Re: [PyMOL] Analysis of docking poses from 2 nmr-ensembles

2016-06-13 Thread Sampson, Jared M. 
Hi James -

First, it will be useful to split the 
states.

split_states ensemble1
split_states ensemble2
delete ensemble1
delete ensemble2

Then, superimpose all structures onto a 
reference structure for easier visualization.  This won't affect your distance 
measurements, but will make it easier to see the changes from one object to the 
next.

python
ref = 'ensemble1_0001'   # your reference object
for obj in cmd.get_names():
if obj != ref:
cmd.super(obj, ref)
python end

For your residue pair analysis, you have to decide what kind of distance you 
want to measure (e.g. CA-CA; average position of all atoms in the residue; 
closest atoms, which would require looping through all atom pairs in each 
residue pair and keeping only the shortest distance).  Then create selection 
strings based on those criteria, use them in 
distance measurement, and print 
them or add them to a variable to be output.  If you want to create and 
visualize distance objects, use `distance` instead of `get_distance` and pass a 
distance object name as the first parameter before the selections.

python
sel1 = "resi 100 and name CA"
sel2 = "resi 200 and name CA"
sel3 = "resi 300 and name CA"
for obj in cmd.get_names():
d12 = cmd.get_distance("{} and {}".format(obj, sel1), "{} and 
{}".format(obj, sel2))
d23 = cmd.get_distance("{} and {}".format(obj, sel2), "{} and 
{}".format(obj, sel3))
print "{}: '{}' to '{}' distance = {}".format(obj, sel1, sel2, d12)
print "{}: '{}' to '{}' distance = {}".format(obj, sel2, sel3, d23)
python end

This is just a very quick example; really there are many different ways to do 
this, and you'll have to find what kind of analysis your particular structure 
needs.  Also, if you want to look at H-bonds, it will be more complicated, 
because the angle is important as well.  In this case you may want to look at 
Thomas' Polarpairs script.

Hope that helps.

Cheers,
Jared



On Jun 13, 2016, at 9:41 AM, James Starlight 
mailto:jmsstarli...@gmail.com>> wrote:

Dear Pymol users!

I am studying protein-protein assosiation using 2 different proteins
as test case by means of variety of computational methods.
For my particular caseI need to compare binding poses emerged as the
result of protein-protein docking (ensemble 1: which  consists of 20
snapshots according to docking ranking) as well as MD simulation
(ensemble 2: which consists of 10 snapshots each of which represents
binding pose which has been established during long MD run).
Loading those two ensembles in pymol as 2 different models (in
NMR-like model format)  I need to performs some analysis  to find some
shared trends in each of them e.g RMSD of the distances between common
residues-pairs found in contact map analysis
or something else. What are most trivial suggestions might be in that
particular case?


Thanks for the suggestions!


James

--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are
consuming the most bandwidth. Provides multi-vendor support for NetFlow,
J-Flow, sFlow and other flows. Make informed decisions using capacity
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
___
PyMOL-users mailing list 
(PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity 
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

[PyMOL] Analysis of docking poses from 2 nmr-ensembles

2016-06-13 Thread James Starlight 
Dear Pymol users!

I am studying protein-protein assosiation using 2 different proteins
as test case by means of variety of computational methods.
For my particular caseI need to compare binding poses emerged as the
result of protein-protein docking (ensemble 1: which  consists of 20
snapshots according to docking ranking) as well as MD simulation
(ensemble 2: which consists of 10 snapshots each of which represents
binding pose which has been established during long MD run).
Loading those two ensembles in pymol as 2 different models (in
NMR-like model format)  I need to performs some analysis  to find some
shared trends in each of them e.g RMSD of the distances between common
residues-pairs found in contact map analysis
or something else. What are most trivial suggestions might be in that
particular case?


Thanks for the suggestions!


James

--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity 
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

[PyMOL] Mutagenesis

2016-06-13 Thread ‪sina f‬ ‪ 
Hi!  I need to perform an operation to mutate five amino acid residues in five 
positions of a pdb file to other19 standard amino acid residues but I need a 
help with scripts (or commands). Could anyone give a hint on how to do it ? 
Thanks !Sara.
--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity 
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] Getting Started

2016-06-13 Thread Julian Heinrich 
Hi Melanie,

have you gone through the 'movie school' (
http://www.pymolwiki.org/index.php/MovieSchool) ?
I know that biomedical animators also like to work with the molecular
flipbook (https://www.molecularflipbook.org/) or bioblender (
http://www.bioblender.eu/).

Cheers,
Julian

On Wed, Jun 8, 2016 at 3:23 PM Melanie Prakash 
wrote:

> Hi!
>
> I was wondering what a good tutorial would be to start with learning
> PyMol. I understand basic movie making commands, but I want to move onto
> developing movies of more complex biological processes.
>
> Currently I'm in the process of understanding how to develop a movie of a
> phosphorylation, and I don't understand several of the commands and
> functions I'm supposed to use. At that level, does one mostly lean on their
> knowledge of PyMol (which is quite young) when designing a movie?
>
> Thanks!
>
> -Melanie
>
> --
> What NetFlow Analyzer can do for you? Monitors network bandwidth and
> traffic
> patterns at an interface-level. Reveals which users, apps, and protocols
> are
> consuming the most bandwidth. Provides multi-vendor support for NetFlow,
> J-Flow, sFlow and other flows. Make informed decisions using capacity
> planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
> ___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity 
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

[PyMOL] APBS plugin on pymol 1.5 does not work

2016-06-13 Thread Yanni Goudeuk 
Hello

I recently installed PyMOL version 1.5 no my MAC 10.9 using HomeBrew.
There were no problems with the installation at all however the APBS plugin
when loaded it gives me this error:

Error: 4
 Exception in Tk callback
  Function:  at 0x106691758> (type: )
  Args: ()
Traceback (innermost last):
  File 
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/Pmw/Pmw_1_3_3/lib/PmwBase.py",
line 1753, in __call__
return apply(self.func, args)
  File 
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/pmg_tk/startup/apbs_tools.py",
line 265, in 
command = lambda s=self: APBSTools2(s))
  File 
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/pmg_tk/startup/apbs_tools.py",
line 628, in __init__
group.pack(fill='both',expand=1, padx=4, pady=5)
  File "", line 1, in pack
None
  File 
"/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/lib-tk/Tkinter.py",
line 1764, in pack_configure
+ self._options(cnf, kw))
: cannot use geometry manager pack inside
.4388449240.4388454480.4388457144.4388479776 which already has slaves
managed by grid

Could someone help me resolve this error please?

Many thanks
goude

--
What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic
patterns at an interface-level. Reveals which users, apps, and protocols are 
consuming the most bandwidth. Provides multi-vendor support for NetFlow, 
J-Flow, sFlow and other flows. Make informed decisions using capacity 
planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e
___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net