[PyMOL] Resetting PyMOL via API for unit testing

[Sampson, Jared M. <jms2435@cu...>]

tl;dr: Is there a way to fully stop and restart PyMOL "sessions" using the API to avoid crossover between unit tests?

Hi everyone -

I'm working on unit testing for a plugin and have been trying to figure out how to test some functionality from within a PyMOL session.  I have a partially working solution, but the problem arises that I can't adequately reinitialize PyMOL between tests, and sometimes end up getting carryover between tests.

Here's a working example of this behavior using the built-in `unittest` testing framework:

```
import unittest

import __main__
__main__.pymol_argv = ['pymol','-qkc']
import pymol
from pymol import cmd

class TestPymolApi(unittest.TestCase):
    def setUp(self):
        pymol.finish_launching()
        cmd.reinitialize()

    def tearDown(self):
        #cmd.quit()  # ***this line hangs if uncommented***
        pass

    def test_1(self):
        '''No value for stored.foo.'''
        from pymol import stored
        with self.assertRaises(AttributeError):
            stored.foo

    def test_2(self):
        '''Sets a value for stored.foo.'''
        from pymol import stored
        stored.foo = 'bar'

    #def test_3(self):
    #    '''Fails due to carryover from test_2.'''
    #    self.test_1()

if __name__ == '__main__':
    unittest.main()
```


Running `python basic_tests.py` yields the following output (each dot represents a successful test):

```
$ python basic_tests.py
..
----------------------------------------------------------------------
Ran 2 tests in 0.043s

OK
```


But if I uncomment `test_3` and re-run (the tests are executed in standard string-sorting order by function name), it fails because the value of `stored.foo` is retained even after reinitialization after `test_2`.  (The `setUp` and `tearDown` functions are run before and after each test, respectively.)

```
$ python basic_tests.py
..F
======================================================================
FAIL: test_3 (__main__.TestPymolApi)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "basic_tests.py", line 32, in test_3
    self.test_1()
  File "basic_tests.py", line 24, in test_1
    stored.foo
AssertionError: AttributeError not raised

----------------------------------------------------------------------
Ran 3 tests in 0.110s

FAILED (failures=1)
```

Maybe this is a bug in `cmd.reinitialize()`?  If not, it is unexpected behavior (at least in my opinion), and could be improved.

Anyway, this is why I'm trying to figure out another way to reset PyMOL using the API.  So if I then uncomment the `cmd.quit()` line to try to get complete shut down and restart of PyMOL, unittest hangs on the tearDown of the first test and I have to interrupt the process with <Ctrl-C>.

I found an old thread<https://sourceforge.net/p/pymol/mailman/message/26469705/>; where Jason mentioned using (admittedly experimental) `pymol2.PyMOL().start/stop()` to, well, start and stop PyMOL sessions.  However, in Open Source PyMOL 1.8.2.1, it appears to be broken:

```
$ python
>>> import pymol2
>>> p = pymol2.PyMOL()
>>> p.start()
Segmentation fault: 11
```

So, again, my question is: Is there any way to reliably start and stop multiple PyMOL sessions or completely reset it using the API?

Looking forward any suggestions or further discussion.

Cheers,
Jared

[PyMOL] Help Download structural alignment

[Clarisa Alvarez <clarisae.alvarez@gm...>]

Hi everyone:
I am writing asking help to download the structural aligment performed in
pymol.
Thanks in advance.
Regards,
Clarisa.

2016-06-14 11:01 GMT-03:00 <pymol-users-request@...>:

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> Today's Topics:
>
>    1. Analysis of docking poses from 2 nmr-ensembles (James Starlight)
>    2. Re: Analysis of docking poses from 2 nmr-ensembles
>       (Sampson, Jared M.)
>    3. Selective valency on bond (McIntyre, Patrick)
>    4. Re: Selective valency on bond (Andreas Warnecke)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 13 Jun 2016 15:41:58 +0200
> From: James Starlight <jmsstarlight@...>
> Subject: [PyMOL] Analysis of docking poses from 2 nmr-ensembles
> To: pymol-users <pymol-users@...>
> Message-ID:
>         <
> CAALQopzzJTYkbY+j_EvpHgvPp2_k_MHMV2HoLhjGf2D5PNRRHw@...>
> Content-Type: text/plain; charset=UTF-8
>
> 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
>
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 13 Jun 2016 16:08:31 +0000
> From: "Sampson, Jared M." <jms2435@...>
> Subject: Re: [PyMOL] Analysis of docking poses from 2 nmr-ensembles
> To: James Starlight <jmsstarlight@...>
> Cc: pymol-users <pymol-users@...>
> Message-ID: <FDAB34D6-3FF3-4737-B61A-A803439793EB@...>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi James -
>
> First, it will be useful to split the states<
> http://www.pymolwiki.org/index.php/Split_states>;.
>
> split_states ensemble1
> split_states ensemble2
> delete ensemble1
> delete ensemble2
>
> Then, superimpose<http://pymolwiki.org/index.php/Super>; 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<
> http://pymolwiki.org/index.php/Get_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<
> http://pymolwiki.org/index.php/Polarpairs>; script.
>
> Hope that helps.
>
> Cheers,
> Jared
>
>
>
> On Jun 13, 2016, at 9:41 AM, James Starlight <jmsstarlight@...
> <mailto:jmsstarlight@...>> 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,
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> -------------- next part --------------
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> ------------------------------
>
> Message: 3
> Date: Mon, 13 Jun 2016 09:56:36 +0000
> From: "McIntyre, Patrick" <pm296@...>
> Subject: [PyMOL] Selective valency on bond
> To: "pymol-users@..."
>         <pymol-users@...>
> Message-ID: <A67054C6-D4F4-4237-BFA0-8FEF107835B5@...>
> Content-Type: text/plain; charset="us-ascii"
>
> Dear PyMol users,
>
> I have a crystal structure of my protein with an unnatural amino acid
> present. This amino acid has a double bond within it, which I would like to
> display as such. However I would like the surrounding protein  side chains
> to not show double bond character. Is this possible at all?
>
> So far, I can either keep valence mode set to '0' and see no double bonds
> across the whole protein, or set to '1' and see all of the double bonds,
> which I don't want.
>
> My question is, is it possible to selectively 'set valency' onto a single
> bond, or is it a global command which is not capable of this fine-tuning? I
> am using MacPyMol if this makes a difference at all?
>
> Thanks for your help,
> Patrick
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 14 Jun 2016 16:01:04 +0200
> From: Andreas Warnecke <4ndreas.warneck3@...>
> Subject: Re: [PyMOL] Selective valency on bond
> To: "McIntyre, Patrick" <pm296@...>
> Cc: "pymol-users@..."
>         <pymol-users@...>
> Message-ID:
>         <
> CAEyFQbUfioDrVnOydHtegsT5HMkQ_ji5BqWngLKO9tviBTTFDg@...>
> Content-Type: text/plain; charset="utf-8"
>
> The easiest way to deal with this is setting the valence or valence_mode
> individually for the object.
>
> set valence, 0, object1
> set valence, 1, object2
>
> Cheers,
>
> Andreas
>
> On Mon, Jun 13, 2016 at 11:56 AM, McIntyre, Patrick <pm296@...
> >
> wrote:
>
> > Dear PyMol users,
> >
> > I have a crystal structure of my protein with an unnatural amino acid
> > present. This amino acid has a double bond within it, which I would like
> to
> > display as such. However I would like the surrounding protein  side
> chains
> > to not show double bond character. Is this possible at all?
> >
> > So far, I can either keep valence mode set to '0' and see no double bonds
> > across the whole protein, or set to '1' and see all of the double bonds,
> > which I don't want.
> >
> > My question is, is it possible to selectively 'set valency' onto a single
> > bond, or is it a global command which is not capable of this
> fine-tuning? I
> > am using MacPyMol if this makes a difference at all?
> >
> > Thanks for your help,
> > Patrick
> >
> >
> ------------------------------------------------------------------------------
> > 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@...)
> > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> > Archives: http://www.mail-archive.com/pymol-users@...
> >
> -------------- next part --------------
> An HTML attachment was scrubbed...
>
> ------------------------------
>
>
> ------------------------------------------------------------------------------
> 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@...
> https://lists.sourceforge.net/lists/listinfo/pymol-users
>
>
> End of PyMOL-users Digest, Vol 121, Issue 3
> *******************************************
>

[PyMOL] How to show one side of the surface of an object

[sunyeping <sunyeping@al...>]

Dear all,
If we show surface of an object in pymol, the surface appears to wrap the object all around. But whether is it possible to show a surface that cover only one side of certain part of that object？ For example, when I draw a surface of the active site that contacts a drug, I wish the surface should look like a curved surface without a thickness suspending over the active residues instead of a volume that wraps all directions of the the active site residues. I remember I saw such figures somewhere but I cann't find them now?
Do you have any idea how draw it?
Thanks a lot.
Yeping Sun 

[PyMOL] helical tilt angle

[Qasim Pars <qasimpars@gm...>]

Dear pymol users,

I have the trajectory file (.xtc file) of a protein using GROMACS. gmx
helixorient tool of GROMACS calculates it for each C-alpha atom of helix as
a function of simulation time. Whereas, I would like to calculate only ONE
helical tilt angle relative to the z -axis of a alpha helix for each frame
of simulation.

Does anyone have a script to calculate the helix tilt angle relative to the
z -axis of a alpha helix?

Any helps will be appreciated.

-- 
Qasim Pars

[PyMOL] problems with loading trajectories and topology from AMBER 14

[Thomas Pochapsky <pochapsk@br...>]

I have had no trouble loading .prmtop and .mdcrd files from AMBER 14 
into MacPyMOL locally, just change the name from .prmtop to .top and 
.mdcrd to .trj, and it works fine.  However, if I try to do the same 
with trajectories and topologies running on an XSEDE node (also using 
AMBER 14), obtained with (as far as I can tell) identical input files, I 
get the following error message:

ObjMolLoadTRJFile-Error: Failed to read expected coordinate value.
   This traj. does not match the loaded parameter/topology file.
   Likely cause: either the atom count or the periodic box settings
   are inconsistent between the two files.
  CmdLoad: "/Users/pochapsk/Box Sync/amber_stuff/MycG.trj" appended into 
object "MycG".
  CmdLoad: 0 total states in the object.


The .rst file coords load fine.


The only odd thing that I notice locally is when the .rst file is 
loaded, the water molecules are not folded back into the periodic box, 
while the .trj files show a symmetric water cube (expected if there are 
periodic boundary conditions).

[PyMOL] VR for Pymol?

[Albert <mailmd2011@gm...>]

Hello:

Does anybody have any idea whether PyMol support Virtual Reality (VR)? 
Can we use the following VR devices to visualize PyMOl in computer?

http://www.polygon.com/2016/1/5/10719326/nvidia-virtual-reality-performance-power

https://www.youtube.com/watch?v=U4JPhUr_d7g

If yes, will any VR device on the market work for PyMol?

Thanks a lot

[PyMOL] 2nd Call For Papers - 23rd Annual Tcl/Tk Conference (Tcl'2016)

[<akupries@sh...>]

Hello pymol-users, fyi ...

23rd Annual Tcl/Tk Conference (Tcl'2016)
http://www.tcl.tk/community/tcl2016/

November 14 - 18, 2016
Crowne Plaza Houston River Oaks
2712 Southwest Freeway, 77098
Houston, Texas, USA

Important Dates:

[[ Attention!
   Registration is open. Please have a look at
        http://www.tcl.tk/community/tcl2016/register.html

   The tutorials are known. See
        http://www.tcl.tk/community/tcl2016/tutorials.html
]]

Abstracts and proposals due   September 12, 2016
Notification to authors       September 19, 2016
WIP and BOF reservations open August 22, 2016
Author materials due          October 24, 2016
Tutorials Start               November 14, 2016
Conference starts             November 16, 2016

Email Contact:                tclconference@...

Submission of Summaries

Tcl/Tk 2016 will be held in Houston, Texas, USA from November 14, 2016 to November 18, 2016.

The program committee is asking for papers and presentation proposals
from anyone using or developing with Tcl/Tk (and extensions). Past
conferences have seen submissions covering a wide variety of topics
including:

* Scientific and engineering applications
* Industrial controls
* Distributed applications and Network Managment
* Object oriented extensions to Tcl/Tk
* New widgets for Tk
* Simulation and application steering with Tcl/Tk
* Tcl/Tk-centric operating environments
* Tcl/Tk on small and embedded devices
* Medical applications and visualization
* Use of different programming paradigms in Tcl/Tk and proposals for new
  directions.
* New areas of exploration for the Tcl/Tk language

Submissions should consist of an abstract of about 100 words and a
summary of not more than two pages, and should be sent as plain text
to tclconference@... no later than September 12, 2016. Authors of accepted
abstracts will have until October 24, 2016 to submit their final
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encouraged.

Printed proceedings will be produced as an on-demand book at lulu.com

The authors will have 30 minutes to present their paper at
the conference.

The program committee will review and evaluate papers according to the
following criteria:

* Quantity and quality of novel content
* Relevance and interest to the Tcl/Tk community
* Suitability of content for presentation at the conference

Proposals may report on commercial or non-commercial systems, but
those with only blatant marketing content will not be accepted.

Application and experience papers need to strike a balance between
background on the application domain and the relevance of Tcl/Tk to
the application. Application and experience papers should clearly
explain how the application or experience illustrates a novel use of
Tcl/Tk, and what lessons the Tcl/Tk community can derive from the
application or experience to apply to their own development efforts.

Papers accompanied by non-disclosure agreements will be returned to
the author(s) unread. All submissions are held in the highest
confidentiality prior to publication in the Proceedings, both as a
matter of policy and in accord with the U. S. Copyright Act of 1976.

The primary author for each accepted paper will receive registration
to the Technical Sessions portion of the conference at a reduced rate.

Other Forms of Participation

The program committee also welcomes proposals for panel discussions of
up to 90 minutes. Proposals should include a list of confirmed
panelists, a title and format, and a panel description with position
statements from each panelist. Panels should have no more than four
speakers, including the panel moderator, and should allow time for
substantial interaction with attendees. Panels are not presentations
of related research papers.

Slots for Works-in-Progress (WIP) presentations and Birds-of-a-Feather
sessions (BOFs) are available on a first-come, first-served basis
starting in August 22, 2016. Specific instructions for reserving WIP
and BOF time slots will be provided in the registration information
available in August 22, 2016. Some WIP and BOF time slots will be held open
for on-site reservation. All attendees with an interesting work in
progress should consider reserving a WIP slot.

Registration Information

More information on the conference is available the conference Web
site (http://www.tcl.tk/community/tcl2016/) and will be published on
various Tcl/Tk-related information channels.

To keep in touch with news regarding the conference and Tcl events in
general, subscribe to the tcl-announce list. See:
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Conference Committee

   * Andreas Kupries Hewlett Packard Enterprise
   * Arjen Markus    Deltares
   * Brian Griffin   Mentor Graphics
   * Clif Flynt      Noumena Corp
   * Gerald Lester   KnG Consulting LLC
   * Joe Mistachkin  Mistachkin Systems
   * Ronald Fox      CAEN Technologies
                     NSCL @ Michigan State University
   * Steve Landers   Digital Smarties

Contact Information     tclconference@...

Tcl'2016 would like to thank those who are sponsoring the conference:

   * Mentor Graphics
   * Tcl Community Association

Re: [PyMOL] Selective valency on bond

[Thomas Holder <thomas.holder@sc...>]

Hi Patrick and Andreas,

"valence" is actually a bond-level setting, so you don't need to create individual objects. This should work:

set_bond valence, 1, organic

Cheers,
  Thomas

On 14 Jun 2016, at 10:01, Andreas Warnecke <4ndreas.warneck3@...> wrote:

> The easiest way to deal with this is setting the valence or valence_mode individually for the object.
> 
> set valence, 0, object1
> set valence, 1, object2
> 
> Cheers,
> 
> Andreas
> 
> On Mon, Jun 13, 2016 at 11:56 AM, McIntyre, Patrick <pm296@...> wrote:
> Dear PyMol users,
> 
> I have a crystal structure of my protein with an unnatural amino acid present. This amino acid has a double bond within it, which I would like to display as such. However I would like the surrounding protein  side chains to not show double bond character. Is this possible at all?
> 
> So far, I can either keep valence mode set to '0' and see no double bonds across the whole protein, or set to '1' and see all of the double bonds, which I don't want.
> 
> My question is, is it possible to selectively 'set valency' onto a single bond, or is it a global command which is not capable of this fine-tuning? I am using MacPyMol if this makes a difference at all?
> 
> Thanks for your help,
> Patrick

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] Selective valency on bond

[Andreas Warnecke <4ndreas.warneck3@gm...>]

The easiest way to deal with this is setting the valence or valence_mode
individually for the object.

set valence, 0, object1
set valence, 1, object2

Cheers,

Andreas

On Mon, Jun 13, 2016 at 11:56 AM, McIntyre, Patrick <pm296@...>
wrote:

> Dear PyMol users,
>
> I have a crystal structure of my protein with an unnatural amino acid
> present. This amino acid has a double bond within it, which I would like to
> display as such. However I would like the surrounding protein  side chains
> to not show double bond character. Is this possible at all?
>
> So far, I can either keep valence mode set to '0' and see no double bonds
> across the whole protein, or set to '1' and see all of the double bonds,
> which I don't want.
>
> My question is, is it possible to selectively 'set valency' onto a single
> bond, or is it a global command which is not capable of this fine-tuning? I
> am using MacPyMol if this makes a difference at all?
>
> Thanks for your help,
> Patrick
>
> ------------------------------------------------------------------------------
> 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@...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@...
>

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

[Sampson, Jared M. <jms2435@cu...>]

Hi James -

First, it will be useful to split the states<http://www.pymolwiki.org/index.php/Split_states>;.

split_states ensemble1
split_states ensemble2
delete ensemble1
delete ensemble2

Then, superimpose<http://pymolwiki.org/index.php/Super>; 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<http://pymolwiki.org/index.php/Get_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<http://pymolwiki.org/index.php/Polarpairs>; script.

Hope that helps.

Cheers,
Jared



On Jun 13, 2016, at 9:41 AM, James Starlight <jmsstarlight@...<mailto:jmsstarlight@...>> 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

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

[James Starlight <jmsstarlight@gm...>]

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

[PyMOL] Mutagenesis

[‪sina f‬ ‪ <sina.pilot90@ya...>]

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.

[PyMOL] Selective valency on bond

[McIntyre, Patrick <pm296@le...>]

Dear PyMol users,

I have a crystal structure of my protein with an unnatural amino acid present. This amino acid has a double bond within it, which I would like to display as such. However I would like the surrounding protein  side chains to not show double bond character. Is this possible at all?

So far, I can either keep valence mode set to '0' and see no double bonds across the whole protein, or set to '1' and see all of the double bonds, which I don't want. 

My question is, is it possible to selectively 'set valency' onto a single bond, or is it a global command which is not capable of this fine-tuning? I am using MacPyMol if this makes a difference at all?

Thanks for your help,
Patrick 

Re: [PyMOL] Getting Started

[Julian Heinrich <julian@jo...>]

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 <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@...)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@...

[PyMOL] APBS plugin on pymol 1.5 does not work

[Yanni Goudeuk <goudeuk@gm...>]

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
<class '_tkinter.TclError'> Exception in Tk callback
  Function: <function <lambda> at 0x106691758> (type: <type 'function'>)
  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 <lambda>
    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 "<string>", 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))
<class '_tkinter.TclError'>: 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

[PyMOL] Getting Started

[Melanie Prakash <melanie.prakash@gm...>]

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

Re: [PyMOL] Details of the morph interpolation?

[Thomas Holder <thomas.holder@sc...>]

Hi Emilia,

On 03 Jun 2016, at 18:39, Emilia C. Arturo (Emily) <eca38@...> wrote:

> Thank you for the reply, Thomas. I have a few items in reply:
> 
> 1) I have not yet tried to change the refinement settings, but (for educational purposes, if nothing else) I would like to know what it is that this particular command that you typed, does: PyMOL> refine(5, "mout", sculpt_field_mask=(0xFFF & ~0x60)). I haven't found any online documentation for sculpt_field_mask.

"sculpt_field_mask" is a bit mask, every bit enables a term. Look at the link to Sculpt.h that I sent in the previous email. 0x60 is the "or" combination of cSculptVDW and cSculptVDW14, and the tilde (~) inverts all bits, so effectively enabling all terms except VDW and VDW14.

> 2) Thank you for showing me how to fix atoms by typing
> 
> PyMOL> flag fix, (selection), set
> 
> before I call the morph command. Now how does one UNfix the atoms in the selection? Navigating Build>Scultping>Clear memory does not do it. Do I really need to exit the session to accomplish the reset (which is what worked for me)?

"unfix" atoms:
PyMOL> flag fix, (selection), clear

> 3) I encountered a warning message about the match command when I type:
> 
> PyMOL> morph mout, sele1, sele2, refinement=0 
> 
> (where sele1 and sele2 both have 4 iron ions each, each labeled 'FE')
> 
> The result is several lines that say 'Match-Warning: unknown residue type 'FE' (using X).' No Fe ions are used/observed in the interpolation. If, however, I type:
> 
> PyMOL> morph mout, sele1, sele2, match=in, refinement=0
> 
> then the Fe ions do appear as part of the interpolation. Why does the 'align' argument (which is default for 'match') ignore the Fe?

This is indeed not obvious. The "align" command uses a BLOSUM62 substitution matrix to score the alignment. Since "FE" is not an amino acid, it gets assigned "X" as the single letter code. With the BLOSUM62 matrix, X matched to X has a score of -1 (penalty). In theory you could modify the file /Applications/MacPyMOL.app/Contents/pymol/data/pymol/matrices/BLOSUM62 and change the X/X score to 1, then PyMOL will align the FE atoms.

> Thank you for your time, Thomas.
> 
> Regards,
> 
> Emily.

Cheers,
  Thomas

> On Tue, May 31, 2016 at 4:44 PM, Thomas Holder <thomas.holder@...> wrote:
> Hi Emily,
> 
> PyMOL's morphing performs two steps: (1) RigiMOL, and (2) refinement of non-backbone atoms by sculpting. The second part can be skipped with "refinement=0".
> 
> Unfortunately, there is no RigiMOL publication or method documentation.
> 
> The sculpting refinement tries to avoid clashes and maintain the local sidechain geometry, based on start and end conformation as references. You are right that sculpting doesn't consider the Ramachandran plot or a real energy force field. But it does consider clashes (it has a VDW term). Check "Build > Sculpting > ...", the bottom part of that submenu lists some of the available terms. The corresponding numerical values can be found here:
> https://sourceforge.net/p/pymol/code/HEAD/tree/trunk/pymol/layer2/Sculpt.h
> 
> The "morph" command refinement uses all sculpting terms. You could customize that, e.g. exclude VDW repulsion, like this:
> 
> PyMOL> morph mout, sele1, sele2, refinement=0
> PyMOL> from epymol.rigimol import refine
> PyMOL> refine(5, "mout", sculpt_field_mask=(0xFFF & ~0x60))
> 
> You can also "fix" atoms, e.g. all non-polymer atoms, like free ions, which tend to bounce around as a result of the refinement:
> 
> PyMOL> morph mout, sele1, sele2, refinement=0
> PyMOL> from epymol.rigimol import refine
> PyMOL> flag fix, (not polymer), set
> PyMOL> refine(5, "mout")
> 
> Hope that helps.
> 
> Cheers,
>   Thomas
> 
> On 30 May 2016, at 12:43, Emilia C. Arturo (Emily) <eca38@...> wrote:
> 
> > Hello.
> >
> > I would like to know more about the type of interpolation that is done when morph is called, and what calculations are done at each refinement cycle. Is there a literature reference or previous forum discussion to which you can point me?
> >
> > From my sifting through the internet, I settled on the likelihood that refinement is done using the "molecular sculpting" algorithm that has been employed since at least this discussion took place in 2002: http://www.mail-archive.com/pymol-users@.../msg00359.html
> > In other words, refinement is not done on the basis of energy differences, Ramachandran plot, interatomic clashes, or other problems with geometry that could arise at each interpolation step.
> >
> > Is that correct? If so, is there a way to customize the refinement that's done?
> >
> > I am using MacPyMOL version 1.7.6.2.
> >
> > Regards,
> >
> > Emily.

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] Details of the morph interpolation?

[Emilia C. Arturo (Emily) <eca38@dr...>]

Thank you for the reply, Thomas. I have a few items in reply:

1) I have not yet tried to change the refinement settings, but (for
educational purposes, if nothing else) I would like to know what it is that
this particular command that you typed, does: PyMOL> refine(5, "mout",
sculpt_field_mask=(0xFFF & ~0x60)). I haven't found any online
documentation for sculpt_field_mask.

2) Thank you for showing me how to fix atoms by typing

PyMOL> flag fix, (selection), set

before I call the morph command. Now how does one UNfix the atoms in the
selection? Navigating Build>Scultping>Clear memory does not do it. Do I
really need to exit the session to accomplish the reset (which is what
worked for me)?

3) I encountered a warning message about the match command when I type:

PyMOL> morph mout, sele1, sele2, refinement=0

(where sele1 and sele2 both have 4 iron ions each, each labeled 'FE')

The result is several lines that say 'Match-Warning: unknown residue type
'FE' (using X).' No Fe ions are used/observed in the interpolation. If,
however, I type:

PyMOL> morph mout, sele1, sele2, match=in, refinement=0

then the Fe ions do appear as part of the interpolation. Why does the
'align' argument (which is default for 'match') ignore the Fe?

Thank you for your time, Thomas.

Regards,

Emily.





On Tue, May 31, 2016 at 4:44 PM, Thomas Holder <
thomas.holder@...> wrote:

> Hi Emily,
>
> PyMOL's morphing performs two steps: (1) RigiMOL, and (2) refinement of
> non-backbone atoms by sculpting. The second part can be skipped with
> "refinement=0".
>
> Unfortunately, there is no RigiMOL publication or method documentation.
>
> The sculpting refinement tries to avoid clashes and maintain the local
> sidechain geometry, based on start and end conformation as references. You
> are right that sculpting doesn't consider the Ramachandran plot or a real
> energy force field. But it does consider clashes (it has a VDW term). Check
> "Build > Sculpting > ...", the bottom part of that submenu lists some of
> the available terms. The corresponding numerical values can be found here:
> https://sourceforge.net/p/pymol/code/HEAD/tree/trunk/pymol/layer2/Sculpt.h
>
> The "morph" command refinement uses all sculpting terms. You could
> customize that, e.g. exclude VDW repulsion, like this:
>
> PyMOL> morph mout, sele1, sele2, refinement=0
> PyMOL> from epymol.rigimol import refine
> PyMOL> refine(5, "mout", sculpt_field_mask=(0xFFF & ~0x60))
>
> You can also "fix" atoms, e.g. all non-polymer atoms, like free ions,
> which tend to bounce around as a result of the refinement:
>
> PyMOL> morph mout, sele1, sele2, refinement=0
> PyMOL> from epymol.rigimol import refine
> PyMOL> flag fix, (not polymer), set
> PyMOL> refine(5, "mout")
>
> Hope that helps.
>
> Cheers,
>   Thomas
>
> On 30 May 2016, at 12:43, Emilia C. Arturo (Emily) <eca38@...>
> wrote:
>
> > Hello.
> >
> > I would like to know more about the type of interpolation that is done
> when morph is called, and what calculations are done at each refinement
> cycle. Is there a literature reference or previous forum discussion to
> which you can point me?
> >
> > From my sifting through the internet, I settled on the likelihood that
> refinement is done using the "molecular sculpting" algorithm that has been
> employed since at least this discussion took place in 2002:
> http://www.mail-archive.com/pymol-users@.../msg00359.html
> > In other words, refinement is not done on the basis of energy
> differences, Ramachandran plot, interatomic clashes, or other problems with
> geometry that could arise at each interpolation step.
> >
> > Is that correct? If so, is there a way to customize the refinement
> that's done?
> >
> > I am using MacPyMOL version 1.7.6.2.
> >
> > Regards,
> >
> > Emily.
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>


-- 
"Study as if you were going to live forever; live as if you were going to
die tomorrow." - Maria Mitchell

"Success is going from failure to failure without losing your enthusiasm."
- Anon.

“We are the people we have been waiting for.”
- A tag line from MIT's Vehicle Design Summit website (http://vds.mit.edu)

[PyMOL] Calling a plugin function from python script

[Ebert Maximilian <m.ebert@um...>]

Hi there,

I am trying to call the spectrumany plugin (or any plugin) from within a python script. I am generating a PSE file from within python in the following fashion:

#!/usr/bin/python
import __main__
__main__.pymol_argv = ['pymol','-qc'] # Pymol: quiet and no GUI
import pymol
pymol.finish_launching()

pdbID = "1G68"
fetchResult = pymol.cmd.fetch(pdbID, type='pdb', quiet=1)
if fetchResult == -1:
	sys.exit("The provided PDB ID %s does not exist"%pdbID)

pymol.cmd.save(“test.pse”)


how would I now call the spectrumany plugin or any plugin function extending to the console in this way? 

cmd.<plugin_name> doesn’t work

thank you!

Re: [PyMOL] Details of the morph interpolation?

[Thomas Holder <thomas.holder@sc...>]

Hi Emily,

PyMOL's morphing performs two steps: (1) RigiMOL, and (2) refinement of non-backbone atoms by sculpting. The second part can be skipped with "refinement=0".

Unfortunately, there is no RigiMOL publication or method documentation.

The sculpting refinement tries to avoid clashes and maintain the local sidechain geometry, based on start and end conformation as references. You are right that sculpting doesn't consider the Ramachandran plot or a real energy force field. But it does consider clashes (it has a VDW term). Check "Build > Sculpting > ...", the bottom part of that submenu lists some of the available terms. The corresponding numerical values can be found here:
https://sourceforge.net/p/pymol/code/HEAD/tree/trunk/pymol/layer2/Sculpt.h

The "morph" command refinement uses all sculpting terms. You could customize that, e.g. exclude VDW repulsion, like this:

PyMOL> morph mout, sele1, sele2, refinement=0
PyMOL> from epymol.rigimol import refine
PyMOL> refine(5, "mout", sculpt_field_mask=(0xFFF & ~0x60))

You can also "fix" atoms, e.g. all non-polymer atoms, like free ions, which tend to bounce around as a result of the refinement:

PyMOL> morph mout, sele1, sele2, refinement=0
PyMOL> from epymol.rigimol import refine
PyMOL> flag fix, (not polymer), set
PyMOL> refine(5, "mout")

Hope that helps.

Cheers,
  Thomas

On 30 May 2016, at 12:43, Emilia C. Arturo (Emily) <eca38@...> wrote:

> Hello.
> 
> I would like to know more about the type of interpolation that is done when morph is called, and what calculations are done at each refinement cycle. Is there a literature reference or previous forum discussion to which you can point me?
> 
> From my sifting through the internet, I settled on the likelihood that refinement is done using the "molecular sculpting" algorithm that has been employed since at least this discussion took place in 2002: http://www.mail-archive.com/pymol-users@.../msg00359.html
> In other words, refinement is not done on the basis of energy differences, Ramachandran plot, interatomic clashes, or other problems with geometry that could arise at each interpolation step. 
> 
> Is that correct? If so, is there a way to customize the refinement that's done?
> 
> I am using MacPyMOL version 1.7.6.2.
> 
> Regards,
> 
> Emily.

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] Numpy in incentive pymol

[Thomas Holder <thomas.holder@sc...>]

Hi Filip,

Incentive PyMOL includes numpy and scipy. However, the 1.8.0.0 release on Windows was missing some dlls, that's why "import numpy" fails. The 1.8.0.7 update fixes that.

Cheers,
  Thomas

On 30 May 2016, at 06:44, Filip Leonarski <leonarski@...> wrote:

> Hi,
> 
>    I have a question - is it possible to have numpy and scipy available in pymol 1.8 incentive version. I have some plugins that worked perfectly well with pymol 1.7, however after upgrade to 1.8 they fail on "import numpy" step.
> 
> Thanks,
> Filip
> 
> -- 
> Filip Leonarski, PhD
> IBMC/CNRS
> 15 rue René Descartes
> 67084 Strasbourg Cedex

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

[PyMOL] migrating Fe ions and the use of 'morph'

[Emilia C. Arturo (Emily) <eca38@dr...>]

Hello all.

I'm struggling to comprehend why the morph function, as called using
MacPyMOL version 1.7.6.2, is making iron ions either migrate out of the
active site during the interpolation, or completely absent from the
interpolation.

I call the morph function like so:  morph morphresult, pdb1, pdb2, match=#,
where in place of '#' I have tried all the arguments available to match; if
#=in, then the iron ion in one, two, or three chains of the four chains in
each of pdb1 and pdb2, migrates out of the active site(s) and into some
nonsensical space; if #=like or any other argument, the iron ions do not
appear in the interpolation. Both pdb1 and pdb2 have four chains, and in
each of the chains is an iron ion labeled identically as 'FE'.

Has anyone a recommendation for how to address this?

Emily.

-- 
"Study as if you were going to live forever; live as if you were going to
die tomorrow." - Maria Mitchell

"Success is going from failure to failure without losing your enthusiasm."
- Anon.

“We are the people we have been waiting for.”
- A tag line from MIT's Vehicle Design Summit website (http://vds.mit.edu)

[PyMOL] Details of the morph interpolation?

[Emilia C. Arturo (Emily) <eca38@dr...>]

Hello.

I would like to know more about the type of interpolation that is done when
morph is called, and what calculations are done at each refinement cycle.
Is there a literature reference or previous forum discussion to which you
can point me?

>From my sifting through the internet, I settled on the likelihood that
refinement is done using the "molecular sculpting" algorithm that has been
employed since at least this discussion took place in 2002:
http://www.mail-archive.com/pymol-users@.../msg00359.html
In other words, refinement is not done on the basis of energy differences,
Ramachandran plot, interatomic clashes, or other problems with geometry
that could arise at each interpolation step.

Is that correct? If so, is there a way to customize the refinement that's
done?

I am using MacPyMOL version 1.7.6.2.

Regards,

Emily.


-- 
"Study as if you were going to live forever; live as if you were going to
die tomorrow." - Maria Mitchell

"Success is going from failure to failure without losing your enthusiasm."
- Anon.

“We are the people we have been waiting for.”
- A tag line from MIT's Vehicle Design Summit website (http://vds.mit.edu)

[PyMOL] Details of the morph interpolation?

[Emilia C. Arturo (Emily) <ecgarturo@gm...>]

Hello.

I would like to know more about the type of interpolation that is done when
morph is called, and what calculations are done at each refinement cycle.
Is there a reference or previous forum discussion to which you can point me?

I am using MacPyMOL version 1.7.6.2.

Regards,

Emily.

-- 
"Study as if you were going to live forever; live as if you were going to
die tomorrow." - Maria Mitchell

"Success is going from failure to failure without losing your enthusiasm."
- Anon.

“We are the people we have been waiting for.”
- A tag line from MIT's Vehicle Design Summit website (http://vds.mit.edu)

[PyMOL] Map issue

[Filip Leonarski <F.L<eonarski@ib...>]

Hi,

    I'm trying to access electron density maps from PyMol. Everything is
fine, when the map is orthorombic. I take map extremities with get_extend
and compare them with shape of array accessed via get_volume_field .
However when map is non-orthorombic I need to shuffle between
fractional/real coordinates. And here is the problem:

I have a map calculated exactly for the unit cell. However map_extend
provides values around 1% smaller. Why can it be?

Thanks,
Filip


-- 
Filip Leonarski, PhD
IBMC/CNRS
15 rue René Descartes
67084 Strasbourg Cedex