if we would like to send a
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