le to run this
interactively. Otherwise, I'm going to just create a very long pml file
with all the commands.
thanks,
Nat
ta working,
what's the minimum amount of annotation that PyMOL requires for a sheet?
PDB seems to use a lot more data which I don't believe I can supply, like
which sheets are parallel/antiparallel to eachother.
thanks,
Nat Echols
nf under SuSE 7). I'm not quite sure what's going on... all
I really need to do is execute a .pml file and run a few system calls for
now, until I create something more rigorous.
thanks,
Nat
> I have a GeForce4 Ti 4600 on a dual 1GHz PowerMac G4 (the old one with
> 133 MHz bus).
I too am using this, though on a Dell running Linux. The performance is
unbelievable; unfortunately the graphics card far outpaces the PC! I have
dual pentium IIIs and 1GB of memory, and the machine will dro
Ds for the
symmetry mates so you can still use a unique atom selection for the original
chain(s).)
-Nat
On Sunday, September 11, 2011, shukunluo wrote:
> Dear Pymol users,
>
> I want to compare the crystal packing and contacts of two different space
groups of the same protein using pymol. He
hat the payment was intended for people who wanted
> to support the future of PyMOL as well as get some high-quality
> documentation and increased personal support.
There were some features that always required payment and were never
open-s
ands.
util.cba("deeppurple")
Or did you want something you could run from a menu?
-Nat
--
Write once. Port to many.
Get the SDK and tools to simplify cross-platform app development. Create
new or port existing
onhere)) doesn't seem to work.
Did you make sure to quote the selection? This worked for me (on MacPyMOL 1.2).
-Nat
--
Write once. Port to many.
Get the SDK and tools to simplify cross-platform app development. Create
ieve is started
with the "-R" command-line flag, but I ended up coding my own. (You
can use the Python getattr() function to automatically pull methods
from the various PyMOL APIs, which saves a lot of time coding
individual wrapper functions). I can send you an example if
ex (and easy to break if the
networking does not behave), but far more powerful.
-Nat
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x27;m using a custom Python installation for this, but I
immediately ran into problems with another library, GLEW:
File
"/net/chevy/raid1/nat/build/intel-linux-2.6-x86_64/base/lib/python2.7/site-packages/pymol/__init__.py",
line 184, in
import pymol
File
"/net/chevy/raid1/n
han PyMOL:
http://robetta.bakerlab.org/
https://modbase.compbio.ucsf.edu/scgi/modweb.cgi
http://swissmodel.expasy.org/
However, the "Mutagenesis Wizard" in PyMOL may be suitable for simple
editing if the only differences between your sequence and the crystal
structure is poi
where else?
thanks,
Nat
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hem. Alternately, you can use the 'bond' and 'unbond'
commands, but this can be non-trivial to do on a large scale.
-Nat
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E 2 AC1 6 HOH A 259 HOH A 261
Obviously this still requires that the authors actually perform the
annotation. It's a poor substitute for having (for instance) entire
PyMOL sessions accompanying a PDB deposition, but I've learned to keep
my
f PyMOL,
you need to download the source bundle for CCTBX, and use the same
python interpreter that PyMOL is using to build CCTBX.
Since building open-source PyMOL is significantly easier and faster
than building CCTBX, and CCTBX has free binaries, I would recommend
(1).
-Nat
-
had to do this, but does your script call
the "ray" command before saving the PNG? As far as I remember this is
required when running in console mode - it can't save an image dump of
the OpenGL view becau
get rid of it:
set internal_gui, 0
-Nat
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5
set ray_shadows = 0
set ray_opaque_background = 0
-Nat
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ile will be located in /path/to/home/.pymolrc."
This should probably be edited to "Unix-type system", since Mac and
Linux behave identically in this case.
-Nat
--
Everyone hates slow websites. So do we.
Mol, it comes back
> with:
>
> File "/Users/adam/pymolrc.pym", line 1
> set auto_zoom = 0
> ^
> SyntaxError: invalid syntax
That's because you're using the wrong file name:
>> "On a linux-type syste
ied:
set normalize_ccp4_maps = 0
?
-Nat
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and resi 1")
cmd.color("skyblue","rov_m1")
cmd.isomesh(name="rov_m2", map="FoFc_map", level="3.0", selection="polymer
and chain A and resi 1")
cmd.color("green","rov_m2")
cmd.isomesh(name="rov_m3", map=
I'm getting the same error for a completely unrelated SourceForge
repository (but strangely, another works fine). I suspect they're having
server problems - it wouldn't be the first time.
-Nat
On Wed, Apr 30, 2014 at 1:39 PM, Andreas Förster wrote:
> Dear all,
>
> try
oms, do this:
align object1, object2, 0, 0
(the zeros specifying the number of refinement cycles, I think)
-Nat
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Apologies if this has been asked/answered already. My rotation student
just showed me how PyMOL animates the transition between scenes, which
makes for some beautiful zooming effects. Is it possible to capture these
in a movie?
thanks,
Nat
Any body know how to fix this. Have people tested this driver? Should I load
an earlier driver?
When dealing with NVidia cards, I've found this is always the first thing
to try whenever a problem arises. Their Linux drivers are updated to
support new hardware and fix old bugs, but they often
I'm trying to make a high-quality figure showing ligand binding in a
cleft, incorporating sticks, electron density, and some combination of
cartoon/surface/lines for the protein. Ray-traced shadows make the
perspective much clearer but also add visual "noise" - for instance, the
electron densi
selections altogether? (I tried changing mouse_selection_mode but this
didn't help, and now it's stuck selecting everything with a single click.)
thanks,
Nat
ydrolysis, you use ADP in both PDB files, and
later re-insert the original ATP in place of the ADP in the first
frame(s). PyMOL makes this very easy.
-Nat
On Fri, May 28, 2010 at 10:49 AM, Thomas Juettemann wrote:
> Hi Chris,
>
> the emails are only sent to you because you subscribed to the pymol-users
> list.
> If you don't want them anymore you need to unsubscribe.
>
> Click on "Show details" at the top of this email. Click then on:
> unsubscribe
Sort of an obscure question, but I've run into problems with a plugin I
wrote - based on what I've seen so far, I'm pretty sure it isn't in 0.99,
but it would be helpful to know what the minimum required vers
I suspect there is some issue with how
you are creating the object. The only settings that I've encountered so far
that can only be applied globally are ray-tracing parameters.
-Nat
--
ThinkGeek and WIRED'
t after that I'm stuck with either a blank
window (if I do nothing else), or a segmentation fault (if I call the "draw"
method).
thanks,
Nat
--
Forrester recently released a report on the Return on Investmen
On Thu, Jan 27, 2011 at 9:54 AM, Schubert, Carsten [PRDUS] <
cschu...@its.jnj.com> wrote:
> I am just getting a blank page when I try to access the Pymol Wiki. Do
> other people see the same problem?
>
Working fine for me (using Safari o
; didn't turn up
anything, and all I could find on Google was that it's handled as part of
the residue ID, e.g. "resi 10A", but that won't do what I want.
Unrelated question: is there a Python method t
just use all uppercase
characters, but I'm worried about the size of the resulting selection
strings. (I managed to crash PyMOL for the first time in years last week
with a very long selection.) Can I instead select for a *blank* insertion
code?
-Nat
---
determine what their structure assignment is, but I never figured out how
to access this info.
If there isn't anything that'll do this, perhaps I'll just write it.
-Nat
I'm planning on yanking the Quadro 2 from a machine we bought as
a server. Would I see any actual performance gain? Which chip is
actually faster, at least for what I'd be using it for?
thanks,
Nat Echols
Gerstein Lab
Yale University
Can PyMOL do coloring by B-factors? I didn't see anything about this in
the manual. If not, I'll go ahead and write a new function, unless
someone else is working on this.
thanks,
Nat Echols
I just discovered that I can't set colors with more than one decimal point
of precision. Is there any way around this? I'm trying to get a
background that blends in with part of a web page.
Nathaniel Echols
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.
--
> 0. Upgrade to 10.2.3 if you have not already done so.
On a side note, did they fix NIS compatability again after breaking it in
10.2? I dropped OS X as soon as I discovered that, since that made it
nearly useless for the environment I work in. If they got it working
again, that and the new X
re
how to get ahold of it (we have a Harvard CHARMm license, at least).
thanks,
Nat
Nathaniel Echols Programmer
n...@bioinfo.mbb.yale.edu
s, myself included), or enter
the commands to assign structure manually in pymol, e.g.
alter , ss='H'
-Nat
> workstation (O2, Octane, Fuel, Onyx)? I've got an old Pentium III PC with 450
> MHz and a (non-stereo) Nvidia GeForce2 MX440 graphics card side-by-side with
> an SGI O2 with a R12000 processor: a simple pymol (0.86) movie of a protein
> sketch at 800x800 resolution and maximum display quality req
> Pymol at least *compiles* under a vast amount of processor
> architectures, if only under Linux:
> http://buildd.debian.org/build.php?arch=&pkg=pymol
> Nothing wrong with testing your code on as much platforms as possible of
> course :)
It's harder than you think. I have a *really* old SGI, whi
> Not at all. The only way to increase ray tracing speed is to
> upgrade your CPU. I think a 100-150 Ghz Pentium 8 is just about
> optimal.
On this note, our collaborators in CS have a test Itanium2 box that I have
an account on - I've been planning to try out a bunch of comp. bio.
softwar
> I'm new with Pymol and I would like your help in the following problem:
> I have a receptor image that I want to emphasize the ligand in its interior.
I'm a big fan of transparent surfaces for this, e.g.:
http://bioinfo.mbb.yale.edu/people/nat/mbp.mpg
> Its a nonpeptidic
and inside the
> protein should not be clipped, but displayed completely.
I assume that PyMOL's clipping planes are simply OpenGL clipping planes,
in which case the answer is "no". They're handled in hardware, not by the
application.
-Nat
> Is there a limitation to the number of atoms or subunits pymol can handle?
> I reset max_triangles from 10^6 to 10^7. Didn't change a thing.
Exactly how much memory does your computer have? And what OS are you
running? I've definitely crashed PyMOL before on a Linux system when I
tried to do t
> Now there is a twist to the story. We also run linux (redhat with 2.4.18
> kernel) on a 2 CPU 930MHz (1GB RAM, Nvidia GeForce2 GTS) PIII. Working
> speed is much slower but no crashes when ray-tracing from the exact same
> pml script.
> Can it be that linux makes better use of its physical memory
I understand the question, but what about this:
http://bioinfo.mbb.yale.edu/people/nat/bilayer.png
There are obviously lots of visible pockets (this is with a solvent
radius of 1.4 - I don't know what the default is), but this seems normal.
If I crank the solvent area up to
This looks terrific. However, I'm having problems building on both Linux
and Irix (using the Intel cc and SGI cc, respectively). It compiles fine,
but './pymol.com -c' fails with "Fatal error: can't initalize module
sglite". It's still right where it should be in contrib/sglite - any idea
why th
I'm trying to make some figures for a review, and I'm seeing weird little
partial spheres show up when I try to ray-trace a polymerase structure:
http://bioinfo.mbb.yale.edu/people/nat/weird.png
They're in the bottom third of the picture, and seem to show up in
the same location i
ut of /tmp.
The Irix binary behaves similarly but I couldn't get the Mac version to work
without installing it.
thanks,
Nat
roblem for me,
but I figured I should check and see if this was a known issue or if I'm
doing something dumb.
-Nat
un multiple invocations of PyMOL at once?
-Nat
if 'foo' is the segid of your kinase,
PyMOL> select kinase, segi foo
PyMOL> color green, segi foo
it doesn't seem to care about any leading or lagging spaces, as far as I
can tell.
On Thu, 16 Oct 2003, Jonathan Ostrem wrote:
> How are segment identifiers used. I have a PDB file with a kinase
Tkinter is a separate Python module that's an interface to the Tcl Tk
library. It's probably just not installed on your system, but it is
included in the RH 9 distribution (tkinter-2.2.2-26.i386.rpm) so it should
be easy to find and install.
On Wed, 22 Oct 2003 fr...@mit.edu wrote:
> Hi PyMOLers
What's been added? I didn't see a changelog. . .
(the 'dss' command, by the way, looks unbelievably awesome.)
On Sat, 25 Oct 2003, Warren L. DeLano wrote:
> (in a whisper)
>
> I'm still in the process of building binaries, but pioneers are welcome
> to start downloading 0.92, if your platform i
> I am not suggesting at all that users should now start coding for PyMOL
> in BASIC - naturally, the best way to extend PyMOL remains to write
> additional program modules in Python. Nevertheless, for people who
> already write code in languages other than Python, the above strategy
> might repres
27;d be nice to have even more control over animation and camera
actions; PyMOL has excellent potential for making really large movies, but
the current movie commands seem tailored for interacting with a small
number of states. I want a molecular version of Maya.
-Nat
On Wed, 4 Feb 2004, Matt Frank
PyMOL will already dump POVRAY format files; you should be able to feed
these to Blender somehow. This looks like it might be useful:
http://jmsoler.free.fr/util/blenderfile/povanim.htm
No idea if it will work well. . . but probably worth a try before writing
something yourself.
On Wed, 10 Mar
> The downloaded script is then executed by Pymol, which can uses Python's
> socket abilities to download PDB files and run Pymol commands on them.
H, I like this idea. Can PyMOL open files directly over the web? It
would be nice to simply type
PyMOL> load http://server/1cll.pdb, calmodulin
er
libraries or tweak torsion angles in PyMOL, with some additions to the
Python layer? $40 isn't a lot of it's a decent partial replacement for
SGI dial boxes.
thanks,
Nat
here a
way to turn off this behavior, other than writing a script to do it each
time? In my case "unbond resnam mg, not resnam mg" does the trick, but
I've had different protein chains or substrates bound together in the
past.
thanks,
Nat
> I have commented out most all the "quality" settings until I can figure
> this thing out.
well, if you comment out the setting for 'ray_trace_frames', it'll be
using OpenGL for rendering. but you've launched on the command line, so
there is no OpenGL. uncomment that line, and see if it works.
> areas of the protein that undergo movement and show general trends. There is
> also a server at Yale (http://www.molmovdb.org/molmovdb/ ) that will perform
> simulated annealing while morphing between two structures, thereby producing
> intermediate structures that violate fewer protein restrain
> Hi, I have pymol 0.97 installed on a sgi workstation. However it keeps
> the old picture when I move the molecule, which seems like a long time
> delay. I wonder if people have similar experience.
What kind of SGI? Anything less powerful than an Octane is going to be
pretty useless for PyMOL.
st get it going on my
computer.)
thanks,
Nat
est of
the view and slides to the left. Normal mouse interaction appears largely
unaffected, although this seems to happen randomly as well.
Is this a known bug, or has anyone else noticed it? I don't recall seeing
it before. This is RedHat 9.0, GeForce Ti 4600, with driver version 6629.
-Nat
> Thanks to the poewrful software I was able to create some protein
> animations using Python. As a mac user I have the option to save
> directly the animation for quick time player. From the options I have
> upom save, I tried 'movie' and 'animation' and both formats show a
> reduced performance w
> There is a well documented bug in Powerpoint 2004 for mac regarding
> movie playback performance which seems to be the problem. There are
> hundreds of posts on Microsoft's support forums. Actually when you
> build the slide in PPT 2004 in edit mode the preview of the movie plays
> fine but not
> I don't have red hat support yet. The problem appears to be that the
> nvidia installer (nvidia...6629pkg2.run) is getting confused as to which
> kernel is running.
Just a couple of quick thoughts --
1) Does /usr/src/linux point to the original installed kernel soruces or
the updated kernel sou
> Please revise, extend, and embellish.
- structure alignment (pretty simple, but a lot of people don't know how
to use the various commands)
- as part of movies, a large section on available 3rd-party apps and
codecs would be very useful (as well as workarounds for PowerPoint
madness)
-Nat
s, name n+ca+c+o
set stick_radius, .5, name n+ca+c+o
set line_radius, .2, ! name n+ca+c+o
When you ray-trace, the 'lines' just look like thinner sticks. This
avoids using multiple objects.
-Nat
e to hear of it. The program I used to use appears to be no longer
actively developed, and it was buggy to begin with.
-Nat
> Fit only works with objects that are identical in terms of atom number,
> chainID, atom name and what not. This is not the case for a protein on
> one side and a protein plus ligand on the other.
I've gotten away with some differences between chains. Sometimes you need
to force it to fit using
you can set the number of cycles of refinement on the command line.
change this:
> align 1kjg & i. 1-99 & n. ca, 1kjh & i. 1-99 & n. ca
to this:
> align 1kjg & i. 1-99 & n. ca, 1kjh & i. 1-99 & n. ca, 0, 0
I forget what the first 0 means; the second means "don't refine." It'll
use all matching
Is there a simple tool for taking a rotation and translation matrix - in
this case, the BIOMT records from a PDB file - and applying it to an
object? Doesn't necessarily have to be in PyMOL; a simple script/program
would do.
thanks,
Nat
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