Re: [PyMOL] Colouring nucleic acids, without changing the colouring of amino acids

[Sampson, Jared]

Hi Brenton -

To avoid coloring e.g. Glycine when you only want to color e.g. guanine, prefix 
the residue name with “D” (as the residues are shown in the Sequence viewer) 
for DNA.  I believe RNA works the same way with “R” as well.

set cartoon_color, green, resn DG

To color the DNA backbone, you could try:

color pink, resn DA+DC+DG+DT and bb.

or, if you know the chain IDs,

color pink, 2XCT and chain A+B+C+D+E and bb.

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/

On Mar 24, 2015, at 11:47 PM, Brenton Horne 
mailto:brentonho...@ymail.com>> wrote:

Hi,

I've seen this (Example 1 on 3DNA) and 
I noticed to colour each nucleic acid differently they used something like:

set cartoon_color, green, resn G

for each of the four different nucleic acids. When I ran this for 2XCT bio 
assembly 1 it coloured amino acids with the same single letter codes as the 
four nucleic acids (e.g., G for guanine [nucleic acid] and glycine [amino]) and 
I wanted to know how to run it just for nucleic acids. I thought that something 
like this for each chain containing nucleic acids:

set cartoon_color, green, /2XCT//E and resn G

would do the trick but that would take forever seeing how 8 separate chains 
contain nucleic acids. While we're on this topic I'd also like to know how to 
colour the backbone and sugars via a more efficient method than doing something 
like this:

color pink, /2XCT//E and bb.


for each chain containing nucleic acids.

Thanks for your time,
Brenton
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Re: [PyMOL] Weird problem with cmd.fetch()

[Irem Altan]

Nevermind, I forgot pymol.finish_launching()
My apologies,
Irem

On Mar 26, 2015, at 9:22 PM, Irem Altan 
mailto:irem.al...@duke.edu>> wrote:

Hi,

When I run the following code, it gives me an error that I don’t understand.

# -*- coding: utf-8 -*-
import random
import pymol
from pymol import cmd, stored
from pymol.exporting import _resn_to_aa as one_letter




def test():
  objSel="protein"
  cmd.fetch('1zv4',objSel)

  print "now im here"

test()


The error it gives is:

Traceback (most recent call last):
  File "testNeig.py", line 16, in 
test()
  File "testNeig.py", line 12, in test
cmd.fetch('1zv4',objSel)
  File "/usr/lib64/python2.6/site-packages/pymol/importing.py", line 1399, in 
fetch
path = setting.get('fetch_path',_self=_self) or '.'
  File "/usr/lib64/python2.6/site-packages/pymol/setting.py", line 1306, in get
_self.unlock(r,_self)
  File "/usr/lib64/python2.6/site-packages/pymol/locking.py", line 79, in unlock
if (thread.get_ident() == pymol.glutThread):
AttributeError: 'module' object has no attribute 'glutThread'

What am I missing?

Thank you,
Irem

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[PyMOL] Weird problem with cmd.fetch()

[Irem Altan]

Hi,

When I run the following code, it gives me an error that I don’t understand.

# -*- coding: utf-8 -*-
import random
import pymol
from pymol import cmd, stored
from pymol.exporting import _resn_to_aa as one_letter




def test():
  objSel="protein"
  cmd.fetch('1zv4',objSel)

  print "now im here"

test()


The error it gives is:

Traceback (most recent call last):
  File "testNeig.py", line 16, in 
test()
  File "testNeig.py", line 12, in test
cmd.fetch('1zv4',objSel)
  File "/usr/lib64/python2.6/site-packages/pymol/importing.py", line 1399, in 
fetch
path = setting.get('fetch_path',_self=_self) or '.'
  File "/usr/lib64/python2.6/site-packages/pymol/setting.py", line 1306, in get
_self.unlock(r,_self)
  File "/usr/lib64/python2.6/site-packages/pymol/locking.py", line 79, in unlock
if (thread.get_ident() == pymol.glutThread):
AttributeError: 'module' object has no attribute 'glutThread'

What am I missing?

Thank you,
Irem
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[PyMOL] Fwd: Location of pdb2pqr.py file for PyMOL use on Windows 7

[Brenton Horne]

Hi,

I've had some trouble with the APBS tools plugin, please see the email 
below which I sent to the pdb2pqr-users list and I felt as I haven't 
received a response so far (granted I only sent it 2 hours ago) I felt I 
should forward this message to PyMOL-users too.



 Forwarded Message 
Subject:Location of pdb2pqr.py file for PyMOL use on Windows 7
Date:   Thu, 26 Mar 2015 16:01:26 +1000
From:   Brenton Horne 
To: pdb2pqr-us...@lists.sourceforge.net



Hi,

I downloaded pdb2pqr-windows-bin64-2.0.0.zip 
, 
unzipped it and realized that pdb2pqr.py was missing from the zipped 
file directory (as I understand it pdb2pqr should be ready to go the way 
it is without running any msi/exe files?). Now I need a pdb2pqr.py 
python script in my PDB2PQR installation to point to in order for PyMOL 
to work for me (as running "Set grid" without it gives the error 
described below), so my question is, "How do I get such a script or 
otherwise overcome this error?"


The PyMOL error described above was:

/Error: could not import pdb2pqr, please check pdb2pqr.py location./

Thanks for your time,
Brenton


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