David,
By default, when HETATMs are loaded from a PDB file, the "ignore" flag
is set, which means that they are excluded from surface & mesh calculations.
You can clear these flags with:
flag ignore,all,clear
rebuild
Alternatively, you can just tell the surface and mesh algorithms to
Fred,
Not currently. To the rest of the list: How important is this to
people? Please send me an email directly if you think it would be an important
feature to add.
Warren
--
mailto:war...@sunesis.com
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341
Kevin,
It looks to me like you are missing Numeric Python. Either you need to
remove the _PYMOL_NUMPY option from the Rules.make, or you need Numpy
installed. There is likely a Fink package which contains it, but I suspect
this dependency may have been missed in the creation of the Fi
Dear PyMOL Users and Friends,
It is with great excitement and anticipation that I announce a new
phase for PyMOL: Beginning April 3rd, 2003, I will be committed FULL-TIME to
the development, documentation, and support of this Open-Source package through
my limited liability company, De
PyMOL's internal raytracer isn't likely to support perspective any time
soon. Instead, I recommend using PovRay.
Cheers,
Warren
> Subject: Re: [PyMOL] different transparencies
>
> DeLano, Warren wrote:
>
> >Because of the way settings work in PyMOL, you will n
Certainly,
For example: to create a selection "near145" consisting of all atoms within 4 A
of residue 145:
select near145, all within 4 of 145/
And to select complete residues:
select near145, byres ( all within 4 of 145/ )
Cheers,
Warren
--
mailto:war...@sunesis.com
Warren L. DeLano, Ph.D.
ATI/Linux Graphics Card Users,
One of our users has been struggling with a strange crash on an ATI Radeon
Mobility chip under Redhat 8.0. Display of cartoon representations generated
an illegal instruction and crashed the program. A workaround has been
discovered: turn of ATI hardware acceler
Roger,
The code is in:
$PYMOL_PATH/modules/pmg_tk/Demo.py
Note that there isn't any demo which displays electrostatic surface potential.
That capability won't present be in PyMOL until the next release, but even then
you'll still need some external program to calculate the protential.
War
The patch can be found at
http://cobra.mih.unibas.ch/dino/pov/index.php3?p=patcho
"help povray" unfortunately has a typo in the url, but is otherwise informative.
Good luck. Unforunately, this stuff is 1.5 years out of date -- I haven't
revisited the triangle situation since then. From what I
Kaushik,
Good questions.
(1) PyMOL doesn't show the solvent accessible surface, rather it shows the
solvent/protein contact surface. The solvent accessible surface area is
usually defined as the surface traced out by the center of a water sphere,
having a radius of about 1.4 angstroms
Of course!
Before you load a PDB file, run the command:
set connect_mode,1
You can put this in your ".pymolrc" file if you want this to be the default
behavior.
Note that with this approach, you'll need to supply ALL connectivity
information, even for standard residues. At some point in the
. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606 FAX:(650)-266-3501
> -Original Message-
> From: Alan Wilter Sousa da Silva [mailto:a...@biof.ufrj.br]
> Sent: Thursday, February 06, 2003 7:41 AM
>
Naveen,
We've had great results with the FireGL series, and the OpenGL performance of
the FireGL X1 is excellent (http://www.spec.org/gpc/opc.data/vp7/summary.html).
However, the trick with these cards is to allow ATI's binary driver
compatibility to dictate your choice of Linux distribution
Anthony,
I agree that we need one, but it doesn't currently exist. The same can be said
for surface calculations, especially when you've loaded a 500 frame MD
trajectory and accidentally "show surface" (doh!).
My advice: save sessions often and make liberal use of PyMOL's logging
capability.
Bartholomeus,
You have run into limitations in PyMOL's handling of single objects.
The answer to both these questions is to split your molecule into multiple
object and color/show independently. Use the "create" command to make copies,
and then use alter to reassign secondary structure codes w
Doug,
(1) I've got a hard deadline to have this capability in the program
less than 1 month from now...not the pot. calc., just the import, rendition,
and coloring.
(2) no clue
Warren
--
mailto:war...@sunesis.com
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceu
Carsten,
You're bumping up against a 63-character limit I currently have for any one
individual argument in PyMOL's internal parser. Obviously I need to either
safeguard that limitation to prevent a crash or eliminate it. You can still do
this in a single selection, as follows
select pock
Jacob,
It look to me like you've found a bug in PyMOL with the manual
approach. What's happening is that the result of a subsequent ignore command
isn't updating the surface which was created before it. The scripted behavior
is correct, since all geometric objects should reflect the c
The SourceForge status page is a good place to look for info on CVS problems:
http://sourceforge.net/docman/display_doc.php?docid=2352&group_id=1
Project CVS Services: Developer (SSH) CVS access online; pserver-based CVS
access and ViewCVS (web-based) access offline
Warren
--
mailto:w
> From: Nukri Sanishvili [mailto:rsanishv...@anl.gov]
> There is a new thing (I'm pretty sure it's a bug, not a
> feature) in 0.86:
> When I Tab for command completion, the command ends with a
> comma when in
> fact = is expected. For example, set cartoon_fl(Tab)at_sheets, not set
> cartoon_fl(
Jack,
What are all those extra "Q" atoms in the pdb file? They look to me like
compromise/placeholder coordinates for NMR-equivalent hydrogens...or something
like that.
To get a reasonable picture, you can get rid of the extra bonds with
unbond elem q*,all
or just nuke the "Q" atoms alto
Tara,
Use Python (and the run command with .py files).
from pymol import cmd
f=open('dist.txt','w')
dst=cmd.distance('tmp','mol1///25/ha','mol1///26/ha')
f.write("%8.3f\n"%dst)
f.close()
You could measure the whole protein this way by putting a loop around the
distance command:
from pymol impo
Stephen,
You're looking for the PyMOL API function "extend":
from pymol import cmd
cmd.extend("ramp_colors",ramp_chain.ramp_colors)
Would then permit the following:
ramp_colors chain A
See "help extend" for more info...
Cheers,
Warren
--
mailto:war...@sunesis.com
Warren L. DeLano, Ph.D.
Inf
Kristl,
It may not be possible to switch PyMOL over to correctly recognizing
these bonds by default, but you should be able to use the "bond" command after
loading to manually create the bonds.
Cheers,
Warren
--
mailto:war...@sunesis.com
Warren L. DeLano, Ph.D.
Informatics Manager
S
Laurence,
This is a bug I found a couple of days ago and remedied -- the 3D hash code
in the raytracer was faulty. In the meantime, you may want to render with
PovRay. Would you please send me a quick email (off the list) with your
version and platform information so that I will know the e
zoom along?
Cheers,
Warren
>
> Chris
>
> - Original Message -
> From: "DeLano, Warren"
> To: "Chris Arthur" ; "pymol-users"
>
> Sent: Monday, December 02, 2002 4:00 PM
> Subject: RE: [PyMOL] Zooming in animations
>
>
> Chr
Chris,
If you are talking about a controlled zoom into a specific active site
region, there isn't any automated way to do this. Peter's "movie.zoom" routine
can help with a general zoom. Try this:
fragment arg
mset 1 x100
movie.zoom 1,100,1,0
mappend 1:move z,-100
rewind
mplay
Cheers,
Wa
Keith,
Thank you for bringing this issue to my attention.
I can confirm that PyMOL doesn't currently read SCALE records. In order
to generate correct crystal symmetry, it requires the input PDB coordinates to
be properly oriented and translated with respect to the crystal latti
Kelley,
Unfortunately PyMOL doesn't have object-specific Z-clip. (That is a
cool idea though, perhaps in the future...)
The closest thing to this you can accomplish is to selectively show or
hide the surface on certain atoms in order to create a view which shows the
full ligan
As some of you may already know, we now have a freelance writer working with
us to rewrite/improve the PyMOL manual. This has been made possible through
the contributions of PyMOL licensees (specifically: Shering-Plough, Incyte,
Pfizer, Karo-Bio, as well as many other small contributors -- t
Bill,
There has been some discussion of this desirable feature, but it doesn't
currently exist.
Cheers,
Warren
> -Original Message-
> From: wgsc...@chemistry.ucsc.edu [mailto:wgsc...@chemistry.ucsc.edu]
> Sent: Tuesday, November 12, 2002 1:27 PM
> To: pymol-users@lists.sourceforge.net
Scott,
> From: Scott Classen [mailto:clas...@uclink.berkeley.edu]
>
> Hello fellow PyMOLers,
> Is the surface in PyMOL a solvent accessible surface or
> a molecular
> surface? It looks like a solvent accessible surface to me. Is
> there any
> way to change the radius of the water probe
Tara:
One easy way is simply
(not hydro)
Wildcards in atom names are currently disabled because nucleic acid chemists
use asterices in atom names. However it is better to use the element symbol,
since there is no guarantee that an atom name will start with the element:
(elem c,n,o,s)
Cheers
The native OSX version doesn't support the Tkinter-based user interface, but
you can use the unaccelerated versions of PyMOL available in Fink or GNU/Darwin.
Warren
> -Original Message-
> From: robert del vecchio [mailto:delve...@cshl.edu]
> Sent: Tuesday, November 05, 2002 9:00 AM
> To
> 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.
>
Not true... just the output is rounded. The exact color is whatever you set it
to.
PyMOL>se
Jules,
Unfortunately, PyMOL molecular editing features are not really
documented yet.
You can move entire object independently using the "MovF" and "RotF"
mouse actions. With the normal three-button mouse configuration in Editing
Mode, that would be shift-middle-click and sh
By default, PyMOL doesn't surface PDB HETATMs.
To surface all atoms,
set surface_mode=1
To surface all atoms except hydrogens,
set surface_mode=2
Cheers,
Warren
> -Original Message-
> From: Kersey Black [mailto:kbl...@jsd.claremont.edu]
> Sent: Wednesday, October 30, 2002 3:09 PM
>
mset 1 x360
movie.roll 1,180,1,axis=y
movie.roll 181,360,1,axis=x
> -Original Message-
> From: Craig Smith [mailto:boiler...@mac.com]
> Sent: Wednesday, October 30, 2002 11:43 AM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] making a two step movie in pymol
>
>
> How do I cr
This is undocumented:
To get a list of settings:
from pymol import setting
print setting.get_name_list()
To get the current value of a setting:
print setting.get_setting_text("bg_rgb")
print setting.get_setting_text("gamma")
To get a list of names with values:
print map(lambda x:[x,setting.ge
Gordon,
I fully agree with your assessment that PyMOL is currently unable to reach
its potential due to a number of factors, including poor documentation.
Nevertheless, I do have a defined plan for eliminating these deficits. It
involves securing funding to hire people under contract
Mark,
Coloring by partial charge should work fine, provided that you supply
partial charges to PyMOL...which isn't trivial. You could either assign them
using the 'alter' command after loading a PDB or SDF file, or you could convert
your molecule into a Chemical Python "model" object, assig
Frank suggested a good approach. You can also do the job within one object:
show surface, (resi 110,128,134,135,120,131,118,138,121,129,132,136)
flag ignore,(not (resi 110,128,134,135,120,131,118,138,121,129,132,136))
rebuild
Cheers,
Warren
-Original Message-
From: Vondelft, Frank
Hi
PyMOL is currently just a little too smart in this area -- it checks to see
whether the CA atoms are connected through C and N atoms. The next version
will support CA traces with just CA positions.
In the meantime, you might want to look into the CGO capability, which lets you
draw arbitrary
> From: Jules Jacobsen [mailto:jo...@hermes.cam.ac.uk]
>
>
> you can change most of the parameters using set dash_n where
> n= length,
> width, gap, radius. Unfortunately dash_color doesn't exist.
>
...but you can change the color of a distance object
color red,dist01
Warren
Thanks for the suggestion?
For now, why not just redefine the existing colors?
No need for a leading underscore...
set_color green= [0.00 , 0.53 , 0.22]
etc.
Note that there are default atom colors such as "carbon", "nitrogen", "oxygen",
"hydrogen", "sulfur", etc. which should also be redefi
Atom selections aren't directly exposed to Python, but you can have PyMOL build
a Python list containing whatever information you need:
Using PyMOL commands:
list=[]
iterate (name ca),list.append((resi,resn))
print list
[('ASP', '1'), ('CYS', '2'), ('ALA', '3'), ('TRP', '4'), ('HIS', '5'), ('LE
the PyMOL folder (as well as
in the "Darwin" sub-folder).
Cheers,
Warren
-Original Message-
From: J. Evan Sadler [mailto:esad...@im.wustl.edu]
Sent: Wednesday, October 16, 2002 8:27 AM
To: DeLano, Warren
Subject: Re: [PyMOL] MacOSX and Three button mice.
Warren,
Great sugg
> From: Kristian Rother
> In this and other recent questions inside and outside this
> forum i have
> discovered that many of them could be solved quite easy if
> there was an
> easy way to access the atomic coordinates directly from the PyMOL API.
>
> Is this achievable somehow?
The actual
> From: J. Evan Sadler [mailto:esad...@im.wustl.edu]
> I have povray3.5 working from within pymol, but adjacent
> colors on surfaces
> show jagged lines instead of smooth. I gather that patching
> povray3.1 fixed
> this. Is there a way to do the same for povray3.5?
I've heard that PovRay3.5 sup
> From: Xavier I. Ambroggio
>
> Dr. Delano,
>
> First of all, thank you for developing PyMOL. I want to
> modify the util.py
> to create another color scheme, similar to the util.cba* schemes. How
> would I do this and what would I need to do with the modified util.py
> script to get the PyMOL
Question 1, CA-trace:
show ribbon
set ribbon_sampling=1
(NOTE: requires all main chain atoms to be present, but not necessarily visible
-- CA-only models will be supported later on).
Question 2, Alignment of structural homologs (requires version 0.82).
load prot1.pdb
load prot2.pdb
align pro
Thanks to the previous responders! In addition, versions 0.82 and beyond
support a more intuitive distance selection phrase:
"... within ... of ..."
For example:
load lig.pdb
load prot.pdb
select site,prot within 6 of lig
show surface, site
Note that if the ligand and protein are in the same
Yep, we ran into the same problem with our ESGI emitters and FireGL2 cards --
we ended up having to buy new StereoGraphics (E-2) emitters for the Linux
machines (~$200).
http://www.qualixdirect.com/
part # SV-008-A-PC-E2
Cheers,
Warren
> -Original Message-
> From: Viktor Hornak [mai
William,
You might want to try using the "top" utility to determine whether or
not some other process is soaking up CPU while PyMOL is
-Original Message-
From: William Scott [mailto:wgsc...@hydrogen.ucsc.edu]
Sent: Saturday, October 05, 2002 7:13 PM
To: pymol-users@lists.source
Samy,
Try increasing your refresh rate. You need a vertical refresh in the 100+
Hz range to avoid flicker. If that doesn't do the trick, then perhaps there is
something wrong with the emitter?
Warren
-Original Message-
From: Samy Meroueh [mailto:m...@gordon.chem.wayne.edu]
Sent: S
Ron,
This appears to be a Windows specific problem. I can view spheres with
1bgy.pdb just fine under Linux (albeit 168 MB of RAM...), but it blows out on
Windows.
However, if you lower the sphere_quality (which only affects OpenGL quality),
it holds together:
load 1bgy.pdb
set sphere
There is also a translate function similar to "rotate", the docs for these
don't exist yet, because the implementation isn't finished. However, feel free
to used them in the following forms:
translate vector,object-name,state
vector needs to be something like [x,y,z]
translate [1,0,0],p
Shohei,
The easiest way to do this is to split the objects and then use the rotate
command.
# save as a ".pml" file...
load 1FJ1.pdb
# split PDB file
create anti=(chain F)
create fab=(chain A,B)
# delete original object
delete 1FJ1
# color objects
color green,fab
color pink,anti
# color
From: George Nicola
>I've tried several settings and commands but cannot figure out how to make
>a simple ball-and-stick representation of a molecule. Can it be done in
>Pymol?
George,
Yes, but it is non-obvious:
hide lines
show sticks
show spheres
set stick_radius=0.1
set sphere_scale=0.25
Hi Jeremy,
If the proteins have significant homology, then you can use the align command:
align prot1ca,prot2
which will perform a sequence alignment of prot1 against prot2, and then an
optimizing fit using the CA positions. I'm not sure if the help text for align
got into 0.82, but the n
David,
I haven't written this into the CGO system, which is pretty rudimentary
and pretty incomplete at present. Transparency is actually tough to get right,
since certain kinds of objects need to be rendered before the transparent
surface -- others after. Then there's the issue of Z-
Serge,
The zoom command in the released version is flaky and sometimes causes
clipping. I've fixed this in the development version and will be preparing a
new release shortly.
The best thing you can do right now is put a large buffer on the zoom
command...
zoom all,20
etc.
You can't raytrace it the background using threads, but if you have everything
in a script, you can launch a separate process to do the work:
"pymol -c script.pml"
or
"pymol -c script.py"
will run PyMOL without a Window. You do need to like against the X11 and
OpenGL libs though...
Cheers,
Scott,
isomesh msh1, map1, 1.5, myobject, carve=2.1
The postfix "carve=2.1" will trim density which is more than 2.1 A from
myobject.
You may want to play around with the exact cutoff...
Cheers,
Warren
> -Original Message-
> From: Scott Classen [mailto:clas...@uclink.berkeley.edu
ving to write out a list?
>
> thanks,
>
> Kaushik Raha.
> Penn State University.
>
> On Friday, September 20, 2002, at 04:07 PM, DeLano, Warren wrote:
>
> > Alex,
> >
> > If the sulfurs are within disulfide bonding distance,
> PyMOL should
>
Alex,
If the sulfurs are within disulfide bonding distance, PyMOL should
connect them by default. If this is not happening, please send me the PDB file
so I can take a look-see.
Otherwise, you can use the "bond" command to attach them:
bond 24/sg,26/sg
bond 56/sb,99/sg
unpick
> From: Peter M. Wolanin [mailto:pwola...@princeton.edu]
> One other thing with pymol and 3D stereo: on our system, at least, it
> seems as though the on-screen rendering is much faster and smoother in
> stero mode than in regular mode. Pymol in its usual mode
> seem much slower
> than spdbv.
It looks like nVidia may have finally answered our pleas for stereo under Linux
: )
Forwarded from Peter Wolanin (with permission):
--
In case you're interested, I was able to get quad-buffered stereo 3D
graphics with pymol on a linux (Redhat 7.3) system after a couple weeks of
false starts.
Okay I found the problem...
This fails:
"mpng mov # will create mov0001.png, mov0002.png, etc."
but this:
"mpng mov
# will create mov0001.png, mov0002.png, etc."
works fine.
The problem is that PyMOL isn't yet 100% tolerant of comments which follow
PyMOL commands on the same line. Unfortu
Jennifer,
That looks like some blatantly buggy behavior in PyMOL. Strange thing is, I
don't get the same behavior on the version I have installed. Thus, I may have
inadvertently fixed this problem...
What version of PyMOL are you using? (under Windows obviously...)
Thanks,
Warren
--
ma
Michael,
None of the official releases have Amber trajectory support (although
the mac 0.84 beta may have an early version of this code). I'm planning on
another release near the end of September.
If you can build from the CVS repository, then you can use the code today:
(1) make sure
Scott,
> From: Scott Classen [mailto:clas...@uclink.berkeley.edu]
> OK I am now trying to make a movie and I have a question
> I start the movie out like this:
>
> mset 1 x72
> mdo 1: turn x,5; turn y,5
> mdo 2: turn x,5; turn y,5
> mdo 3: turn x,5; turn y,5
> mdo 4: turn x,5; turn y,5
> mdo 5:
Yes, the Fink and GNU/Darwin versions of PyMOL are unaccelerated. As far as I
know, the only way to get access to hardware is to call Apple's
platform-specific OpenGL libraries from within a platform-specific window.
I am still working on the native OSX port, but with competition from all the
layer4/Selector.c
http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/pymol/pymol/layer3/Selector.c
search for SELE_ARD_ and SELE_EXP_ in "SelectorModulate1" in
and SELE_BYR1 in "SelectorLogic1"
--
mailto:war...@sunesis.com
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
3
No, not a stupid question. PyMOL doesn't currently provide a means for doing
this -- I'll put it on the list...
Cheers,
Warren
> -Original Message-
> From: Luca Jovine [mailto:lucajov...@mac.com]
> Sent: Thursday, August 08, 2002 4:41 PM
> To: Mailing List PyMol
> Subject: [PyMOL] How t
alter eys/,type='ATOM'
sort
The problem is that, by default, PyMOL doesn't create ribbons for HETATMs
(typically ligands and solvent). With the above command, you're converting
selenocysteine residues into regular atoms and sorting them into place so that
they can be included in the ribbon.
C
Even better: try the "feedback" command:
feedback disable,all,actions
feedback disable,all,results
Will suppress most of PyMOL's normal chatter.
At first I thought this was a bug, but after Russel sent me the files, it turns
out that this reveals an important concept for movie-making with PyMOL...
In order to make movies which associate atom identities through a trajectory ,
you must specify unique identifiers for each atom. Just the at
Jason,
Try turning off "Smooth Loops" in the Cartoon menu.
or
set cartoon_smooth_loops=0
Also potentially useful is
set cartoon_flat_sheets=0
Cheers,
Warren
--
mailto:war...@sunesis.com
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S.
Molecular sculpting works like a real-time energy minimizer, except that it
isn't minimizing the energy. Instead, its just trying to return local atomic
geometries (bonds, angles, chirality, planarity) to the configuration the
molecules possess when they were first loaded into PyMOL.
To actu
Not right now...
In order to build PyMOL without linking to real GL libraries, you'd either need
a fake copy of the GL API, or "#define" out all of the gl calls in PyMOL (many
hours of work).
Sorry!
Warren
--
mailto:war...@sunesis.com
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmac
> So there is no way to run and control PyMol from within
> another python program?
If PYMOL_PATH, LD_LIBRARY_PATH, and TCL_LIBRARY are correctly defined, then you
can launch PyMOL from an external Python program as shown in
examples/devel/start_pymol.py.
However, this is not recommended bec
Trissa,
I think that the line may have been wrapped in your copy of the input file. Try
making sure that entire Python in the script file appears on a single line --
then it should work.
Cheers,
Warren
--
mailto:war...@sunesis.com
Warren L. DeLano, Ph.D.
Informatics Manager
Sunesis Pharmac
Jeff,
It would take a little Python programming, but modules/pymol/util.py
has the rainbow command which can be modified so as to give a more restricted
gradient than the current rainbow.
usage:
load prot.pdb
util.rainbow("prot")
(or just select the rainbow option on the color pop-up
> From: Johan Leckner [mailto:jo...@pasteur.fr]
>
> I'm having problems running PyMol from within another Python program.
This is not the recommended way to run PyMOL and may lead to problems. You can
run Python programs within PyMOL as follows:
from the command-line:
pymol example.py # s
> From: Kristian Rother [mailto:kristian.rot...@berlin.de]
>
> As suggested by Warren, i have made some improvements to the
> ScriptBox,
> which should integrate better into PyMOL now,
Thanks Kristian!
> On my page, there is also a 'quick and dirty' hack for PyMOL.
> FilePipe.py allows to exec
Building ChemPy models is a snap. Just "run" the following Python program from
within PyMOL.
from chempy.models import Indexed
from chempy import Bond, Atom
from whrandom import random
from pymol import cmd
model = Indexed()
# create some atoms
for a in range(1,11):
at = Atom()
at.name
There is another (until now, undocumented way):
flag ignore, not A/49-63/, set
delete indicate
show surface
Would achieve the same effect. If the surface was already computed, then
you'll also need to issue the command:
rebuild
Cheers,
Warren
--
mailto:war...@sunesis.com
Warren L. DeLano, Ph
Zac,
Thanks for the report.
The fact that it happens with Ono too indicates that it is a
driver/openGL-level bug. You can try some things like disabling depth cuing
(set depth_cue=0) or smoothing (set line_smooth=0), but most likely you will
need to wait for a driver upgrade. Please do
My guess is that you may still be showing sticks in the original object,
instead of just cartoons. If you have the same overlapping representation in
two objects, it isn't predictable which will show up in the ray-tracer, and you
can get exactly this behavior, where you see one color in OpenGL
This can only be done over discrete ranges, as follows:
color br0,b>5
color br1,b>10
color br2,b>15
color br3,b>20
color br4,b>25
color br5,b>30
color br6,b>35
color br7,b>40
color br8,b>45
color br9,b>50
Cheers,
Warren
--
mailto:war...@sunesis.com
Warren L. DeLano, Ph.D.
Informatics Manager
Sun
Hi Michel,
PyMOL doesn't surface HETATM's by default. A HEME is labeled a hetero-group
in the PDB and is ignored by the surfacing routine (the ignore flag is set for
those atoms). To fix that, you need to clear the ignore flag for the HEM atoms:
flag ignore, hem/, clear
rebuild
Alternativ
No, not yet. The best thing to do is just study the code for those that
currently exist. The wizard functionality is really a stop-gap measure...in
the future we'll build a more robust user interface.
Cheers,
Warren
--
mailto:war...@sunesis.com
Warren L. DeLano, Ph.D.
Informatics Manager
Michael,
A present, you can't simply "import" the PyMOL program as a module. You
need to use PyMOL as your Python interpreter.
You can use "Run" from the File menu or the "run" command from within PyMOL.
PyMOL>cd c:\some_directory
PyMOL>run myscript.py
Since you are under windows, you can
> From: Marc Saric [mailto:marc.sa...@mpi-dortmund.mpg.de]
> >2. Let's Introduce Your Company To China Government
> (investcn2...@yahoo.com.cn)
> ^ ^ ^ ^
> Shouldn't that have been filtered out?
Absolutely. After digging into the settings, I found that SourceForge doesn't
protect the
Gareth,
That is an unusual error. I suspect it has something to do with your
symbolic links, which isn't the most reliable way to solve the dependency
problem. Instead, delete those symlinks, and modify Rules.make to seek out the
system libraries in the usual location. Rules.linux-rh7x sh
> From: Byron DeLaBarre [mailto:by...@slac.stanford.edu]
>
> Anyone out there know how to prevent bonding of adjacent but
> chemically
> unconnected atoms in pymol?
Two step process:
1. edit the PDB file and replace "ATOM " with "HETATM"
2. after the HETATM's add a single record "CONECT" follo
Image quality:
As Andrey indicated, on typical color lasers and inkjets, you need 300 dots
per final printed inch (~120 pixels/cm) for maximum quality . A small 4"x3"
illustration would need to be 1200x900 pixels ("ray 1200,900"). Full page
11"x8.5" (ray "3300,2550").
Since rendering t
> From: Malcolm E Davis [mailto:malcolm.da...@bms.com]
>
> A follow-up newbie question: Is it possible to map colors
> onto a surface on a per vertex basis?
Not yet, but that functionality is planned for sometime this year in order to
enable painting of surfaces in a non-atomic fashion. For n
> From: Byron DeLaBarre [mailto:by...@slac.stanford.edu]
> Subject: [PyMOL] color association with state?
> Do any pymolers out there know how to associate the color of
> a single object
> with its state?
Sorry, this can't be done with the current versions -- colors are either atomic
or whole-o
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