for asking too much.
I will appreciate your help.
On Fri, Mar 13, 2009 at 12:44 PM, Tsjerk Wassenaar tsje...@gmail.com
wrote:
# Hi Falgun,
# Here's a mail I sent earlier to the lsit. I don't know why it
doesn't show up when searching.
# Anyway, this still is a python proof e-mail. You can
Hi Janek,
You want:
cmd.get_object_list()
For instance, I sometimes want to align a whole lot of things, which I do with:
/for i in cmd.get_object_list(): cmd.align( i, reference )
Hope it helps,
Tsjerk
On Fri, Feb 27, 2009 at 3:44 PM, Jan Kosinski k...@genesilico.pl wrote:
Hi,
I wish to
Kosinski k...@genesilico.pl wrote:
Thanks, that works!
Is there an API reference to pymol for non-sponsor users?
Tsjerk Wassenaar wrote:
Hi Janek,
You want:
cmd.get_object_list()
For instance, I sometimes want to align a whole lot of things, which I do
with:
/for i in cmd.get_object_list
Hi Tanja,
Try:
pymol -qcd 'cmd.help(launching)' pymol_launching.txt
and examine the resulting file :)
Cheers,
Tsjerk
On Wed, Oct 29, 2008 at 7:48 PM, Tanja Mittag tanja.mit...@gmx.de wrote:
Hi!
I would like to run pymol scripts on the command line only without
invoking the x-window
Hi Florian,
Check the selection stuff in Pymol: help selections
For example displaying all residues not farer away than 6 A from any
ligand Atom?
If ligand is your ligand selection and protein the protein part, this
is done simply (intuitively) with:
show sticks, byres protein within 6 of
Hi Christian,
The following works, although it may not be a neat solution:
pymol -d 'cmd.help(selections)'
Mind the quotes.
Hope it helps,
Tsjerk
On Thu, Sep 11, 2008 at 5:48 AM, Christian Seifert
cseif...@bph.ruhr-uni-bochum.de wrote:
Hi.
The command help launch tells me, that the launch
Hi,
Hear, hear! :)
A suggestion might be to pass them through the PRODRG server
(http://davapc1.bioch.dundee.ac.uk/prodrg/) which can be automated and
is capable of providing an energy minimized structure (do mind the
hydrogens/charges/valencies). It would also give you the opportunity
to provide
Hi O.J.,
What exactly do you mean by 'sheared'
(http://mathworld.wolfram.com/Shear.html). What you see is due to the
fact that you show the 'exposed' part of the vdw sphere of an atom
with substituents. I think that if you want to show them whole, you
have to make them a separate object first.
Hi Leo,
AFAIK you can't do it with Pymol, as it would require additional
fonts. Also, it seems tough to me to position to label properly with
respect to the camera. But you have plenty control with
convert/imagemagick (see
http://www.imagemagick.org/Usage/annotating/). That will allow you to
Hi,
This should've gone to the list... (isn't there an option send
replies to list rather than to poster to the mailing list?)
Tsjerk
On Fri, Jun 27, 2008 at 1:34 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Marius,
You want iterate.
You do have to make sure though that the numbering
Hi David,
Regarding the first part of your question, the way to load a python
(not a PyMol) script is:
run axes.py
.. and not @axes.py. The latter is used for loading PyMol scripts
(.pml). You _can_ use python code in a .pml script, but then you
better, or in some cases have to, start with a
Hi Tom,
On Tue, May 27, 2008 at 10:53 PM, Thomas S. Leyh, Ph. D.
l...@aecom.yu.edu wrote:
From time to time I find it valuable to view the suface of a
ligand-binding pocket looking out from the surface's interior. This is
accomplished in a variety of ways - principally, zooming and
Hi Martin,
Now why didn't I ever think of that? So simple... In the .pymolrc you can add:
import os
/def gro( fnm ):\
os.system(editconf -f %s -o /tmp/tmp.pdb % fnm )\
cmd.load( /tmp/tmp.pdb, fnm[:-4] )
cmd.extend( gro, gro )
And it will do what you want...
Cheers,
Tsjerk
On Wed, May
Hi Dave,
As intuitively as could be imagined:
bond n. fe, r. hem and n. n
provided that these selections match your atoms. You can also pick
both atoms with the mouse and then simply issue 'bond'.
Cheers,
Tsjerk
On Sat, May 24, 2008 at 7:50 AM, Charles David Stout d...@scripps.edu wrote:
On Apr 24, 2008, at 2:21 AM, Tsjerk Wassenaar wrote:
Hi Dean,
Good that it works. I suspect the only real difference is the use of
ALPHA, which sets the transparency. Do mind the position of the ALPHA
keyword and it's value, as these are important.
Best,
Tsjerk
On Wed, Apr 23
the ray command, I can't see the shadowed
boundary between boxes like I can before before the ray command.
Thanks again. I really appreciate the tips!
Dean
On Apr 24, 2008, at 2:21 AM, Tsjerk Wassenaar wrote:
Hi Dean,
Good that it works
Hi Dean,
Funny, really. Last week I was just playing around a bit with creating
boxes in pymol, e.g. to create a bounding box, and I wanted to have it
transparent. So here's a script, giving you a function 'rect', which
takes two tuples, specifying the far edges of the box:
rect( [x0,y0,z0],
Hi Horacio,
Do you really need a sphere around (x,y,z)? That's tough. But I'd
reckon it's more meaningful to select all residues within a certain
distance from any atom of the ligand anyway, which is easy:
show sticks, byres protein within 3.5 of ligand
Without 'byres' only the atoms actually
Hi Michael,
I believe this is version specific, but for the 1.0 series the
settings are object specific. So in order to get what you want, you
best create a new object for the parts you want to show the cartoon as
cylinders, and
set cartoon_cylindrical_helices, 1, newobject
Hope it helps,
Hi Hari,
You can do it using:
execfile(/Users/hari/Desktop/test.cgo)
cmd.load_cgo(obj,test)
However, you might find it more convenient to drop the obj = from
the .cgo file and load the thing with:
cmd.load_cgo( eval( open(/Users/hari/Desktop/test.cgo).read() ), test )
Although that seems a
Hi Tom,
Does what you're trying to do come down to:
alter all, vdw=b/100
show spheres
?
Cheers,
Tsjerk
On Fri, Feb 22, 2008 at 1:42 AM, Thomas Stout tst...@exelixis.com wrote:
Hi All --
Yes, I know I want to do something silly here, but does anyone know of a
jiffy that will generate
on..
I don't recommend it for general use or analysis!!
-Tom
-Original Message-
From: DeLano Scientific [mailto:del...@delsci.info]
Sent: Friday, February 22, 2008 11:39 AM
To: 'Tsjerk Wassenaar'; Thomas Stout
Cc: PyMOL-users@lists.sourceforge.net
Subject: RE: [PyMOL] Isotropic
Hi Horacio,
There are several ways of doing this. In a .pml script or on the
command line you can do:
/for i in range( 1, 641 ):\
cmd.load( 2jnk%d_rec.mol2 % i, temp, format=mol2, state=1 )\
cmd.align( temp, ref )\
cmd.save( 2jnkp%d_rec.mol2 % i, temp, format=mol2 )\
cmd.delete( temp )
Hi Moshe,
No it isn't. PyMOL is a molecular viewer/graphics engine, not a
modeling package. However, it's not too hard to do using your
favourite MD package. With the definition of a bond and some energy
minimization you'd get close. If it's for displaying purposes only,
that might even be
Hi Buz,
To my opinion, this is not the best place for your question. Pymol is
a molecular viewer...
But the question itself is basically trivial from the linear algebra
point of view.
If X is your source set of orthogonal vectors and Y is the target,
then you should have some sort of matrix R to
Hi,
'save' will save all atoms by default, not only the visible ones.
cat in Linux will surely be more efficient than loading in Pymol and
saving, but the question related to alignment. cat doesn't do that for
you. So the procedure would be:
load A.pdb,A
load B.pdb,B
align A,B
save
Hi Hally,
It's worthwhile getting on terms with Linux. You mention you start a
blank program suggesting to me you're starting pymol without
anything to be loaded (pymol). It's not true that this can only be
done in the pymol directory. You can do it anywhere, as long as you've
got pymol in your
## (: Python proof E-mail :) ##
# Hi João,
#
# It indeed appears that the attachments are not preserved for the
list (or that one at least)
# You can save the text of this mail as arrow.py and run it instead.
#
# Best,
#
# Tsjerk
from pymol import cmd
from pymol.cgo import *
from math import *
Hi Linda,
You can export it to povray:
open(surface.inc,w).write(cmd.get_povray()[1])
Cheers,
Tsjerk
On Jan 16, 2008 4:55 AM, Lu Lin l...@cs.hku.hk wrote:
Hi all,
Anyone can tell me whether I can export the mesh or surface into a file
(e.g. .wrl/.obj etc.)?
Thanks!!
Linda
Hi Ramakrishna,
On Jan 12, 2008 3:51 PM, rama krishna ram...@gmail.com wrote:
Dear User,
I need to color the Molecule based on generalized order parameter
after running the script data2bfactor
i used the command data2b_res 'mol','datafile'
after that it shows that
IOError: [Errno 2] No
Hi Steve,
You'll need to provide more information if you want to have a chance on a
helpful thought. Maybe you could link the .pdb file and the .xplor map and
show what O does to it.
Cheers,
Tsjerk
On Dec 7, 2007 3:57 PM, W.M. B. butiany...@gmail.com wrote:
Hi, All
I'm trying to make a
Hi Abhinav,
Whitespace matters. In fact, the first two characters in the atom name field
of the pdb file are usually considered indicating the element type. Pymol
also does this. This means that NA will be considered of element type
N, whereas NA will be interpreted as being of element NA.
Hi Mark,
You can also directly change the vdw radius of sodium to its ionic radius:
alter r. na\+,vdw=1.02
rebuild
Cheers,
Tsjerk
On Nov 27, 2007 1:15 AM, Dr. Mark Mayer may...@mail.nih.gov wrote:
hello,
Can't find anything about this in docs or in settings:
Where are sphere diameter
Hi Nagarajan,
I'm not sure whether this is the best way to get what you need. symexp is
intended to regain the crystallographic symmetry, but it seem to me you want
to have the biological unit. The pdb files in the RCSB PDB are usually also
available as biological unit and it should be possible
Hi Paride,
You'll have to build up the plane-with-hole with triangles. Not difficult to
do, but not completely trivial either, especially not if the CGO syntax is
new to you :S
Best,
Tsjerk
On 11/1/07, Paride Legovini legov...@spiro.fisica.unipd.it wrote:
Warren DeLano wrote:
Hi Dave,
Use alter_state:
alter_state 1,selection,x=x+25
or
alter_state 1,selection,(x,y,z)=(x+10,y+10,z+10)
By the way, alter_state allows all sorts of transformations of
coordinates...
Cheers,
Tsjerk
On 10/22/07, David Garboczi dgarbo...@niaid.nih.gov wrote:
I have three molecules
Hi,
I wouldn't use list, since that's a python keyword :S
Use reslist or something.
Cheers,
Tsjerk
On 10/19/07, Piter_ x.pi...@gmail.com wrote:
Hi Martin
May be this will help:
from sets import Set
list =[]
cmd.iterate('het', 'list.append(resn)')
residname =Set(list)
print residname
Hi Frieda,
I had to rewrite the script to get the output desired, now also using a
class definition :p
It works fine for me:
PyMOL@../..\ss.pml
PyMOLclass SSList:\
PyMOLlist = []\
PyMOLdef purge( self, resi, ss ):\
PyMOLif not self.list or self.list[-1][0] != ss:\
PyMOLself.list.append( [ss,
#--- Python proof e-mail ;) ---
# Hi Aaron,
# You can get to the coordinates in the following way:
# First make a model from the selection you want to work on:
sel = cmd.get_model( object )
# Then you can get to the coordinates and modify them without affecting the
view:
for i in
, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Frieda,
There's no such command. You'll have to parse the output you get through a
script which filters it in the way you want. This isn't difficult though
(good python exercise :p).
Best,
Tsjerk
On 10/9/07, Frieda Reichsman frie...@nsm.umass.edu
Hi Gillean,
For what it's worth, I experienced the same... No dashes in the numbers:
1-1
1--1 L
1-2
2--1 L
2-3
3--1 L
...
etc.
The double dash must come from the -1 value used as default for your SSE
class. Better double check what's going on there :)
Cheers,
Tsjerk
On 10/9/07, gilleain
Hi Frieda,
There's no such command. You'll have to parse the output you get through a
script which filters it in the way you want. This isn't difficult though
(good python exercise :p).
Best,
Tsjerk
On 10/9/07, Frieda Reichsman frie...@nsm.umass.edu wrote:
Hi,
I would like to get secondary
Hi,
There's not actually a way to get the default back. Distances are
stored as objects, so you can just use color.
Best,
Tsjerk
On 9/19/07, Lari Lehtio lari.leh...@ki.se wrote:
I do not know how to set the default, so I just use
color grey50, dist*
~L~
Hi Gianluca,
It would have been worthwhile checking the archive of the mailing list:
http://sourceforge.net/mailarchive/message.php?msg_id=8ff898150701110024y4b111ab2ic195813792c4b8d%40mail.gmail.com
It's a script of mine; if you encounter any problems or have
suggestions, feel free to contact
Hi kmeatball,
If you append all structures to the same model, which is what you do
by loading each under the same name into different states, the
connectivity will be determined by the first state. That is, the
topology information (read bond map) is global, and applies to all
states. If you want
Hi Hasan,
Start with the structures superimposed and translate/rotate one/both
away from the/each other. Glue the images together in reversed order
and no one will see the difference...
By the way, it might be nice to start with small
translations/rotations and have them increase quadratically in
Hi Mark,
You could've found this one in the archives of this list. Settings
work on objects, not on selections. The solution is to make an object
for the solid sticks and one for the transparent sticks, using create.
Cheers,
Tsjerk
On 6/26/07, Dr. Mark Mayer may...@mail.nih.gov wrote:
Dear
Hi William,
In contrast to Nick, I read your question as inquiring after a 3D
probability density function. In case I get it wrong, just ignore this
mail.
It is well possible to generate 3D pdfs and display them in Pymol.
Actually, for one project I'm doing that right now. I have modified a
Hi Justin,
If you have a pdb file of your coumarin derivative (which you can
obtain e.g. with the PRODRG server), you can use 'fuse' to attach it
to some amino acid side chain.
By the way, it may be a good idea to try and polish your english a
bit. A question clearly phrased will help people on
Crystallographica D, co-editor
e-mail: mbfro...@post.tau.ac.il
Tel: ++972-3640-8723
Fax: ++972-3640-9407
On Apr 20, 2007, at 9:30 AM, Tsjerk Wassenaar wrote:
Hi Gianluca,
Unfortunately, Pymol offers no such functionality intrinsically. But
this is where python comes in handy. Attached you
Hi Gianluca,
Unfortunately, Pymol offers no such functionality intrinsically. But
this is where python comes in handy. Attached you find a script I
wrote for the purpose. It allows you to shift objects or selections
over the periodic lattice:
run lattice.py
create ObjectCopy,MyObject
shift
Hi Jim,
Hmmm. I think your best option is to color the surface according to
the atoms and write the surface in povray format. This will give you
all the vertices. Just another thought springing to mind, you could
cycle over the atoms using a script, writing away only the part of the
surface
Hi Giacomo,
If you type 'set meshtab', you'll get a listing of the mesh-related settings.
With get mesh_something, you'll get the current (default) value.
Best,
Tsjerk
On 4/17/07, Giacomo Bastianelli gbast...@pasteur.fr wrote:
Dear Users,
I would like to change (using the API Pymol
Hi Adiphol,
It would have been better to state several questions as subjcts, but ok...
1. I would like to show side chain one colour by stick
and its backbone by cartoon another colour. So I tried
to create to same molecules. One with normal backbone
(no1) and the other with backbone and a
Hi Richard,
Why not set stereo_mode,3 and raytrace as it is on the screen? You can
set stereo_angle and stereo_shift to modify the scene.
Cheers,
Tsjerk
On 03 Apr 2007 10:57:36 -0500, Richard Baxter
rbax...@alumni.uchicago.edu wrote:
Dear All,
I used the following commands to generate a
Hi,
A workaround may be to wrap the cgo object in a python object, with a
reload function, as well as with transformation functions.
class CGOWrap:
cgoObject = []
name= []
def translate(self,vector):
def rotate(self,matrix):
def reload(self)
...etc...
The most difficult thing is
Hi David,
The state sort of refers to the frame or model in case of a
multiframe/multimodel (multistate) system. You don't need to use it
with set, it's optional. Just note that dash_length and dash_length
are quite different things.
Best,
Tsjerk
On 3/28/07, David Shin dav...@scripps.edu
Vala,
What do you mean by Calcium Phosphates pymol files? If you mean
structures of calcium phosphate..., try to find them on the web,
searching for pdb files or other formats. Pymol is a molecular
viewer.., it doesn't really come with such files from itself.
Alternatively, since calcium
Hey,
In addition, you may also want to
set cartoon_smooth_loops,0
in order to have your loops nice and wiggly, attaching to your side-chains.
Cheers,
Tsjerk
On 3/6/07, Andreas Forster docandr...@gmail.com wrote:
Hey Gary,
in order to have sidechains be attached to your cartoon
Hi Markus,
You can export the scene to pov-ray format, for which you should be
able to find a converter for vrml.
Best,
Tsjerk
On 3/2/07, Markus Wahl mw...@gwdg.de wrote:
Dear all,
I wondered whether there is a possibility in PyMol to export the
rendered polygon data in any kind of 3D format
Hi Mike,
Easy, add the object name after the set command:
set dash_width,3,dist01
set dash_width,10,dist02
Colouring works normally on objects:
color red, dist01
color green, dist02
Cheers,
Tsjerk
On 2/19/07, Mike Summers summ...@hhmi.umbc.edu wrote:
This works great! Is there any way I
Hi Abhi,
Actually, it was a bit surprising to me to see you're right. Now, for
showing/hiding, it has been dealt with in the code, by allowing the
+ to be left out. However, for selecting (and alter_ing) that
doesn't go, apparently. A workaround is to use
cmd.select(selectionname,r. na\+) or
.
Cheers,
Warren
--
DeLano Scientific LLC
Subscriber Support Services
mailto:del...@delsci.info
-Original Message-
From: pymol-users-boun...@lists.sourceforge.net
[mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf
Of Tsjerk Wassenaar
Sent: Friday, February 02, 2007 2:23 AM
Hi Magnus,
Fuse takes two arguments, you've only given one: (ret and name c15)
and (protein and resi 219 and name n). What you intended was
probably:
fuse ret and name c15, protein and resi 219 and name n
By the way, not any of my business, but what bacteriorhodopsin is
this? Usually, the bond
Ni Hao Feng,
First of all, please do not include an complete daily digest in a
question (or reply) on this or any user list. If required, cut out
only that part which connects to your question or reply.
Then, in addition to Bobs comments, you can also use the terminal or a
script, using the
Hi William,
Maybe the attached python script will be of some use. It contains a
function (and some helper functions) to draw a CGO arrow in PyMOL. It
contains code for drawing a cone for the head of the arrow.
Hope it helps,
Tsjerk
On 1/10/07, William Scott wgsc...@chemistry.ucsc.edu wrote:
Hi Rafael,
You can use
cmd.label(selection,'objectname-+resn+resi')
Do mind the quotes.., the label string is _eval_uated.
Of course, if objn = objectname, it also works as
cmd.label(selection,'objn+-+resn+resi')
Cheers,
Tsjerk
On 12/19/06, Rafael Najmanovich rafael.najmanov...@ebi.ac.uk
Hi DeVill,
If you're building a CGO structure with triangles, you have to make
sure that the normal vectors are correct. These will determine the
inside and outside of the object (and hence the coloring).
Cheers,
Tsjerk
On 12/4/06, DeVill dev...@cs.elte.hu wrote:
Hi!
I have created a
Shivesh,
Well, what would you think of the command 'dist'?
You could have read the manual...
Tsjerk
On 11/24/06, shivesh kumar shivesh_...@yahoo.com wrote:
Dear all,
Is there anyway to calculate the bond distances in pymol and to show the
bond distances also...
thanx in advance
S
shivesh
Hi Pernille,
You're looking for the command:
util.cbc
Best,
Tsjerk
On 11/6/06, Pernille Haste Andersen p...@cbs.dtu.dk wrote:
Hi Everybody,
I frequently use the color by chain option available in the PyMOL
viewer GUI, however I haven't managed to find a corresponding command to
be used in
Hi James,
Maybe you can try another route. The ray_trace_mode, 3 gives very
eye-catching pictures. Make one image intended only to grab attention
and place it large in the centre of your poster. Make another image
you can use to fill your background (chose the x/y-ratio of your
poster for
Hi Martin,
You may also be interested in this script which you can use to draw an
arrow from point A to point B:
cgo_arrow( start, end, radius, head_radius, head_length, name, state )
start = [ x1, y1, z1 ], end = [ x2, y2, z2 ]
For lots of arrows you can use:
cgo_arrows( X, radius,
Hi Eva,
It may be that the secondary structure information is not set
(assuming that you have some secondary structure). You can try to run
'dss' or if that fails you can try to resort to 'util.ss' which may do
the trick. Alternatively, you can set the secondary structure
information manually,
Hi Rinku,
Such a feature is not present in pymol out of the box. It is
possible to write a python script to create a CGO object joining two
given points (with a control point for each) with a smooth dashed
line.
Sorry if this doesn't help you further.
Best,
Tsjerk
On 9/20/06, Rinku Jain
Hi Tom,
Settings (thriugh set) apply to objects and not to subsets of objects.
Try creating an object from your selection first or change the colors
using color.
Best,
Tsjerk
On 9/17/06, Thomas Stout tst...@exelixis.com wrote:
Has anyone successfully set colors for ribbons via a
Hi Dong,
The second argument to cmd.select has to be a string giving the
selection _exactly_ as you would give your second argument on the
command line (but then quoted). Try
cmd.select(name, all within 3.2 of (resi 2 and chain A))
Cheers,
Tsjerk
On 9/15/06, XUESONG DONG
Hi OJ,
I don't know if someone has implemented it already, but it's not a
hard thing to do if you know a little python. You basically need to
fetch the coordinates of the OCNH atoms from a selection and build
planes with CGO (you can have a look at Gareth Stockwells walls.py:
Hi Mahesh,
There is no way to see whether two atoms are connected. Pymol guesses
the connectivity based on the distances between the particles. But to
be certain whether atoms are bonded, you have to look in the PDB file,
which should mention covalent attachment of a ligand. At the end of
the
Hi Michael,
Use:
set ray_opaque_background, off
Cheers,
Tsjerk
On 8/17/06, Michael Weber web...@staff.uni-marburg.de wrote:
Hi guys,
for preparation of a figure I need to combine a PyMOL image export file
(.png) with another image. Is it possible to export the PyMOL data with a
Hi Binbin,
Remember that computers understand things different than we usually
do. You need:
select (resi 367 and chain c) or (resi 366-379 and chain a)
And gives intersection, or gives union...
Tsjerk
On 8/17/06, bm...@leeds.ac.uk bm...@leeds.ac.uk wrote:
Hello there,
I'd want to select
Hi Paul,
This is not possible at present (as has been mentioned in this mailing
list several times...).
Tsjerk
On 8/16/06, Paul Wilhelm Elsinghorst p...@uni-bonn.de wrote:
Hi guys,
let's say we have a scene with two objects. Can I have different
clipping planes for these two objects? For
Hi Chandra,
1. Just load the file on the command line or through the interface
(load). Then to show all structures use 'set all_states,1' or
'split_states' if you want to have them as separate objects.
2. First create an object of the selection.
3. Please read the manual, search the archives
Hi Philippe,
Pymol isn't very good at handling many spheres. However, Povray is
extremely efficient with raytracing scenes consisting of spheres and
if you know the perspective you want to have the image from, you can
convert your atom set to spheres (with desired radii) and apply the
view from
Hi Hasan,
Have a look at label... (and read the manual :))
Cheers,
Tsjerk
On 7/27/06, Demirci, Hasan hasan_demi...@brown.edu wrote:
I have a cross-eye stereo image generated by PYMOL. Is there an easy way of
custom labeling the residues by using PYMOL ?
Or should I use a photo editor
Hi Adrien,
You don't really need the double loop, I'd say. What about:
for i in range(1,20):
cmd.load(o.%03d.1.pdb%i,m1)
cmd.load(o.%03d.2.pdb%i,m2)
cmd.load(o.%03d.3.pdb%i,m3)
cmd.hide(everything)
cmd.show(spheres)
cmd.ray()
cmd.png(o.%03d.png%i)
By the way, note that
Hi Mikael,
As far as I'm aware that is not possible (and definitely not with
run, see 'help run'). What you can do is to define a function in
test.py, which takes the arguments you want. Then, after running the
script you can use the function as you please. If, in addition, you
add to the end of
Hi Petro,
run expects a python script (.py), whereas you're trying to run a
pymol script (.pml). For that you nead '@':
@c:\pict.pml
Cheers,
Tsjerk
On 7/6/06, Piter_ x.pi...@gmail.com wrote:
Hi all
I have some errors if I run script:
PyMOLrun c:\pict.pml
Traceback (most recent call last):
Hi,
You can do this using alter_state:
alter_state 1,selection,(x,y,z) =
(a11*x+a12*y+a13*z+d1, a21*x+a22*y+a23*z+d2,
a31*x+a32*y+a33*z+d3)
where a11-a33 are the matrix elements (check whether they have to be
transposed) and d1-d3 are the elements of the shift vector.
It may
Hi Dong,
My guess is (but ofcourse Warren knows best) that pymol chokes in the
full pathname, including the spaces. Note that under windows the
actual pathname would be D:\DOCUME~1\1LTL.pdb The long pathname is an
alias.
Cheers,
Tsjerk
On 6/29/06, LIU Changdong cd...@ust.hk wrote:
Dear all:
Hi Michael,
The answer to the second question is: yes
alter selection,vdw=1.0
will change the radius of selected atoms to 1.0 angstrom.
Cheers,
Tsjerk
On 6/30/06, Michael Weber web...@staff.uni-marburg.de wrote:
Hi,
I have a question concerning the spheres representation. According to my
Hi Warren et al.
I really like the ray_trace_modes 2 and 3. However, I'd like to fiddle
around with the thickness of the edges, but can't find a setting to do so.
Am I overlooking something, or isn't there any (yet)?
By the way, ray_trace_mode 2 is great for making colouring pictures to get
the
Hi Natasja,
That should be done with (IIRC)
set surface_color,-1
Tsjerk
On 5/24/06, Natasja Brooijmans broo...@wyeth.com wrote:
I accidently used the set surface_color, x command, and then unset. Now
the full surface is colored white. Rather, I want the surface to be colored
by the color
Hi Frank,
These settings apply to objects, if specified.
set cartoon_trace,1,object1
will make it apply only to object1
Cheers,
Tsjerk
On 5/23/06, Frank Murphy f...@mrc-lmb.cam.ac.uk wrote:
Hello,
I was wondering if anyone out there has connived a way to assign
different properties to
Hi Ron,
Check the commands
get_view
set_view
Cheers,
Tsjerk
On 5/23/06, Ronald Chiu rccom...@gmail.com wrote:
Hello All,
Is there any way to show the coordinates for the orientation that a
protein is in?
Lets say you tweak (rotate and turn) a protein in to a particular
orientation, is
Hi Surendra,
split_states is a native Pymol command. If you download from the PDB the
biological unit coordinate file, you can show it using split_states OBJECT
Cheers,
Tsjerk
On 5/18/06, surendra negi negi...@yahoo.com wrote:
Hello pymol,
Is it possible to create biological unit of a
Hi Terry,
There's a bit more to it. In the pymol view, the camera is located at the
origin, so to rotate your coordinates you first have to move the center to
the origin, do the rotation and move the thing back. I've scripted this in
Povray. If you're interested, I can send you the script. You
Hi,
Actually, one of the first of these images I made was of conotoxin floating
above a see. Will that do? I'd still have to add the sunset though ;) O, and
the checkered beach...
In regards the problem of Seth, it's good you've solved it. It is possible
though to remove all statements about
Hi Laura,
You can change the van der Waals radii of atoms using
alter selection, vdw=newradius
Alternatively, you can use the setting sphere_scale (set
sphere_scale,factor), which changes all radii by the given factor. Note that
you need to create different objects to use different factors for
Hi Tiger,
Nick is largely right. The cause for the link to show up is that pymol just
traces through all c-alphas in the object, regardless of chains or
distances. So, selecting the linked residues and hiding the trace should
solve your problem. Also, creating two files will do the trick.
Hi Warren,
I just ran into a bug with pymol 0.99 rc1 on SUSE 10 Linux on my Acer
TravelMate 800, which has an ATI Radeon video card. The problem is that for
atoms with negative x-coordinates the spheres don't show up. When I shift
the coordinates using alter_state the spheres show up again. This
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