From: Thomas Evangelidis [mailto:te8...@mbg.duth.gr]
Sent: Thursday, October 29, 2009 4:56 PM
To: Warren DeLano
Cc: Thomas Evangelidis; email@example.com
Subject: RE: [PyMOL] how to get RMSD from align command
before I write something
To: Warren DeLano
Subject: Re: [PyMOL] how to get RMSD from align command
Now I am more confused. I used align command to measure the overall
RMSD between homologous structures. Apparently align is not
appropriate if not sufficient
Today's questions regarding alignment RMS values suggest to me that I
should re-emphasize what PyMOL is and is not good for:
Please everyone keep in mind that PyMOL is intended to be just a
molecular graphics program, to be used for displaying, comparing, and
Unfortunately, there isn't any way at present to directly expose PyMOL's
internal C coordinate array to Python in an accessible form. Yes,
iterate_state and alter_state are highly inefficient - it would make
more sense to provide a means of exporting and re-importing coordinate
Unfortunately, there is no programmatic way to get this information out of
PyMOL -- my apologies!
From: Michael Zimmermann [mailto:micha...@iastate.edu]
Sent: Mon 10/26/2009 9:04 PM
Subject: [PyMOL] number of h-bonds
1. What type of RMSD is calculated with align comman i.e All Atoms or
It depends on the input selections. If you don't restrict it to backbone
atoms, PyMOL will perform the fit for all matched atoms. Also, it is important
to understand that align is a combined sequence and 3D
You have a rotate command in that script. Did you mean to 'turn' the
camera rather than 'rotate' the atomic coordinates?
From: David Garboczi [mailto:dgarbo...@niaid.nih.gov]
Sent: Thursday, October 22, 2009 7:00 AM
How would this be different from the existing Scene interpolation
You can use the Scene menu to Append a series of scenes of the molecule
(views+representations) and then use Scene - Next, PAGE-DN or the
scene command to interpolate through them.
Actually this is how the draw command works in using the screen-based OpenGL
renderer to create images of arbitrary size. However, the ray-tracer isn't
currently set up to operate that way. Ray might work with an orthoscopic
projection, but with perspective enabled, each frame would
You might try super instead of align (same syntax).
Failing that, you can use pair_fit with explicit selections -- just make sure
the number of atoms is the same in each of the selections.
From: Kerff Frédéric [mailto:fke...@ulg.ac.be]
You may be past the limit of what PyMOL can handle. Regardless, the
64-bit Linux builds are the best at handling large-memory tasks.
Practice with something really simple:
Also, two more things I'd suggest for such a large image (in order to
There is also a more concise option:
select allothers, chain 0:4+C:J+L:Z
Or even more concise, using selection macro: chain/residue/atom
select allothers, 0:4+C:J+L:Z//
From: Marius Retegan [mailto:marius.s.rete...@gmail.com]
Switch the mouse into editing mode, then ctrl-left-click-and-drag on
the label to reposition.
Warren L. DeLano, Ph.D.
(Sent from an iPhone -- please forgive brevity and/or typos!)
On Oct 14, 2009, at 8:03 AM, Per Larsson per.lars...@sbc.su.se
Mark ( indeed all Mac users)
MacPyMOL can be launched in two flavors, based on the name of the
If the executabled is named MacPyMOL, PyMOL launches in the mode you're
familiar with: a single-window Cocoa-based interface.
If the executable is renamed PyMOLX11Hybrid, then PyMOL
i have multiple conformations files (multi pdb) and would like to
compute for each one, the rmsd for each snapshot against the first
Is it possible with pymol to do such a task ?
thank you in advance for the gain of time ... :-)
Yes, using a short Python
Great question with a crummy answer: you can't!
But this seems like a really good idea, at least for primitives stored
in ordinary built-in Python containers. Saving class instances would be
problematic, since session files wouldn't necessarily be restorable in
the absence of
That's a bit odd: usually it either works or it doesn't. Working for 20
seconds at a time may indicate defective hardware (projector, emitter,
graphics card, connector, dead battery, etc.).
But as a first test, pease try using some other stereo-3D-capable
software (e.g. VMD or
I'm not sure what you have in mind other than something like (python code):
for state in cmd.count_states():
cmd.iterate_state(state, selection, expression)
where expression is accumulating coordinates from multiple states
Yes, that is an alternate route. cmd.get_model is likely slower than
cmd.iterate_state, but should work regardless.
From: Sean Law [mailto:magic...@hotmail.com]
Sent: Monday, September 28, 2009 11:58 AM
PyMOL relies entirely upon Python's built-in proxy support (via urllib),
so if you can get a Python script configured to work properly through
your proxy, then PyMOL should work as well.
Based on that traceback, it looks like you have two conflicting versions
of Tcl (8.4 as well as 8.5) linked against and running in the same
process...that could be the source of the crash.
From: Ian Berke
Apologies, but PyMOL can only mutate the standard 20 amino acids.
Note that you have asked that second question before:
Again, there is no special theory behind PyMOL's mutagenesis wizard:
If there are multiple attached atoms, then there may be multiple
dihedrals present. There is a visual indicator which shows what angle
is being measured -- do those indicator match the displayed angle?
From: Vivek Ranjan
In the OpenGL viewer, dashes are always drawn using line primitives, so
dash_radius has no effect until you issue the ray command.
Note that dash_width is generally preferable to dash_radius since it
controls both the OpenGL and ray-traced renditions (so long as
dash_radius is zero).
For what's it's worth, I'm not able to reproduce the problem:
Aside from automatic suppression of output when using the Python API,
I'm getting the exact same behavior with
Yes, but it may not be the answer you want: avoid putting those objects
into groups. At present, groups and grids are interconnected in a
From: T. Andrew Binkowski [mailto:abinkow...@anl.gov]
Sent: Thursday, September 17, 2009
When posting such questions, please always indicate what specific vesion
of PyMOL you are using, since the program continues to evolve with every
release (to reflect numerous end-user suggestions, as enabled by
contributions from our sponsors.)
PyMOL version 1.2r1 should
There is no relationship between ACT and PyMOL, so one wouldn't necessarily
expect them to match in terms of how they name the resulting objects. However,
I suspect there may also be a difference of intent:
Based on a quick glance at PyMOL source code, PyMOL appears to convey a
Note that this kind of stuff is much easier in PyMOL 1.2 without any
(ScreenCasts for PyMOL Sponsors at http://delsci.info/id/media:new12
under Complex Movie Creation -- login first).
Nevertheless, a possible answer is below:
# PyMOL .pml file (tested against PyMOL
For those looking to do Quadro-based stereo 3D under Windows with the new 120
Hz LCD displays, please pay careful attention to which card you purchase if you
expect to do stereo 3D!
nVidia has a page with the facts you need:
Can you describe what you are trying to accomplish (overall) in more
There are different approaches one could take depending on the
The simplest, but limited approach is to use the mset and madd commands
with variable numbers of frames:
# show the initial state (1)
select all_arg_lys, resn arn+lys
From: Maia Cherney [mailto:ch...@ualberta.ca]
Sent: Friday, September 11, 2009 2:03 PM
Subject: Re: [PyMOL] Alignment Objects
Is it posible in pymol to select all
From: Carlos Ríos Vera [mailto:crosv...@gmail.com]
Sent: Saturday, August 29, 2009 4:08 PM
To: David Hall
Cc: Warren DeLano; pymol
Unfortunately, that is hard to do: there is no guarantee that the
proposed (characteristic) path of motion which relates any two spacial
orientations will possess reasonable chemistry or sterics. RigiMOL does
make an attempt to resolve simple conflicts, and the refinement step can
The trick is to leave the phosphate displayed for those residues where
the backbone should still be shown:
hide everything, resi 20-40 and not elem p
From: Bala subramanian [mailto:bala.biophys...@gmail.com]
PyMOL's mutagenesis wizard is purely geometric, and is intended to offer
up Dunbrack rotamers as per:
From: Chandan Choudhury [mailto:iitd...@gmail.com]
the use of frames and
split_states, but I haven't come up with anything.
I've heard about a demo that Warren DeLano put on for the ACS
where, as part of the demo, he showed off some toy example
where he docked a ligand in by hand, complete with having
PyMOL show red/green dots for steric
pymolwiki, the masking and protecting options, and
examining the use of frames and split_states, but I
up with anything.
I've heard about a demo that Warren DeLano put on for
When using the PyMOL launch icons, it is only possible to have one active
version installed (registered) under Windows.
However, you can (1) copy and rename the Program Files \ DeLano Scientific \
PyMOL folder from a correctly installed version, then (2) edit the launch.bat
If building PyMOL from source, then please get APBS in source or binary form
from the APBS sourceforge project: http://apbs.sourceforge.net
From: Hugo G. de Teran [mailto:hugo.te...@usc.es]
Sent: Thursday, August 27, 2009 10:06 AM
Hmm...it appear that QuietException is being thrown when the input pattern
fails to match any valid object name (but without an error message being
The easiest immediate workaround is to simply swallow the exception.
for i in range(10):
ramp_new ramp-name, ...
From: Stephen Graham [mailto:steph...@strubi.ox.ac.uk]
Sent: Tuesday, August 25, 2009 10:09 AM
Subject: [PyMOL] invoke ramp_new without drawing 'ramp' CGO
By default, alter_state expressions are evaluated in the pymol
namespace of the current PyMOL instance, not the cmd (pymol.cmd)
namespace. The reason why it works with 'run' is that run also executes
in pymol by default, and thus, includes any functions you define.
From: Stuart Ballard [mailto:srball...@wisc.edu]
Sent: Monday, August 24, 2009 4:06 PM
To: Warren DeLano
Subject: Re: [PyMOL] Calling scripted
I think this is more an issue of driver support rather than hardware.
However, the latest drivers do not necessarily support older cards.
Please see nVidia's site for details:
and click on the supported hardware tab after searching.
Yes, you need to override the object-specific transparency specification from
unset transparency, object-name
From: Duca, Jose [mailto:jose.d...@spcorp.com]
Sent: Wed 8/19/2009 10:33 AM
The light and lightN settings are direction vectors, not coordinates.
Intensity (reflect setting) is averaged across all such directional
It has recently been suggested that we need better control over
Warren L. DeLano, Ph.D.
Use set_bond instead of set for per-bond properties.
Warren L. DeLano, Ph.D.
(Sent from a mobile device. Please forgive brevity and/or typos!)
On Aug 20, 2009, at 4:18 PM, Sean Moore semo...@mail.ucf.edu wrote:
I am trying to change the
Create a copy of the original chain, modify the chain, and fit the copy to the
original. For example
# PyMOL 1.2 .pml input
fab AAA, orig
create copy, orig
set_dihedral orig///3/C, orig///4/N, orig///4/CA, orig///4/C, 180
fit origCA, copyCA
Use the discrete=1 option to load each PDB state as a separate set of atoms
(instead of as a trajectory -- the default behavior).
load multimodel.pdb, discrete=1
From: S4C6Ar Chung [mailto:s4c...@gmail.com]
Sent: Sat 8/15/2009 9:44
FYI, for Windows users who like to live on the edge...
AxPyMOL is the PyMOL Active Control, which makes it possible to display
live molecular content, including PyMOL PSE and PSW files inside of
PowerPoint (on Windows only). Because we are still having trouble
getting this Windows-based
With the 1.2 release of PyMOL, we have completely switched over to
Numpy. So the first thing to try is to replace:
from Numeric import *
from numpy import *
From: Jed Goldstone [mailto:jedg...@mit.edu]
Sent: Thursday, August 13, 2009
PyMOL isn't the optimal tool for measuring surface area -- perhaps
others on the list can suggest good alternatives.
The only kind of surface area PyMOL can measure well is solvent
accessible area, and it is a bit slow because all it does is sum up
partial areas associated with discrete
set specular, 0
alone should be enough to do the job if all you want to do is turn off
specular lighting -- you can ignore all those other spec_* settings.
However, for a more matte appearance I'd be more inclined to try:
set specular_intensity, 0.2
It sounds like there mayy be something other than canonical amino acids in your
structure which might need to be removed prior to performing a calculation.
These may be alternate conformations of amino acid side chains, ligands, or
other unrecognized groups which cannot be processed
I´m desperate to get some information about PyMol, I need to know it is
possible to measure a distance from a middle of a pi-bond to another atom?
No, this isn't possible directly, but you can do something like the following:
# copy paste demo snippet
You need a keyword argument list as well, so that the effective PyMOL
class instance (_self) can be passed in by keyword (actual use of _self
is only strictly required when you have multiple PyMOLs active in a
single Python interpreter).
# pml input:
def my_fn(*arg, **kwd):
Sorry, there is no way to do this at present (short of manually editing
text files). But thank you for the suggestion!
From: Stuart Ballard [mailto:srball...@wisc.edu]
Sent: Saturday, July 18, 2009 1:58 PM
Just to make sure everyone understands:
Stereo 3D support for these awesome new 120 Hz LCD displays is WINDOWS
ONLY due to the need of a special USB driver for the 3D Vision sync
emitter. Unfortunately, you cannot sync a digital 120 Hz LCD using the
old stereo analog DIN sync connector - it
this just work?
From: Warren DeLano [mailto:war...@delsci.com]
Sent: Friday, July 17, 2009 12:23 PM
Subject: [PyMOL] WARNING: No Mac or Linux support for 120 Hz LCD synchronization
Just to make sure everyone understands:
Minor correction, for geeks who care about technical trivia. I
I don't think [VGA] Modeline timings have any meaning when
generating a true digital display signal...
Apparently the modeline timings do still have significance in terms of
digital information transport, which
Date: Thu, 9 Jul 2009 13:34:53 -0700
From: Warren DeLano war...@delsci.com
Subject: [PyMOL] PyMOL 1.2r1 Released
PyMOL has been known to work great with the Samsung 2233rz for quite
some time, but nVidia had not publicly released any of the required
190-series drivers until today.
Note that, officially speaking, you will need a Quadro graphics card in
order to do OpenGL-based stereo 3D.
Today nVidia issued their first public beta release of their 190-series
driver. Although this release is officially for GeForce hardware, it
seems to work fine for Quadro cards as well. So, if you have the
following hardware setup, then you can at last now use PyMOL in Stereo
3D at full
Although GeForce 3D Vision is not officially supported for Windows XP, I
managed to get it to work with PyMOL. Assuming you have the following
- A 120 Hz LCD: a Samsung 2233RZ or a ViewSonic Fuhzion vx2265wm
- A recent Quadro series graphics card such as
blocks you have to do more than indentation. You have to put a slash
in front of the for statement and end all but the of the blocks with a
Actually, nowadays you can just wrap Python blocks with the statements:
python and python end. For example:
# example pymol
Sorry for the confusion:
Although 32-bit 1.2r0 Windows and Linux builds have been announced, Mac builds,
64-bit Windows Linux builds, as well as final updates to the open-source code
build scripts are still in process. Once the complete 1.2 release is ready,
that fact will be
The movie panel operates on movie frames, not trajectory states, so you need to
create a relationship between them. A one-to-one relationship can be created
using the Python command:
cmd.mset(1 -%d % cmd.count_states())
Or alternatively, you can use the new Movie - Program - State Loop
The difference? $769.99 - $354.99 = $415 exactly.
But seriously, this is a question for Dell, not pymol-users.
For what it is worth, mid $300's is the current per-unit pricing for the
ZM-M220W display - but they originally hit the market at a 2-3X higher
price, so one of those links is
Have you heard?
You Mom Is Open Source! http://winkleman.com/exhibition/view/1628
No, that is not some veiled condemnation of maternal virtue, but rather
the provocative title of Shane Hope http://www.shanehope.info 's
latest Solo Exhibition at the Winkleman Gallery
set label-color, color-name, object-name
set label-color, color-name, selection
# for example
label all, name
set label_color, yellow, arg
set label_color, red, elem c
# note that the other label settings may not work below the per-object level
On Tue, Feb 10, 2009 at 1:54 PM, Warren DeLano
This tripped me up for a while too, but I think the stereo
DIN is an
output (for projector, Z-screens, etc.) not an input.
Suffice it to
Can you wait a week or two? This sort of thing is about to get 100X easier in
From: Charlop-Powers, Zachary [mailto:zachary.charlop-pow...@mssm.edu]
Sent: Thu 6/18/2009 10:11 PM
set cartoon_highlight_color, default
From: Roger Rowlett [mailto:rrowl...@mail.colgate.edu]
Sent: Thursday, June 11, 2009 7:17 AM
Subject: [PyMOL] Disabling cartoon_highlight_color
How do you disable
structs, I suspect we
could extend that to 7 characters plus a null without adversely impacting
PyMOL's memory use characteristics...
From: ABEL Stephane 175950 [mailto:stephane.a...@cea.fr]
Sent: Tuesday, June 09, 2009 12:34 AM
To: Warren DeLano
From: Warren DeLano
Sent: Tuesday, June 09, 2009 12:26 PM
To: ABEL Stephane 175950
Subject: Re: [PyMOL] How to plot residu with a number
Okay, I see -- you're just spilling the top digit
Sorry, I accidentally forgot to CC the list on my response to Jim. Yes,
the culprist is one of the 600+ settings (ray_label_specular to be
exact). Recipe for jet-black labels below...
label all, name
I suspect this is a question PyMOL automatically normalizing the map
values, whereas the other programs might not. For historical reasons,
PyMOL's default behavior is to normalize CCP4 map values upon loading.
To prevent this, issue:
As per http://www.wwpdb.org/documentation/format32/sect9.html , the PDB
residue identifier field is only four characters wide.
So how could you possibly have a PDB file with residue identifiers
larger than ?
From: Stephane Abel
As for the your general question: can you import pymol; from pymol
import cmd; pymol.finish_launching(); etc?
Answer 1: Yes, if you manually compile PyMOL open-source code into an
existing Python interpreter.
Answer 2: Yes, if you run your Python script using PyMOL's built-in
followed by a 90 degree rotation about the camera's ]X-axis should give you a
couple of views with the desired characteristics.
turn x, 90
From: gilleain torrance [mailto:gilleain.torra...@gmail.com]
Apologies for not understanding...
You definitely need orthoscopic, but there's more to it.
fetch 1bna, async=0
from chempy.cpv import average
To: Warren DeLano
Subject: Re: [PyMOL] reorienting a chain
Thank you very much for your advice.
I guess I was not being very clear. what i meant was that i would also
like to save the coordinates of this reoriented polymer. Let me
B all by itself is a selection language keyword for the b-factor property:
select high_b_factor, b 50
So just use a different selection name:
select chB, chain B
From: Jim Remington [mailto:reming...@molbio.uoregon.edu]
You can save a copy of the original and then superimpose the copy back onto it
# using fab command from the latest 1.2 beta to create poly-ala
fab AAA, pol
# create copy of the polymer
create copy, pol
# adjust a torsion
set_dihedral pol///4/N, pol///4/CA, pol///4/C, pol///5/N, 60
PyMOL transforms the output geometry in order to deliver a default view
matching what's seen in the viewer window. To prevent that, you'll need to
effectively eliminate PyMOL's camera transformation by restoring to a
transformation-less identity matrix:
isolevel mesh-name, level
From: hari jayaram [mailto:hari...@gmail.com]
Sent: Wednesday, May 27, 2009 12:29 PM
Subject: [PyMOL] update mesh level to custom value after deleting map object
You can save some time a lot of memory by loading the file and
removing the atoms in a single-line compound statement (with a semicolon
after the load statement).
load 1E3M.pdb; remove not A-C+F//
From: Sean Law
set surface_mode, 1
From: chaix denis [mailto:ch...@cbs.cnrs.fr]
Sent: Tuesday, May 26, 2009 3:55 PM
Cc: Chaix Denis; support; firstname.lastname@example.org
Subject: [PyMOL] surface of ligand
Ad include below, just FYI -- no affiliation with DeLano Scientific --
though we have used products from these companies and found them
It appears that you can now set up a small conference room for
active-stereo 3D visualization with glasses for 4 people
For quite some time now, we have ourselves experienced and continued to
receive complaints regarding graphics artifacts and other glitches with
ATI/AMD Radeon HD graphics chips on multiple platforms. Though we
haven't had time to investigate everything to our satisfaction, it is
Assuming that you are using the most recent PyMOL 1.2 beta build, first
create a Scene for each display you wish to show.
(To do that, show everything the way you want and then select Append
from the Scene menu. Repeat the process for each view / color /
representation you wish to
Sorry, PyMOL only has protein charges coded at present. Perhaps the
APBS project's pdb2pqr utility might be able to assign charges to
canonoical ligands (such as ATP)?
From: Chaix Denis
Ctrl-right-click on the bond
seems to do the trick. Perhaps there's a problem with the version of
PyMOL you're using?
From: Thomas S. Leyh, Ph. D. [mailto:l...@aecom.yu.edu]
It appears the script was flawed:
names = cmd.get_names(sel1)
names = cmd.get_names(selection=sel1)
I've updated it on the Wiki.
From: Shiven Shandilya [mailto:shiven.shandi...@gmail.com]
Sent: Monday, May 11, 2009 4:47 PM
Should be fixed now (in rev 3720).
From: Mark Wehner [mailto:mark.weh...@rub.de]
Sent: Monday, May 11, 2009 12:11 PM
Subject: [PyMOL] Vacuum electrostatics
in the newer version of
This is a weak area for PyMOL. One thing to try is to switch to an animation
with multi-layered transparency, two_sided lighting (and other tweaks) to help
show the entire binding site volume. The approach isn't perfect, but it may
fetch 1gzm, async=0
remove not a//
We don't have vector export, but PyMOL can generate a high-resolution BW
transparent-background raster image as illustrated below:
set ray_trace_mode, 2
set ray_trace_gain, 1
set grid_slot, -2, object-name
for the object you wish to spread across all grid slots.
From: Höfling Martin [mailto:martin.hoefl...@gmx.de]
Sent: Tue 5/5/2009 5:02 AM
Subject: [PyMOL] Grid_mode - reference
# new command in 1.2b5 - fabricate peptide, ALA trimer:
# set a dihedral value ro 180 degrees.
set_dihedral 1/C, 2/N, 2/CA, 2/C, 180
From: Vivek Ranjan [mailto:vran...@gmail.com]
Sent: Tue 5/5/2009 12:09 PM
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