Dear Thomas,
that did the trick! Thank you so much!
Cheers,
Christian
Am 15.11.2013 15:59, schrieb Thomas Holder:
> Hi Christian,
>
> set defer_builds_mode to 3, this will prevent caching the geometry for all
> states.
>
> http://pymolwiki.org/index.php/Defer_builds_mode
>
> Cheers,
> Th
Hi Christian,
set defer_builds_mode to 3, this will prevent caching the geometry for all
states.
http://pymolwiki.org/index.php/Defer_builds_mode
Cheers,
Thomas
On 09 Nov 2013, at 13:58, Christian Becke wrote:
> Dear pymol users,
>
> I'm trying to create a movie, using lsqman and pymol, o
Hi Jianghai,
if your morph has 30 states, this short script will y-rock at the
beginning, the middle, and the end or the morph:
mset 1 x51 -15 x61 -30 x51
movie.rock 1, 40
movie.rock 76, 115
movie.rock 151, 190
Instead of movie.rock, you can also use movie.nutate of course.
See also: http://pym
Sean,
> My mistake, I omitted "set matrix_mode, 1" and realized in Movie School 5
> that not setting this to "1" would cause the object motions to not be
> captured. I will add this to the PyMOL-Wiki.
That tutorial is mostly correct, but as you've noticed, a bit out of
date. Please feel free to
Hi Jordan,
I guess you actually do want the axis in camera space, not in object
space. Unfortunately the origin argument will pick the origin of object
coordinate space and not it's geometric center.
Check the attached script, which I modified slightly. I defined a
"my_rotate" command which
Hi Jordan,
the "rotate" command has a "camera" argument. Does it help if you set
that to zero?
rotate [0,0,1],360, object=3hmx_ant, origin=3hmx_ant, camera=0
Cheers,
Thomas
Jordan Willis wrote, On 09/17/12 02:55:
> Hello,
>
> I'm making a movie, and I think I really got it down! However, I
Hi Georgios Gkouridis,
RigiMOL is an Incentive PyMOL feature. To gain access to this, you'll
need to purchase a copy of PyMOL.
Cheers,
-- Jason
On Fri, Jul 13, 2012 at 3:18 PM, wrote:
> Dear users,
> I would like to create a movie using Pymol between two different
> conformations (structures)
Hi Yuri,
> I was putting together some movies using pymol and I have some
> questions.
> First, how can I gradually make a surface go from solid to transparent?
> Currently what I see is, in scene 1 I have it solid (0% transp.)
> surface. Then after I show some ligands and aa side chains in sce
one more thing: ffmpeg script at that link didn't work for me so i had to
modify it like that
ffmpeg -f image2 -qscale 5 -r 24 -b 9600 -i image%d.png movie.mpg
On Wed, Nov 9, 2011 at 11:22 PM, Vitali Stanevich wrote:
> have a look at this link:
>
> http://strucbio.biologie.uni-konstanz.de/ccp4wi
have a look at this link:
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Morph_with_Chimera
disregard morph part. you can modify script to contain "frames" instead of
"states". i installed ffmpeg from repositories on ubuntu and don't remember
any issues with kodecs.
vitali
On Wed, N
Hi,
Quick time player 7 pro does a great job for me.
Cheers
Tim
Am 11/8/11 9:54 PM, schrieb Troels Emtekær Linnet:
Hi.
I have made a nice little movie in Pymol.
1500 frames.
So now I am wondering what is the best method to export?
At the moment I do export to .png with ray tracing each image.
I used this a long time ago, but after googling for the error "from
bgra to yuv420p" I guess that is a problem with the color space
conversion that memcoder tries to enforce by default. Maybe you could
try imposing the color space by adding -vf "format=bgra", but I think
that the video codec is not
What codec do I need to install??
MEncoder 1.0rc4-4.5.2 (C) 2000-2010 MPlayer Team
Option x264encopts: Unknown suboption nodct_decimat
success: format: 16 data: 0x0 - 0x0
MF file format detected.
[mf] search expr: *.png
[mf] number of files: 537 (4296)
[demux_mf] file type was not set! trying 'ty
On a Linux system you can use the following commands to stick them all together
mencoder mf://*.png -mf fps=25 -ovc x264 -x264encopts
bitrate=3000:threads=auto:frameref=8:bframes=0:nob_adapt:direct_pred=auto:subq=7:mixed_refs:nodct_decimat:no_psnr:me=umh:keyint=25
-ofps 25 -nosound -noskip -of raw
Hi Troels,
One benefit of the Incentive version of PyMOL is the Files > Save
Movie as ... > MPEG feature. If you don't have that or you want to use
a different compressor that's cool. In the past I had great luck with
mencoder (http://www.pymolwiki.org/index.php/Making_Movies)-- but I
think everyo
Hi Brian,
> Speaking of movies, is there a way to control the fade-in and fade-out rate
> of objects between scenes (eg. by changing the value of the transparency
> variable over a series of frames perhaps) using the native pymol movie
> features? Kristian Rother wrote a great movie script a n
Hello everyone,
Speaking of movies, is there a way to control the fade-in and fade-out rate of
objects between scenes (eg. by changing the value of the transparency variable
over a series of frames perhaps) using the native pymol movie features?
Kristian Rother wrote a great movie script a num
Yes, that is exactly what I wanted.
Perfect. Thank you very much.
Am 9/14/11 5:59 PM, schrieb Jason Vertrees:
> Hi Tim,
>
>> I love pymol for creating high quality figures and analysing my
>> structures. But creating movies in pymol is rather tedious... CCP4mg
>> seems to be much easier to use for
Hi Tim,
> I love pymol for creating high quality figures and analysing my
> structures. But creating movies in pymol is rather tedious... CCP4mg
> seems to be much easier to use for creating movies, you just have to
> save a scene and CCP4mg interpolates between the created scenes.
>
> Is there a
Hello Tim,
It sounds like a combination of "mview store" (saving your scenes) and
"mview reinterpolate" (interpolating between them) is what you are looking
for.
http://www.pymolwiki.org/index.php/MovieSchool_4
Unless you mean interpolating between different representations of your
structure. Cou
Hi Jason,
I have the incentive version, but how do I use rigimol? I can't find
documentation for it on the documentation webpage. The link from
http://pymol.org/dsc/dokuwiki/doku.php?id=ip&s=rigimol
seems to be dead.
Thanks, nick
On 05/18/11 15:20, Jason Vertrees wrote:
> Hi Nick,
>
> You ca
Hi Nick,
You can use the "smooth" command
(http://www.pymolwiki.org/index.php/Smooth) on the structure of
choice. Incentive PyMOL comes with a molecular morpher called
"rigimol" that morphs a starting structure into an ending structure.
I suggest trying the "smooth" command first if you already h
If you know a bit of python, you can make a version of the Plugin that will
do this via repeated calls to self.execute('Run APBS',refocus=False).
If this would be a generally useful feature, I could add a movie button to
the plugin so that it would step through all available frames, saving PNGs
fo
Hi Hirdesh,
You don't say what you have, what you want to show and what you tried
to show it. So we can't help you. I would also politely like you to
consider that perhaps we might not be very apt to do your work for
you. We're willing to help though, when you run into problems doing
your own work
Yes:
unset movie_loop
--
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 Martin
Weisel
Sent: Saturday, July 05, 2008 4:07 AM
To:
Hey Claudia,
my favorite way of making movies is importing the folder containing the
png files as frames into ImageReady. There you can assign a delay for
each image separately or all simultaneously to give you a movie of the
desired length.
Verifying this on my computer I just found out th
You can use Martz-Authored PDB Tools / MORPH2
Citation:
MORPH2 generates a series of interpolated frames between two PDB files. The PDB
files must match, atom by atom, in the same order. The interpolation is linear:
each atom "moves" in a straight line between its start and end positions. The
o
Hi Hasan,
Start with the structures superimposed and translate/rotate one/both
away from the/each other. Glue the images together in reversed order
and no one will see the difference...
By the way, it might be nice to start with small
translations/rotations and have them increase quadratically in
Use the "translate" command to move one/both of the pdb molecules until
they superimpose. Just interpolate the distance depending on how many
frames you want to do and the distance separated.
Cheers,
JTM
"We can be sure that if a detailed understanding of the molecular basis of
chemo-therapeutic
Shivesh,
Given that this is your third post on the same topic, an important point
needs to be made:
It is not reasonable for one user to expect other PyMOL mailing list
participants to teach them how to use the software, especially for involved
tasks such as movie-making. Open source is largel
Dear Shivesh-
There are a variety of approaches. For very biased reasons, I suggest
you look at:
http://www.pymolwiki.org/index.php/Slerpy
Cheers,
Joel
>>> "shivesh kumar" <2shiv...@gmail.com> 2/1/2007 3:37 AM >>>
Dear all,
How can I make a movie of crystal structure using PYMOL.Thanx i
Since this is your second message regarding the same problem... Did
you try searching the the pymolwiki.org site? Or just google for
commands/scripts to make a movie on pymol?
Here is a link that may help:
http://pymolwiki.org/index.php/Slerpy
Best,
Shiven
On 2/1/07, shivesh kumar <2shiv...@gm
Hi Adrien,
You don't really need the double loop, I'd say. What about:
for i in range(1,20):
cmd.load("o.%03d.1.pdb"%i,"m1")
cmd.load("o.%03d.2.pdb"%i,"m2")
cmd.load("o.%03d.3.pdb"%i,"m3")
cmd.hide("everything")
cmd.show("spheres")
cmd.ray()
cmd.png("o.%03d.png"%i)
By the w
ot;Grégori Gerebtzoff"
To: "'Karsten Seidel'" ;
Sent: Friday, July 07, 2006 2:28 AM
Subject: Re: [PyMOL] Movie to Powerpoint
The problem with animated gif is the color limitation to 254 + one
transparent colors, whereas PyMOL generated png's have millions of col
-GIFs
unless for websites and such.
Hope this helps. Best of Luck!
cheers,
nick
- Original Message -
From: "Grégori Gerebtzoff"
To: "'Karsten Seidel'" ;
Sent: Friday, July 07, 2006 2:28 AM
Subject: Re: [PyMOL] Movie to Powerpoint
The problem
users@lists.sourceforge.net
Subject: Re: [PyMOL] Movie to Powerpoint
Hi there,
first of all, let me say hello to all list subscribers, as I'm new here.
I've been evaluating PyMOL for a couple of months now, coming from Molmol.
Chiradip, one option next to creating an MPEG file is to make a
Hi there,
first of all, let me say hello to all list subscribers, as I'm new here.
I've been evaluating PyMOL for a couple of months now, coming from Molmol.
Chiradip, one option next to creating an MPEG file is to make an
animated GIF. Unfortunately, I don't know a free program under Windows
For this purpose I've been using mencoder (http://www.mplayerhq.hu) which is
open source and gives access to a wide range of codecs (mpeg-1, mpeg-2,
mpeg-4 (divx), realmedia, mov, avi, asf, flash etc). Here is the batch file
I used to encode a video in two-pass divx encoding (the frames were in the
There some cool free tools out there in cyberspace, one of them is Slide
Show Movie Maker by Joern Thiemann
http://www.joern-thiemann.de/tools/SSMM/index.html
Although it is not meant as a live movie maker but for slide shows, it
just a matter of frames pr. second, right ;-)
First you need to co
Video mach seems to work
chiradip chatterjee wrote:
Hi Friends
I am a new Windows pymol user.
I made a movie in Pymol and saved the 120 ray traced
*.png frames.
Now I want to convert the *.png files to MPEG files
and then directly convert/run the movie in the
Powerpoint presentation.
can anyone
Best one I have found is mpeg_encoder from Berkeley, free but runs on linux
Also Adobe premiere but $$$
Cheers,
JTM
"We can be sure that if a detailed understanding of the molecular basis of
chemo-therapeutic activity were to be obtained, the advance of medicine would
be greatly accelerated."
e.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> Satya Arjunan
> Sent: Thursday, February 16, 2006 6:11 PM
> To: EPF (Esben Peter Friis); pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] movie of diffusion of atoms/molecules
>
> Hi Esben and List,
>
> Thank you
Hi Esben and List,
Thank you for your answering my questions. I realize now that it would
be better to just represent a molecule as a sphere with diameter
corresponding to the protein's diameter because like you said, with 4000
molecules, I don't need atomistic detail.
Here is my situation:
Hi Satya
You can use the command "translate" to move the individual objects in pymol. Is
takes a list of 3 floating points numbers as the translational vector.
I don't know how Pymol would handle 4000 objects, but an alternative might be
to load them as states within one object, and then use
Raul,
Load them in to the same object in a serial fashion -- i.e. where you specify
the object state for each molecule loaded. You may also want to set the
discrete object to 1 in order to avoid extra bonds.
Cheers,
Warren
--
Warren L. DeLano, Ph.D.
Principal Scientist
Dave,
Try the move command;
move x, value and move y, value for the translation
move z, value for zoom in and zoom out
Greg
Jmarie,
The latest betas do this in real-time, but there isn't yet a facility to
writing out a static movie of that form. As you might expect, there is
broad agreement that such a capability is very much needed.
Cheers,
Warren
--
Warren L. DeLano, Ph.D.
Principal Scientist
Hi Alexander,
That all seems a bit complicated (for me anyway) but the one thing I
think your missing is the "util.mroll(1,120,1)" command. There is an
example in the user manual pages 50/51
Hope this helps
J
Alexandra Deaconescu wrote:
Hello:
I am trying to generate a movie ( a 360 degr
SAMPEG:
http://rachmaninoff.informatik.uni-mannheim.de/sampeg/
Works beautifully- very high quality movies most of the time. I've fully
automated animations with PyMOL this way. Images need to be converted
into Targa format first, but this is pretty standard.
--
> do you have any recommendations for a program under linux that assembles all
> the individual png pictures into a movie for a PowerPoint/OpenOffice
> presentation?
Dear Dirk,
I have tried mpeg_encode from Berkeley very successfully.
Its a command-line tool that makes a MPEG-1 movie from a s
Don't you hate it when users outsmart the programmer?
This is a tough one. The only solution I can think of is not memory
efficient, but it should work:
Load each frame of the movie into a separate segment or chain. This
should allow you to independently address each frame...
# assume that the
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