Hi!
I wonder if it is possible with a cmd.set(something) to change the length
of allowed string length of objects name.
As far as I can count, it is now possible with 16 characters.
I would like to change this to 20 or so.
Best
Troels
Hi.
I wonder if it is possible to interact with the mutagenesis wizard from the
command line?
I am trying to determine best mutants for FRET labelling, by predicting the
pka value/reactivity for a possible cysteine.
I would like to make a script that loops over the residues in my protein,
A).splitlines()[3]
print cmd.identify(chain A and name N)[0]
print cmd.identify(chain A and name C)[-1]
Troels Emtekær Linnet
Karl-Liebknecht-Straße 53, 2 RE http://maps.google.dk/
04107 Leipzig, Tyskland
Mobil: +49 1577-8944752
2011/8/22 Yotam Avital yota...@gmail.com
Hi.
I have a xyz file
number, pymol assign an internal index.
This is handsome, if your xyz file, pdb file does not have an id.
Troels Emtekær Linnet
Karl-Liebknecht-Straße 53, 2 RE http://maps.google.dk/
04107 Leipzig, Tyskland
Mobil: +49 1577-8944752
2011/8/22 Yotam Avital yota...@gmail.com
The xyz http
propka
Troels Emtekær Linnet
Karl-Liebknecht-Straße 53, 2 RE http://maps.google.dk/
04107 Leipzig, Tyskland
Mobil: +49 1577-8944752
2011/8/22 Martin Hediger ma@bluewin.ch
**
Hi Troels
It's indeed possible.
The wizards are available through the cmd module.
# Initialize
load
Thanks!
Your comments are gold!
I put the warning on the propka page.
http://pymolwiki.org/index.php/Propka#Mutagenesis_analysis
Best
Troels
Troels Emtekær Linnet
Karl-Liebknecht-Straße 53, 2 RE http://maps.google.dk/
04107 Leipzig, Tyskland
Mobil: +49 1577-8944752
2011/8/22 Martin Hediger
Hi PyMOL'ers.
I am happy to announce, that I have finished working on a script that
fetches the pKa values of your protein.
The script contacts, download results, processes the files, and write a
pymol command that make pka atoms, labels,
colors, bonds, distances and such.
See more here:
Hi.
If one writes a pymol script, and calls an external function, the pymol
script continues its operation before waiting for the success of the
external function.
Is it possible to give a keyword, so it waits for the external function
before preceding?
Kind of the same function with:
fetch
])
if / in rawinputstring:
rawinputstring = rawinputstring.split(/)
answer = float(rawinputstring[0])/float(rawinputstring[1])
print(Your answer you long for is:%s%(answer))
23.08.2011 15:55, Troels Emtekær Linnet yazmış:
Thats because the raw_input is a string
would be happy to
hear about it.
Troels Emtekær Linnet
Karl-Liebknecht-Straße 53, 2 RE http://maps.google.dk/
04107 Leipzig, Tyskland
Mobil: +49 1577-8944752
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Thanks, but as you say, it is not working. :-)
Another one out there?
Best
Troels
Troels Emtekær Linnet
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04107 Leipzig, Tyskland
Mobil: +49 1577-8944752
2011/8/24 Thomas Juettemann juettem...@gmail.com
Hi Troels,
about 8 month again I
Hi.
I was very happy to find a post how to easy install pymol 1.4 from source on
windows.
1) Install python, 2.5, or 2.6 or 2.7 for windows.
2) Download appropriate installer from:
http://www.lfd.uci.edu/~gohlke/pythonlibs/#pymol Select according to your
python version.
3) Run it
4) PyMOL is
:\\Python27\\PyMOL\\PyMOL.cmd\ %*
2011/8/24 Troels Emtekær Linnet tlin...@gmail.com
Hi.
I was very happy to find a post how to easy install pymol 1.4 from source
on windows.
1) Install python, 2.5, or 2.6 or 2.7 for windows.
2) Download appropriate installer from:
http://www.lfd.uci.edu/~gohlke
Check this, and tell if it works.
http://pymolwiki.org/index.php/Matrix_Copy
Troels Emtekær Linnet
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04107 Leipzig, Tyskland
Mobil: +49 1577-8944752
2011/8/25 Bjoern-oliver Gohlke
bjoern-oliver.goh...@student.uni-tuebingen.de
The error I
don't want the logtime function
propka.propka(molecule=resi[0],resi=resi[1],logtime=i)
cmd.refresh()
i = i + 1
python end
zoom all
hth
Martin
On 23.08.11 10:48, Troels Emtekær Linnet wrote:
Hi.
If one writes a pymol script, and calls an external function, the pymol
script
that function.
It's about 3 AM my time and I'm sure there's a better solution--but
this might work for now.
Cheers,
-- Jason
2011/8/26 Troels Emtekær Linnet tlin...@gmail.com:
Well, I cant get it to work.
Pymol speeds ahead of calling propka.propka
Can you give an example
a coordinate point.
- crossprod(Vector1, Vector2): Makes a crossproduct between two vectors
- crosspoint(Pos1, crossprod): Returns the endpoint for the Position plus
the crossproduct vector. Suitable if one would like to rotate around a
crossvector.
Best
Troels Emtekær Linnet
So.
cmd.(something) ALWAYS has to be in string format.
So there is the cmd.frame wrong.
Then you dont quit the mutagenesis wizard
And you have a space in the cmd.save
*It total, try:*
#Initialize
fetch 1shr, async=0
create test, 1shr
cmd.wizard(mutagenesis)
cmd.do(refresh_wizard)
# Mutate
You have to make .pml file and put the python commands inside pymol blocks.
Try look here for an example.
http://www.pymolwiki.org/index.php/Propka#Mutagenesis_analysis
Troels Emtekær Linnet
Karl-Liebknecht-Straße 53, 2 RE http://maps.google.dk/
04107 Leipzig, Tyskland
Mobil: +49 1577-8944752
Well, not hard.
I made a script that can rotate a molecule around a line.
And I made a large tutorial to take one through the available functions of
this script.
It is a pymol command file, .pml.
Check out:
http://www.pymolwiki.org/index.php/Rotkit
Troels Emtekær Linnet
Karl-Liebknecht-Straße
Have you tried
delete all and not obj1
Troels Emtekær Linnet
Karl-Liebknecht-Straße 53, 2 RE http://maps.google.dk/
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Mobil: +49 1577-8944752
2011/9/13 Андрей Гончар gontc...@gmail.com
Hi all! I have a question about wildcards usage in pymol.
For example if I want
)
### Select frame 1, which is most probable
cmd.frame(1)
cmd.get_wizard().apply()
### Stop the wizard
cmd.set_wizard(done)
python end
Troels Emtekær Linnet
2011/9/22 Fabio Gozzo fgo...@gmail.com
Hi Pymolers,
I need to perform a batch operation but I need a help with script
And to save it, add this python block
python
for PDB in PDBs:
cmd.save(%s-K.pdb%PDB,%s%PDB)
python end
Troels Emtekær Linnet
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04107 Leipzig, Tyskland
Mobil: +49 1577-8944752
2011/9/22 Troels Emtekær Linnet tlin...@gmail.com
# Firs
If you need rotations around an line, instead of axis, check out
http://www.pymolwiki.org/index.php/Rotkit
Troels Emtekær Linnet
Karl-Liebknecht-Straße 53, 2 RE http://maps.google.dk/
04107 Leipzig, Tyskland
Mobil: +49 1577-8944752
2011/10/7 kanika sharma ksharma...@gmail.com
Hello everyone
. rotate it at a atep of 60 degrees till 240 degree..
2011/10/8 Troels Emtekær Linnet tlin...@gmail.com
If you need rotations around an line, instead of axis, check out
http://www.pymolwiki.org/index.php/Rotkit
Troels Emtekær Linnet
Karl-Liebknecht-Straße 53, 2 RE http://maps.google.dk
#Running_PyMOL_in_batch_mode
pymol -cq
Troels Emtekær Linnet
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04107 Leipzig, Tyskland
Mobil: +49 1577-8944752
2011/10/17 grantaka36 grantak...@gmail.com
Hi Thomas,
I appreciate your advice very much, testing and cannot find green
signal yet as [2
What version do you have installed?
Troels Emtekær Linnet
Karl-Liebknecht-Straße 53, 2 RE http://maps.google.dk/
04107 Leipzig, Tyskland
Mobil: +49 1577-8944752
2011/10/17 Tao-wei Huang yelve...@gmail.com
Hi all,
I have problems with starting pymol in ubuntu. When I started it from
?
Can it be done faster with the MPEG method?
Best
Troels
Troels Emtekær Linnet
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4300 Holbæk
Mobil: +45 60210234
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http://p.sf.net/sfu/rsa
(http://www.videolan.org/) or ffmpeg
(http://ffmpeg.org/) now. If the PyMOLWiki's out of date, please feel
free to update it.
Cheers,
-- Jason
2011/11/8 Troels Emtekær Linnet tlin...@gmail.com:
Hi.
I have made a nice little movie in Pymol.
1500 frames.
So now I am wondering what
Hi Pymolers.
I sometimes find small errors in my scripts, which I then correct.
But then I get a little sad, that now my unfinished script still lives
out there.
So I think, why is the pymolwiki scripts not under subversion control?
Then authors could push corrections to their scripts to the
experience should throw in some experience. :-)
Best
Troels
Troels Emtekær Linnet
Slotsvej 2
4300 Holbæk
Mobil: +45 60210234
2011/11/10 Jason Vertrees jason.vertr...@schrodinger.com
Hi Justin,
I started this some time ago and also announced it on the mailing list.
But
it didn't caught
Hi Gals and Gils.
I have struggled with making a movie easy and fast. The MPEG way is just
snappy snappy fast.
I was pleased to see that installation instructions has been updated for
the pymol open source.
I added installation instructions (Ubuntu/Mint) with MPEG support for the
opensource
Using pseudo atoms
http://www.pymolwiki.org/index.php/Pseudoatom
using pos=
pseudoatom tmpPoint2, resi=40, chain=ZZ, b=40, color=tv_blue, pos=[-10, 0, 10]
Troels Emtekær Linnet
Slotsvej 2
4300 Holbæk
Mobil: +45 60210234
2011/11/14 ABEL Stephane 175950 stephane.a...@cea.fr
Dear all,
I
of file in front of
function
Area=forster.numintegrator(fluarray, col1=0, col2=1)
Best
Troels
Troels Emtekær Linnet
Slotsvej 2
4300 Holbæk
Mobil: +45 60210234
2011/11/23 James Starlight jmsstarli...@gmail.com
Thanks Thomas!
Those scripts works fine. Could you tell me if there any way
Have you told PyMOL to import the functions from a module?
What have you written in PyMOL?
/T
Troels Emtekær Linnet
Slotsvej 2
4300 Holbæk
Mobil: +45 60210234
2011/11/24 James Starlight jmsstarli...@gmail.com
Dear PyMol Users!
I've decided to make this topic for all questions wich could
of python.
Please consider how you ask questions.
Best
Troels
Troels Emtekær Linnet
Slotsvej 2
4300 Holbæk
Mobil: +45 60210234
2011/11/24 James Starlight jmsstarli...@gmail.com
Troels,
no I just typed command name
cealign ref, target
on another loptop I have more modern version
Try Following this script.
http://www.pymolwiki.org/index.php/Linux_Install#Ubuntu.2FMint_Compile_and_install_with_MPEG_support
Please report if you are successful.
It would be interesting to see how it works on CentOS
/T
2011/12/2 grantaka36 grantak...@gmail.com
Referring the following,
.
Cheers,
Marius
2011/12/2 Troels Emtekær Linnet tlin...@gmail.com:
Try Following this script.
http://www.pymolwiki.org/index.php/Linux_Install#Ubuntu.2FMint_Compile_and_install_with_MPEG_support
Please report if you are successful.
It would be interesting to see how it works on CentOS
Hi.
I sometimes see, that you can do
select polymer
select organic
Is there a list somewhere with these keywords and what they select?
Best
Troels
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Troels,
pymol/layer3/Selector.c near line 355.
Cheers,
-- Jason
2011/12/4 Troels Emtekær Linnet tlin...@gmail.com:
Hi.
I sometimes see, that you can do
select polymer
select organic
Is there a list somewhere with these keywords and what they select?
Best
Troels
Hi Andrew.
I experienced something similar for the autodock_plugin.
http://www.pymolwiki.org/index.php/Autodock_plugin
During my trials, I notified two things for autodock.
It did not like funny atom names or Alternative configuration
Could this be a case for your protein / ligand?
I don't know
Can this plugin solve it:
http://www.pymolwiki.org/index.php/Rotamer_Toggle
Note, that you have to collect the script yourself, and replace
the original pymol menu.py file.
Not a easy solution to problem.
Note, it the script: http://www.pymolwiki.org/index.php/Rotkit
You can mutate through a
Hi guys.
I am trying to use the plugin: MSMShttp://www.pymolwiki.org/index.php/Msms on
a win machine.
The plugin is dependent on a shell script: pdb_to_xyzrn
But I cant execute it on a win machine, and I won't install cygwin.
Can someone help me convert the shell script to a python script?
Or
Case closed.
Thanks to Hongbo Zhu for a solution.
Best
Troels
2011/12/12 Troels Emtekær Linnet tlin...@gmail.com
Hi guys.
I am trying to use the plugin: MSMShttp://www.pymolwiki.org/index.php/Msms
on
a win machine.
The plugin is dependent on a shell script: pdb_to_xyzrn
But I cant
Or just use this script
http://www.pymolwiki.org/index.php/RemoveAlt
Troels Emtekær Linnet
Slotsvej 2
4300 Holbæk
Mobil: +45 60210234
2011/12/13 Joel Tyndall joel.tynd...@otago.ac.nz
Mark,
You could always simply edit the pdb file (remove the trans option).
Simply open up the pdb file
or so.
/T
Troels Emtekær Linnet
Slotsvej 2
4300 Holbæk
Mobil: +45 60210234
2011/12/15 James Davidson j.david...@vernalis.com
**
Dear All,
I am currently having a problem with the distance command when applied to
merged objects. The real case is actually when I remove a ligand from
2011-12-19 12:32:21.901 Python[243:5d03] *** Terminating app due to
uncaught exception 'NSInvalidArgumentException', reason*:
'-[GLUTApplication _setup:]:* unrecognized
--
Do you have glut installed ?
Hi Vivek.
I will suggest looking at:
http://pymolwiki.org/index.php/Rotkit
Best
Troels Linnet
2011/12/29 Jason Vertrees jason.vertr...@schrodinger.com
Vivek,
Yes, it is. Please read the web page I suggested.
Cheers,
Jason
Sent from my android.
On Dec 28, 2011 9:04 PM, Vivek Ranjan
Hi Thomas.
Great work!
That looks like a real handsome plugin.
I succeded to get some of the scripts from the git repository to work out
of the box. :-)
And I love the info box.
But I see some funny behavior, which you probably are working on hard
alreadt.
1) New click boxes open behind the
or so.
So, in somehow the subversion home-build pymol, is using the paths from the
pre-installed librabries.
I used this recipe, when i builded pymol:
http://www.pymolwiki.org/index.php/Linux_Install#Ubuntu.2FMint_compile_and_install_with_MPEG_support
I must have good something wrong.
Troels Emtekær
Venkatramanan Krishnamani.
How about posting it on http://www.pymolwiki.org/index.php/Category:Plugins
Then it will newer get lost. :-)
Best
Troels
Troels Emtekær Linnet
Slotsvej 2
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Mobil: +45 60210234
2012/1/13 Venkatramanan Krishnamani ve...@andrew.cmu.edu
hi everyone,
I
Have you checked the right path?
Write in pymol cmd.
pwd
And check if the file is there.
Could it be that easy?
Troels Emtekær Linnet
Slotsvej 2
4300 Holbæk
Mobil: +45 60210234
2012/1/13 tusi t...@enzim.hu
I have got the same result: no png image has been generated.
Can you try doing
Hi you all.
I need to build a cys residue for a script, to align it to a residue.
I am looking at the command: frag cys
cmd.do(frag cys)
but by script does not wait for frag to complete, and speed on.
Is there a cmd.frag ?
Or how can i find more information on frag?
Cheers
Found it.
cmd.fragment
under modules/pymol/creating.py
Troels Emtekær Linnet
Slotsvej 2
4300 Holbæk
Mobil: +45 60210234
2012/1/13 Troels Emtekær Linnet tlin...@gmail.com
Hi you all.
I need to build a cys residue for a script, to align it to a residue.
I am looking at the command: frag
Hi James.
I moved the script under the git repository yesterday, and took care of the
bug.
The script look a little different now.
So try the new one again from:
http://www.pymolwiki.org/index.php/findseqhttp://www.pymolwiki.org/index.php/Findseq
The follow the guide on the page.
# Find the
Maybe this could be interesting to.
http://www.pymolwiki.org/index.php/Color_by_conservation
This script reads an alignment object and colors the protein objects in the
alignment by the sequence conservation found in the alignment.
I tried to update a little list with the different methods
or
@ script.py
from PyMol shell!
then I use script_command ( e.g findSeq ) and further script syntax for my
tasks
e.g findSeq s.g 1f88
works perfect but
the above command for the ensemmble of pdbs give me error.
James
2012/1/16 Troels Emtekær Linnet tlin...@gmail.com
It depends
looks very
easy.
I normally have only seen Jmol application for this:
http://www.proteopedia.org/wiki/index.php/4ins
God work!
Troels Emtekær Linnet
Slotsvej 2
4300 Holbæk
Mobil: +45 60210234
2012/1/16 Takanori Nakane t.nak...@mail.mfour.med.kyoto-u.ac.jp
Dear Pymol users,
I wrote a Pymol
There is now a description available at:
http://pymolwiki.org/index.php/Pymol2glmol
If you use a webpage for teaching, you should really try this plugin out.
/Troels Linnet
2012/1/16 Takanori Nakane t.nak...@mail.mfour.med.kyoto-u.ac.jp
Dear Pymol users,
I wrote a Pymol script to export
I am not able to reach the site?
Is it down?
Troels Emtekær Linnet
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Emtekær Linnet tlin...@gmail.com:
I am not able to reach the site?
Is it down?
Troels Emtekær Linnet
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Hi guys.
Ehh. I have a newly installed Mint 12 box with gnome 3.
I have that annoying thing, that when I click a text .pdb files, it opens
with gedit.
Then I can right click and select .pdb files to open with pymol.
But when I then click a .txt file, it opens it with pymol.
Grrr...
I know its
/
If you want to visualize the pKa, try this Pymol script.
http://www.pymolwiki.org/index.php/Propka
Troels Emtekær Linnet
Lyongade 24. 4.mf, 2300 København S
Mobil: +45 60210234
2012/2/3 Xiaoshan Min xs...@yahoo.com
Hi Pymoler,
I want to present a structure to non-structural biologist
Hi.
I have a pdb file, which is a modelled structure from another sequence.
I want to check the amino acid sequence in the structure.
Does anyone know a one-liner in pymol which will extract the sequence
in one-letter code?
best
Troels
Thanks!
I put it on the wiki:
http://pymolwiki.org/index.php/Get_fastastr
Cheers
2012/2/8 Thomas Holder spel...@users.sourceforge.net
print cmd.get_fastastr('all')
Cheers,
Thomas
On 02/08/2012 03:24 PM, Troels Emtekær Linnet wrote:
Hi.
I have a pdb file, which is a modelled
Hi.
We have builded svn pymol at our unilabs linux computers.
Is there a way to tell pymol it should look for .pymolrc and .pymolrc.py
other places than the users home library?
Or can you run the commands in these files in another way?
Best
Troels
Thanks!
It worked. :-)
Troels Emtekær Linnet
2012/2/13 Justin Lecher j.lec...@fz-juelich.de
On 13.02.2012 20:27, Jason Vertrees 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
Troels Emtekær Linnet
Lyongade 24. 4.mf, 2300 København S
Mobil: +45 60210234
2012/2/14 Thomas Stout tst...@exelixis.com
Hi All -
I am trying to compile the open-source code for PyMOL for the first time
(on CentOS) and running into all sorts of issues. Is there a listing
somewhere
If you need publication citation, I would go for the
Cealign ww.pymolwiki.org/index.php/Cealign
There is references you can read and understand. :-)
See a list of alignment methods and tools
http://www.pymolwiki.org/index.php/Align#SEE_ALSO
Best
T
Troels Emtekær Linnet
Lyongade 24. 4.mf
Hi.
I can confirm that you can compile pymol 1.5.0.1 on RHEL 6, with python
2.6.6 from the RHEL repositories.
http://www.pymolwiki.org/index.php/Linux_Install#Red_Hat_Enterprise_Linux_RHEL_6_compile_and_install_with_MPEG_support_for_x86_64_bit
Still splash screen 1.3.x ... Funny bug.
Best
You can see the requirements here:
http://www.pymolwiki.org/index.php/Linux_Install#Red_Hat_Enterprise_Linux_RHEL_6_compile_and_install_with_MPEG_support_for_x86_64_bit
Troels Emtekær Linnet
Lyongade 24. 4.mf, 2300 København S
Mobil: +45 60210234
2012/2/24 Andreas Förster docandr...@gmail.com
Hi pymolers.
I was trying to test our lab pymol installation from home.
But i ran into an error in freeglut, when executing over SSH.
I have found a solution, but is unsure what it does, and if means something
for
speed and 3D rendering.
*When I ran:*
*[software@elvis ~]$ pymol*
*freeglut
Try install tkinter
Tkinter uses tcl 8.4 (something...)
Troels Emtekær Linnet
Lyongade 24. 4.mf, 2300 København S
Mobil: +45 60210234
2012/2/27 greipel.joac...@mh-hannover.de
Hi Jason,
I just installed pymol 1.5.0.3 on our linux machines and the segfault in
libtcl8.5.so upon help-about
Sorry for being rude, it was not meant in that way.
I was just puzzled by the fact, that you would be graded higher if you
don't use the command line.
That is just weird.
Back to the question.
Suhaila, you should try to explore the action button.
First get a protein, which is good to
Have you tried this:
http://www.pymolwiki.org/index.php/Examples_of_nucleic_acid_cartoons
Best
Troels Emtekær Linnet
2012/4/2 Francis E Reyes francis.re...@colorado.edu
Tricky one I tried hide cartoon, name P but no go..
instead cartoon skip will do it.
On Apr 2, 2012, at 2:50 PM
If you have some name scheme for your molecules, you could figure it out
from this:
You want to make a python block:
python
do python code here
python end
Then define a loop, and figure out to call your naming scheme.
Do a calculation, and add the result to an array or something.
Hi.
I tried to compile the latest svn -rev 3998.
I think I have problem with the MyPNG.c file?
($HOME/pymolsvn2/svnpymol/layer0/MyPNG.c)
It is referring to *png.h* which I believe is in the package: *libpng-devel*
I have a RHEL 6.2 system.
I cant find it in the RHEL repositories, epel and
,
-- Jason
On Wed, May 16, 2012 at 12:00 PM, Troels Emtekær Linnet
tlin...@gmail.com wrote:
Hi.
I tried to compile the latest svn -rev 3998.
I think I have problem with the MyPNG.c file?
($HOME/pymolsvn2/svnpymol/layer0/MyPNG.c)
It is referring to png.h which I believe is in the package
Troels Emtekær Linnet
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How about using python blocks:
python
resis = [[1DSB,*,30,red],[1ERT,*,32,green]]
for p,c,r,col in resis:
cmd.fetch(p,async=0)
cmd.refresh()
cmd.show(cartoon,p) cmd.color(col,p)python end
2012/6/18 Yotam Avital yota...@gmail.com
I may have asked this question
project to pursue?
Best
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PhD student
SBiNLab, Copenhagen University
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threat landscape has changed
.
The Uniprot_features http://pymolwiki.org/index.php/Uniprot_features is
probably what I am looking for.
So I will try that out.
Best
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2012/7/14 Thomas Holder spel...@users.sourceforge.net
indeed, the SITE records could easily be parsed and made available as
named selections.
Similar
Once again Thomas Holder have done a very nice work, and made a solution.
Check it out here:
http://www.pymolwiki.org/index.php/Select_sites
fetch 1sgt, async=0import select_sites
select_sites
It works really brilliant.
Best
Troels Emtekær Linnet
2012/7/14 Troels Emtekær Linnet tlin
*
*c:\python27\pymol\pymol-script-repo\modules\mole\whrandom\random.py*
The package is included in the project Pymol-script-repo project.
http://www.pymolwiki.org/index.php/Git
http://www.pymolwiki.org/index.php/Git_install
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Troels
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/pymollib
export LIBGL_ALWAYS_INDIRECT=no
/usr/bin/python /xxx/software/pymolsvn/modules/pymol/__init__.py $@
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2012/7/24 Matthew Baumgartner mp...@pitt.edu
Hi,
I wrote a short script that I am going to use
],chainresnresi3[i][3])
cmd.get_wizard().do_select(selection)
cmd.frame(1)
cmd.get_wizard().apply()
python end
cmd.set_wizard(done)
*pdb1.fasta*
pdb1
CVGLTSW
*pdb2.fasta*
pdb2
ALTWSIK
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2012/9/14 Maurício
(my_protein, my_objects[i], 1, (i+1))
cmd.remove(my_objects[i])
cmd.delete(my_objects[i])
python end
show_as cartoon, my_protein
save my_protein.pdb, my_protein, state=0
set movie_fps, 1
mplay
-
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Mobil
of OGA and chain B
show sticks, OGA_*
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2012/9/29 Mona Kab Omir kzq...@alumni.ku.dk
Hei
I have a question about how to introduce hydrogen bonds between ligands
and target molecule in pymol that runs on linux
, 0)*
*print cmd.get_setting_text('depth_cue')*
*
*
*#set ray_shadows, off*
*print cmd.get_setting_text('ray_shadows')*
*cmd.set(ray_shadows, off)*
*print cmd.get_setting_text('ray_shadows')*
*
*
*#ray 1280,1024*
*#cmd.ray(1280,1024)*
*
*
*#png 1dw1.png*
*#cmd.png(1dw1.png)*
Troels Emtekær Linnet
be meaning full on CentOS ?
Please report how it goes :-)
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2012/9/27 Christian Roth christian.r...@bbz.uni-leipzig.de
Dear all,
we have with our system Ubuntu a problem with APBS in the new pymol 1.5.
We
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What is the atom name of EFP.ligand:A:EFP999?
Can you check your pdb file? Do you rename them before running the plugin?
Den 26/10/2012 23.26 skrev Ragnar Thomsen rthoms...@gmail.com:
I have a problem when running the autodock plugin for PyMOL. I followed the
tutorial at
if those fragments are surface exposed or
internal.
What tools does pymol have to find out if the residues are surface exposed?
Or is there another easy tool?
Best
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Thanks!
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2012/10/31 Abdullah Kahraman abdul...@imsb.biol.ethz.ch
Dear Troels,
Personally I don't use PyMol for this problem. Rather I use the
application NACCESS (http://www.bioinf.manchester.ac.uk/naccess
Hi mehdi.
Look for inspiration here.
http://www.pymolwiki.org/index.php/Dynamic_mesh
fetch 1HWK, async=1
fetch 1HWK, 1hwk_map, type=2fofc, async=1
Best
Den 01/11/2012 18.09 skrev Mehdi Talebzadeh Farooji mahdi...@yahoo.com:
Dear All,
I am trying to create a electron density map for the pdb
might also want to try this.
That is the repository with all scripts from Pymolwiki, to work out of the
box.
http://pymolwiki.org/index.php/Git_intro
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2013/1/3 Andreas Förster docandr...@gmail.com
Dear all
How about.
import select_sites
sites 1a3l
set_bond stick_radius, 0.1, resi 213
extract Fe_atom, resi 213 and name Fe
Wiki
http://www.pymolwiki.org/index.php/Select_sites
http://www.pymolwiki.org/index.php/Set_bond
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Troels
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$@
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2013/2/7 m.r...@5-cent.us
Hi, folks,
If there's a howto or FAQ on this, please give me a pointer.
We've recently install pymol on several systems. We're running CentOS 6.3
Hi Michael.
Something similar has been made to show the SITES labels of a pdb file,
for quick referencing of a crystal structure.
http://pymolwiki.org/index.php/Select_sites
You could look into how that is written, and provide something similar for
an NMR structure?
Best
Troels
Troels Emtekær
There should be No asterixs.
I tried to mark the part in bold via email.
best
2013/2/12 mark m.r...@5-cent.us
On 02/11/13 09:30, Troels Emtekær Linnet wrote:
Hi.
Well, I don't know really what you wan't, but I remember pain with
graphics and computers. :-)
I see the same error (X
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