The source of 1.9.0.0 is likely the subversion repository, which also has
the history that shows the changes.
https://sourceforge.net/p/pymol/code/4184/log/?path=/trunk
As for pymol 2.0 coming to open source, the announcement for 2.0 said the
improvements would be pushed to the open source
The transform matrix you’re using is the identity matrix, so it won’t have any
effect.
-David
> On Jan 11, 2018, at 6:54 PM, Benjamin Bailly wrote:
>
> Hi Thomas,
>
> Thanks for your reply.
>
> So if I am correct, for my protein get_coords fetches a very large matrix of
You can use the partial argument of the load command to get two sessions
together.
load session1.pse
load session2.pse, partial=1
> On Dec 28, 2017, at 6:03 PM, david gae wrote:
>
> Dear Maria,
>
> I don’t think there is a direct way to connect two sessions together. One
For some reason, the people doing brew have decided to stop supporting
compiling tcl-tk with X11 support. Not 100% sure, but I'm pretty certain
pymol cannot use tcl-tk with aqua.
If you already had pymol installed, this seems to eliminate the external
gui. If you didn't, new installations of
PyMol doesn’t display any atoms for a region of the protein for the same reason
the rcsb doesn’t for that area. The crystallographer deposited a structure
without coordinates for residues 25-38.
http://www.rcsb.org/pdb/explore/remediatedSequence.do?structureId=1AX8
I think if you install "msgpack-devel”, it will compile and install.
Generally, header files (which is what is included in C++ files) are in *-devel
packages. The regular msgpack package just contains the shared library for use
by programs already compiled against msgpack.
-David
> On Jun 7,
PyMol does not use QM methods. It also does not "determine the structures of
molecules".
-David
> On Jun 1, 2017, at 12:38 AM, Susmita/Rajib wrote:
>
> Thank you, Dr. Tyugashev, for replying to my query.
> Doesn't PyMol also use those QM methods to determine the
It sounds like you may need to change surface mode to include hets
https://pymolwiki.org/index.php/Surface_mode
-David
> On May 24, 2017, at 4:45 AM, 刘艳超 wrote:
>
>
> Dear Madem/Sir,
>
> I am a user of Pymol software. Pymol facilitates me a lot during my study. I
>
Hi,
I maintain the pymol package for openSUSE. I'm considering packaging a
python3 version alongside the python2 version. Are there maintainers of
other distributions that have done so? Do you rename /usr/bin/pymol to
/usr/bin/pymol3 for your python3 version? I'm looking to see if there is a
When debugging, it is good to stop running pymol as a command line app and
just run your script in a pymol gui and see what it is going on.
In this case, you would find your selections have zero atoms. Why? Because
you are basing them on something like "resn 102" , which is using the
residue name
, Ahmad Abdelzaher <underoath...@gmail.com>
>> wrote:
>>
>>> Well I'm assuming the selection goes in the argument of cmd.centerofmass(),
>>> however, does it have to be an atom? How should I calculate the center of
>>> mass for an entire protein?
>>&
It returns the x, y, and z coordinates of the center of mass as a list of 3
floats, presumably in that order?
Is there another question? The page describes the arguments and their defaults
so I am unsure what is lacking.
-David
> On Apr 5, 2017, at 10:29 PM, Ahmad Abdelzaher
The error is due to you not surrounding AlnAB in quotes, so python treats it as
a variable which has not been defined.
That said, align modifies the coordinates of the existing object, the object
created just shows the correspondence of residues used for alignment. To save
the superimposed
https://pymolwiki.org/index.php/Retain_order
> On Nov 14, 2016, at 3:04 PM, Subha K wrote:
>
> Hi There,
>
> Just wondering if there is a way to have the same order of atoms (with that
> of the initial loaded file) while saving a pdb file with pymol?
>
> I came across
https://pymolwiki.org/index.php/Read_Pdbstr
-David
> On Oct 26, 2016, at 3:55 AM, Albert Solernou wrote:
>
> Dear All,
> I was wondering if there was a way to load a PDB file stored in memory
> instead of disk, i. e., a memory file, defined through StringIO or
>
Every time you loop through the list of files, you set X=1 ; you do your X=X+1
in a loop that will only run once ( because glob.glob(“lig.pdb”) is only going
to return a list of length 1 that has lig.pdb) , so you set X=1 , then X=2,
then back to X=1 before you process the next entry. That is
Select the protein you want and the dna, then save the selection as a PDB.
There are many ways to make a selection; visually, the easiest might be:
You said you’ve removed the DNA from the protein-dna complex, so now you should
have:
(1) an object that has just your protein that you want in
Do you have the python code from freemol.org ?
-David
> On Jul 8, 2016, at 7:02 AM, Ioannis Michalopoulos
> wrote:
>
>> On Friday 08 of July 2016 11:10:08 Folmer Fredslund wrote:
>> Dear Ioannis,
>>
>>> On 2016-07-08 09:04, Ioannis Michalopoulos wrote:
>>> Dear PyMOL
http://www.poissonboltzmann.org
psize.py and pdb2pqr.py are part of pdb2pqr
The others are part of apbs
> On Jul 6, 2016, at 5:15 AM, Yanni wrote:
>
> Hello
>
> I'm using pymol 1.7 on OS X 10.11.5.
> XQuartz version: 2.7.9
> python version: 2.7.12
>
>
Feel free to send me the files off list.
-David Hall
> On May 6, 2016, at 1:54 PM, Stephen Kerry <stephen.kerr...@outlook.com> wrote:
>
> Dear All,
>
> I have a protein complex scene that I need to create a large, high resolution
> (1200 dpi) ray traced image of, but
You need to add “,async=0” to your fetch calls.
http://pymolwiki.org/index.php/Fetch
> On Apr 28, 2016, at 4:51 AM, James Starlight wrote:
>
> Hi,
>
> My script is
>
> pdb_array=("1UBI" "1IGD" "1G33" "1CC7" "4LGJ" "5A2H")
> pdb_array_store=$template/pymol
>
>
> #
Make a file at ~/.pymolrc
-David
> On Apr 8, 2016, at 10:35 AM, harold steinberg
> wrote:
>
> where in OS X is pymolrc located?
>
>> On Apr 7, 2016, at 2:39 PM, Thomas Holder
>> wrote:
>>
>> pymolrc
>
> H. Adam Steinberg
> 7904
I think you can use cmd.do
cmd.do("com /DARPin2//A/37-135/CA, object=com2”)
-David
> On Apr 1, 2016, at 8:48 AM, Honegger Annemarie wrote:
>
> Hi!
>
> I am trying to automate some model building tasks
>
> this loop in my pml script works just fine, it generates models
Doesn’t using --install-lib mean you are explicitly telling it to put the files
in your modules directory instead of creating any lib/python type directories?
> On Mar 5, 2016, at 2:50 PM, Albert wrote:
>
> Hello:
>
> I am using the following command line to compile
would something like these work for you?
fetch 1rna, async=0
as cartoon
set cartoon_ring_mode, 1
cartoon skip
show sticks
set cartoon_ladder_mode, 0
> On Jan 28, 2016, at 6:28 PM, COSTA Maria
> wrote:
>
> Hi,
>
> I would like to know if it is possible to
Well, yes, programs do use the CONECT records, including pymol
http://pymolwiki.org/index.php/Connect_mode
Removing bonds is http://pymolwiki.org/index.php/Unbond
Atoms can be translated using the command line
http://pymolwiki.org/index.php/Editing_atoms#Get_coordinates_from_Python
Or in edit
Ubuntu’s universe repository has a 32-bit version of pymol?
http://packages.ubuntu.com/precise/pymol
Obviously, being a 4-year old distro, it is an older release, but it may still
work with the plugin.
-David
> On Jan 6, 2016, at 2:39 PM, Joe Gauthier wrote:
>
>
set_bond stick_color, color, selection
For more info on what is used to create the ball and stick preset, see:
http://sourceforge.net/p/pymol/code/HEAD/tree/trunk/pymol/modules/pymol/preset.py#l144
-David
> On Dec 17, 2015, at 2:35 AM, ANURAG SANKHYAN wrote:
>
> Dear
Try the last comment on:
https://github.com/Homebrew/homebrew-science/issues/2273
-David
On Fri, Dec 11, 2015 at 3:39 AM, Chris Swain wrote:
> Hi,
>
> I maintain a list of science applications that work under El Capitan (
>
http://pymolwiki.org/index.php/Save ??
-David
> On Nov 24, 2015, at 9:45 PM, Smith Liu wrote:
>
> Dear All,
>
> Suppose the original PDB was not oriented. Once we have it oriented by pymol,
> is any way we can save the new PDB oriented?
>
> Smith
>
>
>
>
>
Assuming you are ok with overwriting the B-factors
stored.y=[]
iterate_state 1, prot, stored.y.append(y) % prot here should be replaced
with your pymol object name
alter prot, b=stored.y.pop(0) % again, replace prot with your pymol object
name
On Wed, Nov 18, 2015 at 7:49 AM, Smith Liu
I forgot:
spectrum b
at the end.
On Wed, Nov 18, 2015 at 8:11 AM, David Hall <li...@cowsandmilk.net> wrote:
> Assuming you are ok with overwriting the B-factors
>
>
> stored.y=[]
> iterate_state 1, prot, stored.y.append(y) % prot here should be replaced
> with your p
he PDB and save it as another file? Can you introduce to me a server
of software which can delete the original b-factors in the original PDB and
have the ys pasted on the b-factors positions in the PDB file?
Smith
At 2015-11-18 21:13:05, "David Hall" <li...@cowsandmilk.ne
I would disagree with your assertion that they use pymol to "insert" the
protein into the membrane. They use the program they wrote, g_membed, to
insert the protein. They used pymol to overlap them for the beginning of
the simulation. That is, they use pymol to place the atoms of the protein
on
able from http://freemol.org <http://freemol.org/>
>
> Hans, what Windows version do you use? I can't reproduce this problem on
> Windows 7 or 8.
>
> Cheers,
> Thomas
>
> -Original Message-
>
> David Hall <li...@cowsandmilk.net <mailto:li...@c
there is no mpeg_encode.exe binary.
mpeg_encode, as far as I am aware, has long been abandoned. You can find
what I believe is the last version of the source code (1.5c) at
https://build.opensuse.org/package/show/home:cowsandmilk/mpeg_encode , you
can download by clicking the files with the up
You can set:
pse_export_version
to the 3-part version of pymol you would like to use as an export version.
-David
> On Oct 18, 2015, at 3:48 AM, Takanori Nakane
> wrote:
>
> Hi,
>
> It looks like the structure of PyMOL session (what
> we got from
presumably:
http://sourceforge.net/p/pymol/code/HEAD/tree/trunk/pymol/modules/pymol/preset.py#l164
On Mon, Oct 5, 2015 at 5:42 AM, Clavel wrote:
> Hello everyone,
>
> I would like to create my own command within the pymol environement.
>
> I have currently a set of points in
What version of PyMol are you using?
On Aug 27, 2015, at 7:50 AM, Christian Trindler
christian.trind...@unibas.ch wrote:
Hello,
I’ve been trying to make a pseudoatom/sphere simply by typing:
pseudoatom name
into the command line of Pymol, but it only gives me the following error
I vastly prefer calling the python program from pymol
You can call any python program using pymol as:
pymol -r program.py — arg1 arg2 arg3
Or, my full preferred method is:
pymol -qrck program.py — arg1 arg2 arg3
These make it quieter, stay on the command line, and not read the .pymolrc file
PyMOLrun fitting.py,main
Do I need to import Pymol module in the shell script to use the pymol scripts
like you did in python?
Am I missing something?
Thanks
--
Gazal
On Fri, Jul 10, 2015 at 11:36 PM, David Hall li...@cowsandmilk.net
mailto:li...@cowsandmilk.net wrote:
http
http://www.pymolwiki.org/index.php/Command_Line_Options
http://www.pymolwiki.org/index.php/Command_Line_Options
see the -c and -r options. I also use -q
pymol -qcr script.py — arg1 arg2 arg3
On Jul 10, 2015, at 8:44 AM, Gazal gazal...@gmail.com wrote:
Hi,
I'm trying to find the RMSD
This is the problem.
Pymol’s working directory is not where you have this file. So, the script never
loads.
On Jul 10, 2015, at 12:20 PM, ABEL Stephane 175950 stephane.a...@cea.fr
wrote:
No such file or directory: './loadB2Fact.py'
On Jul 6, 2015, at 10:44 AM, Albert mailmd2...@gmail.com wrote:
Hello:
I am just wondering is it possible to rotate the torsion angle of a
molecule in Pymol? I search in pymolwiki, and I only find how to
translate a molecule or move the atom positions, but I didn't find
anything
PyMol's License can be found at:
http://sourceforge.net/p/pymol/code/HEAD/tree/trunk/pymol/LICENSE
Generally, this is considered a permissive license (
https://en.wikipedia.org/wiki/Permissive_free_software_licence ).
If you plan to use it in a commercial tool, you should pay for a couple
hours
preset.ball_and_stick('r. STI’)
On Apr 23, 2015, at 12:52 PM, Brenton Horne brentonho...@ymail.com wrote:
Hi,
I recently read this reply
(http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg13248.html
There is an INSTALL file that provides instructions. The first step,
calling ./configure , generates pdb2pqr.py from pdb2pqr.py.in
If you want to manually do it, it just changes the first line in the file
to point to your python installation. But, since there's a whole bunch of
other things
you can set cartoon_ring_color ?
On Mar 9, 2015, at 11:20 AM, Quentin Vicens qvic...@unistra.fr wrote:
Hi folks,
I'm wondering how to get rid of the default green shine that's present in the
middle of every ring (see attached snapshot) following commands such as:
spectrum
http://pymolwiki.org/index.php/Ball_and_Stick ?
You used the handmade method on that page. Generally, I like using the
preset better.
On Sun, Feb 1, 2015 at 11:42 PM, Seera Suryanarayana paluso...@gmail.com
wrote:
Dear Pymol Users
I would like to represent the protein what I have in ball and
This occurs when retain_order is set before loading a protein.
You have to:
unset retain_order
Then load your protein again.
You might say: I didn't set retain_order. This is likely true. Some very
popular pymol plugins set it when loaded, most famously the autodock plugin.
-David
On Tue, Jan
On Jan 23, 2015, at 7:32 PM, McCully, Dwayne (NIH/NIAMS) [C]
dmccu...@mail.nih.gov wrote:
When running python setup.py build in the pymol directory of version
1.7.4.0,
I get an error that stops pymol from compiling (see below). Does anyone know
how
to fix this problem.
Dwayne
(2) assuming you didn't change it when installing fink, fink will install
pymol in the /sw/bin directory.
(4) this is fink setting environment variables such as PATH. You can add a
line to your .bashrc to source it so it will be sourced every time you open
a terminal.
On Mon, Jan 19, 2015 at
my experience shows that when you have two HETATM residues one after another,
pymol never shows this bond because the crystallographer never put a CONECT
record for it, which pymol wants.
eg for 1674, there is not CONECT showing 1676 as being bonded and since they
are HETATM , pymol decides to
where are you getting this from? I don’t see a LINE command in
pymol/modules/cgo.py
-David
On Dec 22, 2014, at 11:40 AM, Robert Hanson hans...@stolaf.edu wrote:
OK. I will look at the PyMOL code if I need to. For instance:
LINE has eight parameters. I don't know what the first two
colored by chain
set cartoon_ladder_radius, 2
set cartoon_tube_radius, 2
set ray_trace_mode, 1
-David
On Dec 13, 2014, at 1:22 AM, Jacob Lewis jl...@uowmail.edu.au wrote:
Hi,
Does anyone know how to show DNA like this in pymol?
PastedGraphic-1.tiff
Cheers,
Jacob
I'm a little confused by what PDB assemblies you are talking about that are
distributed as multi-state structures, but assuming they are similar to NMR
models... you can use intra_fit (
http://www.pymolwiki.org/index.php/Intra_fit )
For example, with 2kgx, we start out with chain a in state 1 and
http://www.pymolwiki.org/index.php/Connect_mode
-David
On Oct 6, 2014, at 6:35 PM, Markus Heller mhel...@cdrd.ca wrote:
Hello,
How can I get PYMOL to use the CONECT table from a PDB file? My protein is
glycosylated, and I'd like to properly and automatically display the
glycosides
I am very unsure of your question, but I believe you're asking if you have
a PDB id, how to load that into pymol. For that, you can use the fetch
command ( http://www.pymolwiki.org/index.php/Fetch )
You type:
fetch 1acb
into the pymol interface and it will download pdb id 1acb and load it into
Have you tried doing show as surface
It appears the wrl file has a bunch of extra information from the cartoon
representation, which could confuse shapeways?
-David
On Sun, May 4, 2014 at 4:49 AM, Grateful Frog gratefulf...@gmail.comwrote:
Hi Jared everyone,
First, thanks for all your
set_bond line_color, color_name, n. CA+CB
will color all bonds between CA and CB whatever color you put in as
color_name
If you're doing sticks instead of lines, you should use
set_bond stick_color, color_name, n. CA+CB
-David
On Mon, Mar 3, 2014 at 10:01 PM, I-Ji Jung u5205...@anu.edu.au
I think there's a bug in python's code, not pymol's
In the file that it describes at the end ( C:\Python27\lib\mimetypes.py ) ,
you should change line 250 from:
except UnicodeEncodeError:
to
except (UnicodeEncodeError,UnicodeDecodeError):
keeping the indentation in the file and so on. Then the
I couldn't reproduce the exact error message you received, but I will note:
(1) your splitting of lines leaves out the chain, so chain is never defined
(2) line 9 of your python is missing an opening quotation mark before (resi
matching the closing quotation mark right before the % sign
(3) line
For a definition of TTT , see http://pymolwiki.org/index.php/Object_Matrix
You'll notice that set_object_ttt takes a 16-member list that corresponds to
this matrix.
-David
On Aug 12, 2013, at 11:48 AM, Павел Томашевский croov...@gmail.com wrote:
Thank you Thomas, translate and rotate works
Jason can fill you in if there's an update, but the latest status update I'm
aware of was:
http://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg11572.html
-David
-David
On Monday, July 29, 2013 at 11:04 AM, H. Adam Steinberg wrote:
It would be great if we could control PyMOL
, 2013-04-26 19:15 EDT, David Hall li...@cowsandmilk.net
wrote:
Hi Thomas,
I'm running into issues with color compatibility between 1.6 and
earlier versions when opening pses
(a) when I open any 1.5 pse in 1.6, I see a bunch of errors like:
Setting-Error: type read mismatch (color
by default, macports installs tcl with the +corefoundation variant (see
http://guide.macports.org/#using.variants )
if you do:
sudo port install tcl -corefoundation
that will solve the problem.
-David
On Mon, May 6, 2013 at 8:26 PM, Rhitankar Pal rhitan...@gmail.com wrote:
Dear Thomas,
? Are these issues happening because
OSX 10.8.2 comes with preinstalled tcl and tk ?
Thanks
Rhitankar
On Tue, May 7, 2013 at 12:30 PM, David Hall li...@cowsandmilk.net wrote:
by default, macports installs tcl with the +corefoundation variant (see
http://guide.macports.org/#using.variants
what method did you use for installation?
--
David Hall
On Wednesday, May 1, 2013 at 11:53 AM, Rhitankar Pal wrote:
I am having some issues after installing pymol in Mac OS 10.8.2. It seems
the program is installed but when I try to open in using command line
pymol it doesn't show
Hi Steve,
I'll suggest a workaround to having pymol cache the files:
(1) Install the DropBox app
(2) Favorite your PDB files in that app, this will cache those files
locally within the DropBox app for offline access
(3) From the dropbox app, you can open PDB files in Pymol using the
button in
http://pymolwiki.org/index.php/Set_Key
http://pymolwiki.org/index.php/Extend is also useful.
-David
On Tuesday, October 23, 2012 at 6:02 AM, Boris Kheyfets wrote:
Hello PyMOL users,
Menus
=
Is there a way I can add custom menu in PyMOL?
Ideally I'd like to be able to call
You don't need a license for the open source version.
If you provided details on what OS/distribution you are building on, people may
try to replicate and understand why the python version hung. In my experience,
using setup.py generally worked out of the box.
-David
On Oct 4, 2012, at 9:22
, the same
thing happens. Interestingly, while the desktop background and any app
on the screens are impacted, the mouse cursor is not.
Note, the incentive build PyMolX11Hybrid does not have this problem.
Thanks for any help,
David Hall
The main technology I've seen used for interactive publications is ActiveICM
(see http://www.molsoft.com/activeicm.html#aipub ). In my lab, we regularly
include pymol sessions as supplementary material to help people understand our
results.
-David
On Friday, July 13, 2012 at 6:41 AM, Troels
Hi Suhaila,
Correct me if I'm wrong but you want create *new* GUI elements for
pymol to enhance your application, right?
To my knowledge, there is not a great tutorial on this, but I can give
you some pointers to plugins that do this currently and hopefully you
can backfill some knowledge.
The
On Tue, Mar 20, 2012 at 8:44 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Thomas,
'Wrong', certainly in the context it was given in, is a statement of
judgment. It suggest that there is a failure in the functioning, and
is a criticism to the developer, becoming a wrongdoer. My argument
http://pymolwiki.org/index.php/Axes
-David
On Feb 27, 2012, at 5:38 AM, Gudrun Lotze gudrun.lo...@gmx.net wrote:
Dear all,
is it possible to show in Pymol a little coordinate cross with axes x,y,z,
for example like in VMD, please?
I have a protein made from dummy atoms and there is no
On Mon, Feb 13, 2012 at 2:27 PM, Jason Vertrees
jason.vertr...@schrodinger.com wrote:
Greetings,
It is my pleasure to announce the release of open source PyMOL
v1.5.0.1. The source code has been committed to the open-source
repository. It is revision 3976. An svn tag and downloadable bz2
I think super does not handle nucleic acid sequences well.
super ec-5s, hm-5s, seq=-1
works.
I'll leave it to someone else to say what that does. I just noted
that align works, super doesn't, guessed it had to do with sequence
and noted that for align, the default value of seq was -1 and for
On Fri, Jan 13, 2012 at 4:34 AM, tusi t...@enzim.hu wrote:
Dear All,
After updating to Ubuntu natty (11.04), cmd.do('png filename') does not
work. When I execute the following commands in pymol I get the wanted
png picture:
load tmp.pdb tmp
png tmp.png
but, if I execute the following
about invalid selections because it thinks the selections are
empty.
-David
On Fri, Jan 13, 2012 at 8:37 AM, David Hall li...@cowsandmilk.net wrote:
I think super does not handle nucleic acid sequences well.
super ec-5s, hm-5s, seq=-1
works.
I'll leave it to someone else to say what that does
the builds on
https://build.opensuse.org/package/show?package=pymolproject=devel%3Alanguages%3Apython
for opensuse 11.3 and 11.4 use gcc4.5 successfully. I blame ubuntu or
linux mint.
-David
On Dec 2, 2011, at 10:21 AM, Marius Retegan marius.s.rete...@gmail.com wrote:
Could you please
Assuming you're using a recent version of openSUSE (11.3, 11.4, or
Factory), feel free to grab the svn compiled version from
http://software.opensuse.org/download.html?project=devel:languages:pythonpackage=pymol
-David
2011/9/11 Troels Emtekær Linnet tlin...@gmail.com:
This should get you on
Resolves fine for me.
-David
On Mar 22, 2011, at 12:30 PM, Jason Vertrees jason.vertr...@schrodinger.com
wrote:
Hi Roger,
On Tue, Mar 22, 2011 at 9:20 AM, Roger Rowlett rrowl...@colgate.edu wrote:
Hmm. At the RCSB site, I can see that the ftp server is ftp.wwpdb.org and it
is currently
No idea if this will fix your problem, but what I've found is portable
across binaries from Delano Scientific/Schroedinger and
OS/self-compiled versions of pymol is to instead run:
pymol -r examply.py -- mymolecule.xyz
(or if I'm making pngs, usually pymol -qrck examply.py -- mymolecule.xyz )
Jmol certainly is not the only thing able to do that.
In the applet world, you have at least OpenAstexViewer
http://openastexviewer.net/web/ , but I also imagine it is possible to build a
(jogl-accellerated) applet using jymol http://www.pymol.org/jymol , but I'm
fairly certain it is not open
Has anyone else run into a problem with label_size in pymol 1.3 on
Mac? For both my fink and macports build, it doesn't work. The
baseline of the text moves, but the size doesn't change.
It does work when I compile from pymol trunk on my linux box. I don't
see anything in the changelog or svn
. If they support non-orthogonal DX
maps out of the box, that might be a quick and easy solution.
Cheers,
-Michael
On Fri, Oct 15, 2010 at 5:51 PM, David Hall li...@cowsandmilk.net wrote:
I have long been happy reading .dx files produced by apbs and my own
programs into pymol. Everything works great
I have long been happy reading .dx files produced by apbs and my own
programs into pymol. Everything works great.
Interestingly, when I save a .dx file from OpenDX (http://opendx.org),
pymol seems to not be able to read it.
I've attached two files that come from OpenDX's samples directory
where
In preparing my test for the odd request that I just sent, I came
across what seems to be a bug in super. It has to do with this weird
nucleic acid thing I was talking about.
Here's the script this time:
from pymol import cmd
cmd.fetch('1acb', async=0)
cmd.fetch('1acb', '1acb_2', async=0)
I realize this is an edge case, where behavior is not always well
defined in programs, but I have a request for a behavior (and the
behavior actually seemed to change between 1.2 and 1.3)
My example script:
from pymol import cmd
cmd.fetch('1acb', async=0)
cmd.fetch('1acb', '1acb_2', async=0)
The quick answer is Don't use an evaluation build.
You have 3 main options:
1) become a sponsor and get builds of the latest code
http://pymol.org/funding.html
2) use the free builds that are several years old http://pymol.org/rel/099/
3) build pymol from source. There are instructions on
Is it possible to load a pdb file and have pymol skip making bonds?
There's a bunch of undocumented options to load, but I don't think any
of them do what I want. I have a file where there's a bunch of
jumbled atoms and there's no relation between them, just thousands in
the same place and pymol
actually, you can ignore this email, it seems pymol was having issues
because there were a bunch of CONECT records, if I delete those, pymol
actually loads it really fast. Kind of odd behavior, but interesting.
-David
On Thu, Apr 22, 2010 at 2:14 PM, David Hall li...@cowsandmilk.net wrote
.
-David
On Thu, Apr 22, 2010 at 2:43 PM, Jason Vertrees
jason.vertr...@schrodinger.com wrote:
Hi David,
Check out the connect_mode setting:
set connect_mode, 1
# no bonds
fetch 1cll
Cheers,
-- Jason
On Thu, Apr 22, 2010 at 2:14 PM, David Hall li...@cowsandmilk.net wrote:
Is it possible
I think what you're asking for is one of the examples included in the
PyMol source code. You can do this manually using the mutagenesis
wizard, but it is possible to drive this wizard through scripts. The
two examples can be found at:
I think you'll be saddened to discover that if you try what Petr (the
original poster) was doing, sys.argv[0] won't work.
$ cat test.py
print sys.argv[0]
$ pymol -qrc test.py
PyMOLrun test.py,main
/sw/lib/pymol-py26/modules/pymol/__init__.py
This quite clearly gives the behavior that Petr had
The error below shows that you don't have gcc, which means you have to
install Apple's Developer tools to compile pymol.
That said, the easiest way right now is probably using macports.
Follow the instructions at http://www.macports.org/install.php for
installing macports, then you can run port
rms and fit gave you different values? They have never given me different
values.
Example:
from pymol import cmd
cmd.fetch('1nmr')
cmd.split_states('1nmr')
for i in xrange(1,21):
for j in xrange(1,21):
prot_i = '1nmr_%04d' %i
prot_j = '1nmr_%04d' %j
rms_val =
to be currently running Fedora or even Linux to
participate. So, if you have some time to spare this week, you can
run all the tests on your system and hopefully help move open source
graphics on linux forward.
Announcement and details can be found at:
http://lwn.net/Articles/383156/
-David Hall
I know little of the apbs-pymol integration, but in general, you can
use the PROPKA support built into PDB2PQR to assign protonation at
different pHs and then feed your pqr to apbs.
See http://www.poissonboltzmann.org/pdb2pqr/user-guide/using-pdb2pqr
for the --with-ph option.
There's also a
1 - 100 of 133 matches
Mail list logo