representatives.
From: Sean Law magic...@hotmail.commailto:magic...@hotmail.com
Date: Wednesday, June 4, 2014 4:17 PM
To: Sampson, Jared jared.samp...@nyumc.orgmailto:jared.samp...@nyumc.org
Cc:
pymol-users@lists.sourceforge.netmailto:pymol-users@lists.sourceforge.net
pymol-users
Hi PyMOLers,
I have a c-alpha only model and I would like to visualize both helices and
sheets based on my own custom SS assignments (via alter). Altering a
residue's SS assignment to helix or loop (ss=H or ss=L) is fine and can be
visualized. However, altering a residue's SS assignment to
to indicate your SS assignments in
another cartoon mode?
Cheers,
Jared
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/
On Jun 4, 2014, at 1:50 PM, Sean Law magic...@hotmail.com wrote:
Hi PyMOLers,
I have a c-alpha only model and I would
Hi PyMOLers,
I am trying to use the built-in functionality to draw a user-defined ellipsoid
and I am doing this by adding an extra ANISOU line in my PDB. Here is a test
case:
ATOM 2 CA ALA D 500 -1.217 1.844 -2.065 1.00 1.00
CAANISOU2 CA ALA D 50026170
I too have encountered a similar problem and was hoping that somebody had a
suggestion for this. I've tried using CEALIGN to attempt to align the
molecules and then hoped that I could simply use some atom-atom pairwise
distances to map one set of atoms onto another but CEALIGN doesn't seem to
Hi PyMOL Community,
I have a PyMOL script that I have written that starts with the following kind
of format:
-from pymol import cmdfrom re import *
def test (*args, **kwargs):
var1=0 sel=
for key in kwargs:if (key == var1): var1=int(kwargs[var1])
elif (key ==
Takanori,
I've tried the following:
for a in range(1,8): cmd.mdo(a,hide sphere; select test, input_object_name
c. b i. 19 around 4 resn HOH; show sphere, test)
where HOH is the residue name for water (so I want to know only the waters
within a 4 Angstrom radius of residue number 19).
Hi PyMOLers,
I was wondering if it were possible to have a selection update itself for every
frame. Specifically, I have a simulation trajectory of a protein in a water
box and I want to show only the waters that are within 5 Angstroms of the
protein binding site. Obviously, as the
Takanori,
Thanks for pointing that out!
I might be misunderstanding the usage but it does seem a bit tedious to have to
go through each frame (if I had 1000+ frames) and then make a selection.
I'm hoping that this isn't the only solution and that there's some other
setting/command that I can
Jason (and PyMOLers),
To clarify, B.dcd matches the number of atoms in B.pdb and A.dcd also matches
the number of atoms in A.pdb. In the previous example, if I perform steps 3
and 4 first then it works in loading B.dcd into object B. Then, if I try to
open up A.pdb into a separate PyMOL
Hi PyMOLers,
I noticed some strange behaviour when I do the following:
1) Load A.pdb into MacPyMOL via pymol A.pdb2) Load a CHARMM simulation
trajectory into object A via load A.dcd, A
3) Load a completely different structure (must have different number of atoms
than A.pdb), B.pdb, into a
Hi PyMOLers,
I had written a script called jump.py which is used to jump between frames
after loading in a trajectory:
http://www.pymolwiki.org/index.php/Jump
Originally, I was using this on a PC and am now on a MAC (at work). For some
unknown reason, the default key PgDn doesn't seem to
Hi PyMOLers,
I have set movie_panel=1 in MacPyMOL but I don't see the normal movie
controls as in the Windows version of PyMOL which is typically situated below
the viewing area. Can somebody tell me where it went?
Thanks
Sean
Hi PyMOLers,
Can anybody tell me if there's a way to read in a protein structure file (PSF).
This is a common file format in simulation programs such as CHARMM and NAMD
and basically gives similar information to the PDB file.
Any suggestions would be greatly appreciated.
Thank you for your
...@gmail.com
To: magic...@hotmail.com
CC: pymol-users@lists.sourceforge.net
Hi Sean,
The .psf file format is for a topological desription (bonds, angles, etc), not
for coordinates afaik.
Cheers,
Tsjerk
On Dec 7, 2011 6:25 PM, Sean Law magic...@hotmail.com wrote:
Hi PyMOLers,
Can anybody
Hi PyMOLers,
I have tried installing both PyMOL 1.3 and PyMOL 1.4.1 on OpenSuse (old Pentium
4) and am finding that when I load a molecule and click Show -- Sticks that
the entire molecular gets colored blue (originally the green default lines
color). After trying to change the color (Color
If you find that get_dihedral is slow then you can try using the code from
pucker.py which contains a section on calculating dihedrals for the nucleotide
sugar pucker:
http://pymolwiki.org/index.php/Pucker
Sean
Hi PyMOLers,Can somebody offer an explanation for the possible values that can
be used with the movie.produce command?produce filename [, mode [, first [,
last [, preserve [, encoder [, quality [, quiet ]]]Any clarification of the
scope of each option would be appreciated.ThanksSean
Hi PyMOL Community,
I have a trajectory file loaded into PyMOL but I would like to play the movie
in reverse order. Is there a way to achieve this within PyMOL? I know that I
could do this by outputting the states as PNG files and then reversing them in
an external program but I would like
Cunliang,
There is a script available on the PyMOL-Wiki that calculates either the
center-of-mass OR the center-of-geometry.
Please see http://www.pymolwiki.org/index.php/Center_Of_Mass
It uses the pseudoatom function to generate a sphere at the desired center of
mass.
Hope this answers
Hi,
That was my first instinct as well and I tried that. However, the problem is
that rotating the molecules gets very tricky since the molecules are now no
longer in the same plane. So, if I translate one of them either towards or
away from me and then rotate, that molecule will rotate
Hi PyMOLers,
I was wondering if anybody had a solution for independent when using
grid_mode=on. I want to be able to show, side-by-side, the same structure
where one structure is zoomed in on a specific part on the biomolecule and
the other object is zoomed out (viewing the entire molecule).
Hi PyMOLers,
Is there a way to display PDB atom numbers when you right click on an atom? It
normally gives information like object/segment/chain/resn/resid/name but I want
a quick way of comparing the atom number with the PDB atom numbering.
Thanks!
Sean
Hi PyMOLers,
I was wondering if this problem was exclusive for my case. I was using
pair_fit (rather than super/align) to superimpose two conformations of the
same structure and noticed two things:
1) After being superimposed, BOTH structures (source and target) end up moving
rather than
Jason,
Being a complete novice when it comes to movie making, I decided to finally
take the plunge. First, I tested your commands on the prototypical 1nmr file
which worked great with the commands that you had described. However, when I
tested the same commands on a 212 state DCD file the
Hi PyMOLers,
I'm not sure if this is a bug or not but when I draw CGO shapes in PyMOL and
then later decide to give the shape a different color, I can't seem to change
the color of the CGO object by simply clicking on C from the internal GUI and
selecting the desired color. Instead, I need
Hi All,
I just wanted to let everyone know that there were some minor bugs in the
modevectors.py script (originally written by me) that were discovered (and
debugged) by a fellow PyMOLer (Raul Mendez). These bugs only affected the
usability of the script and should not affect the output. I
Hi PyMOLers,
I have been tackling this problem (on and off) for quite some time now but
without any luck. I have been trying to create CGO triangles using the
following simple sample script:
###
from pymol.cgo import *
from math import *
from pymol import
Hi All,
I was wondering if anybody knew how to save MPEG movies in PyMOL via command
line (I am using v1.3). I understand that movies can be saved via File-Save
Movie As-MPEG but I want a full screen sized movie (full screen mode) where
only commands issued via command line can be accessed
Hi All,
I have re-written the center-of-mass script found on the Wiki (which was
actually only calculating center-of-geometry). This script provides three
improvements to the previous script: 1) The real center-of-mass can be
calculated based on a table of atomic masses, 2) pseudoatoms are
Hi All,
I noticed that when I write a script that prints something in PyMOL that there
appears to be a limitation to the continuous length that can be printed to the
external GUI. Here is an example script:
#
from pymol import cmd
def testing ():
Hi All,
I have written a quick little script to jump through various frames from an MD
simulation loaded into PyMOL:
###
from pymol import cmd
import time
def jump (*args, **kwargs):
#Example: jump 1, 10, 20
#This will jump from frame 1
Hi All,
I'm not sure if this is a bug in PyMOL but I found that when you make a
selection, show it as spheres representation, and then turn on the transparency
(to anything but off), none of the now transparent spheres be selected via a
mouse-click in the viewing area. Thus, if I selected 5
Hi all,
Being a user of Adobe products, I am use to having a very customizable working
environment so that you could easily improve overall workflow and decrease
fumbling time. I find myself wanting my productivity to increase when using
PyMOL. While I do input a lot of my commands by hand,
Hi,
Another idea that came to mind while staring at MD trajectories all day is the
ability to display measured values (distance, angle, dihedral, etc) in a
localized or boxed in area (maybe even under the list of objects). The main
use for a measurement area would be to make it easier to
Hi all,
Another feature that I find myself always wanting is a kill script button
and/or command. This comes in handy when I am testing a new python script and,
accidentally, throw in an infinite loop. It would be nice to have some sort of
kill switch not only for python scripts but even
Is it possible to include a function that could easily add or delete states
(from the beginning, middle, or end of a set of states)?
Something with the following syntax:
delete_states 14 #Deletes state 14
delete_states 10-20 #Delete states 10-20
Jason,
I would LOVE to see CEalign built along with PyMOL. +1
Sean
_
Say Happy New Year with Messenger for Mobile.
Jason,
Here are some features that I have discussed with Warren in the in the past:
1) Vector graphics output (preferably in Adobe Illustrator format, SVG,
postscript, or PDF format). I tend to make all of my posters and publication
figures in Adobe illustrator (due to its scalability) and
Hi All,
I have two structures that are homologous. One structure #1 contains 100
states and structure #2 contains only one state. I would like to align each
state of structure #1 to structure #2 based upon some selection. From what I
can understand, if I say:
align struct1, struct2
This
and alter_state are highly
inefficient – it would make more sense to provide a means of exporting and
re-importing coordinate sets via either native Python lists or, even better,
NumPy arrays. In what form do you have the current coordinate data?
Cheers,
Warren
From: Sean Law
for that trajectory that is renumbered by PyMOL
or
2) Retain the RESID (see PyMOL-Wiki)
Since this was done on a whim, please use at your own risk until it is further
developed. Hope this helps!
Sean Law
Michigan State University
Hi All,
I was wondering if there was a faster way to replace all coordinates. I've
used commands such as iterate_state and alter_state before but they are far too
slow since they have to iterate over each atom. Instead, I want to replace one
set of coordinates that correspond to a specific
Hi PyMOL Users,
I was wondering if there was a smart way of having a script iterate over all
(or some) of the states. I know that there are the usual iterate and
iterate_state commands available but it appears that it makes for clumsier
code. More specifically, I'm looking to use the
I think I figured it out (though, it wasn't documented). What I needed was to
use:
cmd.get_model(selection, STATE)
I think that's the correct usage? What I needed was to loop through a
selection and then to calculate the sugar pucker information. However, not all
atoms from the selection
Oscar,
If you visit the PyMOL-Wiki, you will find a script called modevectors.py:
http://www.pymolwiki.org/index.php/Modevectors
There are several examples there that will allow you to customize the arrows.
Sean
Dear all,
Is it possible to show normal model/vectors of the selected
I was wondering if AxPyMOL could handle a .pse file that loaded two pdb
structures in powerpoint.
I've simply created a .pse file by fetching 2bmv and 2hhb. Then I loaded this
onto my PC laptop while in powerpoint. Other slides in the same presentation
with a single pdb file works fine.
Hi PyMOLers,
I am trying to write a python script that will allow a user to provide an
unlimited number of positional arguments for a function. I am use to the
following scheme for defining a function and its arguments:
def some_function ( x, y, z, file=false):
#DO SOMETHING
return
Where
Hi all,
I am playing around with the new PyMOL 1.2 release and was hoping to use the
Movie Panel in conjunction with a loaded DCD trajectory file. However, after
loading the MD trajectory and setting movie_panel to 1 I don't see the
prescribed time line below the viewing area. Of course, if
.
Anyway, you already mention joining opposite faces of the box - well
just use the axes calculated half-way through the first function.
Hope this helps.
gilleain
On Tue, Jun 2, 2009 at 11:41 PM, Sean Law magic...@hotmail.com wrote:
Hi,
For the past couple of days I've been trying to find
From: matthew.frank...@imclone.com
Date: Wed, 3 Jun 2009 15:13:25 -0400
Sean Law magic...@hotmail.com wrote on 06/03/2009 12:52:45 PM:
Warren,
After a deja vu moment, I realized that I had posed a similar
question to you before about this (although, we didn't really have
should be invariant to 180 degree rotations about the Y or X axes
respectively.
Cheers,
Warren
From: Sean Law
[mailto:magic...@hotmail.com]
Sent: Wed 6/3/2009 12:28
PM
To: matthew.frank...@imclone.com
Cc:
pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Principal Axes
of Rotation
Hi PyMOLers,
I was wondering if there is a way to load part of a PDB file if you know a
priori what you want thereby saving time/memory?
Currently, I have a system that is ~160,000 atoms (protein-DNA complex with
explicit water molecules taken from an MD simulation). When I load more than
Hi All,
While ray tracing a scene with 10 x-large proteins in grid mode at 3600, 3600
(width, height) I ran out of RAM (2 GB). I tried it again by writing
everything into a script and using pymol -qc which still ran out of memory. I
read somewhere that POVRAY is less of a memory hog so I
Hi Warren,
I know that there has been some discussion on implementing a vector-based
figure export. I was wondering if there were any updates on this? I think
that this would be an amazing feature to have. Thanks!
Sean
_
Hi Bala,
Recently, I added a new python script to the PyMOLWiki. Search for
modevectors or arrows and you should find the method for drawing arrows
with TONS of examples. I'm not sure if that's what you are looking for but you
should be able to find your answer amidst the script.
Sean
Hi,
I noticed that version 1.1 is said to have Cone representation available as
cgo so I downloaded the windows binary and tested it out but I haven't been
able to get it to work. Any clarification on how to get this to work would be
greatly appreciated. A sample code is written below.
) is below.
Sean
from pymol.cgo import *# get constants
from math import *
from pymol import cmd
def pucker(selection):
# Author: Sean Law
# Institute: Michigan State University
# E-mail: s...@msu.edu
obj_name = selection
objects = cmd.get_names(selection)
for obj
? Thanks in advance!
Sean
=
from pymol.cgo import *# get constants
from math import *
from pymol import cmd
def pucker(selection):
# Author: Sean Law
# Institute: Michigan State University
# E-mail: s...@msu.edu
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