Keana,
This is a problem with at least one mac web browser...for some
reason the .gz gets removed from the file upon download, but the file is
still compressed.
If you replace the .gz, then the file will uncompress and open
properly when you double-click on it.
Cheers,
Todd,
Unfortunately that is not a problem PyMOL was designed to solve, and off the
top of my head I can't think of any way to bend it around to do this --
you're talking about a different rendering scheme. I think it amounts to
the following: trace every sharp edge, and outline every round
Nuno,
For a couple of reasons, I curently believe that electrostatic calculations
based on point charge models are not valid near or within the protein surface
-- you need to be at least one atom radius beyond the molecular envelope in
order to draw physically meaningful interpretations.
Frank,
PyMOL's atom selection language is based on logical operators over sets of
atoms.
and is the intersection and or the union. You're looking for
create forst2, (resi 1 or resi 32 or resi 356)
Using macros, this can be reduced to:
create forst, 1+32+356/
Please see the manual:
...@lists.sourceforge.net] On Behalf Of
Jose Avalos
Sent: Thursday, February 05, 2004 8:56 AM
To: Warren DeLano
Cc: 'Nat Echols'; 'Matt Franklin'; pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] Zoom in a movie
Sorry for the basic question, but I can't get the mdo command
to work
PyMOL Users:
Regarding default setting:.
1) How many people will object if I change PyMOL's default cartoon settings
so that loops are not initially smoothed? (cartoon_smooth_loop = off by
default)
The reasoning behind this is that gross smoothing is really only appropriate
for
PyMOLers,
In the past, some of you may have encountered a problem with printing the
PDF version of the PyMOL Users manual.
The problem has now been fixed -- so print away!
http://pymol.sourceforge.net/html/index.html
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano,
Yunfeng,
That is because the Mac still doesn't support Tcl/Tk out of the box.
You'll either need to install Fink http://fink.sourceforge.net/ ,
X11, and the Fink version of PyMOL
http://fink.sourceforge.net/pdb/package.php/pymol, or if you're willing to
consider becoming a
Leigh,
Get_dihedral can do what you need -- I think the problem is that you
need to be more narrow in your atom selections. Otherwise, 9/C will match
every atom named C, in every residue 9, and in every protein loaded.
With two proteins loaded:
load prot1.pdb
load prot2.pdb
You'll
Eric,
For now,
set retain_order, on
Before writing out your PDB file -- that will insure that nothing changes.
I'll look into whether the default behavior can be changed before the next
release...
Cheers,
Warren
-Original Message-
From:
Bjorn,
Whoops! That is definitely an oversight -- I'll see what I can do
to correct this. In the meantime, you may need to save a separate session
file for each labeled scene.
Cheers,
Warren
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
John,
color red, 5paa and elem o
The problem with using asterices as wildcards in atom names is that some
ill-conceived PDB files actually use them in atom names.
However, PyMOL does support the use of a terminal wildcard in some cases,
such as with the delete command...
create obj01,
-Original Message-
From: Charlie
Sent: Wednesday, February 18, 2004 8:56 AM
To: Warren DeLano
Subject: Re: [PyMOL] selecting multiple atoms ie oxygen
Warren DeLano wrote:
John,
color red, 5paa and elem o
The problem with using asterices as wildcards in atom names
Dan,
I think it's fair to say that PyMOL's currently molecular building
capabilities are at the stage of a technology
demonstration/proof-of-concept, but very little effort has yet been expended
toward making them useful for real work.
Part of that is because we don't yet have
Matt,
Try:
set selection_width, 6
set selection_width, 7
set selection_width, 8
Cheers,
Warren
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
Matthew Zimmerman
Sent: Thursday,
Morri has a good point:
The standalone pymol-0_xx-bin-linux-libc6-i386.tgz binary builds
should be capable of running on virtually any current x86-based Linux
system: RH, SUSE, Debian, Fedora, or whatever.
So, if you're having trouble with compilation or use of
Rongjin,
PyMOL can certainly color surfaces by atom color and other properties.
show surface
color green, elem c
color violet, elem n+o
But Grasp's hydrophobicity function may be doing something more
sophisticated then that...
Cheers,
Warren
-Original Message-
From:
Dieter,
Yes, there is a practical limit which depends on (1) the amount of
RAM and (2) the operating system. For reasons I don't completely
understand, PyMOL isn't able to get as much memory under Windows as under
Linux or OSX on equivalent system.
There are some things you can do to
Mads,
The only way to accomplish this that I can think of would be to
perform the normal expansion of all symmetry-related molecules within a
cutoff and then use a Python script to delete those objects which don't fit
a criteria.
One such criteria might be the presence of a
John,
You're not doing anything wrong -- there's just a little confusion
here about how settings work: they're global for an object or for the whole
system. The current value is what is always used. To get different sphere
sizes, use the alter command to change the vdw radii of the
Neema,
This is a fundamental limitation in PyMOL's current architecture...
B factors are an atomic rather than a coordinate property. It may be
possible to address this in the future, but not yet...sorry.
The clusy workaround is to load each PDB file into a separate
Michael,
PyMOL will only insert TER records when residue identifiers are
non-sequential.
Cheers,
Warren
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
Michael George Lerner
Sent: Monday, March 08,
Jason,
Thanks for the kind words.
It has been a while since anyone's tried to build/run PyMOL on a
64-bit system...it may not currently be 64-bit clean. We don't currently
have any Opteron hardware, but if you can build under -g, crash the program
under GDB, and then send me the
Ilya,
PyMOL treats insertion codes as part of the residue identifier:
select my_sele, resi 324A
Cheers,
Warren
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
Ilya Venger
Sent: Tuesday, March
Some users have reported problems with PyMOL on SGI hardware, particularly
after upgrading IRIX. We now know what it going on:
It seems that SGI broke the critical pthread library in several recent
versions of IRIX. In order to get PyMOL and other pthread-dependent
programs to run reliably on
Fred,
I think Lieven answered the second part, so I'll answer the first:
PyMOL's surfaces are discrete approximations of the solvent contact surface
(the surface of waters in contact with the protein at all possible
positions).
I generally think of the solvent accessible surface as being the
Fred,
Using the -c command line option will launch the command-line
version of PYMOL (no display required). You may also wish to use -q to
suppress the splash information.
pymol -cq pymol_script.pml
or
pymol -cq python_program.py
Cheers,
Warren
-Original
Gareth,
You need to provide normal vectors too. Otherwise OpenGL the
raytracer won't be able to light them correctly.
Cheers,
Warren
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
Gareth
Einat,
That is a longstanding goal of the PyMOL project, but there are various
hurdles to be surmounted, including creating an API for embedding PyMOL and
a secure API/language-subset for controlling it via the network. Another
problem is that each platform has a different optimal technology for
Ken,
set ray_interior_color, color-name
eg:
set ray_interior_color, grey30
To restore default:
set ray_interior_color, -1
Cheers,
Warren
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On
Sergio,
PyMOL probably isn't the best tool for doing this, but it can be done:
To add to a free N-terminus, pick (ctrl-middle-click) the N-terminal
nitrogen, and then press Alt-Letter (on Macs, Option-Letter) for the amino
acid you want:
For example: Alt-G adds a glycine
To add onto the
Sent: Tuesday, March 30, 2004 12:31 PM
To: Warren DeLano
Subject: multi-instances of pymol on OS X
Hi, Warren,
Is it possible that I can run multiple instances of pymol on OS X?
After I opened pymol, if I double click pymol again it won't
open a new pymol but just return
Franz,
I agree that it would nice for PyMOL to handle this automatically, but I
personally think that extra long CA-CB bonds look almost as goofy as
sidechains hanging in space.
As it stands, there are two ways to handle this annoyance manually, assuming
that you're using version 0.95 beta:
Thomas,
The trick for handling these sorts of situations is to load the
first PDB file into PyMOL using reasonable atom distances. So long as no
new atoms are added in subsequent PDB files, PyMOL will continue to use the
connectivity from the first state.
The only way to
Lihua,
You're correct: 'id' doesn't currently have the capability of selecting by
range or even using a list. However, we can probably add that behavior in a
future version.
In the meantime, you could tap Python for the task, but it will be slow:
select myrange, none
for a in
PyMOLers:
Yesterday marked DeLano Scientific's one year anniversary as a full-time
business. In addition to popping the cork on a bottle of champagne, we
celebrated with the release of version 0.95!
http://pymol.sf.net
http://pymol.sf.net/obtaining.html
Thank you to everyone who made the
Mado,
PyMOL's current labeling is inflexible. The only way to change position
automatically is to insert spaces at the front of the label:
label (name ca), %s-%s%(resn,resi)
The font selections are limited:
normal: set label_font_id, 0
bigger: set label_font_id, 1
smaller: set
David,
There isn't currently a programmatic way of doing this, but it wouldn't be
too hard to make one. I'll put onto the todo list support for commands
like: ray 1024; ray width=800; height=600; where the second axis is
calculated.
Note that we're currently missing an API function for getting
load ref4.pdb, ref, discrete=1
then apply the overall coloring:
spectrum b, selection=ref
Cheers,
Warren
-Original Message-
From: Tony
Sent: Monday, April 05, 2004 2:08 PM
To: Warren DeLano
Subject: colors and states
Warren,
I have figured out how to move (rotate) my domains
Dan,
That's the not expected result, but indeed you have a problem --
each of those subunits will have identical atoms. To resolve this, assign a
unique segment identifier to each subunit:
load 1c8e.pdb1, 1c8e
split_states 1c8e
delete 1c8e
alter all, segi = model[-4:]
rewind
save
Frank,
PyMOL adds hydrogens based on the hybridization and formal charge of an
atom...if you're not getting the right number of hydrogen, then you probably
need to adjust either the valences of the bonds it participates in, or the
formal charge.
A) To adjust valences:
1) enable show valences
Yes, it's called spectrum...but it looks like the docs don't exist yet.
PyMOLspectrum ?
Usage: spectrum [ expression [, palette [, selection [, minimum [, maximum
[, byres [, quiet ]]]
eg:
spectrum b
spectrum q
spectrum b, selection=my_obj
spectrum b, minimum=5, maximum=60
spectrum count,
1) I would like to show certain residues and have no problem
getting the ones I want selected and displayed as sticks or
whatever. The problem is color. When I change the color of
the selection, it changes the color of the associated section
of the ribbon. I would like to leave the
Tony,
First, enable stick_ball
show sticks
set stick_ball, on
That will put rounded-ends on sticks.
If you wall a ball stick representation, then also do something like the
following:
set stick_radius, 0.12
set stick_ball_ratio, 2
And if you want bond valences as well:
set
Ken's answer covers it...the following just provide a little more in-depth
coverage:
What has happened is that PyMOL now supports the picking of multiple atoms,
so use of the lb and rb selections is less necessary. Picking and selecting
are not the same thing in PyMOL. Selections are merely
Jason,
The problem is that your script is changing the setting for the specific
object-state by passing it an explicit object name and state number.
cmd.set( sphere_transparency, str(val), spheres, 0, 1, 1 )
As an important compatibility consideration, I recommend for all API
functions that
must I do c10+c11+c12...c50?
Yes, unfortunately. However, this long selection:
select tails1, r. pop n.
c17+c18+c19+c20+c21+c22+c23+c24+c25+c26+c27+c28+c29+c30+c31+ca
1+ca2+c36
+c37+c38+c39+c40+c41+c42+c43+c44+c45+c46+c47+c48+c49+c50
Can be replaced with some Python code in your script:
,
Warren
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
Dr. Daniel James White PhD
Sent: Wednesday, April 14, 2004 7:47 AM
To: Warren DeLano
Cc: pymol-users@lists.sourceforge.net
Subject: [PyMOL] Re: give
Mark,
Despite the performance drop, I'm a big fan of presenting within PowerPoint
-- I think it is simply the best solution for Windows.
Note that within PowerPoint:
- you can have your movie play automatically
- you can start and stop the movie with a mouse click in order to discuss
My thoughts on Yasara:
I'm jealous! Yasara is beautiful, fluid, polished, and significantly ahead
of PyMOL in several key technical areas. To me, Yasara seems like the
Matrix of molecular graphics: its perceptive experience is a quantum leap
beyond PyMOL, VMD, and other conventional programs,
Joyce ( friends),
I think that these kinds of RAPTOR-specific questions are best
followed up with Bioinformatics Solutions (
http://www.bioinformaticssolutions.com ) first, rather than being posted to
PyMOL-users. We're not (yet) familiar with how their interface works, so it
is hard for
Mark,
The sphere_scale setting is a multiplier of the atom's VDW radius.
If you want to set exact radii, use alter:
alter selection, vdw=number
eg. alter (all), vdw=1.0
rebuild
Cheers,
Warren
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
Mark,
The sphere_scale setting is a multiplier of the atom's VDW radius.
If you want to set exact radii, use alter:
alter selection, vdw=number
eg. alter (all), vdw=1.0
rebuild
Cheers,
Warren
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
Mark,
The sphere_scale setting is a multiplier of the atom's VDW radius.
If you want to set exact radii, use alter:
alter selection, vdw=number
eg. alter (all), vdw=1.0
rebuild
Cheers,
Warren
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
Christian,
This isn't implemented yet, but it is on the to do list.
Cheers,
Warren
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
Christian Rummey
Sent: Thursday, April 22, 2004 2:35 AM
To:
Ack! Sorry to hear this.
The two things that determine memory usage when rendering are:
1) the total number of primitives (spheres, triangles, cylinder [i.e. lines]
etc.)
2) the value of hash_max
#1 may not be easily remedied for your scene
#2 can be improved by setting hash_max to something
Hi Jason,
I see you have hash_max set to 400 -- that's the problem.
In empirical testing, I found that there is rarely a reason to go above 200
with this setting. Having a hash table that is too finely sampled is no
better than having one too coarsely sampled. PyMOL's default of 100 is
is there any way of showing movement of a
molecule in a static image, for example as speed lines or a
blur between the two states? If this makes any sense please
let me know if you have some ideas!Mike,
Motion blur in PyMOL is possible, but the process is a bit tedious. You
need to
Einari,
I can't get white surface look really
white. Is there a way to do this ?
Yes: increased the ambient light setting.
set ambient, 0.4
ray
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice
Heinz-Uwe,
For 0.95:
The inversion function was changed in version 0.95 to take advantage
of multiple picked atoms. To invert a center, Ctrl-middle-click to pick the
center atom as pk1 and two stationary atoms as pk2 and pk3. Then type
Ctrl-E to invert.
For 0.93:
Tony,
In order to enter multi-line Python code on the command line, you
need to use explicit end-of-line continuations. Otherwise, PyMOL won't know
where your Python code stops and PyMOL commands again begin.
from pymol.cgo import *
from pymol import cmd
set cgo_sphere_quality, 3
def
Michael,
This is what can sometime happen when you update system libraries
underneath vendor-supplied OpenGL drivers. If you reinstall your graphics
drivers after the update, then the problem should go away.
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren L. DeLano, Ph.D.
Yes,
Assuming you're running 0.95:
Put the mouse into Editing Mode (Mouse menu or click on the mouse matrix).
Insure that no atoms are currently picked (i.e. there are no pk
selections). Click unpick if there are...
You can now independently rotate and translate objects with
PyMOL-Users,
I've been unhappy with the way the user interface for selection works in
PyMOL and am planning a change. Going forward:
1) There will the concept of an active selection.
2) The enabled (visible) selection will be the active selection.
3) Only one selection can be enabled/active
To: Warren DeLano; pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] Linux Beta Version with Sequence Viewer
Hi Warren
This is GREAT!
I was going to suggest this for the future development, but (as usual
:-) you're ahead.
Very good points:
* possible to chose between atoms
Actually, this too was anticipated ; ). On Windows:
for PyMOL commands, simply use
pymolrc
(no extention -- I suppose pymolrc.txt or pymolrc.pml would've made more
sense...)
or for Python code:
pymolrc.py
pymolrc.pym
Cheers,
Warren
--
mailto:war...@delanoscientific.com
Warren
PyMOLer's,
Lots of good feedback on the sequence viewer has been coming in -- thank you
everyone, and please keep it up. I've got about a week's work of changes to
make, but will continue to push out new releases as they are ready.
I did want to draw your attention to the fact that up until the
Randy,
For some reason this approach has turned out to be unstable, so I've
basically placed it on unsupported status until someone with a better
understanding of Python interactive mode than me can take a look at it.
Are you aware that the PyMOL command line is also a Python
Hi Tony Friends,
I just wanted to draw your attention to the fact that rTools should
(in theory) work with the 0.95 OSX-X11 hybrid version, which has an native
Aqua-based OpenGL window and an X11-based Tcl/Tk gui. I specifically
created that version to insure that Mac users wouldn't be
Peter,
set all_states, on
Cheers,
Warren
--
mailto:war...@delsci.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
Bill,
Fit is an extremely finicky command...it only works when the two
objects have matched identifiers for each atom to be superimposed (name,
resi, resn, chain, segi, alt). Align won't help you because you're using
RNA. So you'll need to use pair_fit, which requires that you specify a
Konrad,
There are several options for loading map data into PyMOL now:
XPLOR (format=xplor)
CCP4 (format=ccpy)
O/BRIX (format=brix)
In addition, you can use the following non-crystallographic formats:
Delphi/Grasp PHI files (format=phi)
AVS FLD files (as output from MEAD) (format=fld)
and in
-users-ad...@lists.sourceforge.net] On Behalf Of
Robert Schwarzenbacher
Sent: Wednesday, June 23, 2004 11:47 PM
To: Warren DeLano
Cc: pymol-users@lists.sourceforge.net
Subject: [PyMOL] cartoon and alternates
hi there,
I get broken cartoons with alternate conformations. Is there
a quick way
(Warren DeLano)
2. cartoon and alternates (Robert Schwarzenbacher)
3. RE: cartoon and alternates (Warren DeLano)
4. Question about rotation (Qun Wan)
5. Questions about rotation view (Qun Wan)
--__--__--
Message: 1
From: Warren DeLano war...@delanoscientific.com
To: 'Steve
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
Nalam, Madhavi
Sent: Friday, June 25, 2004 1:48 PM
To: Warren DeLano; pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] superposition of structures
Qun,
This is something that is easist to do with the Fitting wizard.
Starting with the ATP, click successive matched pairs of atoms in the ATP
and then the ADP. When you have enouch pairs, click Fit. That should be
all you need to do.
Cheers,
Warren
--
mailto:war...@delsci.com
Warren
will hash_max 500 be even better?
Thanks,
Scott
On Jul 5, 2004, at 10:56 AM, Warren DeLano wrote:
Scott,
The optimal hash_max is somewhat scenery-dependent, but
values in
the 180-250 range tend to be best for multiprocessor
situations with lots
Vladimir,
Michael and I have been working on streamlining the process for
using ABPS with PyMOL and are almost at the point where PyMOL can generate
the necessary PQR file (for proteins at least) from an ordinary PDB file
lacking hydrogens, c-terminal carboxylates, etc. PyMOL can also
Qun,
PyMOL doesn't (yet) have the ability to calculate Possion Boltzmann
electrostatic potentiallys. You'll need to use an external tool like GRASP
or APBS to perform that task.
If spectrum b doesn't produce the desired result, then there is
probably some strange B-value present
PyMOLers,
Electrostatics purists will undoubtedly question the wisdom of this action,
but in the latest Windows beta version of PyMOL, I have added an
experimental and as-yet-unvalidated automatic way to calculate and display
vacuum electrostatic potentials (computed with a constant homogenous
Jason
Ah, I found the problem:
Sticks represent bonds, not atoms. Normally, in order to see a bond, *BOTH*
atoms involved have to have either sticks or lines shown. That's why you
weren't seeing anything until increasing the radius of the selection sphere,
which included the first bond atom
PyMOLers,
The official 0.96 version of PyMOL had been released. As you've likely come
to expect, this isn't so much a formal release as a quality-controlled build
containing many of the recent beta features. Of greatest interest will
probably be:
1) The sequence viewer.
2) Built-in support
This question just came in about the sequence viewer...I'm anonymously
copying it to the mailing list since it is bound to come up frequently:
Hey Warren,
I just downloaded the new version of PyMOL and was playing
with the new sequence view. Is it possible to do a
structural alignment
Ramesh,
You can do something like this...
For a solvent accessible PSA approximation:
set dot_density, 3
remove hydro
remove solvent
show dots
set dot_solvent, on
get_area elem N+O
get_area elem C+S
get_area all
For molecular PSA approximation
set dot_density, 3
remove hydro
remove solvent
Ramesh,
Thanks for this report. So far I haven't been able to reproduce the crash
under Linux or IRIX...
If other people encounter this same problem or other problems with the new
releases, then please send a report to supp...@delsci.com that includes your
operating system details. If pattens
Douglas,
I don't think PyMOL can handle negative selections yet. Just make
them positive:
alter all, resi=int(resi)+100
etc.
Cheers,
Warren
--
mailto:war...@delsci.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-4020
Dan,
Yes, those files aren't really valid PDBs, but you can probably
solve this by assigning a distinct chain to the waters and rebuilding:
alter hoh/, chain='X'
sort
Cheers,
Warren
--
mailto:war...@delsci.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice
Following up on Bill's report...
We've updated to version 10.3.5 all the Mac's we have access to and have not
been able to reproduce the reported problem. The configurations tested are:
Mono on an LCD:
MacPYMOL 0.95 on a dual G5 with an ATI Radeon 9600 (RV350)
MacPyMOL 0.95 on a dual G4
Ian,
Yes, I have gotten PyMOL to work with the laptop version of this display
(just Windows so far). The stereo effect is quite good. However, your head
does need to be in just this right spot in order to get the effect. After
15 minutes, I learned to do this automatically, moving slightly off
Anthony,
New in version 0.97 is a get_angle function that takes three single-atom
selections. There is also a get_distance that is more efficient than the
distance command (which creates objects)...
See help get_angle
To set up a loop, you'll need to generate a list of selections
# for
That's good advice, except that you'll lose any bonds between the two
selections...
the following example will keep those bonds (by duplicating atoms)
create protein2, (selection_1)
create protein3, ((not selection_1) extend 1)
set line_width=1.2, protein2
set line_width=2.0, protein3
Cheers,
Charles,
It's a design limitation that hasn't yet been remedied. For the time being,
please just shift residues into a positive range via a command such as the
following:
alter all, resi=int(resi)+100
Cheers,
Warren
Note that if you have alphanumeric residue identifers 110A, 110B, then
you'll
Why do you think pymol cannot be sold? The copyright license
does not seem to imply this[1], and such a restriction would
render pymol not Open Source.
Warren, can you tell us what you think on this?
Michael Carly,
Yes, in my world, open-source means available to all people and for all
)
for atm in mdl.atom: atm.b = 10
cmd.load_model(mdl, new_obj)
label new_obj, b
Cheers,
Warren
--
mailto:war...@delsci.com
Warren L. DeLano, Ph.D.
Principal Scientist
DeLano Scientific LLC
Voice (650)-346-1154
Fax (650)-593-402
Thanks,
Charlie
Warren DeLano wrote:
Charles
Ben,
Thanks for the great benchmarks! PyMOL is definitely showing non-linear
behavior when it comes to loading a lot of objects...I don't know why this
is exactly, but I can tell you that I didn't originally envision (and thus
optimize PYMOL for) loading of so many objects.
As it currently
PyMOL Users who:
1. don't normally need to share session files with others
2. want to load a lot of structures into PyMOL
3. like living on the bleeding edge
4. will provide feedback on problems encountered
may wish to try the latest 0.98beta05 executables for Win/Linux/Mac-X11
posted
PyMOL Users,
A major PyMOL sponsor is having problems with the Mobility Radeon 9000 chip
on their Dell laptops under Windows XP. I am curious to know whether others
have seen or are encountering similar problems with this chipset. The issue
is as follows:
When attempting to choose atoms using
Roger,
CMYK and RGB are non-equivalent, and there will always be some mangling like
what you describe. The CMYK color mode in PyMOL is an attempt to constrain
PyMOL to using the a subset of RGB values that can be mapped reliably into
the CMYK color space, at least via Photoshop. It's not a
://delsci.com/beta ).
Cheers,
Warren
-Original Message-
From: pymol-users-ad...@lists.sourceforge.net
[mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of
Warren DeLano
Sent: Monday, September 13, 2004 8:34 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] ATI Mobility
Mary,
You can write a Python loop like the following:
f=open(distance.txt,w)
pairs = ( \
( 45/ca, 47/ca), \
( 45/ca, 49/ca), \
( 45/ca, 51/ca), \
)
for a in pairs:\
f.write(%-10s %-10s %8.3f\n%(a[0],a[1],cmd.get_distance(a[0],a[1])))
f.close()
will create a file like:
45/ca 47/ca
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