Might I recommend a conda based solution.
https://installpython3.com/chromebook/ <https://installpython3.com/chromebook/>
Install miniconda on your Chromebook using the attached link.
Then you can simply use conda to install pymol
conda install -c schrodinger pymol
Jordan Willis, PhD
Probably could use load_object instead.
def load_object(type,object,name,state=0,finish=1,discrete=0,
quiet=1,zoom=-1,_self=cmd):
'''
DESCRIPTION
"load_object" is a general developer function for loading Python objects
into PyMOL.
> On Oct 26, 2016, at
If you really want to use pymol, this works
#!/bin/bash
#myscript.bash
for i in `cat $1` ; do pymol -d "fetch $i" -c ; done
Then on the command line
>chmod +x myscript.bash; ./myscript.bash mylist.txt
> On Apr 27, 2016, at 2:55 AM, Jordan Willis wrote:
>
> Must you
Must you use pymol?
Try directly from the PDB
#!/bin/bash
#myscript.bash
for i in `cat $1` ; do wget http://www.rcsb.org/pdb/files/${i}.pdb ; done
Then on the command line
>chmod +x myscript.bash; ./myscript.bash mylist.txt
J
> On Apr 27, 2016, at 2:41 AM, James Starlight wrote:
>
> D
Hi,
Is there a way to iterate through the names that have been grouped?
iterate
doesn’t seem to do it because it kills my pymol app.
Jordan
--
Site24x7 APM Insight: Get Deep Visibility into Application Performance
APM
an get
> this oriented pdb?
>
> Smith
>
>
>
>
>
> At 2015-11-28 15:37:10, "Jordan Willis" wrote:
> get view takes in camera coordinates. You can’t open a PDB and it have know
> anything about the camera view. You will have to grab the view, save it
> s
> <http://www.pymolwiki.org/index.php/Transform_selection> there is another
> script.
>
> I do not know how to use this scripts to realize my purpose.
>
> Smith
>
>
>
>
>
>
>
>
> At 2015-11-28 15:07:18, "Jordan Willis" wrote:
&
ed.py"
> does not work?
>
>
> Smith
>
>
>
>
>
> At 2015-11-28 13:11:25, "Jordan Willis" wrote:
> try running
>
>
> find ~/ -name “newpdb.pdb”
>
>
>> On Nov 27, 2015, at 9:08 PM, Smith Liu > <mailto:smith_liu..
try running
find ~/ -name “newpdb.pdb”
> On Nov 27, 2015, at 9:08 PM, Smith Liu wrote:
>
>
> Dear All,
>
> Osvaldo is new here for this question, so I repeat it a little. By pymol I
> open a pdb and orient it and I want to save the oriented pdb. First I input
> command "orient" after lo
ller named
> MacPyMOL-v1.7.x.x-syspython.dmg). It simply does not bundle a Python
> distribution, but uses /usr/bin/python2.7 to run MacPyMOL.
>
> Related:
> https://sourceforge.net/p/pymol/mailman/message/33531659/
>
> Cheers,
> Thomas
>
> On 21 Jun 2015, at 21:44, Jordan
Hi,
I’m trying to use the pandas library with MacPymol 1.7.05 but get the following
with import pandas.
File "/Library/Python/2.7/site-packages/pandas/__init__.py", line 6, in
from . import hashtable, tslib, lib
File "numpy.pxd", line 157, in init pandas.hashtable
(pandas/hashtable.c
ke I’m doing.
Jordan
> On Jun 15, 2015, at 11:59 PM, Tsjerk Wassenaar wrote:
>
> Hi Jordan,
>
> Yes, although I don't have the answer at hand, it has been given on the user
> list several times. You can find it in the archives.
>
> Cheers,
>
> Tsjerk
&
Hi,
I have a dictionary that has a bunch of values I want to assign to b-factors in
order to color by. In my script:
for residue in data:
cmd.alter(“resi
{}”.format(residue[‘resnum’]),”b={}”.format(residue[‘value’]))
This executes the alter command for each residue. For some reason, its tak
PyMOL
The PyMOL Molecular Graphics System, Version 1.7.4 Schrödinger, LLC.
JyMOL
The JyMOL Molecular Graphics System, Version 1.7.4 Schrödinger, LLC.
AxPyMOL
The AxPyMOL Molecular Graphics Plugin for PowerPoint, Version 1.7.4
Schrödinger, LLC.
> On Apr 18, 2015, at 11:08 PM, leila karami
Hi everyone
This has always bugged me a bit, but how do I color by chain if I have two of
the same models loaded in? For instance, if they have the same chain
designation, util.cbc(obj01) and util.bc(obj02) will color them with the same
scheme. I assumed it was the “first_color” command, but it
much easier with ‘remove’
> reinitialize
> fetch 1Z92, type=pdb1
> as cartoon
> bg_color white
>
> color red, ss h
> color yellow, ss s
> color green, ss l+"
>
> remove /1Z92//A
On Feb 28, 2015, at 12:28 AM, Brenton Horne wrote:
> Hi,
>
> I've got this pml code:
> delete all
> fetch 1Z92, ty
Hi Lau,
If you install from command line, it will most likely install to
/usr/local/bin/. The problem is, your icons probably link to the app you
uninstalled. I would try to find the /usr/local/bin/pymol in your finder
window, then drag the binary to your desktop in you want an icon. If you rea
Does anyone know why PyMoL renders the PDBs 3U2S and 3U4E without connecting
backbone atoms at residue 100G and 100H? Are the bond distances for these two
residue types not within the right parameters? SimpleViewer and JalView both
bridge this connection.
Thanks,
Jordan
Hi,
I know Pymol has a built-in sequence alignment function that ‘align’ uses
before it does alignment. I was wondering how one could access this function
generically for any given strings. I wanted to use this in a module and don’t
want to rely on importing alignment modules from other package
Hi,
I have a really just awful way of doing this and was wondering if there is a
pymol solution that would make it easier.
Here is the problem.
Given two protein sequences, align their corresponding amino acids. The
position of each of the strings is not known, just the sequence.
Ex.
Protei
Is it possible to get the pymol module for interpreters other than the built in
one for pymol?
Python2.7.6 in this case? The build only seems to come with pymol.
Jordan
--
Learn Graph Databases - Download FREE O'Reilly
Hi,
I stumbled across this email:
https://www.mail-archive.com/pymol-users@lists.sourceforge.net/msg08945.html
Wondering if it was still unimplemented or if I’m missing it somewhere
Jordan
--
Learn Graph Databases - Do
I think...
What is happening is that the color command should take in a name like “color
yellow, i. 1" or a CMYK color vector. When you are saying “color 1” it is just
starting at the first index of CMYK which is black.
There is a command for your problem though. Just say util.color_chains() an
I’m using powerpoint for mac, so I don’t have the luxury of Axpymol (any plans
for OSX?)
I wanted to make a movie that iterates through scenes of a PyMol session and
pauses there until I hit the “next” button on powerpoint. My workaround was to
simply make a movie that went trough all scenes an
A super hack way is this:
hide all
python
my_list = cmd.get_object_list() # gets all objects loaded
index = 0
def next_thing():
global index
cmd.show('sticks', my_list[index])
cmd.hide('sticks', my_list[index - 1])
index += 1
def last_thing():
global index
index -= 1
Oh, I see what your saying. This is a python question.
from sys import argv
c_arg1 = argv[1]
c_arg2 = argv[2]
from pymol import cmd, stored
def align_heme(arg1, arg2 ):
cmd.load(arg1)
cmd.load(arg2)
cmd align(arg1,arg2)
#cmd.create(obj1, arg1) #There is no need
angstrom
J
On Dec 12, 2013, at 3:41 AM, Ahmet yıldırım wrote:
> Dear users,
>
> What is the unit of RMSD in pymol? Nanometer or angstrom?
>
> PyMOL>align structure1 & n. ca, structure2 & n. ca
>
> --
> Ahmet Yıldırım
>
> -
rather :)
colors = [‘red’,’blue’]
fetch 1nmr, discrete=1, async=0
as ribbon
set all_states
for model,color in zip(range(cmd.count_states()),colors): cmd.color(str(color),
"state %s" % x)
On Nov 13, 2013, at 12:23 AM, Jordan Willis wrote:
> zip it like this
>
> co
zip it like this
colors = [‘red’,’blue’]
fetch 1nmr, discrete=1, async=0
as ribbon
set all_states
for color, model in zip(range(cmd.count_states()),colors):
cmd.color(str(color), "state %s" % x)
On Nov 12, 2013, at 11:32 PM, Jerome BENOIT wrote:
> Hello Jason,
>
> thanks for your hint.
>
> Un
For some reason David, you have to pass the **kwargs keyword list too. I'm not
sure why but this worked for me,
python
from pymol import cmd, stored, CmdException
class Helix():
def __init__(self,selection):
self.selection = selection
def my_module(*args,**kwargs):
helices = [He
Could you just initialize your helix class with the object at the time of
creation? Also why are you passing the superclass object to Helix?
> class Helix():
> def __init__(self,selection):
> self.selection = selection
>
> def my_module(*selections):
> helices = [Helix(x) for x i
do you have numpy and psico installed?
http://www.pymolwiki.org/index.php/Psico
Psico has that particular command.
Jordan
On Sep 21, 2013, at 8:45 AM, Ananya Chatterjee wrote:
> Dear all,
>
> After simulation of my protein I have aligned the initial and the final
> structure and I could see
git/repo"
I would really appreciate the help,
J
----
Jordan Willis
Vanderbilt Medical Center
jwillis0...@gmail.com
--
How ServiceNow helps IT people transform IT departments:
Hello,
I'm all over the place with storing scenes, views, states etc.
One thing I can't get to the bottom of, especially going through the
documentation, is when one should use interpolate vs. reinterpolate. In Movie
School 5, they seem to be used interchangeably. It seems to me that it should
Hello,
I'm using MacPymol 1.5.0.4
When I save a ray traced .PNG file with set ray_opaque_background, 0 It does
gives me a transparent background when I put the picture into other apps, e.g.
Powerpoint. However, when I save it as a .mov file, I can see that pymol is
trying for a transparent bac
I know you have asked for frames, but I assume that each frame is mapped to a
state. The selection logic allows for you to specify the state.
So if the waters of interest are in state 1,40:
python
for i in range(1,41):
cmd.select("wat_"+i,"byres in within 6 of
",state=i)
python end
J
> 'sel
It seems the difference I was looking for was
pymol something.pml -- arg1 arg2 arg3
I was missing the --
Thanks
Jordan
On Jun 26, 2013, at 4:21 AM, lievb...@vub.ac.be wrote:
> On Wednesday 26 June 2013 08:52:39 Jordan Willis wrote:
>> I'm looking to pass a .pml file, do s
Hello,
I'm looking to pass a .pml file, do some stuff, and then save it as a session.
Pymol -c My.pml looks like a good option. I'm trying to write hundreds of
sessions each with different arguments. I was wondering if its possible to pass
command line arguments that can then be seen by the py
er your
> question exactly, but might be usefull):
>
> label foo and n. CA, "foo"
>
> Hope this helps,
> Folmer
>
>
> 2013/5/21 Jordan Willis
> Hello,
>
> This should be straightforward,
>
> Is it possible to label selections by their name?
&
Hello,
This should be straightforward,
Is it possible to label selections by their name?
If I have a selection named "foo" and I say label foo, "foo", it of course
labels all the atoms. Is it possible to get one label for the entire selection
without using pseudoatoms?
Jordan
--
Hi everyone,
I was wondering if there is an easy way to show distances as a function of
state. As you show each state (using the play button or mplay), can you show
the distance measurement changing? For now it just keeps the distance of the
first state shown. I could script this but first wou
Does it have to be a pymol script. Renumbering pdbs is the bread and butter of
biopython pdb module:
#!/blue/meilerlab/apps/Linux2/x86_64/bin/python2.5
import sys
from Bio.PDB import *
from optparse import OptionParser
import warnings
def main():
usage = "%prog input.pdb output.pdb"
parse
Hi,
I have 3 different conformations of the same structure and I was wondering what
is the easiest possible way to morph 3 conformations.
Morpheasy works fantastic for two conformations, and this makes around 80
frames. I can then reinitialize and do the other two states. I have no idea how
to
t additional
frames. However if I didn't want to map 1 state to 1 frame, this makes it
impossible.
For instance
#show each state for 3 frames
madd 1 -30 x90
seems impossible now,
but close enough,
Jordan
On Nov 10, 2012, at 11:46 PM, Jordan Willis wrote:
> Hi List,
>
>
Hi List,
I figured out a hack way to fix my last question. That's ok, because I have
another one. In my movie I have some objects with multiple states, and some
objects with one. Is there a way to use mset (or in my case madd) for the
multiple state objects and disregard the other objects?
For
Hello,
I'm having trouble with a movie I'm making. My very last scene which stores my
objects in a different place is trying to reinterpolate them with the starting
objects. In one scene I align them with each other and I just want to work from
that alignment. However, pymol moves them back to
Does every MODEL ENDMDL have a unique Connection list?
Can you show me your PDB file?
Jordan
On Oct 5, 2012, at 1:59 AM, Vishwas Vasisht wrote:
> Hi Thomas,
>
> Thanks, it works for single frame. But when I use multiple frame (using
> MODEL and ENDMDL), the connections which i speci
Was my message received by the pymol group about combining camera and object
motions at the same time? It said it was held for review. I have "copy myself"
on the mailman server, but I never seem to receive my own posting.
Jordan
On Sep 19, 2012, at 5:35 AM, Thomas Holder wrote:
> Hi Mona,
>
Hello,
**First, I'd like to apologize if you are receiving this message more than
once. I kept sending it from the wrong email name**
I'm making a movie, and I think I really got it down! However, I'm having
trouble with independent rotations.
I have nine independent objects, of which three I
Hello,
I'm making a movie, and I think I really got it down! However, I'm having
trouble with independent rotations.
I have nine independent objects, of which three I'm trying to get to rotate
their own z-axis. Is this possible? Let me show you what I mean :)
frame 30
rotate [0,0,1],360
I have the same problems. If you use the pymol pqr grid instead of the pdb2pqr,
you will find that it works.
Sent from my iPhone
On Aug 8, 2012, at 6:24 PM, Warren Gallin wrote:
> Hi,
>
>I am trying to generate some electrostatic surfaces using the APB plugin,
> but I am getting the foll
I'm thinking a good work around is simply this.
Select the binding site of the amino acids and ligand in pymol.
Then copy those selected aa's and atoms to another object:
save -> model -> copied_object as output.pdb
output.pdb will then contain all the x,y,z coordinates of only what was
Hi Pymol!
I have a question about movies, but has nothing to do with the movie commands,
so don't worry.
I have 750 states that are dumped directly into pymol where each "move" from
my modeling program, is a new state. I want to compare this to the input
structure which only has one state.
I
Hello,
I was wondering if anyone could help me with some state mapping for movies. I
have 1000 states or so that are output from a dynamics simulation automatically
to pymol. I was wondering two things:
1. Can I hide the lines for state 500-1000 and show the lines for 1-500? I have
all the sta
Hello,
What I want to do seems so simple, I just can't find the documentation. Would
anyone know how to just change the colors of only certain states when they are
appended to the same object?
For instance I have a simulation that shows atoms moving all over the place for
states 1-300 and a ni
Oh duh,
You are saying the .pdb is read as a "plain text file"
You would then have to add a new mime type ".pdb" to the source XML file that
gnome reads in /usr/share/mime/packages/freedesktop.org.xml
http://library.gnome.org/admin/system-admin-guide/stable/mimetypes-source-xml.html.en
Sorry
Hmm,
Have you tried putting a .txt and .pdb file on your desktop. Right click either
one and click Properties. There is an Open With tab. It should say "Open this
file and other .txt files with" and then you can select gedit. Conversely do
the same for .pdb files.
Jordan
On Jan 29, 2012, a
Is this a one time deal? Or a script you need to make for multiple proteins.
You could probably transfer the volume by making TLG a new object. create TLG,
protein_1 and resi (residue numbers of TLG).
Then align TLG to the new protein X where you want it.
align TLG, proteinX and resi (where yo
58 matches
Mail list logo
