Hi Ian,
As this may be of broader interest, I forward it to the pymol user list too.
You can clip the scene using an intersection. Let's say that you have
the object you want to clip stored as a povray include file
"object.inc". Then you can get the clipped object as:
//###
pymol_object = union
Hi,
I'm having some trouble accessing a function defined at top level with
alter_state in a python script launching pymol. Maybe I shouldn't be
wanting to do this, but what I'm trying, and failing to do is
exemplified by this script:
###
#!/usr/bin/env python
import pymol
if __name__ == "__mai
Hi Andreas,
In the meantime, you can set double labels by using a pseudoatom,
labeling it with the second part, and placing the label at the spot
desired.
Cheers,
Tsjerk
On Wed, Mar 30, 2011 at 3:59 AM, Jason Vertrees
wrote:
> Hi Andreas,
>
> This is currently not possible. If this is a featu
Hi Kanika,
You can also use pseudoatoms. If you have the positions:
pseudoatom coms,pos=[x1,y1,z1]
pseudoatom coms,pos=[x2,y2,z2]
bond coms,coms
Or, if you just have the chains:
pseudoatom coms, chain a
pseudoatom coms, chain b
bond coms, coms
Alternatively you can use CGO objects. But pseudo
Hi :)
The radius of gyration is not that tough. Here's a python script to do
it in pymol. Do note that the hydrodynamic radius is something
related, but different.
from pymol import cmd
import math
def rgyrate(selection):
# Get the atoms for the selection
model=cmd.get_model(selection).atom
Hi Francois,
That information is in the view matrix you get from get_view. The
first nine numbers are the rotation matrix R. The next three numbers
are the camera position c, followed by the three numbers denoting
origin of rotation o. Then to transform your protein coordinates, as
in the PDB, to
Hi Kanika, Jason,
cmd.get_legal_name is only called in 'com' if no object name is given.
The quickest workaround thus is to provide an object name for the
'com' object as third argument.
Of course, it still is wise to upgrade and benefit from all those cool
new features :)
Cheers,
Tsjerk
On Mo
Hi Jason,
I run into a segfault with Pymol 1.4 rev 3938 on my EEE PC, running
Ubuntu 9.04. The segfault occurs when loading the PDB file. It happens
regardless of the contents of the PDB file, but loading something with
hetatms gives some insight in how far it goes:
PyMOL>load ../../../3lzt.pdb
H
ndary structure assignments.
> ObjectMolecule: Read crystal symmetry information.
> Symmetry: Found 1 symmetry operators.
> ObjectMoleculeGuessValences(1,0): Unreasonable connectivity in heteroatom,
> unsuccessful in guessing valences.
> CmdLoad: "../../3lzt.pdb" loaded a
Molecule: Read crystal symmetry information.
>>> Symmetry: Found 1 symmetry operators.
>>> ObjectMoleculeGuessValences(1,0): Unreasonable connectivity in heteroatom,
>>> unsuccessful in guessing valences.
>>> CmdLoad: "../../3lzt.pdb" loaded as &quo
:)
Cheers, and thumbs up for Jason!
Tsjerk
On Mon, Apr 11, 2011 at 2:03 PM, Tsjerk Wassenaar wrote:
> Hi,
>
> The problem did not occur on another machine (Intel Core i7, 64bit),
> running Ubuntu 10.10.
> On my EeePC loading a python CGO file worked fine, while loading an
> empty P
Hi Kanika,
> alter_state 1, 1a8y_a, 1a8y,(x,y,z)=(-0.5*x + 0.886025*y, 0.886025*x +
> 0.5*y, -z)
This doesn't work like that. It should probably be
alter_state 1, 1a8y_a,(x,y,z)=(-0.5*x + 0.886025*y, 0.886025*x + 0.5*y, -z)
> then i saved the molecule in pymol from file-->save molecule-->1a8y_
Hi Kanika,
No, the spacing, or in this case the lack of it, is correct. The
coordinate section of the pdb file is %8.3f%8.3f%8.3f, i.e. each
coordinate eight characters wide with three decimal precision.
Cheers,
Tsjerk
On Mon, Apr 25, 2011 at 12:28 PM, kanika sharma wrote:
> i have attached a
Hi,
The first line is okay, but the rest seems to have an extra space,
indeed. You can remove it from the script using:
sed -i 's/^ //' script.py
Hope it helps,
Tsjerk
On Thu, May 26, 2011 at 4:33 AM, Michael Lerner wrote:
> Hi Ivan,
> There's definitely a bug in that script. It looks like mo
Hi Spyros,
In cases like these, I think it's usually best to use colours for the
selections and for the overlap:
color cyan, selection1
color yellow, selection2
color hotpink, selection1 and selection2
Hope it helps,
Tsjerk
On Tue, Jul 12, 2011 at 1:14 AM, Spyros Charonis wrote:
> Hello PyMOL
Hey Ram,
It's scriptable, but not very doable on this Android :p
The best solution would involve a generator funtion that takes a file
pattern and a number, using glob to expand the file list, and using yield at
each cycle.
For a pythonista that should make sense ;) I may take it up when I'm typin
at 9:56 PM, Marius Retegan
wrote:
> You could try something like this in a terminal
>
> for i in $(seq 1 1 100); do pymol $i.pdb; done
>
> if your file name are 1.pdb, 2.pdb ... 100.pdb
>
> Marius
>
> On Fri, Jul 15, 2011 at 9:00 PM, Tsjerk Wassenaar wrote:
>> Hey
Hi Babban,
For modeling the polymers you probably want to try a docking program.
Maybe HADDOCK suits your needs...
Hope it helps,
Tsjerk
On Sun, Jul 31, 2011 at 1:42 AM, Babban Mia wrote:
> Dear users,
>
> Is there some program to calculate the zeta potential or streaming
> potential
> of prot
Hey,
I noticed with coarse grained structures that cartoon_trace_atoms
really traces all atoms; you may need to restrict the selection:
set cartoon_trace_atoms
show cartoon, n. ca+cb
Hope it helps,
Tsjerk
On Wed, Aug 17, 2011 at 1:24 AM, Jason Vertrees
wrote:
> Hi Baptiste,
>
>> My pymol vers
Hey :)
Here is an all Python solution to load a .gro file, including the box
vectors. It simply converts to PDB format and calls cmd.read_pdbstr...
It supports multimodel files. I'll probably add a mechanism to
identify chains from breaks, as the .gro format does not use chain
identifiers, and may
solvated system > 100.000 atoms I have problems with water
> molecules. Is it possible to handle gro files with more than 100.000 atoms
> and residues?
> Best
>
> On Thu, Aug 18, 2011 at 9:39 AM, Tsjerk Wassenaar wrote:
>>
>> Hey :)
>>
>> Here is an all
2011 at 9:07 PM, Michael Lerner wrote:
>
>
> On Thu, Aug 18, 2011 at 3:39 AM, Tsjerk Wassenaar wrote:
>>
>> Hey :)
>>
>> Here is an all Python solution to load a .gro file, including the box
>> vectors. It simply converts to PDB format and calls cmd.rea
Hey Björn,
The mesh will be in Pymol camera coordinates, not in PDB coordinates.
You'll have to take the object_matrix (cmd.get_object_matrix) and
apply it to the protein to convert it to the same space if you are to
use it outside of Pymol.
Hope it helps,
Tsjerk
On Mon, Aug 22, 2011 at 8:12 PM
Hi Tanya,
Does it say more than "syntax error"? Can you send the whole output?
(copy crom the grey screen). In addition, can you send the pymolrc
file as attachment? There might be something to do with line endings;
so don't paste it in the mail, but attach the actual file that fails.
Cheers,
Ts
Hi Bjoern,
Please do also give a more explicit account of what you want to
achieve in the end and what you've tried to get there, including the
commands used.
Cheers,
Tsjerk
2011/8/25 Troels Emtekær Linnet :
> Check this, and tell if it works.
>
> http://pymolwiki.org/index.php/Matrix_Copy
>
>
Hi Adam,
Here's an alternative script... The command is pplanes (peptide-planes):
run triangles.py
pplanes selection[, color[, alpha[, state[, name
Hope it helps,
Tsjerk
On Thu, Aug 25, 2011 at 5:34 PM, H. Adam Steinberg wrote:
> Hi all,
> Can anyone help me with a problem that I am havi
Hi Suda,
Do you mean different structures of the same molecule or different
molecules? For a multistate object, there is intra_fit. for selections
comprising multiple objects it's not currently possible. But it's
being worked on.
Cheers,
Tsjerk
On Mon, Aug 29, 2011 at 8:43 AM, Suda Ravindran w
Hi Arne,
Unfortunately that is not possible. You could export the scene to
POV-Ray format and make the modifications there.
Cheers,
Tsjerk
On Tue, Aug 30, 2011 at 11:37 PM, Arne Dieckmann
wrote:
> Hi all,
>
> I would be interested in creating custom textures for spheres in pymol. More
> expli
Hi Lina,
In most cases, you can set it back to default by setting it to -1.
To know what the default value is, you can use 'get setting_name', before
you start fiddling with the setting.
Hope it helps,
Tsjerk
On Sep 15, 2011 4:12 AM, "lina" wrote:
Hi,
when I tried to set something,
let's s
Hi Suda,
Do you mean the number of residues in helix c.q. sheet or the number
of helices and the number of sheets? The former is pretty easy. You
can do
select ss s
select ss h
to get the numbers for sheet and helices, respectively. To use the
numbers in a script, use cmd.select('ss s') and cmd.
Hi Anasuya,
This sound like one of those very good reasons to have a go at Python,
and leave Perl behind... Together with all the plain reasons to leave
Perl behind :) First of all, check http://xkcd.com/353/
Assuming the file is called list.txt and you have all pdb files at
hand (which is not st
I just can't help myself...
> (for instance, a rainbow colour scheme based on survey trip?)
Can he do a colour scheme based on LSD trip too?
But it's cool :)
Cheers,
Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecula
Hi Lina,
Can you tell more? What version are you using, what system are you on, do
you use a .pymolrc, and what exactly do you do?
Cheers,
Tsjerk
On Oct 9, 2011 5:05 PM, "lina" wrote:
On Sun, Oct 9, 2011 at 10:50 PM, lina wrote: > >
Hi, > > I met the followi...
Still something abnormal.
W
2011, at 1:04, Tsjerk Wassenaar wrote:
>
> Hi Lina,
>
> Can you tell more? What version are you using, what system are you on, do
> you use a .pymolrc, and what exactly do you do?
>
> Version 1.4.
> Debian amd64
> I did use .pymolrc.
> Please kindly notice the problem jus
Hi Lina,
Not really a Pymol question, is it?
On linux you can use sed:
sed '/^\(ATOM\|HETA\)/s/^\(.\{72\}\)/\1/' filein.pdb > fileout.pdb
That means:
/^\(ATOM\|HETA\)/ :: Match lines starting with ATOM or with HETA, and
on those lines execute:
s/^\(.\{72\}\)/\1/ :: Subsitute the
t; On Tue, Oct 11, 2011 at 4:24 PM, Thomas Holder
> wrote:
>>
>> On 10/11/2011 10:16 AM, Tsjerk Wassenaar wrote:
>>>
>>> Not really a Pymol question, is it?
>>
>> well, it's the segment identifier column, so you can do with PyMOL:
>>
>> set p
Hi Martin,
You can use b and q as selection keywords (help selections):
color red, b < 0
color blue, b > 0
Or you can use 'spectrum' (help spectrum):
spectrum b, red_white_blue
Hope it helps,
Tsjerk
On Oct 13, 2011 12:58 AM, "Martin Hediger" wrote:
Dear List
I have the below model of three
triction on how the PQR file is to be formatted? I was reading
> PQR is not as strict as PDB format, so I believe the file I posted should be
> a valid PQR format.
>
> Martin
>
>
>
>
>
>
>
> Am 13.10.11 06:17, schrieb Tsjerk Wassenaar:
>
> Hi Martin,
>
Hi Андрей,
That is not possible.
You set a new property on a chempy model instance. load_model converts
that model into an internal representation, simply neglecting the new
property. get_model creates a fresh chempy model instance, which has
no .name property.
If you really, really want to do i
Hi George,
You might want to use cmd.get_model() to make your life easier. It turns a
selection into a chempy model, which has an attribute .atom, containing all
the corresponding atoms with names, identifiers, coordinates, etc.
Check scripts on the pymolwiki that do comparable things.
Hope it h
Selam Ahmet,
I cordially suggest to have a look at
http://catb.org/~esr/faqs/smart-questions.html to phrase your question
more effectively, such that we can provide more tailored help. It
would have been nice to have an example that we could try ourselves.
I find that as preparation for MD simula
Hi Jack,
Unfortunately, that is not possible. The ray-trace mode affects the
behaviour/display of edges during raytracing, It's basically doing
edge detection, similar to what can be done in image processing
afterwards. So, it's similar to having an image and wanting to enhance
edges on some, but
Hey :)
Does the script pasted below do what you want? It does not move the
molecule(s), but it returns a list of occupied bins with the ids,
names and chains of residues in it.
Hope it helps,
Tsjerk
###
from pymol import cmd
def _bin(x,d):
d = float(d)
a,b,n = min(x),(1-1e-16)/(max(x)
Right, forgot to mention that the bin is given as the coordinates of
the lower corner, relative to the minimal coordinates.
Cheers,
Tsjerk
On Thu, Oct 27, 2011 at 6:02 PM, Tsjerk Wassenaar wrote:
> Hey :)
>
> Does the script pasted below do what you want? It does not move the
>
Hi Troels,
> I think to get the return values of a script, you need to put them
> inside python boxes
I'd assume it'd be a Python script :) But also for a PyMOL script,
it's not exactly true. However, then there should be no space before
the equality sign. This should work:
theCenter=COM(...)
ps
Hi Daniel,
set auto_zoom,0
Cheers,
Tsjerk
On Wed, Nov 16, 2011 at 11:02 AM, Daniel Larsson wrote:
> Hi,
>
> Is it possible to disable the automatic zoom of the view to fit the newly
> created object when one issues the create command?
>
> Daniel
> -
Hi Martin,
The temporary namespace for an atom means that variables like 'resn'
can be used to refer to the attribute with that name on the atom
instance.
You are right that iterate is here used to iterate over a single atom.
That does seem a bit odd :p But it seems to be a more straightforward
w
Hi Martin,
It should be RMSD indeed. Mind that the final RMSD from align is obtained
after optimizing the fit by leaving out outliers.
Cheers,
Tsjerk
On Nov 29, 2011 10:07 AM, "Martin Hediger" wrote:
Is the RMS the same as RMSD? PyMOL writes "RMS" when using align.
Martin
Am 11.11.11 14:
Hi Martin,
Here's a fourth option (and the technique worth noting :p ):
print len( set( [(i.chain,i.resi,i.resn) for i in
cmd.get_model(selection).atom] ) )
Cheers,
Tsjerk
On Tue, Nov 29, 2011 at 4:26 PM, Jason Vertrees
wrote:
> Hi Martin,
>
> You get three options:
>
> (1) You can count alph
Hi Martin,
It does an alignment, finding matching pairs of atoms, removing
outliers and calculating the RMSD over the remaining matches.
Cheers,
Tsjerk
On Wed, Nov 30, 2011 at 11:05 AM, Martin Hediger wrote:
> How does PyMOL calculate the RMSD between two structures where the
> number of atoms
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" wrote:
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
Hi Lina,
In addition, you can split out a specific state using:
create StateX, selection, state=X
Check out 'help create'
Cheers,
Tsjerk
On Thu, Dec 15, 2011 at 6:26 AM, Jason Vertrees
wrote:
> Lina,
>
> To jump to any given state, X, just type,
>
> set state, X
>
> If you want a specific ob
Hey :)
You could copy the state to the b-factor field:
fetch 1nmr, async=1
split_states 1nmr
for i in range(1,cmd.count_states()+1): cmd.alter("1nmr_%04d"%i,"b=%d"%i)
delete 1nmr
spectrum b
Cheers,
Tsjerk
On Mon, Dec 19, 2011 at 7:38 AM, Jason Vertrees
wrote:
> Hi Jacob,
>
> You cannot use th
Hey Anasuya,
On Fri, Mar 2, 2012 at 5:13 PM, Anasuya Dighe wrote:
> What's going wrong with this code?
> ___CODE___
> from pymol import cmd
>
> def process_line(x):
> pdbid,res,chain,num = x.split()
> cmd.load(pdbid)
> cmd.select("target","(resn %s and chain %s and resi %s)"%(res,chain
Hi Suheila,
That is really not straightforward under Windows. To run any Gromacs
tools under Windows, the preferred way to install is using Cygwin. But
that will pose a problem coupling to Pymol. I'd say you're out of
luck, sorry.
Cheers,
Tsjerk
On Wed, Mar 7, 2012 at 4:15 PM, Suhaila Haji Moh
Hi Suheila,
Are you running both pymol and gromacs on the virtual machine?
Are tge gromacs binaries installed in /usr/bin or /usr/local/bin or
otherwise globally available?
Cheers,
Tsjerk
On Mar 11, 2012 10:00 PM, "Suhaila Haji Mohd Hussin" <
bell_beaut...@hotmail.com> wrote:
The problem I'm
Hi Suhaila,
>From what I understand from the wiki, you have to have a match between
the PDB and the contact map. If your contact map was made on a
structure with multiple chains, all chains will be in there. If you
want to select a single chain, you have to extract that chain from
thhe PDB file, t
Hi Suhaila,
It looks like it's trying to load the XPM file, in stead of the
jpg/png. How did you invoke Pymol and what commands did you give?
Cheers,
Tsjerk
On Tue, Mar 13, 2012 at 1:49 PM, Suhaila Haji Mohd Hussin
wrote:
> Hello everyone especially to people who have used Contact Map Visualiz
Hi Suhaila,
mogrify modifies in-place, causing a mismatch between the extension
and the format. I guess that the script decides based on the
extension, and thus fails. Better is to use convert:
convert contactmap.xpm contactmap.png
Do make sure that the conversion goes well. I'm not exactly sure
Hi Suheila,
The CMV requires the contact map and the structure to match. So to get
what you want, it's easiest to load the structure in pymol, and save
only the part you want to analyze:
save helix.pdb, ss h
save sheet.pdb, ss s
Then you can run g_mdmat on each of those, and load the result back
Hi James,
In addition to Thomas' answer... What is _wrong_ about the TER
statement? Your chain is broken, indicated by the nonconsecutive
numbers. That means you have two distinct molecules, and they are
separated by a TER statement. Doesn't seem wrong. Yeah, they might be
the same chain, but havi
s,
Tsjerk
On Tue, Mar 20, 2012 at 1:14 PM, Thomas Holder
wrote:
> On 03/20/2012 11:35 AM, Tsjerk Wassenaar wrote:
>>
>> In addition to Thomas' answer... What is _wrong_ about the TER
>> statement? Your chain is broken, indicated by the nonconsecutive
>> numbers.
Next time... :p
Tsjerk
On Tue, Mar 20, 2012 at 2:48 PM, David Hall wrote:
> On Tue, Mar 20, 2012 at 8:44 AM, Tsjerk Wassenaar wrote:
>> Hi Thomas,
>>
>> 'Wrong', certainly in the context it was given in, is a statement of
>> judgment. It suggest that the
Hi Suheila,
What were the exact commands you used, and what error did it come up with?
Just saying you tried mogrify and convert and the error was still there
isn't very informative to us.
Cheers,
Tsjerk
On Mar 18, 2012 2:39 PM, "Suhaila Haji Mohd Hussin" <
bell_beaut...@hotmail.com> wrote:
I
Hi,
Why can't you use set_name tun1, ..., etc? The attempt trying to change
names is quite odd, and won't do what you want anyway.
You could use
basename="your_tag"
cmd.set_name(cmd.get_object_list()[0], basename+"_subtag")
... and so on.
Cheers,
Tsjerk
On Mar 21, 2012 6:56 AM, "Sajeewa Pemasi
g residues ( e.g in loops
> of GPCRs or other flexible regions) ?
>
> James
>
> 21 марта 2012 г. 10:38 пользователь Tsjerk Wassenaar
> написал:
>
>> Hi James,
>>
>> Broken refers to non-continuity of a chain, i.e. missing residues. Broken
>> does not
Hi Gudrun,
If you raytrace an image it is written to disk and loaded into the
viewport. If the imge is larger than the viewport it is displayed
smaller with the real resolution mentioned underneath. If you save the
image, using 'png', it is saved in the large format, without the black
padding.
Ch
Hi Boris,
PBC have not yet found their way to the main pymol code. What kind of stuff
do you need? lattice.py is quite convenient for shifting. For (a)symmetry
mates, you can use the scripts suggested by Thomas. If you need something
else, pbc operations are not very hard to script.
Cheers,
Tsje
Error:
> unable to initialize plugin 'SuperSymPlugin12'.
>
> lattice.py: that shift the structure. I want to display some more cells of it.
>
> With great respect,
> Boris.
>
> P.S. I have a cell - I'd like to see if its homogeneous. For that I
> need to put several
Hey,
Of course you can also escape the asterisk (just for the record):
remove resn \*\*\*\*
Cheers,
Tsjerk
On Wed, May 30, 2012 at 8:28 AM, Thomas Holder
wrote:
> Hi Martin,
>
>> when visualising data out of a GOLD docking run, where the software
>> has added lone pairs to active site residue
Beautiful people,
I was trying to make an image with a surface, with part of the surface
opened to show the inside. I tried to clip the surface by hiding
everything within a distance from a pseudoatom, but I ended up editing
by hand selecting atoms with the mouse, left click, hide, surface. I
was
e/... breaks down to
a click + key press operation.
cmd.set_key('F1', cmd.show, ('surface', 'sele'))
cmd.set_key('F2', cmd.hide, ('surface', 'sele'))
If you really want to map the mouse click operation you need to write a
wizard,
... so a wizard seems the way to go.
Thnx,
T.
On Jun 9, 2012 10:56 AM, "Tsjerk Wassenaar" wrote:
Hi Thomas,
The problem is a bit more complicated than that. I just want to be able to
turn on/off some representation by just clicking the atom. I don't want to
select, pres
Hi Michael,
The answer used to be "you can write out the surface as mesh in vrml or
povray format, from which you can extract the vertices". I think it's still
the proper answer.
Cheers,
Tsjerk
On Jun 11, 2012 5:26 PM, "Michael Lerner" wrote:
Hi all,
If I have a surface representation, is th
Hi Sean,
The pymol syntax for getting help on a command is "help command". I
think it is a wrapper around the python help function, for which the
syntax is "help(command)". In your case, it would only show something
like:
test(*args,**kwargs)
You can write a docstring, e.g. similar to the ones i
Hi Shane,
I've been playing with a virus 60mer on an intel core i7 workstation with
6Gb memory with good response. Just make sure you use the latest incentive
or open source version and have a good graphics card.
Cheers,
Tsjerk
On Jun 14, 2012 11:49 PM, "Shane Neeley" wrote:
Hi,
Does anyone
Hi Darrell,
> When using the plugin, I find it useful to use smooth loops and smooth
> strands. Unfortunately, the script puts the supporting struts at the
> C-alpha positions, not the splined positions that you get with smoothing.
> The trick is to "show" a "line" representation of just the C-alp
Hi Malai,
Check whether all residues have unique identifiers (residue id + chain id).
I often see this happen for multiple chains with no or identical
identifiers, in which different residues share the same number.
Cheers,
Tsjerk
On Jul 21, 2012 12:46 AM, "Jason Vertrees"
wrote:
Hi Malai,
Wh
Hi Andrei,
You only specified the width. The next argument should then be the height,
for which you filled in 'ray'. So pymol tries to make a number of that,
which fails.
Cheers,
Tsjerk
On Sep 13, 2012 7:45 PM, "Andrei Tudor" wrote:
Hello,
I installed pymol a few days ago from source. Everyt
Hi :)
You can also add
cmd.disable('all')
cmd.enable(cur_obj)
To have all other objects turned off. This is one I'm definitely going to use :)
Cheers,
Tsjerk
On Thu, Sep 20, 2012 at 6:32 PM, Jason Vertrees
wrote:
> Hi Martin,
>
>> Is it possible to somehow assign "page up" or "page down" key
Hi Stephane,
print cmd.count_atoms("byres resn URE within 3.5 of peptide")/8
Cheers,
Tsjerk
On Fri, Sep 28, 2012 at 2:59 PM, ABEL Stephane 175950
wrote:
> Dear pymol users,
>
> I would like to obtain with Pymol (v1.3) the number of urea molecules in the
> first shell of a peptide. To do this
t; Cheers,
>
> -- Jason
>
> On Fri, Sep 28, 2012 at 10:03 AM, ABEL Stephane 175950
> wrote:
>> for the pymol-users mailing list archive and to close my message
>>
>> Tsjerk Wassenaar gave the command :
>>
>>
Hi Dave,
You can set the chain identifier for each object
alter object, chain="A"
And then you can create a new object
create alltogether, chain A+B+C+D
That object you can then use for fitting.
Hope it helps,
Tsjerk
On Wed, Oct 3, 2012 at 7:22 PM, Bourgaize David wrote:
> Hello, all.
>
>
Hi Vitaly,
Try
for i in cmd.get_object_list(): cmd.get_model(i).get_coord_list() or
cmd.delete(i)
Ciao!
Tsjerk
On Tue, Dec 11, 2012 at 9:31 AM, V.V. wrote:
> Hello,
> Is there a quick way to delete the objects that do not contain any atoms?
>
> Thank you in advance,
> Vitaly
>
>
>
Hey :)
Can't resist the challenge...
For any given ensemble, you can draw a trace through the C-alphas using the
following lines, illustrated here for the NMR ensemble '1NMR':
# Get the structure
fetch 1nmr
# Get the number of states
n = cmd.count_states('1nmr')
# Collect the C-alpha coordinate
versity Research Lecturer
> Division of Structural Biology
> Wellcome Trust Centre for Human Genetics
> University of Oxford
> Roosevelt Drive,
> Oxford OX3 7BN, UK
>
> Email: jonat...@strubi.ox.ac.uk, Web: www.strubi.ox.ac.uk
> Tel: (+44) - 1865 - 287561, FAX: (+44) - 1
Hi Anasuya,
Happy New Year!
sphere_mode only controls the appearance. You probably want to try
sphere_scale.
Enjoy,
Tsjerk
On Mon, Dec 31, 2012 at 12:14 PM, Anasuya Dighe
wrote:
> Hi,
>
> I am representing C-alpha atoms of binding site as spheres.
> I am using the set sphere_mode command to
Hi,
I would be in favor of SVG format, because it is human
readable/editable/scriptable. The other formats are harder to deal with,
without using some external program, and SVG can be converted into either
of them anyway. In addition, SVG is suitable for use on webpages.
Cheers,
Tsjerk
On Tue,
Hi Yamei,
There's nothing wrong with your approach. If you like the results, and
they illustrate the point your trying to make, it's good.
Cheers,
Tsjerk
On Thu, Feb 21, 2013 at 9:22 AM, Yamei Yu wrote:
> Hi All,
>
> I want to generate a stereo image for a structure. I use
> pymol-diaplay-Ster
Hi,
If you want to draw all bonds for all pairs between two selections,
you can just use bond:
bond sele and n. ca, sele and n. ca
Hope it helps,
Tsjerk
On Thu, Feb 21, 2013 at 9:19 PM, Robert Campbell
wrote:
> Hi Anasuya,
>
> On Thu, 21 Feb 2013 17:10:40 +0530
> Anasuya Dighe wrote:
>
>>
>
Hi Stephane,
You can convert a Gromacs run input file (.tpr) to a pdb file with
CONECT records using the Gromacs tool 'editconf' with the '-conect'
flag. The CONECT records will be set according to the bonds in the
topology. Pymol will read the CONECT records and set the bonds. If you
have a traje
Hi Stephane,
You don't have phi/psi angles, so determining secondary structure is a
bit problematic. What you can do is draw a trace through the backbone
beads and set the secondary structure representation explicitly.
You'll have to make sure to exclude connections between chains.
set cartoon_tr
# Hey :)
# Here is a work around...
# First import the numpy module
import numpy
# Then store the viewing matrix as 6 by 3 numpy array.
M=numpy.array(cmd.get_view()).reshape(6,3)
# Now place a pseudoatom at the position of the camera
# Turn off autozoom to keep the view
set auto_zoom, 0
scale=1
Hi Anasuya,
You can make the selections in PyMOL and save each chain separately. But if
you have to do batch processing, you're probably better off using sed:
sed -n "/^.\{21\}P/p" 1a55.pdb > 1a55_P.pdb
sed -n "/^.\{21\}Q/p" 1a55.pdb > 1a55_Q.pdb
sed -n "/^.\{21\}R/p" 1a55.pdb > 1a55_R.pdb
To au
Hi Wilson,
I don't know how to reset the color scheme, but maybe something along the
following lines can help out:
# set the colors (change to your liking):
colors = ("green","cyan","magenta","yellow")
# create a color iterator:
python
def colit():
i = 0
while True:
yield colors
Hi Tim,
No, that is not possible. And a workaround isn't simple. You can wrap the
CGO object and place it each time you need it, using the information stored
in the viewing matrix.
Cheers,
Tsjerk
On Tue, Apr 16, 2013 at 1:43 AM, Someone Else wrote:
> Hi,
>
> is it possible to define a CGO ob
Hi Bharat,
Not exactly a Pymol question, is it? But in case you're using a list of
simple vectors as tuples or lists you can easily add them the Python way,
provided that the list is not too long (or it'll be slow):
vecs = [(a,b,c),(d,e,f),...]
v = [sum(i) for i in zip(vecs)]
Alternatively, you
Hi Bob,
I notice that this question has not yet been answered, unless you have
received private answers. To start with the second question, this list is
followed by those who are most involved in the code, and, AFAIK, there is
no specific developers list (I do care to know if there is :P). Also fo
Hi Thomas,
Probably something like this should do something close to what you need:
sed -n '/^\(ATOM\|HETATM\)/s/^.\{16\}\(.\{10\}\)/\1 \0/p' file.pdb | sort
-n -k 3 | cut -b 11-
Hope it helps,
Tsjerk
On Thu, May 30, 2013 at 10:21 AM, Thomas Evangelidis wrote:
> Dear PyMOL users/developers,
Hi Sid,
Have a look at this:
http://pymolwiki.org/index.php/Spectrum_states
Hope it helps,
Tsjerk
On Sun, Jun 2, 2013 at 8:06 PM, Sridharan, Sudharsan <
sridhar...@medimmune.com> wrote:
> Hi all,
>
>
>
> Sorry this may be a naive question and probably has a simple answer but I
> haven’t bee
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