Hello pymol Gurus,
I previously made a figure where the protien is cut in half and you can
see the ligand binding cavity. However, I have forgot how to reproduce it.
My problem is that I want to show a slab of the internal surface not just
the interior part of the external surface. Can anyone hel
OK Thomas,
Thank you for your comments, I will try to upgrade to a more recent version of
pymol.
A bientot,
Cheers
Stephane
De : Thomas Holder [thomas.hol...@schrodinger.com]
Date d'envoi : vendredi 10 mai 2013 20:48
À : ABEL Stephane 175950
Cc: pymol
Hi Stephane,
psico requires python 2.6 or 2.7. I also made a python 2.5 backport [1]. But
PyMOL 0.99rc6 is way too old, it ships with python 2.3.
[1] https://github.com/speleo3/pymol-psico/tree/backport
Cheers,
Thomas
On May 10, 2013, at 8:20 PM, ABEL Stephane 175950 wrote:
> Hello
>
> I
Hi Jason
It is exactly what I want !!!
Merci beaucoup
Cheers
Stephane
De : Jason Vertrees [jason.vertr...@schrodinger.com]
Date d'envoi : vendredi 10 mai 2013 20:25
À : ABEL Stephane 175950
Objet : Re: [PyMOL] Replicate a cubic unit cell in the x, y, z
Hi DJ,
It sounds like you're using the "transparency" setting instead of
"cartoon_transparency". For example instead of
movie_fade transparency, 1, 0., 40, 1.
you likely want
movie_fade cartoon_transparency, 1, 0., 40, 1.
Cheers,
-- Jason
On Fri, May 10, 2013 at 3:50 AM, Dhananjay wrote:
Hello
I have downloaded the Psico module of T. Holder to use the command supercell. I
have followed the wiki http://www.pymolwiki.org/index.php/Psico and
https://github.com/speleo3/pymol-psico/.
I did the followings:
1) Installed the ccbtx and numpy librairies
2) Dowloaded the Psico archive
Bachar Cheaib wrote:
> This record "REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC" does
> not tell us if a structure is really multi
> or monomeric in the pdb file.
>
Right, that tells you what it is in vivo.
To see what it is in the pdb file, i.e. contents of the asymmetric unit,
look
Hello Bachar,
On Fri, 2013-05-10 14:29 EDT, Bachar Cheaib
wrote:
> Dear pymol users,
>
> I have wondered whether someone know how to know if a such structure in
> pdb file is multi-mer or mono-mer biologically speaking? Somehow in the
> related publication of structure this information is pr
Hello Bachar,
On Fri, 2013-05-10 14:29 EDT, Bachar Cheaib
wrote:
> Dear pymol users,
>
> I have wondered whether someone know how to know if a such structure in
> pdb file is multi-mer or mono-mer biologically speaking? Somehow in the
> related publication of structure this information is pr
Dear pymol users,
I have wondered whether someone know how to know if a such structure in pdb
file is multi-mer or mono-mer biologically speaking? Somehow in the related
publication of structure this information is present in occurrence and in
pdb also is not nonintuitive to catch without the BI
Hi all,
I want to know if is possible to replicate a cubic unit cell in the x, y, z
directions (as with the "graphic representation -> periodic" command in VMD)
with pymol(v1.3)? if yes how I can do that ?
Thanks in advance
Stephane
Dear all,
I am trying to animate set of proteins.
Each protein has two conformations.
I wanted to show first confirmation as cartoon, followed by fade out it and
fade in the second confirmation.
I could use movie_fade.py script successfully, however, it fades the
surface to cartoon.
I just want
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