Dear PyMOL users,
I would like to make a movie showing a slice-through a cryo-EM map.
Something similar to Video 1s (produced using Chimera) in PMIDs
30602789 and 30602790:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6364807/PMC6364807/bin/NIHMS80767-supplement-Supplementary_Video_1.mp4
https:/
Hi Clarisa,
You can pass "width" and "height" arguments to the "mpng" command, like this:
mpng fileprefix, width=720, height=480
See also https://pymolwiki.org/index.php/mpng
Hope that helps.
Cheers,
Thomas
> On Jan 29, 2019, at 5:47 PM, Clarisa Alvarez
> wrote:
>
> Could anyone help m
Could anyone help me how i could change resolution of my png images make to
perform a video, that changes resolution when i open with movie maer.
Thanks in advance.
Clarisa.
___
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pymol-users@li
Hello everyone!
I want to know if I can perform a movie in educational pymol, it seems it
is not allowed, thanks in advance!!
Clarisa.
--
___
PyMOL-users mailing list (PyMOL-users
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
Dear pymol users,
I'm trying to create a movie, using lsqman and pymol, of a molecule of
~1700 residues (HETATMs deleted, no hydrogens, alternative conformations
removed). I created 60 pdb files with lsqman and loaded them (as
different states of the molecule) into pymol. In the default "lines"
Hi Appu,
interpolation between two conformations is called "morphing". You can do
this with the incentive version of PyMOL, which includes an additional
component called RigiMOL.
With incentive PyMOL 1.6, you can morph directly from the object menu:
A > generate > morph
See also:
http://pymolwik
Dear All,
I am working on an enzyme which close it active site when
react with substrate. I have solved the structure in both open and closed
conformation. Now i want to make the movie of showing a series of change in
going from open to close conformation. please tell me how to mk
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
Hi,
I have a pdb containing the morphing. I can play the movie with the loaded pdb
file. Now I want to start the movie with rocking the first state for a few
seconds and end the movie with rocking the last state for a few seconds. How
do I do that? Can I rock or nutate a state in the middle
Hi,
I have a pdb containing the morphing. I can play the movie with the loaded pdb
file. Now I want to start the movie with rocking the first state for a few
seconds and end the movie with rocking the last state for a few seconds. How
do I do that? Can I rock a state in the middle for a few
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
Hello,
**First, I'd like to apologize if you are receiving this message more than
once. I kept sending it from the wrong email name**
I'm making a movie, and I think I really got it down! However, I'm having
trouble with independent rotations.
I have nine independent objects, of which three I
Hello,
I'm making a movie, and I think I really got it down! However, I'm having
trouble with independent rotations.
I have nine independent objects, of which three I'm trying to get to rotate
their own z-axis. Is this possible? Let me show you what I mean :)
frame 30
rotate [0,0,1],360
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)
Dear users,
I would like to create a movie using Pymol between two different
conformations (structures) of a protein 1NL3_coli and 1MN6coli. I read
this can be done with rigimol. I am giving the following commands and
getting an error when giving the following command
> rigimol.morph ( "m_in"
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
Dear Users,
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 scene 2, I
Hi folks,
on OS10.5, and 10.6 Macs running MacPymol 1.2r1, we are trying to
export movies as Quicktime with H.264 which results in a one-frame
movie only, despite every frame being displayed on screen during the
write. Looking online led me to bug #1545548 back in 2006
http://sourceforge.ne
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.
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.
set ray_trace_frames = 1
That takes a long time.
And what program should I use to pack them together? The easy wasy?
Hi Guridis,
you need to store object matrices with the "mview store" command and use
"rotate" instead of "turn" (object versus camera rotation).
And you should avoid "B" as object name, because it's the b-factor
keyword in the PyMOL selection language.
mset 1x100
frame 1
mview store, object=mo
I want to make a movie with two objects.One object should remain
static(A) while the other(B) should rotate 90 degrees in x-axis. I
cannot keep object A immobile.
The commands i am using are:
> show surface,A
> show surface,B
> super B,A
> mset 1x100
> frame 1
> scene 001,store
> mview store,s
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 mo
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
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
Dear users or developers,
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
a variable into a string. The load loads
>> files and super superposes one structure onto another.
>>
>> Hope that helps.
>>
>>
>> Andreas
>>
>>
>>
>> On 10/07/2011 12:05, Babban Mia wrote:
>>>
>>> Hello Everyo
Dear MfG, formerly known as Holfelder, here's an expanded script:
load x_1.pdb
zoom
#orient molecule at this point as you desire
ray
png x_1
disable x_1
for i in range (2,10001): \
cmd.load("x_%d.pdb" %i) \
cmd.super("x_%d" %i, "x_1") \
cmd.ray() \
cmd.png("x_%05d" %i) \
cmd.di
s % notation substitutes a variable into a string. The load loads
> files and super superposes one structure onto another.
>
> Hope that helps.
>
>
> Andreas
>
>
>
> On 10/07/2011 12:05, Babban Mia wrote:
> > Hello Everyone
> >
> > I have got
one structure onto another.
Hope that helps.
Andreas
On 10/07/2011 12:05, Babban Mia wrote:
> Hello Everyone
>
> I have got a doubt relating to making PYMOL MOVIE.
> I have like 10,000 PDBs named x_1.pdb .x_23.pdb and so on
>
> I want to make a movie which essentially
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
Hi,
can pymol interpolate between states in a movie? Suppose I have
coordinates of a docking process with several states, and I would like
to animate that process, but smoothly. I would
madd 1 x15
madd 2 x15
.
.
.
but would like pymol to interpolate in those 15 frames between state 1
and 2, then
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
I am trying to figure out how to design a movie that will preform a morph
between two conformations of a protein, while having each chain move as a
rigid body, and recalculate the electrostatic surface for each midstate
between conformations. Can anyone offer me some suggestions on how to do
this?
Hi Aiko,
That's impressive for only using PyMOL one day. As a solution, just add,
mview reinterpolate
right before
frame 433.
So, at the end of your file you should have:
frame 432
set_view (\
0.264227241,0.815219104,0.515365601,\
-0.842250228, -0.065306552,0.53512
; Sent: Friday, February 11, 2011 5:52 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] pymol movie scripting for beginners questions
>
> Dear Mailing list!
>
> I have just started using pymol to make a molecular movie of a protein
> ligand
Dear Mailing list!
I have just started using pymol to make a molecular movie of a protein
ligand system.
What I came up with is:
###
reinitialize
set matrix_mode, 1
set movie_panel, 1
set scene_buttons, 1
set cache_frames,
ly load either of them into a PyMol movie.
> I'm trying to combine them give a 64 states movie.
>
> That's what I did:
> load nmr1.pdb,mov
> load nmr2.pdb,mov,33
> mplay
>
> Since these two files are not superimposed in the first place, the first 32
> frames sho
Dear All,
I have two NMR.pdb files that describe the same molecule. They are 32 states
each. It's possible to separately load either of them into a PyMol movie.
I'm trying to combine them give a 64 states movie.
That's what I did:
load nmr1.pdb,mov
load nmr2.pdb,mov,33
mplay
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
Hi All,
I want to prepare movie for my presentation representing various properties
of protein and bound ligand. Can anyone help me for the same
--
Hirdesh Kumar Sharma
M.S. (Pharm) Final Semester
Centre for Pharmacoinformatics
A-212; Research Block A
NIPER,
Sector 67, S.A.S. Nagar, Mohali
Punja
Magnus,
Use 'madd' in place of the second (any and subsequent) 'mset' commands.
Cheers,
Warren
> -Original Message-
> From: Magnus Andersson [mailto:m...@farma.ku.dk]
> Sent: Monday, March 16, 2009 10:39 AM
> To: pymol-users@lists.sourceforge.net
> S
Hi,
I have a problem appending two scenes in a movie. First I want to make a
turn of the protein. Then I want to move between a series of 50 morphs of
a conformational change of the protein. The problem is that the last mset
command seems to override the first, so that I only see the last scene an
nal Message-
> From: liyang [mailto:liy...@moon.ibp.ac.cn]
> Sent: Monday, March 02, 2009 9:49 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Question about Pymol movie
>
> Dear all,
>I got two small molecule binded protein structures, during
> the reactio
Dear all,
I got two small molecule binded protein structures, during the
reaction, this molecule moves from one site to another. Given the
two pdb files, can I make a movie to simulate the whole process
in Pymol? Any suggestion will be appreciated.
--
Open WebMail Project (http://openwebmail.
: pymol-users@lists.sourceforge.net
Subject: [PyMOL] movie between frames
Hi there,
I loaded a number of cgos into different states using the 'load_cgo'
command:
cmd.load_cgo(obj1,'cgo1',1)
cmd.load_cgo(obj2,'cgo2',2)
...
cmd.mplay() produces a nice movie
Hi there,
I loaded a number of cgos into different states using the 'load_cgo'
command:
cmd.load_cgo(obj1,'cgo1',1)
cmd.load_cgo(obj2,'cgo2',2)
...
cmd.mplay() produces a nice movie in an endless loop. Is there a
possibility to stop the movie once it has reached the last frame (sth.
like cmd.mpla
Hi everyone,
I wonder if it is possible to change the color of the morph movie.
For example I want to start morhing one color and end up with another color
while it is morphing.
Thanks.
Hasan Demirci
Department of Molecular Biology, Cellular Biology & Biochemistry
Brown University
69 Brown Stree
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
Dear list,
I'm trying to prepare a movie in mpeg format transforming the Pymol png frames
into tga and then merging them with makempeg. I cannot get, however, a
reasonable frame rate: the final movie is too quick and unacceptable for a
Powerpoitn presentation (which is what I would need it fo
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
Hi,
I have two pdb files that I want to superimpose them onto each other. (I know
how to do this part)
however, at the same time i want to generate a movie showing those two pdb
files going into each other.
Does anyone know how to do it?
Thanks in advance.
Hasan Demirci
Department of Molecular
this open-source endeavor!" -WLD
_
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of shivesh
kumar
Sent: Thursday, February 08, 2007 1:29 AM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] movie in pymol
Dear all,
Dear all,
I am trying to make a movie in pymol with two structure of the same
protein.one is crystal structure and one is NMR structure.The N-terminal part
of crystal structure is in open conformation whereas that of NMR is closed.What
command should I use.Is it possible to make the movie with
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
Dear all,
How can I make the movie.I have .pdb file.
First I have to load the file,then mset.Then what is util.mrock.Please help.
Thanx in advance.
Shivesh
shivesh
-
Food fight? Enjoy some healthy debate
in the Yahoo! Answers Food & Drink Q&A.
Dear all,
How can I make a movie of crystal structure using PYMOL.Thanx in advance.
Shivesh
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
Dear Pymol uers,
Sorry for this probably basic question but the "search" option for this
mailing list seems to be out of order on the sourceforge website...
I'm trying to make a movie with 3 molecules for each frame. As each molecule
is in a separate pdb file, I would like to find a way to do s
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
have been added/modified.
Hope this helps!
Cheers,
Greg
-Original Message-
From: chiradip chatterjee [mailto:chiradi...@yahoo.co.uk]
Sent: mercredi, 5. juillet 2006 22:15
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Movie to Powerpoint
Hi Friends
I am a new Windows pymol user.
I
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
dicine
University of Alberta
ja...@biochem.ualberta.ca
*
- Original Message -
From: chiradip chatterjee
Date: Wednesday, July 5, 2006 3:14 pm
Subject: [PyMOL] Movie to Powerpoint
> Hi Friends
> I am a new Windows pymol user.
> I made a movie in Pymol and sav
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 please help me in this regard
Thanks
Chiradip
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
t;stick" together:
pymol> alter my_object, vdw=3.0
pymol> show spheres, my_object
pymol> sort
Cheers,
Esben
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net on behalf of Satya Arjunan
Sent: Sat 2006-02-11 03:56
To: pymol-users@lists.sourceforge.net
Subj
Cheers,
Esben
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net on behalf of Satya Arjunan
Sent: Sat 2006-02-11 03:56
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] movie of diffusion of atoms/molecules
Hi all,
I would like to use Pymol to visualize 3D simulation of latt
Hi all,
I would like to use Pymol to visualize 3D simulation of lattice-based
diffusion of molecules. The simulator provides the 3D coordinates (or
the translational direction since they have fixed diffusion distance) of
the molecules at everytime step. At the end of the simulation, I would
l
ers-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
> Raúl Mera
> Sent: Wednesday, November 09, 2005 9:37 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] movie from chempy objets
>
> Greetings
>
> I need to create pseud
Greetings
I need to create pseudo-atoms with Van der Waals
radius defined by me, I know how to do it using
chempy, and loading the chempy objets into pymol, but
i need to create several chempy objets and show them
in pymol as frames of a movie. (i.e getting a movie of
an objetc which VdW radius ch
Dear all:
I would like to make a simple movie of a structure ( a full rotation
about the y axis) with a very strong fog effect. I have tried playing
with depth_cue, ray_trace_fog settings as shown below but I do not get
as strong a fog effect as I would like. Adjusting the clip planes
w
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
Hi, all.
This is my next installment of what is probably another dumb question from a
new user, but
I'm trying to learn how to construct movies, and havind some success. However,
I cannot seem to create anything that involves translating multiple objects and
zooming in on a particular area
ol-users-ad...@lists.sourceforge.net
> [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Jmarie
> Sent: Wednesday, March 09, 2005 9:12 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] Movie (one more)
>
> Hi,
>
> Is it possible to record as a movie, the p
Hi,
Is it possible to record as a movie, the passage between 2 (or more)
store scenes (F1,F2…)?
It seems that Pymol calculated all the states between two different
store scenes. It would be easier for make complex movie with zoom and
change of orientations.
--
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
Hello:
I am trying to generate a movie ( a 360 degree rotation around the y
axis) using the mset and mdo commands. I can play the animation alright
in Pymol, but when I am trying to save it as either a
Quicktime file or a series of pngs (that I would like to create an
animation of in ImageRead
Hi!
I am trying to figure out how to make a movie with several panels,
i.e., one panel showing large protein structure domain movements, the
other on the same screen showing the corresponding detailed structural
changes at the domain interface. It would be nice to interlacing these
two together so
Dear Pymollers,
I have some basic Pymol questions because of some constraints that I have
with my computer systems. I have a URGENT need to do some complicated
animations for some upcoming talks. I have two computer systems:
Mac G4 Powerbook: 400 MHz, 1 Gig Ram, Pymol 0.9 installed through Fink
Hi List!
I'm trying to make some movie script. I read a bit about in several
places. By now I'm almost getting what I want, but I need help, follows
my partial script:
---
del all
load c1/forcedin.pdb,c1
load c2/forcedin.pdb,c2
frame 1
hide all
run Pymol/stride_ss
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