mistake in this domain...
Regards
Johannes
Tsjerk Wassenaar wrote:
Hi Johannes,
It's not that hard. The clipping planes are defined by the z coordinate (in
the viewing matrix). So you can get the atoms for a selection, transform to
get the new z coordinate only, and check whether it's
Hi Martin,
The wiki way should work. The only thing I can think of is that you're
not doing what you think you're doing :S
Did you copy paste the commands from the wiki? Did you get an error?
What version are you using?
but, the selection kind of does not work for me (I'm assuming the operator
Hi Kanika,
In 3HHZ.pdb, I find:
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: 22-MERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, K, L, M, N,
REMARK 350AND CHAINS: O, R
REMARK 350 BIOMT1 1 1.00 0.00 0.00
Hi Chad, Kanika,
Symexp is for generating symmetry mates, not for (re)constructing
biological assemblies.
If the BIOMT record gives an identity matrix, it means that there is
no further information for building a biological unit. The biological
unit is most likely contained in the PDB file. Note
Hi Kanika,
Let's say your protein is called 'protein'. Then you can obtain the other
unit corresponding to your second biomt operation as:
create unit2, protein
alter_state 1,unit2,(y,z)=(-y,40.6-z)
Note this is a shorthand specific to your case. For a full biomt record (R
t), with R being the
28, 2011 at 12:39 PM, Tsjerk Wassenaar tsje...@gmail.com
wrote:
Hi Kanika,
Let's say your protein is called 'protein'. Then you can obtain the other
unit corresponding to your second biomt operation as:
create unit2, protein
alter_state 1,unit2,(y,z)=(-y,40.6-z)
Note this is a shorthand
Hi Kanika,
You're right about the columns for translation and rotation. But since in
your case it's an identity matrix, it's not going to help you achieve your
goal.
Cheers,
Tsjerk
On Feb 26, 2011 8:14 AM, kanika sharma ksharma...@gmail.com wrote:
Does anyone know how to apply these
Hi Johannes,
It's not that hard. The clipping planes are defined by the z coordinate (in
the viewing matrix). So you can get the atoms for a selection, transform to
get the new z coordinate only, and check whether it's in between the planes:
m = cmd.get_model(selection).atom
v = cmd.get_view()
m
Hi John, Folmer,
First, in reply to Folmer's comment, it did cross my mind whether it
was necessary to call Pymol from a script, rather than the reverse.
But John gave an example with the file to load as command line
argument (./examply.py mymolecule.xyz). If the filename is required
internally
faster.
Any reason for this?
On 02/17/2011 04:33 PM, Tsjerk Wassenaar wrote:
Hi John,
Is this what you're looking for?:
http://www.pymolwiki.org/index.php/Launching_From_a_Script
Cheers,
Tsjerk
On Thu, Feb 17, 2011 at 8:19 AM, John Russolamaro...@gmail.com wrote:
Hi,
I'm sorry
Hi John,
Is this what you're looking for?:
http://www.pymolwiki.org/index.php/Launching_From_a_Script
Cheers,
Tsjerk
On Thu, Feb 17, 2011 at 8:19 AM, John Russo lamaro...@gmail.com wrote:
Hi,
I'm sorry for making such beginner's questions but searching the manual,
google
or the wiki
Hi,
Wouldn't you get about the same if you did:
import string
proper = set([ i.resi for i in cmd.get_model('all').atom if not
i.resi[-1] in string.ascii_letters ])
I admit, there is a pattern with my previous posts :p And I know, the
import statement can be added as
Hi Martin,
I have trouble to see how the window buffer size could be negative.
Probably it should be
zlib.decompress(pdbFile.read()[22:], zlib.MAX_WBITS)
Downloading in compressed form is much more efficient. But otherwise I
don't think it should give you trouble doing it like that.
Cheers,
Really Jason, the volumetric images on the site are superb! Is the
code already in the svn version? I'd really like to get my hands on it
and incorporate use it scriptwise :)
On another note, you might be interested in the routines laid down in
doi 10.1109/TVCG.2009.138 If you care, I could
Hi Bradley,
The first argument is the setting, which is a string, and the second is the
value for that setting, which is also a string, to be interpreted according
to the setting. Actually, for sphere_scale it's also not size, but a
multiplication factor to the size.
Hope it helps,
Tsjerk
On
Hi Seth,
So you just want to have all unique chain identifiers for the
'polymer' selection? Does the following give what you want?:
polychains = set([i.chain for i in cmd.get_model('polymer')])
Hope it helps,
Tsjerk
On Sun, Jan 23, 2011 at 10:04 AM, Seth Harris set...@gmail.com wrote:
Hi
Oops... That should've been:
polychains = set([i.chain for i in cmd.get_model('polymer').atom])
Sorry for that. :p
Tsjerk
On Sun, Jan 23, 2011 at 10:32 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Seth,
So you just want to have all unique chain identifiers for the
'polymer' selection
This should of course have been sent to the list... Apologies.
Tsjerk
-- Forwarded message --
From: Tsjerk Wassenaar tsje...@gmail.com
Date: Thu, Jan 13, 2011 at 10:47 AM
Subject: all_states failure with 500 or more models
To: Jason Vertrees jason.vertr...@schrodinger.com
Hi
Hi Jason,
It appears that Pymol segfaults rendering when a cgo object spans
multiple states, and all_states is set on:
from pymol import cmd
set all_states,1
cmd.load_cgo([COLOR,1,1,0,SPHERE,3,0,0,1],name=bla,state=2)
cmd.load_cgo([COLOR,1,0,0,SPHERE,0,0,0,2],name=bla,state=3)
ray
This
Ni Hao Cun Zhang
The real 'problem' is that Pymol does not allow selection based on
coordinates. Probably this should be on the wish list (and easy to
implement). Expressions are allowed, for instance selecting based on
b-factor or occupancy.
In your script, you can use some shortcuts. Maybe
atom has which index. Thats why i was hoping to find a way to get the
'linenumber-dependent' index of an atom.
Thanks for your help so far.
Martin
On 31.10.10 18:31, Tsjerk Wassenaar wrote:
Hi Martin,
So it seems I was right :D
ID is an atomic property, read from the PDB file, whereas
Hi Martin,
So it seems I was right :D
ID is an atomic property, read from the PDB file, whereas index is an
'internal' identifier. Following Jasons comments, ID is not changed upon
additions/deletions, whereas index does.
For your purpose, you probably want to make sure that the IDs are
Hi,
The tutorial states that the quality needs to be increased prior to
ray-tracing. But it seems to me that the {sphere,stick}_quality
settings apply to the OpenGL rendering, whereas the raytracer uses
'real' spheres and cylinders. Even when setting sphere_quality to 0,
'ray' will still give
...
-- Forwarded message --
From: Tsjerk Wassenaar tsje...@gmail.com
Date: Mon, Oct 25, 2010 at 12:39 PM
Subject: Re: [PyMOL] Question about Iterate and Edit-Mode
To: Martin Hediger ma@bluewin.ch
Hi Martin,
Without diving into the source, I think it is more like:
for i
Never get used to that only-reply-to-sender policy...
-- Forwarded message --
From: Tsjerk Wassenaar tsje...@gmail.com
Date: Mon, Oct 25, 2010 at 12:30 PM
Subject: Re: [PyMOL] What is the difference between Atom ID and Index
To: Martin Hediger ma@bluewin.ch
Hi Martin,
ID
Hi Ramiro,
Assuming your rings are nicely planar, and representing the ring as:
1-2-3
| |
6-5-4
you can get the plane normal vector as the vector cross product from
(3)-(1) and (5)-(1).
Doing so for both rings gives you the two normal vectors. The angle
then follows from the dot product of
(cpv.get_angle(dir1, dir2))
python end
Cheers,
Thomas
On Thu, 2010-09-23 at 13:02 +0200, Tsjerk Wassenaar wrote:
Hi Ramiro,
A bit of linear algebra wouldn't hurt... :p
In python:
def vsub(a,b): return a[0]-b[0], a[1]-b[1], a[2]-b[2]
def dot(a,b): return a[0]*b[0]+a[1]*b[1]+a[2]*b[2]
def svmul(s
Hi Renuka,
Are you sure that's what you want? It will read something like:
for i in __import__(glob).glob(cluster_*.sdf): cmd.load(i)
But I think it's more elegant to use two commands for this... :-P
import glob
for i in glob.glob(cluster_*.sdf): cmd.load(i)
May seem like a small difference,
Hi Sebastien,
If you have multiple poses of the same molecule in your sdf file, you
can translate them into a multi-model PDB file, writing the score and
rmsd values to the bfactor and occupancy field. This you can then load
into pymol, allowing you to step through the poses. With the command
Hi Sdat5885,
Have you started a fresh session, or did you a. load a session file or
b. did some other things you didn't mention before? It may be that you
have specifically set the highlight color for your protein. The
default is not grey, but whatever color the C alpha atom has. You
might want
Hi Vivek,
Your workflow sort of reminds me of http://xkcd.com/763/ :)
First of all, make sure that you find a way with a minimal number of
operations. Every time you do something, you may negatively influence
the image quality. Also make sure to always use PNG format for
intermediate stages,
Hi Prija,
You can do it with a bit of Python
ss = [ i.ss for i in cmd.get_model(n. ca).atom ]
print Helix content: %5.2f%% % (100.0*ss.count(H)/len(ss))
print Sheet content: %5.2f%% % (100.0*ss.count(S)/len(ss))
The first line gets a list of the secondary structure flags of the
selection n. ca.
Hi,
Okay, maybe I should delve into the code for this, but I (and probably
Joao too) was wondering how (if) Pymol determines the valence of a
bond. I.e. can Pymol distinguish between ethane, ethene, and ethyne?
Cheers,
Tsjerk
On Thu, Jul 1, 2010 at 5:58 PM, João Rodrigues anar...@gmail.com
Hi Robert,
There's still the basic documentation on the commands, which in the
case of save goes (check the NOTES):
PyMOLhelp save
DESCRIPTION
save writes selected atoms to a file. The file format is
autodetected if the extesion is .pdb, .pse, .mol, .mmod, or
.pkl
Note that
as dimer or monomer)
c) the structure is not yet been solved and not reported as yet.
So according your reply, does that mean the only possibility left is docking
? because others are not working for me at all.
Thank you again for suggestions.
On Wed, May 19, 2010 at 6:31 PM, Tsjerk
Hi Afonso,
Can you tell which newspaper? And does it show the date? :)
Seriously, it's difficult to make out more, unless you give more
information, like a link to the image, or the series of commands you
used to get to the point you're at. What you describe might be caused
by two interfering
Hi Tom,
Okay, I thought you wanted to trace out a path through space for the
camera. But for your purpose, it doesn't matter how the things are
defined internally. That's just a matter of representation, which can
be interconverted.
What you really want is to place the center of your active site
Hi Alastair,
The CGO file should come out something like:
cgo_obj = [
BEGIN, TRIANGLES, ALPHA, 1.0,
COLOR, 1.0, 1.0, 1.0,
NORMAL, -1.70693, -11.93375, 23.78227,
VERTEX, 39.96822, 39.96822, -36.33474,
VERTEX, 34.37814, 37.81595, -37.81595,
VERTEX, 38.78347,
not a ready way to generate a VDW surface
colored by atom name. It's doable by checking each triangle for its
adjacent atom and coloring accordingly, but this seems such a common task
I'm surprised there's not already code available for it.
Best,
Alastair
Tsjerk Wassenaar wrote:
Hi Alastair
Hi Rob, Jenna,
Be aware that the symmetry data (symexp) need not be equal to the
biological unit transformations (remark biomt), even though it will
often match.
And since I'm posting anyway, here's another possibility:
load 1b8e.pdb, A
create B,A
alter_state 1,B,(x,y,z)=(-x,y,33.43-z)
Cheers,
Hi Jenna,
I think you already managed (using 'save'). And of course there are
two times as many coordinates in a dimer, so the saved file will be
twice the size. By the way, before saving, you might want to make sure
the chains get different chain IDs, so you can easily address them
later:
alter
Hi Afonso,
If you want to connect one object to another, you want to check out
the fuse command (help fuse)
fuse atom_to_be_connected_from_object1, atom_to_be_connected_from_object2
Hope it helps,
Tsjerk
On Sun, Mar 28, 2010 at 4:33 PM, Afonso Duarte afonsomdua...@gmail.com wrote:
Dear All,
:
In newer PyMOLs this is as simple as:
print cmd.get_atom_coords(oneAtom)
where 'oneAtom' is an object or selection of one atom in PyMOL.
For example,
load $TUT/1hpv.pdb
print cmd.get_atom_coords(A/30/CA);
-- Jason
- Show quoted text -
On Mon, Mar 22, 2010 at 9:04 AM, Tsjerk Wassenaar tsje
Hi Mohan,
You can use iterate_state, which would be the pymol approach:
coords = {}
iterate_state 1,n. ca,coords[i]=(x,y,z)
Or you can take a lower level approach; the python one:
for i in cmd.get_model('n. ca').atom:
print i.coord
cmd.get_model builds you a ChemPy model from a given
Hi Michael,
Have you had a look at 'help selections'?
I am wondering how to select molecules in Pymol.
What exactly do you mean here? The molecule for a certain atom? The
molecule as in 'chain' (if it's a macromolecule), or as in 'residue'
(if it's a ligand/cofactor/solvent)?
The system I am
But it is very doable using grep/cut, you'll just have to use the -b
flag that allows you to cut columns:
grep CA .pdb | cut -b 13-26,30-54
Cheers,
Tsjerk
On Mon, Mar 22, 2010 at 3:58 PM, Robert Campbell
robert.campb...@queensu.ca wrote:
Hi Jed,
On Mon, 22 Mar 2010 10:23:34 -0400 Jed
Hi Jason, e.a.
I would really like to be able to echo my session command line history
to a file. I'm not sure whether I just missed something, or that it's
not in yet. If the latter is the case, I'd like to put it forward as a
feature request. Otherwise, I'd be eager to be enlightened. I found
Hi Folmer,
How silly. Now checked and found it in the manual even! Why didn't I
check that before? Well, thnx a 1e6 anyway.
Cheers,
Tsjerk
On Thu, Mar 18, 2010 at 10:22 AM, Folmer Fredslund folm...@gmail.com wrote:
Dear Tsjerk,
On 18 March 2010 10:08, Tsjerk Wassenaar tsje...@gmail.com
Tsjerk on this, maybe in the .pymolrc?
And auto_show_sticks would be very useful to me!
Cheers,
Greg
-Original Message-
From: Tsjerk Wassenaar [mailto:tsje...@gmail.com]
Sent: Tuesday, March 16, 2010 6:17 AM
To: Jason Vertrees
Cc: pymol-users@lists.sourceforge.net; David Hall
Subject
Hi Jason,
Along those lines, would it be possible to have a 'default' which can
be set to a list of settings related to appearance? That might be more
concise than to have everything in a separate setting.
set default,[cartoon, lines, nonbonded, cbaw]
The default value as pymol starts up now
Hi Mohan Raj,
i am new to pymol. i dont know how the coordinates are made in pdb file.
This is not really related to Pymol. Maybe you should go to
www.rcsb.org/pdb and have a look around.
cold someone tell me? how do we arrive at the coordinates from crystal
structure.
Do you mean from a
response was from John Archie, who sent me a link
I'll bounce here to the list:
http://www.unicom.com/pw/reply-to-harmful.html
It poses some compelling arguments, but you should've pressed 'reply-to-all' ;)
Thanks anyway.
Cheers,
Tsjerk
On Wed, Mar 10, 2010 at 6:18 AM, Tsjerk Wassenaar tsje
I never get used to Pymol doing reply-to-sender in stead of reply-to-list :|
-- Forwarded message --
From: Tsjerk Wassenaar tsje...@gmail.com
Date: Tue, Mar 9, 2010 at 11:51 AM
Subject: Re: [PyMOL] succinct secondary structure 'readout'
To: Ferdinand Alte ferdinand.a
Hi Justin,
I can change it, but there are some good reasons for leaving it as is.
Can you expand on that?
Cheers,
Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.
Computational Chemist
Medicinal Chemist
Neuropharmacologist
Hi Ferdi,
It is better to post such questions to the user list. As you've
noticed I also answer mails there. But I'm not the only one, and
you'll get access to a whole community. Besides, the posts get
archived for future reference. Aside from that, it is commonly
regarded impolite to address
Hi Jon,
I think you're out of luck. The color of cartoon representation is
controlled only by the CAs, which is also used to trace the cartoon.
Probably using spheres is still the best option. Just make sure that
you set both cartoon_smooth_loops and cartoon_flat_sheets to 0, so
that these trace
Hi Mohan Raj,
From the description it is clear that Pymol is a *visualization*
program. So, no, it can not do simulations of any sort.
Cheers,
Tsjerk
On Wed, Feb 24, 2010 at 1:36 PM, mohan raj mohanrajdec2...@gmail.com wrote:
hi all:
i am a new to pymol. could some one tell me more
Hi Gabriela,
If you only want to get the molecule back in view and rotate/translate
it to your liking, you can use commands like:
#declare Protein = union { #include protein.inc }
#declare Center = (min_extent(Protein)+max_extent(Protein))/2;
object { Protein translate -Center }
If you want to
Hi David,
Sorry to be more on the programmatic than on your pragmatic side.
That seems like a modification that makes it less flexible. Now I can't do:
ray 2.5in, 20cm, dpi=300
Okay, let's say you could do:
ray 2.5, 20, units=(in,cm), resolution=300
providing either a single string, or a
Hi Sean e.a.,
In reply to your messages, first an overview as I picked up from the
other mails:
1. eMovie integration (Simon Kolstoe)
2. Powerpoint plugin (Roger Rowlett)
3. Enhanced morphing (ibid)
4. Foolproof download (David Hall)
5. DynoPlot integration (ibid)
6. Improved undo/redo (ibid)
7.
On Thu, Jan 21, 2010 at 10:47 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Sean e.a.,
I really meant Jason e.a. :$
T.
--
Tsjerk A. Wassenaar, Ph.D.
Computational Chemist
Medicinal Chemist
Neuropharmacologist
Hi David,
Doesn't png already take a size and resolution argument?
cmd.png(string filename, int width, int height, float dpi, int ray, int
quiet)
so, now I do cmd.png('1acb.png', 5,4,units=in, dpi=300) ?
Errm, that only makes sense if the viewport itself is resampled
somehow when you don't
Hi,
So what happens if you try it after ray-tracing?
T.
On Thu, Jan 21, 2010 at 5:17 PM, David Hall li...@cowsandmilk.net wrote:
On Thu, Jan 21, 2010 at 9:46 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Errm, that only makes sense if the viewport itself is resampled
somehow when you don't
Hi,
ray 10cm, 20cm, dpi=300?
ray 2.5in, 5in, dpi=300?
I'd slightly modify that to read:
ray 10,10,units=cm,resolution=300
where units can be pixels (default), cm, inches, meters, yards, lightyears...
Cheers,
Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.
Computational Chemist
Medicinal Chemist
Hi Jason,
Now what will come first? Pymol viewer for Android, for Mobile Windows
or for iPhone? Would be so cool to show off at a conference, and use
multi-touch to operate :p
Cheers,
Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.
Computational Chemist
Medicinal Chemist
Neuropharmacologist
Hi Mateusz,
The first guess would be that you're not in the right directory, since
Pymol can't find the file. That seems a bit awkward, as I guess
they're in the same directory as converged.nam, or aren't they? To
see what is in the directory, you can call cmd.ls() at the start of
the script. For
in from a file, then it
works fine. Puzzling.
Thanks,
Matt
On Tue, Nov 10, 2009 at 4:51 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Mateusz,
The first guess would be that you're not in the right directory, since
Pymol can't find the file. That seems a bit awkward, as I guess
Hi Thomas,
Say, the first system is x and the second y, where y=R(x+s) is the
first transformation. Then the reverse transformation follows as
y = R(x + s)
y = Rx + Rs
Rx = y - Rs
x = t(R)(y-Rs)
Note that that is also equal to: x = t(R)y - s
Hope it helps,
Tsjerk
On Mon, Nov 9, 2009 at
Hmm, this should've been replied to the list. The info may be useful to others.
Tsjerk
-- Forwarded message --
From: Tsjerk Wassenaar tsje...@gmail.com
Date: Mon, Nov 9, 2009 at 5:02 PM
Subject: Re: [PyMOL] asymmetric transformation matrices
To: Thomas Evangelidis te8
This is really sad news. It leaves me with a sense of surrealism. I
wish his family a lot of strength.
Tsjerk
On Thu, Nov 5, 2009 at 8:33 PM, Thomas Grant tgr...@hwi.buffalo.edu wrote:
For those of you who are not subscribed to the CCP4 Bulletin Board.
-- Forwarded message --
: Tsjerk Wassenaar tsje...@gmail.com
Subject: Re: [PyMOL] Saving high resolution images
To: Thomas Stout tst...@exelixis.com
Cc: pymol-users@lists.sourceforge.net
Message-ID:
8ff898150910230227k12719cedv8656233c7e67d...@mail.gmail.com
Content-Type: text/plain; charset=ISO-8859-1
Hi
' part for me and sorry to have
then added my own assumptions to the mix!! (as I worried about in my last
paragraph!)
-Seth
On Sat, Oct 24, 2009 at 2:41 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Seth,
Rendering in parts does not avoid taking the whole scene in memory.
That is a more
Hey :)
Why revert to powerpoint and or photoshop? First of all, it's not the
image resolution (dpi) that counts, it's the number of pixels, the
geometry. That you can give as argument to ray. Second, if you want a
distance between images of 63 mm, you seem to want a total image
length of 126 mm,
Oww, that hurts! I knew it should be somewhere, but it was right there
with the 'png' command: the dpi setting:
png image.png, dpi=300
So, no need to edit anything afterwards...
Cheers,
Tsjerk
On Sun, Oct 11, 2009 at 11:31 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hey :)
Why revert
Hi,
At present I'm setting some variables in the globals()
dictionary/global scope, but when I save the session, these variables
are lost. What would be the best way to preserve them? (This question
may also be interpreted as: what does Pymol write to a session file?).
Cheers,
Tsjerk
--
... This should've gone to the list ... :S
TAW
-- Forwarded message --
Hi Warren (e.a.),
First, as a side note, your first post had 'for state in
cmd.count_states():' whereas it seems it should read 'for state in
range(cmd.count_states()):'.
I find myself doing something
Hi pkb bioinfo (which I do hope is not your real name),
Did you actually paste the script or did you retype it?
from pymol import cmd
from glob import glob
lst = glob(*.pdb)
lst.sort()
for fil in lst:
cmd.load(fil,tmp)
O, and just when I pressed send (which also made firefox crash for
some reason), it struck me that you only load files, which means that
you're only appending states. But you don't specify a state to
calculate the distance, which means the first is taken again and
again. You might want to add a
Hi :)
Some people are just not lazy enough ;) Lazy people like me spend a
good deal of effort thinking about how to avoid efforts like writing
repetitive lines :p And then you could come up with:
from math import sin,pi
mset 1 x300
for i in range(200,301): cmd.mdo( i, set
Hi Jason,
You would want to have an optional argument for the circle normal
vector, I think...
Maybe I'll turn to it later; it shouldn't be much work.
Cheers,
Tsjerk
On Fri, Jul 31, 2009 at 9:54 PM, Jason Vertreesj...@cs.dartmouth.edu wrote:
Hello PyMOLers,
A few weeks ago someone asked
Hi,
You can draw a CGO circle in the yz plane using:
x1,y1,z1 = -0.1, 0, 0 # start point
r1,g1,b1 = 1,0,0 # color (red)
x2,y2,z2 = 0.1, 0, 0 # end point
r2,g2,b2 = 1,1,0 # color (yellow)
radius = 10
cmd.load_cgo( [ 9.0, x1, y1, z1, x2, y2, z2, radius, r1, g1, b1, r2,
g2, b2 ], cylinder1 )
To
Hi Jouko,
I think you went through the Python and Pymol tutorials a bit too fast
;) You're writing a Python script to be loaded with 'run'. That means
you have to adhere to Python API and can't use the Pymol specific
language. E.g. you can't use 'png pdb', but have to use 'cmd.png(pdb)'
in which
the tab was lost, so this time I am adding the
script file as an attachment.
Thanks,
Jouko
P.S. I found that @/home/jouko/b_color8.plm and
cmd.do(@/home/jouko/b_color8.plm) both work.
Original message
Date: Tue, 7 Jul 2009 09:17:53 +0200
From: Tsjerk Wassenaar tsje...@gmail.com
Hi Miro,
This one's in the archive, but it was also in my gmail archive, which
made it easy to dig up. The setting you need is transparency_mode:
set transparency_mode,1
This should give you the behaviour you expect for multiple transparent
surfaces. In addition, you may want to have a look at
Hi Matthew,
Why don't you use:
cmd.iterate( sele + and n. ca, ...
to avoid doing a lot of work for nothing... (you may want to check
whether a selection is given to avoid an error though)
Cheers,
Tsjerk
On Thu, Jun 4, 2009 at 5:37 PM, Matthew O'Meara mattjome...@gmail.com wrote:
Thanks
/photo/udk9a4AzhpdI2RfQvclciw?feat=directlink
)
Pymol should probably update the help povray description so that it does
not mislead anymore.
Thanks !!
Abhi
On Mon, May 18, 2009 at 11:55 AM, Tsjerk Wassenaar tsje...@gmail.com
wrote:
Hi Abhi,
I had a look and found that POV-Ray does not have
Hi Hirdesh,
You don't say what you have, what you want to show and what you tried
to show it. So we can't help you. I would also politely like you to
consider that perhaps we might not be very apt to do your work for
you. We're willing to help though, when you run into problems doing
your own
(cmd.get_povray()[1])
-Original Message-
From: Tsjerk Wassenaar [mailto:tsje...@gmail.com]
Sent: Thu 5/14/2009 1:47 PM
To: Sean Law
Cc: pymol-users
Subject: Re: [PyMOL] POVRAY Usage
Hi Sean,
Unfortunately, getting a good image through POV-Ray requires editing
the POV-Ray file
Hi Sean,
Unfortunately, getting a good image through POV-Ray requires editing
the POV-Ray file. You can write the scene to disk with the following
commands
pov=open(protein.pov,w)
pov.write(cmd.get_povray()[0])
pov.write(#include \povray.inc\)
pov.close()
Hi Sean,
Sorry about that. Tried from the top of my head and the evening had
past too far for that already. These vectors define the directions to
distribute the lights - you basically create an area of light sources.
So you need to set two vectors:
area_light 5,0,0,0,5,0,5,5
This will generate
Hi Abhi,
I got and read the e-mail through the list, but would have to test
with pymol 1.0 before being able to give a sensible reply. As I'm now
underway that's a bit too much for me :) I'll come back on this one
later.
By the way, you only sent this mail this afternoon. Don't expect
instant
Hi Carsten e.a.,
I am thinking that if it would be possible to write out the orientation
of the clipping planes/slabs as PovRay objects, they could be used as
bounding objects in PovRay. Since the placement of the clipping planes
is easily achieved in Pymol this could be done interactively.
Hi,
This is about the way I do it :) To make life easier, I have a
function to write the POV-Ray file in two pieces, using an #include
statement to include the object description in the overall scene setup
file. I've found this much easier to work with, since it allows to
change the light and
Hi Nir,
Pymol just draws bonds based on distances, not based on topological
information. If atoms are within contact distance, a bond will be
drawn, whatever the atoms are. If one feels need for an additional
bond, it is possible to add them using:
bond selection1, selection2
This will draw
Obviously that should read 'resn asn' in stead of 'resn asp'. Sorry for that.
Tsjerk
On Tue, Mar 31, 2009 at 9:56 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Nir,
Pymol just draws bonds based on distances, not based on topological
information. If atoms are within contact distance
at 12:45 AM, Tsjerk Wassenaar tsje...@gmail.com
wrote:
Hi Thomas,
You're not really specific here, so I'll give the most general reply:
show spheres, hetatm
By the way, these compounds will definitely be drawn either as sticks
or as nonbonded upon loading of the structure. You may not easily
Hi Cedric,
In general terms, you can do such things with alter_state. More
specifically, you may want to start scripting, reading in the file
(assuming it's from a file) and doing the transformation. One thing
that's not directly clear is whether t is pre- or post-shifting. You
can directly read
Hi Thomas,
You're not really specific here, so I'll give the most general reply:
show spheres, hetatm
By the way, these compounds will definitely be drawn either as sticks
or as nonbonded upon loading of the structure. You may not easily see
them, but if they're in the file, they'll be drawn.
providing more specific examples in the help file.
The label come up white and small; can the color, font size, or position be
controlled?
Thanks
C. D. Stout
3-23-09
Tsjerk Wassenaar wrote:
Hi Charles,
What do you mean with obscure? I've always thought the examples were
Hi Magnus,
The command is 'alter', not 'alter resi' or 'alter_resi'. The function
is therefore 'cmd.alter()', which takes as first argument a selection
string and as second an operation string (expression). The key aspects
to understand are that (most) commands have associated functions
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