Hi,
With regard to sandboxing, there is PyPy:
http://pypy.readthedocs.org/en/latest/sandbox.html
although this would be a little complicated, as it's not just a
cPython package or extension or whatever, but an alternative to
cPython...
Oh, and in general, there does exist some precedent for thi
Hi,
Although most of the time the strands in a sheet have clear 'sides',
this won't always be true. Keitaro already mentioned the possibility
of twisted strands, but you can also get two sheets that share the
'same' long strand - well, depending on the SSE assignment algorithm,
I suppose.
Jellyro
Hi,
I might be wrong, but might it be that you need the axis through the
structure that minimises the distance of all the points to it. Or, to
put it another way, the least-square-plane through the structure, the
normal to that plane, and a thir axis perpendicular to both.
If this is the case, yo
On Tue, Mar 31, 2009 at 9:45 PM, Sean Law wrote:
> the performance is lightning fast. Can anybody help me improve the overall
> performance or suggest an alternative? Thanks in advance!
A kind of alternative would be to use a custom dihedral command, that
avoids evaluating selections:
def tors
Hi,
I think that it probably is possible to do this from within pymol, and
probably quite convenient for single molecules.
However, there are two other possible approaches, which would be
helpful for multiple molecules.
Firstly, there is a program called 'dang' made by the Richardson group:
htt
Hi,
I recognise that code comment :)
Actually, it seems that pymol now includes numpy, I will change my
script and see if it still works.
In the meantime, if you just want axially-aligned bounding boxes, try
this script (not by me):
http://www.pymolwiki.org/index.php/DrawMinBoundingBox
at le
Hello,
Possibly.
I have python code that attempts to parse dssp files. Add that to a
script to call dssp (not so hard) and then call the parsing code, then
annotate the structure with the result...
Maybe all this already exists somewhere?
gilleain
On Fri, Nov 28, 2008 at 1:39 PM, DimitryASupla
Hmmm.
I'm probably over-complicating matters, but:
def before_load():
cmd.delete("all")
def after_load():
cmd.as("cartoon")
cmd.hide("nonbonded")
def wrapped_load(filename):
before_load()
cmd.load(filename)
after_load()
cmd.extend("wrapped_load", wrapped_load)
gilleain
"select hetatm and resname atp" or "select hetatm and r. atp"
see also: "help selections"
gilleain
On Tue, Sep 23, 2008 at 7:18 PM, Paul Shannon
wrote:
> What command will select a HETATM of ATP? I am looking at 1ATP.pdb,
> in which the ATP molecule appears
> as shown below.
>
> I found 'selec
Ah, the problem is the "def" in front of the function call. It should be either:
set_symmetry 1a2p, 60, 60, 80, 90, 90, 120, P6122
(in the pymol command window or in a .pml script) or
cmd.set_symmetry("1a2p", 60, 60, 80, 90, 90, 120, spacegroup="P6122")
in a python script.
gilleain
On We
Hi,
There are many. One way is to use PyMol (or, indeed many other
viewers). So I did it like this:
fetch 1a25
show cartoon
create chaina, chain a
create chainb, chain b
delete 1a25
align chaina, chainb
color red, chain a
color blue, chain b
I guess that this could be generalised into a script t
Hi,
Wouldn't it be better to use a program written especially for this
purpose, like dang/dangle from the richardson group, or dssp (, or
others I don't know of)?
Of course, you may have a specific reason for using pymol, so this is
just a suggestion!
gilleain torrance
On Wed, Jun 1
8, in this case) get put
into the cartoon as 'part' of the peptide backbone, sort of.
Just thought I would mention it, in case this is considered a bug...
gilleain torrance
Hmm. Running scripts has always worked for me on a mac.
Could it be a tab/space problem, or just a character missing at the
end from a copy/paste?
gilleain torrance
On Thu, Feb 28, 2008 at 2:50 PM, Sadler, Evan wrote:
> I can run scripts by pasting them, but they fail when I try to read t
Hi everyone,
Sorry for posting my replies to the list; I hope this is all generally
useful.
Firstly, the bug: the obvious cause is if the line "if ss == currentType:"
is never true. In that case, it is making a list of one-residue sses, with,
as Tsjerk correctly pointed out, the default end of -1.
Hi Frieda,
That's odd. It seems to work okay for mulitchain proteins (I'll add
some extra bits to handle chains).
The "--" in the output is weird. It suggests that either the start
numbers end in a dash or the end number start with a dash. It's
difficult to diagnose the bug, if bug there is, with
rate_sses
They were fun to code, anyway.
gilleain torrance
On 10/9/07, Tsjerk Wassenaar wrote:
>
> 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
> /whil
Hi,
On the subject of "circular variance circle plots for dihedral
angles". If we are talking about the same thing, I have implemented
some of this in python if anyone wants it.
That is, I had to calculate the circular means and std dev for lists
of torsion angles, and used the method described i
Hmmm.
With a little messing around, it seems that this works at the pymol prompt:
for x in range(10): cmd.label("(name ca and resi %d)" % x, '"%s%s\" %
(resi, resn)')
The only difference is in the quoting. Double quotes inside single quotes.
gilleain
On 7/4/07, Clark, Louis wrote:
Dear
Hi,
Firstly, I can see why there is a syntax error for the alter_state command:
cmd.alter_state ("1",("1AW3 and name fe"),((x,y,z)=(x-a,y-b,z-c))")
has the quotes in the wrong place. I guess it should be:
cmd.alter_state("1","(1AW3 and name fe)","((x,y,z)=(x-a,y-b,z-c))")
I can make eve
Hi,
You can save the structure as a pdb file:
save name.pdb, selection-name
that might do what you want. Type help save for more details.
gilleain torrance
On 3/15/07, Juliana R Cortines wrote:
Hi all-
I was wondering if it is possible to generate coordinates in a .pdb file
from the
Hi Rafael,
There is a lot of info on the wiki:
http://www.pymolwiki.org
also, there is a help system in pymol (type "help"). The run command
is what you want for running scripts.
gilleain torrance
On 2/27/07, Rafael Fernández Leiro wrote:
Hello, firstly excuse my english. I
object as a parameter.
So, no, not that I can see.
gilleain torrance
On 2/23/07, Anthony Armstrong wrote:
Hi Folks,
When using the distance wizard is there a way to change the number of
decimal places output to the label from 2 to 1?
Thanks,
Tony
Anthony A. Armstrong
Department of Biop
file, structure names, comments, etc.
In fact, a truly clever thing would be to store the session along with
the image, and you could browse sessions by looking at thumbnail
images...
Anyway, just a thought.
gilleain torrance
dding missing hydrogen atoms." - seems perfect :)
gilleain torrance
On 12/6/06, Stuart Endo-Streeter wrote:
You should take a look at the program Reduce from the Richardson lab at Duke,
it adds protons and is written in C++. It will take a pdb and without
requiring modification or formating a
Hi,
I don't know how simple you want it, but python lets you print just like:
print cmd.distance(a, b)
assuming that a and b are strings that are atom selections. See
http://www.pymolwiki.org/index.php/Translate_And_Measure
for a more complex example! :)
gilleain
On 11/7/06, Giacomo B
ummm.
PY-mol not handling perl is not really a bug...
:)
gilleain
On 9/16/06, vijay wrote:
dear pymol users,
I got a bug in pymol with .pl file produced by
pdbsum clefts (see this link,
http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetPage.pl?pdbcod
Hi,
Yes, the wizards are just pymol classes in individual modules in the
wizard/ subdirectory of the main pymol. So, on the mac :
/Applications/MacPyMOL.app/pymol/modules/pymol/wizard/measurement.py
but, I guess in a similar place in other installations.
I've tried my hand briefly at wizard pr
Hi Björn,
Odd. I can't reproduce this. I load 1a2p and 1a12 into states one and
two, hide, show cartoon, and bingo - I have two cartoons (in two
different states).
What happens if you load the first pdbfile twice? Or use another file
instead of p2? Or a newer version (I'm using MacPyMol 1.0.0b03
Hi,
this is a good idea, and a fairly easy one to implement. do you mean
present all of the pdb files (or the like) from a chosen directory in a
list, and load each molecule via a double-click?
Yes. Exactly. Probably with the directory as a button/textelement at the top
of the list? Whateve
2) filelist:
Yes. Yes it does. Although typing "load " works too...
What I should have said was that I often find myself (and others in our
group have in the past) looking at a whole bunch of structures, one after
the other. When you are looking at 100s of structures in a row it gets
tiring to k
Hi,
Some suggestions:
1) Header file display.
2) Filelist : show a directory as a list, to avoid repeated "load" commands.
3) Ramachandran plots : I keep meaning to try dynoplot on the hybrid
pymol, but never do.
4) Secondary structure display.
Oh the list is endless! But number one suggestion
".pymolrc" or "pymolrc". see :
http://www.pymolwiki.org/index.php/Launching_PyMOL
gilleain
On 5/11/06, Praedor Atrebates wrote:
I would like to make some settings I use permanent and default in pymol
because every time I start pymol or reinitialize and load a new pdb/pse I
have to make a se
due.lower())
cmd.set_geometry ??
cmd.save(aa.pdb, "all")
Unfortunately, I'm not sure the set_geometry command is right.
gilleain torrance
On 3/14/06, Alan wrote:
> Hello List,
>
> I would like to have any help.
>
> I want to build several 3-peptides, like AAA, FFF,
Hello,
yes. maybe. if you are talking about printing to standard error, then :
import sys
sys.stderr.write("hello, stderr!")
will do it.
if, on the other hand, you mean something more complicated to do with
manipulating the shell ("redirection"...?) than I don'
Hello,
This is only my opinion right...
But it seems to me that converting hbonds into secondary structure
elements (helices, strands, paperclips...) can be tricky at the
boundaries when bonds are just too short or just the other side of the
correct angle.
To illustrate this with 1m6q (which is
Hi,
I found out how to do ... something ... like this the other day.
I too have had this problem. Even if you switch to 2-button selecting,
I can't seem to zoom, no matter what finger-twisting combinations I
try!
I do have a usb mouse, but I wonder if this is now vital, or merely
still convenient?
gilleain torrance
On 2/7/06, andr...@biochem.utah.edu
"...get at..."? "...display..."?
To access the B-factors, you can use "iterate" - as in "iterate resi 1,
print round(b, 2)". That will print out the b-factor for each atom in the
first residue.
gilleain torrance
On 1/16/06, Bingding Huang wrote:
>
Hi,
I tried a similar, but simpler, example :
def mol2png(name):
cmd.png(name)
cmd.delete(name)
called as 'mol2png("1a2pA")', given that I have an object called "1a2pA"
loaded.
It works just fine on my laptop (mac).
Odd.
gilleain torrance
On 1/6/06,
Hi,
I've noticed this too, it can be quite frustrating. Oddly, the histories for
the two windows (main, and command) seem to be different.
I have never managed to work out what the problem is, but I sometimes wonder
if it is to do with whether a function returns a result or not? (Wild guess!
:)
Hi,
The link to the beta99:
http://delsci.com/beta/macpymol-0_99beta29.tar.gz
says "Page not found".
I wouldn't normally worry, but since using recent betas, my screen
goes odd when waking from sleep. Which isn't much to worry about
either (assuming it is caused by pymol, which I don't kno
Matrix()
rx, ry, rz = 1, 2, 3
cmd.load_callback(Cone(), 'cone')
Gilleain Torrance
On 8 Nov 2005, at 06:44, Andrew Wollacott wrote:
Hey all,
I recently made a cone class that will display cones using pymol
cgo's. I built the cones using triangles as suggested by Warren Now
I nee
ol/opengl/gl/
__init__.py", line 21, in ?
import _opengl
ImportError: No module named _opengl
Not sure why, as there is a:
/System/Library/Frameworks/Python.Framework/Versions/Current/lib/
python2.3/site-packages/pymol/opengl/gl/_opengl.so
in existance.
gilleain torrance
On 14 Oct 2005,
't need to be opening the files "out" or
"full" inside the loop, or re-reading the data from "amb".
Hth.
gilleain torrance
On 25 Oct 2005, at 10:45, andrea spitaleri wrote:
Hi again, reading my post I found the bottleneckshame on me :)
here it is:
Hi,
Works great for me!
Very nice to have access to the system python.
gilleain torrance
On 14 Oct 2005, at 16:50, Warren DeLano wrote:
For cutting-edge Mac users, there is a new MacPyMOL for Tiger that
integrates into a single window and links to the system Python instead
of bringing its
Which parts are missing? Looks fine to me...
Although the pdb file has some horrible features. Some residues are
multiply defined (eg 170 in chain H) and there is some kind of poly-
calcium binding tail in chain L.
gilleain torrance
On 14 Oct 2005, at 10:43,
wrote:
Hi everybody
I am
disable('two')" at the
end instead of 'hide', then it seems to do what you wanted it to do...
gilleain torrance
On 10 Oct 2005, at 22:12, Terry Jones wrote:
Hi. I've run into a slight pymol UI problem with cgo objects and I'm
wondering if I should be doing somet
interpreting.
gilleain torrance
On 3 Oct 2005, at 12:20, Terry Jones wrote:
Hi all
I've written some python code that I want to run from inside pymol
using
the File/Run command. After some playing around looking at error
messages
and the pymol source, I saw that pymol is reading my f
the 'model' variable correctly to whatever it was
set to at the top of the loop.
gilleain torrance
On 15 Sep 2005, at 01:50, Xavier Deupi wrote:
Hi,
I'm trying to write a script to load a series of model peptides and
superimpose them to a template structure.
The part that
Of course, this assumes you have purchased a QuickTime Pro (tm) key for £20
($25)...
gilleain
On 20/7/05 23:44, "Reinhold Penner" wrote:
> Xavier,
>
> since you're on a Mac, it's easy enough to just fire up QuickTime
> Player and select File->Open Image Sequence. This will prompt you to
> sel
probably a bit
inefficient (could use the Numeric module) and b) you can't ray-trace
callback objects.
Hope this is helpful!
gilleain torrance
On 11/7/05 10:27, "tanri...@stud.uni-frankfurt.de"
wrote:
> Hi everybody,
>
> I want to vizualize 3D-ellipsoids around molecule
e of a question for Mr DeLano
:) Calculating pairwise like this is always going to be computationally
expensive, but I don't know ways to speed this up.
gilleain torrance
On 5/7/05 15:17, "Andrea Spitaleri" wrote:
>> HBA = cmd.distance('HBA', '(lig and acc)&#
_distance in a loop:
for donor in atoms_Don:
for acceptor in atoms_Acc:
DistOut.write("%s" % cmd.get_distance(donor, acceptor))
or something.
gilleain torrance
On 5/7/05 11:50, "Andrea Spitaleri" wrote:
> Hi guys,
> I am trying to make a script to
stance objects (using cmd.distance) to show them.
Also, it is entirely possible that there is a way to do this more easily in
pymol that I missed :)
gilleain torrance
On 12/6/05 20:00, "Marty Taylor" wrote:
> Hello,
>
> I am looking for a tool to help me build structural
glitch is the change from Numeric to numarray. This can be 'fixed'
('hacked') by using *cough*perl*cough*:
perl -i -p -e 's/Numeric/numarray/g' *.py */*.py
which should substitiute all instances of 'Numeric' with 'numarray'.
gilleain torrance
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