Hi Ron,
Check the commands
get_view
set_view
Cheers,
Tsjerk
On 5/23/06, Ronald Chiu 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 there any way to tell
Hi Natasja,
That should be done with (IIRC)
set surface_color,-1
Tsjerk
On 5/24/06, Natasja Brooijmans 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 of the underlying
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 l
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 wrote:
Dear all:
After I inst
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 wrote:
Hi,
I have a question concerning the "spheres" representation. According to my
rough estimation the sphere
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 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_ wrote:
Hi all
I have some errors if I run script:
PyMOL>run c:\pict.pml
Traceback (most recent call last):
File "C:\Progr
Hi Vladimir,
In addition to the solution of Robert (which could be regarded the
best solution in a sense) and for the sake of completeness, you could
also directly change the vdw radii:
alter name ca,vdw=1.5*vdw
alter name cb,vdw=0.5*vdw
This will also change the appearance of other representat
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 o
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 w
Hi Hasan,
Have a look at "label"... (and read the manual :))
Cheers,
Tsjerk
On 7/27/06, Demirci, Hasan 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 program to label everything
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 P
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 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 wrote:
Hi guys,
let's say we have a scene with two objects. Can I have different
clipping planes for these two objects? For now I tried
clip
Hi Michael,
Use:
set ray_opaque_background, off
Cheers,
Tsjerk
On 8/17/06, Michael Weber 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
transparent background? Or does anybod
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 wrote:
Hello there,
I'd want to select residue from differ
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 pdb
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:
http://www.ebi.ac.uk
Hi Orla,
You're not making clear what kind of effects you want to investigate.
Basically, it is possible to delete amino acids using pymol, but you
could as well use a text editor. If the purpose is to have a 'correct'
starting structure for further study (e.g. MD simulation), it's
unlikely to wo
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 wrote:
Hi,
I
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 wrote:
Has anyone successfully set colors for ribbons via a non-trivial atom
selection?
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 wro
Hi Abhinav,
Try:
unbond r. cys and n. sg, r. cys and n. sg
which removes all bonds present between sulphur atoms of cysteine residues.
Best,
Tsjerk
On 10/11/06, Abhinav Verma wrote:
Hello,
pymol finds the disulphide bonds very nicely when you load a pdb file.
What I want is, to tell hi
Hi Nian,
You can only do that by moving the helix (backbone) atoms outward with
respect to the helix axes. It is possible to write a script for that,
but it wouldn't really be simple.
Best,
Tsjerk
On 10/11/06, Nian Huang wrote:
Hi,
"set cartoon_helix_radius" works only in cylinder mo
Hi Feng,
Start out with reading the manual, in particular the section regarding
selections. Then be sure to no the atom names you want to select and
use
select (name atomname1,atomname2,...)
To be sure not to grab any other molecules, you may want to make it read
select (name atomname1,atomnam
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, us
Hi Martin,
As far as I know there is no such plugin yet for gromacs trajectories.
But you can convert the gromacs trajectory to a multimodel .pdb file
using gromacs utility trjconv and load that in pymol. Alternatively,
you could take up the effort of writing a plugin and have a look at
the way A
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 ray-tra
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, head_radi
Hi Pernille,
You're looking for the command:
util.cbc
Best,
Tsjerk
On 11/6/06, Pernille Haste Andersen 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 the Tcl/Tk GUI
Shivesh,
Well, what would you think of the command 'dist'?
You could have read the manual...
Tsjerk
On 11/24/06, shivesh kumar 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 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 wrote:
Hi!
I have created a plug-in that generate
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 wrote:
Hi There,
Is
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 comm
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 wrote:
Let's ask on the pymol mail
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 bon
Hi Maarten,
Your dist-results show up as new objects. You can colour them using
the command color , or using the sidebar.
Cheers,
Tsjerk
On 1/22/07, Maarten Dewilde wrote:
Dear All,
Can anybody please tell me how to change the dash color from standard yellow
to something else (the yellow
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\+")
na\+")
which actually works, but probably shouldn't.
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.ne
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 wrote:
This works great! Is there any way I can draw two
different
Dear Bernhard,
The user manual is quite informative where it comes to making
selections. There is not a polar/nonpolar grouping made for you, but
you can easily select the residues based on their names (resn or r.).
select basic, (resn lys,his,arg)
As a side note, on this as well as all other u
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 wrote:
Dear all,
I wondered whether there is a possibility in PyMol to export the
rendered polygon data in any kind of 3D format such as wrl o
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 wrote:
Hey Gary,
in order to have sidechains be attached to your cartoon representation, the
cartoons mus
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 phosphat
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 wrote:
This regards
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 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
wrote:
Dear All,
I used the following commands to generate a nice wall-eye stereo figure
(at
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 si
Hi Giacomo,
If you type 'set mesh', 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 wrote:
Dear Users,
I would like to change (using the API Pymol commands)
the features of the m
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 1,0,0
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 belon
ographica 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. 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
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
progr
Hi Richard,
What about
set solvent_radius,3
That seems to do the trick for me.
Cheers,
Tsjerk
On 5/22/07, Richard Gillilan wrote:
In the past I have used PyMol pretty successfully to visualize low-
resolution x-ray solution scattering results in which each "atom" in
a pdb file is actually
Hi Nick,
Unfortunately, there's nothing you can do about it. mpng just writes
out the frames one after the other, with raytrace_frames set
raytraycing each of them. cache_frames just puts each (rendered) frame
in memory, so Pymol can cycle through them sort of smoothly after all
frames are render
Hi Thomas,
Just a as a note. A focal blur is not like a fog, but results from
sort of averaging a series of images, with the in-focus plane being
well-defined and the planes in front and in the back blurred according
to the distance from the in-focus plane (and the aperture). Not
completely trivi
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 wrote:
Dear All,
I'm trying t
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 Andy,
Do you mean something like:
show surface, byres Obj1 within 3 of Obj2
show surface, byres Obj2 within 3 of Obj1
Be sure to have the peptide and the protein as separate objects,
otherwise this won't work. You can of course also drop the 'byres'
statement if you want...
Hope it helps,
T
Hi Nicole,
So, marking Warrens words, the question is, did anything else in your
configuration change? Hardware, operating system, device drivers? That
is a more likely cause for your problem. Otherwise, is the problem
reproducible? Good behaviour with before version, bad behaviour with
'fixed' ve
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 wan
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 m
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 wrote:
> I do not know how to set the default, so I just use
>
> >color grey50, dist*
>
> ~L~
>
> ___
Hi Jianghai,
> How can I show the carbonyl oxygen as a stick?
show sticks, (n. c,o)
> What is the best way to show the backbone nitrogen?
show sticks, (n. n,h)
Cheers,
Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
Hi Greg,
In addition to Warrens reply, you don't have to repeat the code eight times
if you use a bit of python:
/for i in range(9): cmd.set_color( "blue"+str(i), [ 0.0, 0.0, 0.2+i*0.1 ] ),
cmd.color( "blue"+str(i), "chain " + "ABCDEFGH"[i] )
You can use all the arithmetic you want to get a nice
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 wrote:
>
> Hi,
>
> I would like to get secondary structure informa
#--- 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 range(len(se
Hi Frieda,
In addition to my previous mail, the following works for me:
sslist=[]
iterate n. ca, sslist.append( [resn,resi,ss] )
/i=1, j=len(sslist)-1
/while i 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 wa
entation,
> that takes a function and applys it to each sse. I don't know if these
> programs are compatible with very early versions of python, bytheway.
>
> http://www.pymolwiki.org/index.php/Iterate_sses
>
> They were fun to code, anyway.
>
> gilleain torrance
&g
and got a
> readout like the following, for each object in the file.
>
> [['MET', '1', 'S'], ['GLN', '2', 'S'], ['VAL', '3', 'S'], ['PHE', '4',
> 'S'], ['ILE&#x
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,
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
PyMOL>class SSList:\
PyMOL>list = []\
PyMOL>def purge( self, resi, ss ):\
PyMOL>if not self.list or self.list[-1][0] != ss:\
PyMOL>self.list.append( [ss
Hi Greg,
You shouldn't physically merge the .pdb files. Just load all the .pdb files,
set the settings and save it as a .pse. This could of course be scripted. If
you want to apply the settings from a certain .pse, load that one store the
view and if any settings need be applied to the other model
Hi,
I wouldn't use "list", since that's a python keyword :S
Use "reslist" or something.
Cheers,
Tsjerk
On 10/19/07, Piter_ wrote:
>
> Hi Martin
> May be this will help:
>
> from sets import Set
> list =[]
> cmd.iterate('het', 'list.append(resn)')
> residname =Set(list)
> print residname
>
> Be
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 wrote:
>
> I have three molecules aligned on each other. I
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 wrote:
>
> Warren DeLano wrote:
> >
> http://pymol.svn.sourceforge.net/view
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 to
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 wrote:
> hello,
>
> Can't find anything about this in docs or in settings:
>
> Where are sphere diameter settings controll
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
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. wrote:
> Hi, All
>
> I'm trying to make a picture of active sit
Hi Ramakrishna,
On Jan 12, 2008 3:51 PM, rama krishna 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 such file
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 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 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 you
## (: 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 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 AB-aligned.pdb
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 enough.
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.d
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 s
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 wrote:
>
>
> Hi All --
>
> Yes, I know I want to do something silly here, but does anyone know of a
> "jiffy" that will generate anisotropic t
in regard to the values of the atoms around themetc etc etc... The
> caveats go on..
>
> I don't recommend it for general use or analysis!!
> -Tom
>
>
> -Original Message-
> From: DeLano Scientific [mailto:del...@delsci.info]
> Sent: Friday, Febru
Hi Andy,
You can get the representation of the surface in terms of a set of
triangles by saving as .wrl (VRML object) or in povray format
(cmd.get_povray()).
Cheers,
Tsjerk
On Fri, Feb 29, 2008 at 3:35 PM, Andy Cheesman
wrote:
> Hi people
>
> I've been using pymol to render molecule models wh
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,
Tsj
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 wi
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], [x1,
efore 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. I suspect the only real difference is the use of
&g
er than 1 that seems to got away.
> > > 2) One other obj (spheroid) which I had set at transparent
> > disappears
> > > when viewed through a transparent box after issuing the ray command.
> > > 3) Also when I issue the ray command, I can't see the shadowed
> >
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 wrote:
> How does one bond
Hi Tom,
On Tue, May 27, 2008 at 10:53 PM, Thomas S. Leyh, Ph. D.
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 clipping. It
> wou
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