>
> Hi, Rob,
>
thank you for you reply and modification of the script. now Ican calculate
the surface area. but when I calculate the surface of part protein, it seem
that the surface area including the surface adjacent with other residues,
means the sum of two fragments is much larger than whole
Dear All,
I am making some figures using ray. When the processing is finished I get a
strange pattern (like newspaper paper pattern) in my cartoon
representations, Spheres and sticks representations are OK only the cartoon.
I have tried to change the options on the cartoon representation but with
Hi Afonso,
Can you tell which newspaper? And does it show the date? :)
Seriously, it's difficult to make out more, unless you give more
information, like a link to the image, or the series of commands you
used to get to the point you're at. What you describe might be caused
by two interfering surf
Hi Sujuan,
On Tue, 18 May 2010 15:58:59 +0800 sujuan wang wrote:
> thank you for you reply and modification of the script. now Ican calculate
> the surface area. but when I calculate the surface of part protein, it seem
> that the surface area including the surface adjacent with other residues,
thank you Thomas,
It worked for me :)
On Tue, May 18, 2010 at 3:23 PM, Thomas Holder <
spel...@users.sourceforge.net> wrote:
> use the PISA web service, you can upload a PDB file there and get
> detailed summary for all interfaces in your complex.
>
> http://www.ebi.ac.uk/msd-srv/prot_int/cg
Hi Tsjerk,
I found the reason of the problem. It wasn't a texture error (I checked that
before) but for some strange reason if I have the same molecule loaded twice
in cartoon with 40% gray and if both are visible I will get that effect. PS
: the reason why I have the same pdb open is make it easi
Hi i was wondering if anybody have a script that can calculate surface energy
of a crystal surface
Also i need to find electrostatic potential map in a crystal surface but the
Vacuum does not work on it is there any other scripts i can use
Thank you all
That's exactly what I just found out!
Thanks! but I don't understand why sometimes it happens and other times it
does not happen.
Cheers
Afonso
On Tue, May 18, 2010 at 4:17 PM, Matthew Franklin <
matthew.frank...@imclone.com> wrote:
> I suspect Afonso's talking about a moire / halftone dot pat
I suspect Afonso's talking about a moire / halftone dot pattern like the one at
this link:
http://www.uvm.edu/~hag/presentations/maze2004/moire.html
I have no idea what would cause this, but if you have two identical copies of a
molecule, in the same representation, strange things can happen.
Hi Afonso,
I haven't seen this before. It seems to be a different texture. Did
you touch any of the settings (like ray_texture)? Surely you didn't
just use 'ray' after you loaded the structure. It wouldn't have shown
up as cartoon to begin with. If you give the full set of commands you
used, it wi
I forgot a step in my command list before; the copy of the molecule has to be a
different color from the parent molecule. (Perhaps that was obvious, but I
thought I should state it.) This may be why you see it some times and not
others: you have to have both copies with their visibility turned
Hello Humayun,
You can use the pisa server at the EBI to find all kinds of information about
your dimer (and other assemblies that may be present) by simply uploading your
pdb file here:
http://www.ebi.ac.uk/msd-srv/prot_int/cgi-bin/piserver
have a nice day,
Eric
__
Eri
Hi Eric,
There's a script on the PyMOLWiki that accomplishes the selection
part. You can then use get_area for the area calculation. Check out
http://pymolwiki.org/index.php/InterfaceResidues.
Cheers,
-- Jason
On Tue, May 18, 2010 at 11:08 AM, Eric Larson wrote:
> Hello Humayun,
>
> You can
Hello, I'm new to this board.
I came across a certain problem with the mutagenesis tool. I got a pdb-file
with amino acids that are partly displayed as 2 rotamers (so one amino acid
displayed in two different ways in the Viewer).
Usually, the mutagenesis tool works fine, but if you try to mutate
Hi I am using a subversion build of pymol built using setuptools i,e
"python setup.py install" on 64 bit ubuntu Lucid Lynx 10.04.
I can use the main program without any problems , but when I try to
install and run the apbs plugin , pymol segmentation faults
immediately.
Incidentally , doing a Hel
Hello,
I would like to do the following: I have a large protein loaded in
pymol. I would like to select all atoms within a radius around a point.
I know about "select within", however, this command requires the second
selection to be an atom. I would prefer if the center of the sphere is
not neces
Dear Nicolas,
As for the semi-transparent sphere, there are a number of ways to do that.
One option: You could create a new object named new_obj with an atom at the
center point and use "alter new_obj, vdw=radius" to make the sphere. Then
use "set sphere_transparency, 0.5, new_obj"
Alternatively
Hi Michael,
thanks!
nick
On Tue, 2010-05-18 at 23:55 -0500, Michael Zimmermann wrote:
> Dear Nicolas,
>
> As for the semi-transparent sphere, there are a number of ways to do
> that. One option: You could create a new object named new_obj with an
> atom at the center point and use "alter new
Dear All,
I have been trying to generate physiological relevant Hexameric structure of
my recently solved trimer structure by using Symmetry Mates in Pymol, but I
am unable to find appropriate hexamer even with all type of symmetry options
available in Pymol (different distances)
Surface contact o
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