Hi List,
just to tell you the solution I finally used:
python
for x in range(400):
cmd.frame(x+1)
cmd.ray(1920,1080)
cmd.png("path/" + str(x+1) + ".png")
python end
Thank you,
Max
On 2012-05-16, at 4:46 PM, Maximilian Ebert wrote:
> Dear list,
>
> I try to export my P
Hi,
Just observed something weird. When I try loading protein -ligand complexes as
frames of a movie (same protein but different ligands for different frames),
some of the ligand structures get completely messed up when viewed as sticks or
lines. Right now I'm using spheres instead, but wonderi
Hi Ritu,
Could you elaborate on "some of the ligand structures get completely messed
up when viewed as sticks or lines"?
To get the best possible answer a few more details would help.
Best regards,
Folmer
2012/5/23 Rituparna Sengupta
> Hi,
>
> Just observed something weird. When I try loading
Hi. I want to make a figure of an RNA molecules similar to the DNA
molecule shown here:
http://kpwu.files.wordpress.com/2011/07/2l8q-cartoon-ring-v1.png
However, I want each nucleotide type (A,T/U,G,C) colored differently. I
managed to get everything but the center of the ring colored the way I
Hi,
Sorry about the lack of description in the previous post.
The chemicals show incorrect bond connections. Some of the rings go missing. In
all, the structure changes and just by looking at it, its possible to tell that
the structure is not right. I didn't see much details though, except that
Hi again Ritu,
This does seem odd. I have no idea what might be wrong, but could you
provide an example pdb, or a png of the output you see?
I would personally try to strip all extra information from the ligand pdb
(so only ATOM and HETATM records is included) and then try loading that pdb.
Best
On Wed, May 23, 2012 at 10:20 AM, Rituparna Sengupta wrote:
> Sorry about the lack of description in the previous post.
> The chemicals show incorrect bond connections. Some of the rings go missing.
> In all, the structure changes and just by looking at it, its possible to tell
> that the struct
Ritu,
just an idea. It could be that your PDB files contains CONECT records
for your ligands. Those bonds are defined by atom number or atom index I
believe. There could be a conflict between the different files you are
loading. Try stripping the CONECT records and see if that helps.
HTH
Hi DMS,
fetch 3r8t, async=0
as cartoon
set cartoon_ring_mode, 3
set cartoon_nucleic_acid_color, magenta
# use 'resn' and the one letter nucleotide codes
color blue, resn A
color green, resn C
color yellow, resn T+U
color orange, resn G
Cheers,
-- Jason
On Wed, May 23, 2012 at 12:44 PM, Daro
Thank you Jason,
Actually this is exactly where I got stuck. With the commands below, each of
the
bases is colored differently *except* the center of the ring, which is set to a
constant value (green in this case). What I'm wanting is to have each base
appear as a single solid color.
DMS
On
Hello DMS,
I think you have to do 3 steps like:
select all_A, resn A
set cartoon_ring_color, red, all_A
color red, all_A
and then do other 3 groups in the same way.
It works for me to show different colors for different types of nucleotides
while the color of "ring and bond" in "single" nucleot
Thanks kpwu. That's the secret! I did not know that I could do that!
DMS
On May 23, 2012, at 8:37 PM, homespuner wrote:
> Hello DMS,
>
> I think you have to do 3 steps like:
>
> select all_A, resn A
> set cartoon_ring_color, red, all_A
> color red, all_A
>
> and then do other 3 groups in the s
regarding CONECT records and whether to use them, try:
set connect_mode, 1
load youfile.pdb
See also:
http://www.pymolwiki.org/index.php/Connect_mode
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg10413.html
Cheers,
Thomas
Nat Echols wrote, On 05/23/12 20:01:
> On Wed, May
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