Hi Orla,
* Orla O'Sullivan orla.osulli...@teagasc.ie [2006-04-28 11:37] wrote:
Is there any way to change an L-alanine to a D-alanine in pymol
Sure. In the build menu there is an entry:
Invert (pk2)-(pk1)-(pk3) [Ctrl-E]
pk1 is the atom whose configuration is to be inverted. pk2 and pk3
Hi Fei,
* Fei Xu f...@rutchem.rutgers.edu [2006-04-19 11:55] wrote:
Hi!:
I met a scaling problem.
I created many pdb files along one trajectory of DNA movement. I loaded
each pdb file in pymol to create a picture, that is, one frame of the
trajectory. Pymol shows each molecule in an optimal
Hi Vanessa,
* Vanessa Oklejas vokle...@stanford.edu [2006-02-10 11:18] wrote:
Hi All,
Does anyone know how to delete bonds between atoms in PyMol?
You can use the unbond command:
PyMOLunbond ?
Usage: unbond [ atom1 [, atom2 ]]
You can pick the two atoms with the mouse (such that they
Hi Aaron,
* Aaron New aaron...@gmail.com [2006-02-09 09:36] wrote:
I have selected atoms near an object of interest, and extended this via
byres to a selection of the other atoms that are part of the same residue.
Is there any way to output a file that would have the coordinates of the
atoms
Alexander,
* alexander.paut...@bc.boehringer-ingelheim.com wrote:
I would like to color my protein according to B-factor with a self-defined
spectral palette (In this case I have put sequence conservation into the
Bfactor this column). I found that
spectrum b, blue_white_red,
* J. Evan Sadler esad...@im.wustl.edu [2005-11-23 13:08] wrote:
I need a list of the secondary structure assigned to each residue by dss in
pymol. Is there a simple way to write this information to a file, or dump it
to the screen?
To dump it to the screen, try:
iterate object name n. ca,
Sebastien,
* Sebastien Moretti sebastien.more...@igs.cnrs-mrs.fr [2005-10-17 08:41]
wrote:
Sebastien,
I cannot
change the color for rendering modes I defined.
I do not understand what you mean by this.
Cheers,
Warren
I mean that the color, for cartoon view, is unchangeable when
Hi,
* Jianghai Zhu z...@purdue.edu [2005-08-24 01:59] wrote:
I could not get cctbx work under either MacPymol or PymolX11Hybrid in
Mac OS X. Anywhere I can find some instructions to get cctbx work in
OS X?
There is a page on the cctbx with special instructions for using it on
the Mac:
Hi Sabuj,
* Sabuj Pattanayek sabuj.pattana...@vanderbilt.edu [2005-08-22 18:03] wrote:
Hi,
Thank you for replying.
In fact this is what I did. Gentoo automatically compiles pymol (pymol
ebuild) with all required dependencies against the system-wide
python-2.4.1. I then manually
Hi folks,
* Warren DeLano war...@delsci.com [2005-08-10 16:41] wrote:
James,
PyMol would allow one to enter a peptide sequence (generally short in
length) to create a template structure that can then be used
Just hold down ALT/OPTION and type in the peptide sequence. The
numbering
Hi,
I just felt like making a correction to the language I used. It seems a
few words went missing!
* Robert Campbell r...@post.queensu.ca [2005-08-11 11:28] wrote:
I had already written a script to do this, but making it easier to
specify the exact phi/psi angles to use. I borrowed bits
Hi Blanton,
* Blanton Tolbert blanton_tolb...@urmc.rochester.edu [2005-08-11 11:53] wrote:
Hi pymolers
is it possible to generate a template nucleic acid structures from
sequence in pymol?
Not as far as I've found. There are other programs that can do this:
B (aka Biomer)
Hellow Sebastien,
* Sebastien Moretti sebastien.more...@igs.cnrs-mrs.fr [2005-08-01 08:48]
wrote:
Hello Sebastien,
Hello,
Is there a way to expand the names panel to be able to read object and
selection names larger than 16 characters ?
At the bottom left corner of the panel, just to
Hi Ramon,
* Ramon Crehuet rcs...@iiqab.csic.es [2005-07-29 12:55] wrote:
Hi all,
I have a problem with intra_fit. After reading two (or more) pdb
into the same molecule, it does not recognise atoms for other states. I
always get the message (this is for a short example):
PyMOLintra_fit
Hello Sebastien,
* Sebastien Moretti sebastien.more...@igs.cnrs-mrs.fr [2005-07-28 08:47]
wrote:
Hello,
Is there a way to expand the names panel to be able to read object and
selection names larger than 16 characters ?
At the bottom left corner of the panel, just to the left of the VCR
Hi,
* Michael George Lerner mler...@umich.edu [2005-07-06 09:28] wrote:
with my editing to put the original e-mail in the correct location
On Wed, 6 Jul 2005, Sebastien Gerega wrote:
Is there a way to list the residues that are in a selection? For example
if I use the command select near,
Andre,
* tree javer...@utmb.edu [2005-06-20 23:31] wrote:
The Wiki (http://www.pymolwiki.org/) has some information about this.
It also shows you how to change some properties to make things easier to
fit.
Intra_Rms (http://www.pymolwiki.org/index.php/Intra_Rms), and Fit
Hi Paula,
* Paula Salgado pa...@strubi.ox.ac.uk [2005-04-27 10:44] wrote:
Hi,
Is it possible to save an r3d file in pymol for exporting into other
render programs like povray? I would like to test rendering in other
programs...
I use the following script to save an input file for povray:
Hi Shohei,
* Shohei Koide sko...@uchicago.edu [2005-04-12 15:39] wrote:
Hi,
I would like to use different stick radii for the backbone and side chains
(e.g. thicker sticks for BB and thinner ones for SC). The command set
stick_radius=X seems to set the global stick radius, so I cannot use
Dear Folks,
* I r...@post.queensu.ca [2005-03-29 16:27] wrote:
After playing around with
this I finally got tired of doing it manually, so of course I wrote a
python script to do this. It uses the alter command (so it isn't fast!)
to modify the alt, name, resn, resi, chain, and segi values
Dear Folks,
I know a number of people have stumbled over the difficulty of
calculating RMSD values for structures of non-identical sequences.
While teaching a class that introduced students to the use of PyMOL
to look at protein structures and to the study of certain structurally
homologous
To add to what Cameron said:
* Cameron Mura cm...@ucsd.edu [2005-03-24 09:44] wrote:
Hi Hyun-Chul,
It's easy to use PyMOL to build protein fragments in standard geometries
(Build menu in the Tcl/Tk GUI window), but I'm not sure about DNA.
Three non-PyMOL methods that I'm aware of are:
Hi,
Daniel Farrell [Monday, March 07, 2005 1:23 PM] wrote:
I want to create a lot of distance objects (in the hundreds)
between particular atomic pairs. Obviously I can make a
script like the following, inserting the exact atomic
selections that I want:
distance distobj12 =
Hi Einat,
* Einat Sitbon einat_sit...@hotmail.com [2005-03-03 14:27] wrote:
1) Secondary structure can be viewed as cartoons, or as colors. The problem
is the boundaries are not the same. If I color a strand by secondary
structure, it seems that the following loop is a strand as well. I?m
Hi,
* Lisa Craig licr...@sfu.ca [2005-01-27 20:43] wrote:
How do I select side chains without selecting the backbone atoms?
Add ! n. n+ca+c+o or in long form and not name n+ca+c+o to your
selection. So to colour all arginine and lysine side chains blue:
color blue, r. arg+lys ! n.
Hi,
* Jeffrey N. Agar a...@chem.uga.edu [2005-01-18 14:07] wrote:
also, typing the following example from the users manual gives invalid
syntax with an arrow pointing to the m in file_list =glob(mov*.pdb):
2) The following is a Python program (with a .py or .pym extension)
which uses a
Hi Roger,
* Roger Dodd rb...@cam.ac.uk [2004-10-07 16:33] wrote:
I am trying to prepare a figure illustrating a fairly complex packing
arrangement in a large H32 (R32) unit cell, where the packing may
actually have some biological relevance. To try and show the packing
I've been
Dear Marcelo,
* castilho casti...@if.sc.usp.br [2004-08-23 17:02] wrote:
My name is Marcelo and I am a basic-level pymol user. I work with docking
programs and I am trying to make pymol our default program for analysing
docking results...this brings me to some questions:
Is it possible to
Dear PyMOLers,
A couple of users of my scripts had contacted me about problems with my
draw_symops_cctbx.py and all_axes_new.py scripts. I've (I think) solved
those problems and added a new functionality requested by one of them.
The main problem was getting anything using cctbx to run properly
Hi Jason,
* Jason Vertrees javer...@utmb.edu [2004-04-14 22:55] wrote:
Master Users,
I'm a bit new to PyMol and still trying to master selections. I've read
the documentation and played with quite a few macromolecules now and
still have some problems with selections.
For example, I
Dear PyMOLers,
It was brought to my attention yesterday that 2 of my scripts had
problems with their selection routines, so I've put repaired versions up
on my web site. They are:
color_by_attype.py
seq_select.py
The problems arose if you had more than one object up with multiple
chains and
Hi PyMOLers,
I've added a new script to my PyMOL script archive. Have you ever wanted
to highlight in the display a particular sequence and couldn't be
bothered to look up the residue numbers? Me, too. So I wrote a little
script called seq_select.py that creates a named selection of an object
* Robert Campbell r...@post.queensu.ca [2004-03-04 16:24] wrote:
To the PyMOLers out there.
This isn't particularly exciting news, but if you use my color_b.py and
data2bfactor.py scripts, you may be interested in the update versions
that I've just put on my web site.
Ops
To the PyMOLers out there.
This isn't particularly exciting news, but if you use my color_b.py and
data2bfactor.py scripts, you may be interested in the update versions
that I've just put on my web site.
There is now a function in data2bfactor.py that loads data into the
occupancy column,
* Lieven Buts lie...@ultr.vub.ac.be [2004-03-02 09:03] wrote:
On Tuesday 02 March 2004 07:56, Matt Franklin wrote:
[...snip...] I then realized that I
had absolutely no idea how to restore the default surface coloring!
(Except by quitting and restarting...)
set surface_color, default
Michael,
* Michael Banck mba...@gmx.net [2004-02-19 12:24] wrote:
On Thu, Feb 19, 2004 at 08:22:14AM +0100, Thomas Siegmund wrote:
For me PyMol on SuSE 8.2 crashed always when raytracing a line element.
That seems to be identical to Debian Bug #229080
(http://bugs.debian.org/229080)
* Tsjerk Wassenaar t.a.wassen...@chem.rug.nl [2004-02-19 04:30] wrote:
Hi Guys,
I seem to have some trouble rendering with povray. The render starts and
finishes fine, and the image is created, but Pymol crashes with a
segmentation fault as soon as the rendering is done. The image is not
Leigh,
* le...@rsvs.ulaval.ca le...@rsvs.ulaval.ca [2004-02-11 15:18] wrote:
I am trying to use the get_dihedral routine. If I've got just one object
it works as expected. For example:
PyMOLget_dihedral 9/C, 10/N, 10/CA, 10/C (I type in)
cmd.get_dihedral: -49.721 degrees. (pymol
* Michael Bovee mbo...@uvm.edu [2003-12-16 14:27] wrote:
Hmm. When I try this I get a syntax error:
__
PyMOLload EcHRSade.pdb
Executive: object EcHRSade created.
PyMOLhide
PyMOLshow cartoon
PyMOLdss EcHRSade
Traceback (most recent call
Hi Loic,
* Loic BERTRAND l...@cryst.bioc.cam.ac.uk [2003-12-03 18:42] wrote:
I want to generate a ray-traced image with a white background and a
very strong fog effect. I tried to play around with the ray_trace_fog,
ray_trace_fog_start and fog parameters but could not manage to do it.
Jack,
* Jack Howarth howa...@bromo.med.uc.edu [2003-11-11 11:17] wrote:
What exactly is the recommended approach for installing
and maintaining custom pymol python scripts? While I have seen
messages describing custom pymol scripts, their installation isn't
described. Should I put them
Dear PyMOLers,
It was brought to my attention recently that the draw_cell.py and
draw_symops_cctbx.py scripts on my web site were broken due to changes
in the cctbx interface. It had been a while since I used the scripts
myself, and I hadn't kept abreast of Ralf's changes ...
Then Warren kindly
* Robert Campbell r...@post.queensu.ca [2003-10-10 13:04] wrote:
snip all that stuff about the new scripts
P.S. Warren, there is still a problem with drawing CGO cylinders
and sausages along the (1,-1,1) direction -- they don't appear unless
you ray trace the image:
As an example:
load
Hi Jason,
* jkyano jky...@scripps.edu [2003-10-01 11:51] wrote:
I am looking for a free program or script that can spit out sidechain
hydrophobicity in the B factor column so that I can color a surface by
hydrophobicity using the color_b.py script.
I have a data2bfactor.py script that will
Hi Stephen,
* Stephen Graham steph...@mail.usyd.edu.au [2003-09-18 21:02] wrote:
First up: Is there any way to tell PyMol *not* to change its view when
loading a
PDB file? For viewing in general, and for movies w/ morphs (etc.) in
particular
it would be nice to not have to re-set the view
Warren,
* Warren L. DeLano war...@delanoscientific.com [2003-09-09 17:42] wrote:
If you're willing to switch into Python, there is an
undocumented read_pdbstr function which can take a PDB file as a
string variable. See modules/pymol/importing.py for the code.
Temporary files are
* Stefan Reinelt stefan.rein...@mpimf-heidelberg.mpg.de [2003-06-19 15:19]
wrote:
Hey there,
I try to get a nonbonded as a simple ball without any sticks out of it.
Any ideas ?
Try:
hide nonbonded, selection if desired
show nb_spheres, selection if desired
Cheers,
Robert
--
Robert L.
Hi Folks,
Some of you may have been using my color_b.py script for colouring by
the value of the B-factor. Thanks to the stimulus of one user, I've
updated it to have a variety of colouring gradients. You can now select
from the following options:
Gradients:
'bwr' blue-white-red (like
* Nat Echols n...@bioinfo.mbb.yale.edu [2003-05-13 15:38] wrote:
I'm new with Pymol and I would like your help in the following problem:
I have a receptor image that I want to emphasize the ligand in its interior.
I'm a big fan of transparent surfaces for this, e.g.:
Hello,
* cami...@mrc-lmb.cam.ac.uk cami...@mrc-lmb.cam.ac.uk [2003-04-29 14:08]
wrote:
Hello Pymol community,
I'm experiencing a problem when colouring a pdb by secondary
structure. The colour bleeds from the ends of helices and sheets into
loop.
for example, if I were to
* yibin xu yibin...@jcu.edu.au [2003-04-21 13:30] wrote:
A little question. I want to color all carbons of my ligand to yellow
and keep oxygen-red and nitrogen-blue. How to do that? Thanks in
advance.
color yellow , (ligand and e;c)
where ligand is some method of selecting your ligand. It
* Armand Tepper wjwtep...@yahoo.com [2003-04-15 04:09] wrote:
Dear all,
1) In a future version of Pymol, would it be possible
to parametrize the POVray output such that all
textures, finishes etc. are declared once as variables
(e.g. something like #declare carbon_texture =
texture) ?
Rajarshi and Gareth,
* Gareth Stockwell gar...@ebi.ac.uk [2003-04-02 08:40] wrote:
Rajarshi,
With a bit of work you could add such a feature to the script, by using
compiled graphics objects (CGOs). The PyMOL documentation explains how
to use them.
Gareth
On Tue, 2003-04-01 at 21:42,
Hi Cameron
On 2003-02-28 12:48 you wrote:
If possible, how does one color a PDB representation in PyMOL by the
B-factor field??
Yes, have a look at my color_b.py script in the PyMOL part of my web
site:
http://biophysics.med.jhmi.edu/rlc/work/pymol
You need to do a run color_b.py first,
* cheom-gil cheong cheomgilche...@hotmail.com [2003-02-27 12:37] wrote:
I want to reduce the width of helices and the strands and the thickness of
the strand to make better-looking figures. Does anyone did that before? It
must be some setting parameters but I cannot find it in my manual.
Hi,
On 2003-02-26 14:54 Andreas wrote:
how to write the PovRay file out? (I do not want to embed PoyRay as the
renderer.)
I also don't use povray directly as I like to edit the povray input
file.
I use the following script:
# make_pov.py
Hi,
On 2003-02-26 11:36 Mathews wrote:
I am looking for a way to change the stick color by maintaining the atom
color.
Extra info:
Using the set color_sphere command to change the colors of the spheres,
changes the colors of the atoms to one specific color. I would like to have
Hi,
* xiaofeng qian xiaofengq...@hotmail.com [2002-12-16 20:47] wrote:
Does anybody know how to display the electrondensity map in the wall-side
stereo way(not cross-eye way)?
You can switch to wall-eyed, by changing the sign of the stereo angle.
You will need to alter the stereo_shift as
Quyen,
* Quyen Hoang hoa...@mcmail.cis.mcmaster.ca [2002-09-05 15:32] wrote:
I would like to read CCP4 electron-density maps into PyMol, but I don't
know how (explore maps loaded fine). Would someone please give me a quick
summary of the procedure.
Thank you!
simply doing:
load
* dee...@iastate.edu dee...@iastate.edu [2002-08-20 07:03] wrote:
On Sat, Aug 17, 2002 at 10:23:46PM +0200, Bartholomeus Kuettner wrote:
Hello there!
I followed mailing list instructions to create cgo based labels via a python
script. Unfortunately, the labels are not in plane but more
Warren,
I have found a CGO-drawing problem for which I cannot find a solution.
I've been trying to perfect my script for drawing symmetry axes of
crystal structures. I noticed that the script wasn't drawing all of the
axes that it should have (i.e. not all of those that were listed by the
Dear PyMOLers,
I've revised the B-factor colouring script that I published on this list
back on May 24th. The function now allows you to choose the style of
colour ramp (blue-magenta-red or rainbow), the way in which the B-value
ranges are chosen (histogram or smooth ramp) plus the number of
Dear PyMOLers,
Nat Echols n...@mail.csb.yale.edu [2002-05-23 10:25] wrote:
Can PyMOL do coloring by B-factors? I didn't see anything
about this in
the manual. If not, I'll go ahead and write a new function, unless
someone else is working on this.
* DeLano, Warren
101 - 163 of 163 matches
Mail list logo
