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
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
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
* 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
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
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
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
* 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 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,
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,
* 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) ?
* 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
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
* 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.:
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
* 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.
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
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
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
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
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
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.
* 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
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,
* 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
* 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
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,
* 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
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
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 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,
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
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
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
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,
* 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 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,
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 =
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:
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
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
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
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:
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,
* 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,
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 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
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 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)
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,
* 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:
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
* 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,
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,
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
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 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 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
Hello Raúl,
* Raúl Mera butil_li...@yahoo.com [2006-06-07 04:32] wrote:
Hello all,
I'm writing a Pymol plugin which creates many chempy
objects (of the class Indexed) and displays the
objects as diferent states of a structure. The atoms
in the objects are not standar (they are dummy atoms
Hi Arvind,
* Arvind Marathe arv...@mbu.iisc.ernet.in [2006-06-09 00:14] wrote:
Hi all,
my system is a newly installed debian-3.1 linux. 'pymol' seems to be part
of the installed package. But when I try to open pymol, I get the
following error:
Hi,
* Joel Tyndall joel.tynd...@otago.ac.nz [2006-07-15 14:29] wrote:
Hi andrea,
you can easily do this by
split_states my_struct
dele my_struct
for the NMR ensemble, then I would use the action menu, align function
and align them to state_1. This is in effect aligning the
Hi Jonathan,
* Jonathan Stuckey sblood@yahoo.com [2006-08-15 12:03] wrote:
How can I change the surface_quality of an electron
density map surface? set surface_quality=-1 does not
do anything.
The surface_quality parameter affects the quality of molecular surfaces,
not isosurfaces. To
Hi folks,
* Michael Lerner mgler...@gmail.com [2006-08-21 12:26] wrote:
I think he means for you to have a Load button as part of your
plugin. That button would first record the path to the file and then
call through to cmd.load().
Perhaps what Ron needs to do is not use the cmd.load()
Hi Andrea,
* andrea carotti and...@chimfarm.unipg.it [2007-02-02 14:13] wrote:
Hi all,
is there the possibility to change the line width of the distance
measure between two atoms?
set dash_width, 3
If you like using a white background like I do, you can also change the
dash color using the
Hi Richard,
* Richard Gillilan r...@cornell.edu [2007-02-19 10:22] wrote:
I'm probably making a simpler mistake here, or perhaps there is
something wrong with my installation or paths.
I'm trying to load and display the simple cgo example in the manual.
I created a file named arrows
Hi Adiphol
* adi di adipho...@yahoo.com [2007-05-11 10:26] wrote:
Dear all,
I am trying to put on the electron density. I only
have .mtz file but I have a look at the manual and the
program need XPLOR file. How can I get the XPLOR file
or do I need to convert the mtz file to this - if so
Hi Vaheh,
* Oganesyan, Vaheh oganesy...@medimmune.com [2007-05-30 09:45] wrote:
I did not get much luck with those recommendations either. I was doing
exactly the same. Something is phishy with my pymol and/or APBS installation.
I did check for different pdb files, so it is not pdb related.
Hi David,
* David A. Horita dhor...@wfubmc.edu [2007-06-14 11:52] wrote:
Hi,
While I've seen a number of examples of good graphics cards to use with
Pymol, I'd like some feedback on what an acceptable low-end is for a
Windows laptop computer. Specifically, is the Intel GMA950 completely
Hi Martin,
* Martin Höfling martin.hoefl...@physik.uni-muenchen.de [2007-06-26 15:15]
wrote:
Hi there,
i am trying to map b factors on a surface representation.
I am using spectrum b,blue_white_red,mymol and the colors are fine. Is there
a
way to fine tune the color spectrum, such as
* Andreas Henschel a...@biotec.tu-dresden.de [2007-06-27 15:49] wrote:
Hi Julio,
If I understood you right, you can simply use translate, eg.:
translate [20,0,0], mol_to_dislocate
The important thing is that turn and move modify the camera, while
translate and rotate modify the
Hi Louis,
* Clark, Louis louis.cl...@codexis.com [2007-07-04 12:01] wrote:
Dear user-group,
I'm trying to learn how to use python commands inside pymol .pml
scripts. I seem to be missing some understanding about how the
interface works. Could somebody tell me how to fix this command
To all you colouring aficionados,
I've updated the color_b.py script on my web page to include Mark Wall's
addition of user-defined, 3-colour, gradients. Now you can type on the
command line something like:
color_b selection, gradient=user, user_rgb=(0.,.3,1.,.8,.8,.8,1.,.8,0.)
to get
Hi Abhi,
On Thu, 23 Aug 2007 12:51:10 -0700, Abhinav Verma
abhinav1...@gmail.com wrote:
I want to align different models of a multimodel pdb file.
How can I do that without extracting models as identical pdb.
cheers,
Abhi
Try the intra_fit command.
Cheers,
Rob
--
Robert L. Campbell,
Dear Tomoko,
On Tue, 18 Sep 2007 21:40:34 +0900 (JST), Tomoko Niwa
outp...@yahoo.co.jp wrote:
Dear all
I am a beginner in Python programming.
I would like to get lists of resn (residue names), resi (residue
identifiers) and atom ID of a selection.
For example, in case of
Hi Tom,
On Thu, 04 Oct 2007 11:20:35 -0700, Tom tl...@optonline.net wrote:
From time to time, I have a need to manually move objects relative to
one another. For example, manual docking of a ligand requires that it the
translated and rotated relative to its binding pocket. It there a
Hello John,
On Thu, 22 Nov 2007 12:36:32 -0800 (PST), JJ josh8...@yahoo.com
wrote:
Hello:
Im new at pymol and would like to obtain the
coordinates of the dots that make up the
solvent-accessible surface. I can obtain the vertices
using cmd.get_povray()[1], but that will give me a
list of
On Sat, 12 Jan 2008 20:21:37 +0530, rama krishna ram...@gmail.com 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
Hi Buz,
On Wed, 30 Jan 2008 14:41:00 -0500, Buz Barstow b...@mac.com wrote:
Does anyone know of a script that is capable of displaying the
surfaces identified by msms in pymol?
I have a script called msms_cgo.py that you can download from:
Hi again, Dimitry,
On Tue, 12 Feb 2008 09:10:23 -0500, Robert Campbell
robert.campb...@queensu.ca wrote:
Hello Dimitry,
On Tue, 12 Feb 2008 16:43:28 +0300, DimitryASuplatov
gene...@gmail.com wrote:
Hello,
I have a .pdb1 file with biological unit. It consists of two frames
Hi Tomoko,
On Mon, 05 May 2008 18:26:17 +0900, Tomoko Niwa tmk.n...@gmail.com
wrote:
Thanks for kind advices.
Whatif and PISA worked excellently, but I want to get the list within Pymol.
By parsing the pymol modules, I found
hb = cmd.find_pairs(((byres +sss1+) and n;n),
Hi Gary,
On Tue, 20 May 2008 12:12:43 +0200, Gary Hunter
gary.hun...@um.edu.mt wrote:
I am displaying pdb files of metalloenzymes, and like to show the metal ions
as spheres.
I select the metal and use showspheres
Fine
Somehow recently I must have done something to reset the vdw radius of
Hi,
On Fri, 27 Jun 2008 13:25:02 -0400, Michael Lerner mgler...@gmail.com
wrote:
This is probably a fairly basic question, but I'm stumped. I want to
visualize electron densities along with my PDB file. So, say I'm interested
in 2DJX. I go to the PDB and download 2DJX.pdb and 2djx-sf.cif.
Dear Morri,
On Fri, 22 Aug 2008 13:35:32 -0700, Morri Feldman
morrifeld...@gmail.com wrote:
Dear Rob,
I'm interested in using your variability script with a substitution matrix.
Would you please send me an example of a substitution matrix file? Thanks
for writing such a useful script.
Dear Pietro,
On Thu, 11 Sep 2008 13:18:20 +0100, Pietro Roversi
pietro.rove...@path.ox.ac.uk wrote:
Dear everyone,
I want to represent a domain of my molecule as a low
resolution solid shape.
I have chosen surface representation but the surface is clipped,
exposing
Hi Abhinav,
On Thu, 29 Jan 2009 13:10:25 -0800, Abhinav Kumar
abhin...@slac.stanford.edu wrote:
Is there someway to select and show conserved residues when a bunch of
superimposed structures are loaded into Pymol?
And if so, can identical and similar residues be selected separately?
I don't
Hi Dave,
On Tue, 03 Feb 2009 16:33:28 -0500, David Garboczi
dgarbo...@niaid.nih.gov wrote:
I am examining packing in several space groups by issuing the command
symexp foo, foo.pdb, sele, 10
If I select the whole reference molecule, I think that I should get
all the symmates within 10 A
Hi Sébastien,
On Mon, 02 Mar 2009 18:21:15 +0100, sconill...@chimie.u-strasbg.fr wrote:
Hi all (for the second time today ...),
I have a problem using the fit function. When I try to do this :
fit (fittest1 and resn P and !h.), (2VT4 and resn P and !h.)
I have this message error :
Hi Peter,
On Fri, 03 Apr 2009 02:38:03 +0530, peter hudson
peter.hudson.pe...@gmail.com wrote:
Hello all
I am trying to upload the ED map on pymol. but, it is not visible on the
screen. Although i checked at pymol wiki and i did as it is given on the
wiki.
For example.
I took ccp4
Hi Tom
On Fri, 15 May 2009 14:57:36 -0700, Thomas Stout tst...@exelixis.com wrote:
What version of PyMOL does this work with? I've been trying your commands
with versions 1.1 and 1.2b and while PyMOL reports that the primitives have
been processed, nothing is written to the file protein.pov
On Fri, 03 Jul 2009 16:18:10 +0200, Raluca Mihaela ANDREI r.and...@sns.it
wrote:
Hi!
Can somebody tell me why I can't create surfaces for the
oligosaccharide chains?
By default, the surface and mesh commands ignore all atoms in HETATM records
in a PDB file. You can change that with:
set
Dear Joseph,
On Tue, 07 Jul 2009 11:00:10 +0200, Andre Joseph andrejos...@gmail.com
wrote:
Dear Delano Scientific support
I've been fetching source code from the sourceforge repositories yesterday.
I've no error or warning during ./configure, make or make install
steps.
However, when I
Hi Mirek,
On Mon, 10 Aug 2009 11:21:39 -0700 Warren DeLano war...@delsci.com wrote:
PyMOL isn't the optimal tool for measuring surface area -- perhaps
others on the list can suggest good alternatives.
I like MSMS for this. I have a script that will calculate the area (both
solvent exposed
Hi David
On Thu, 10 Sep 2009 14:47:43 -0700 (PDT) David Hall dwash59_2...@yahoo.com
wrote:
Is there any documentation on getting information out of alignment objects
into scripts? I tried looking around the wiki, but I didn't see anything.
I'm just wondering things like if I have a residue
Hi Mark and Sean,
On Sat, 07 Nov 2009 10:05:59 -0500 Sean Law magic...@hotmail.com wrote:
Sorry for the earlier confusion. I think I found a hackish way of getting
a gray spectrum:
snip Sean's extensive explanation
I know I'm biased, since I wrote the color_b.py script, but I fail to see
Hi Sean,
On Mon, 09 Nov 2009 10:58:53 -0500 Sean Law magic...@hotmail.com wrote:
Robert,
I would have to agree with you. I've used many of your scripts and have
also learned a lot from them and think that the color B script is pretty
robust and helpful.
Thanks.
I could be wrong but
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