pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] Problem With Dynamic_Gromacs Plugin

[Stephen P. M. <s.m...@sb...>]

I just downloaded, compiled and installed gromacs-2020 without any 
warnings or errors.  However when I attempt opening the Dynamic_Gromacs 
2.2.1 plugin I get the error:

'module' object has no attribute 'showerror' and everything stops.

Now, the plugin has been working with the Debian Stretch default 
gromacs-2019.1. Further, with the gromacs 2020 installation gmx command 
executes correctly at the command line.

I may be wrong, but, might this be a PyMOL  error?

Thanks in advance.

-- 
Stephen P. Molnar, Ph.D.
www.molecular-modeling.net
614.312.7528 (c)
Skype:  smolnar1

Re: [PyMOL] Ray tracing transparent sticks

[Jarrett J. <jar...@sc...>]

Hello,

Which version are you using? We had this regression in 2.3.0 but was fixed
in the 2.3.2 patch update.

On Thu, Jan 30, 2020 at 9:34 AM Ioannis Riziotis <riz...@eb...> wrote:

> Hello!
>
> I have been trying to ray trace stick representations with transparency
> (i.e. stick_transparency = 0.5). Although surface transparency is visible
> in ray tracing, transparent sticks always appear opaque in the rendered
> image.
>
> Is there a way to resolve this? Note that in OpenGL, stick transparency
> appears normal; the problem is only in ray tracing.
>
> Thank you very much.
>
> All the best,
> Yannis
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>


-- 

*Jarrett Johnson* | Senior Developer
[image: Schrodinger Logo] <https://www.schrodinger.com/>

[PyMOL] Ray tracing transparent sticks

[Ioannis R. <riz...@eb...>]

Hello!

I have been trying to ray trace stick representations with transparency (i.e. stick_transparency = 0.5). Although surface transparency is visible in ray tracing, transparent sticks always appear opaque in the rendered image. 

Is there a way to resolve this? Note that in OpenGL, stick transparency appears normal; the problem is only in ray tracing.

Thank you very much.

All the best,
Yannis

Re: [PyMOL] Problem with PDB file export

[Ofir S. L. <ofi...@gm...>]

Hi Ezra,
Good call, I knew it had to be foolish because it worked yesterday.

Thanks!!
Ofir

‫בתאריך יום ד׳, 22 בינו׳ 2020 ב-16:10 מאת ‪Ezra Peisach‬‏ <‪
ezr...@rc...‬‏>:‬

> The dots and question marks are appropriate. You did not export a PDB
> file, but instead an mmCIF/PDBx file.
>
> For an explanation of what the fields mean, you can look at
> http://mmcif.wwpdb.org/docs/tutorials/content/atomic-description.html
>
>
> On 1/21/20 9:46 PM, Ofir Shein Lumbroso wrote:
>
> Hi all,
> I'm a new user of PyMOL and I'm trying to export a PDB file from a PyMOL
> session and It seems to have some errors. I'm using the default settings
> and I'm getting some dots and question marks in the exported PDB file, can
> you please help?
>
> I attached a corrupted PDB file for example.
>
> Thanks!
> Ofir
>
> --
> *Ofir Shein-Lumbroso*
> *m:* +61 406 276 801  |  *e: *ofi...@gm...
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 
*Ofir Shein-Lumbroso*
*m:* +61 406 276 801  |  *e: *ofi...@gm...

Re: [PyMOL] Problem with PDB file export

[Ezra P. <ezr...@rc...>]

The dots and question marks are appropriate. You did not export a PDB 
file, but instead an mmCIF/PDBx file.

For an explanation of what the fields mean, you can look at 
http://mmcif.wwpdb.org/docs/tutorials/content/atomic-description.html


On 1/21/20 9:46 PM, Ofir Shein Lumbroso wrote:
> Hi all,
> I'm a new user of PyMOL and I'm trying to export a PDB file from a 
> PyMOL session and It seems to have some errors. I'm using the default 
> settings and I'm getting some dots and question marks in the 
> exported PDB file, can you please help?
>
> I attached a corrupted PDB file for example.
>
> Thanks!
> Ofir
>
> -- 
> *Ofir Shein-Lumbroso*
> *m:* +61 406 276 801  | *e: *ofi...@gm... 
> <mailto:ofi...@gm...>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] Problem with PDB file export

[Jarrett J. <jar...@sc...>]

  Hello,

Can I ask which version of PyMOL you're using? I don't see anything wrong
on my end.

On Tue, Jan 21, 2020 at 9:48 PM Ofir Shein Lumbroso <ofi...@gm...>
wrote:

> Hi all,
> I'm a new user of PyMOL and I'm trying to export a PDB file from a PyMOL
> session and It seems to have some errors. I'm using the default settings
> and I'm getting some dots and question marks in the exported PDB file, can
> you please help?
>
> I attached a corrupted PDB file for example.
>
> Thanks!
> Ofir
>
> --
> *Ofir Shein-Lumbroso*
> *m:* +61 406 276 801  |  *e: *ofi...@gm...
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 

*Jarrett Johnson* | Senior Developer
[image: Schrodinger Logo] <https://www.schrodinger.com/>

[PyMOL] Problem with PDB file export

[Ofir S. L. <ofi...@gm...>]

Hi all,
I'm a new user of PyMOL and I'm trying to export a PDB file from a PyMOL
session and It seems to have some errors. I'm using the default settings
and I'm getting some dots and question marks in the exported PDB file, can
you please help?

I attached a corrupted PDB file for example.

Thanks!
Ofir

-- 
*Ofir Shein-Lumbroso*
*m:* +61 406 276 801  |  *e: *ofi...@gm...

[PyMOL] Issues when displaying surfaces of two objects in two distinct display grids

[Vedat D. <ved...@gm...>]

Hi altogether, 

using Pymol open source 2.4, I'm trying to simultaneously display two
objects (OB1 & OB2) side-by-side in a grid (>Display>Grid>By object). So
I have one object (OB1) on the left part and one (OB2) on the right.

Now, in order to have two surfaces on the left covering different areas
of the protein, I need to partially duplicate the object on the left
(OB1). Both surfaces on the left are shown properly.

But if I do the same with the second object (OB2, on the right part of
the screen), I run into issues: for none of the objects created as
duplicates (copies) from OB2 I am able to display the corresponding
surface. For the original object (OB2) it works. But this is not what I
want.

Does anyone know what's going on and how to circumvent this problem?

Many thanks in advance & best wishes,

Vedat

Re: [PyMOL] How to print the time stample on each frame of the movie for molecular dynamics trajectory in Pymol?

[Thomas H. <tho...@sc...>]

Hi Yeping,

It's possible to create a such a label, but unfortunately it's a bit complicated. The following script places a label with 2500 states in the upper right corner of the display area.

# create a discrete multi-state object with one labeled atom per state
pseudoatom tmp, label=pending
python
for i in range(2500):
    cmd.label("tmp", "'{} ps'".format(i * 80))
    cmd.create('timestaple', 'tmp', 1, i + 1, discrete=1)
python end
delete tmp
# anchor the label in the upper right corner
set label_screen_point, [1, 1, 0], timestaple
set label_relative_mode, 1, timestaple
# align the label to the bottom left of the anchor
set label_position, [-1, -1, 0], timestaple


Those label settings are documented here:
https://pymol.org/d/setting:label

Hope that helps.

Cheers,
  Thomas


> On Jan 15, 2020, at 5:22 AM, sunyeping via PyMOL-users <pym...@li...> wrote:
> 
> Dear All,
> 
> I load a molecular dynamics (gromacs) trajectory into Pymol and wish to make a movie with it. The trajectory contains 2500 frames, corresponding to 200 ns simulation time, so each frame represents 80 ps. I wish to print time stample on each stample. For example, on the first frame, " 0 ns" is printed; on the second frame, "80 ps" is printed; on the third frame, "160 ps" is printed. How I cannot find any clue how to do this. Could you have any clue how to finish this task? 
> 
> Best regards,
> Yeping Sun
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] diaplay actural sizes in Pymol

[Thomas H. <tho...@sc...>]

Hi Ting,

This will display the assemblies (biological units) in a grid. The result should look like in the attached image.

set assembly
set all_states
set grid_mode
fetch 1igt 1s58 3j3i 2ztn 6ui6 5wtf 3iyo, type=mmtf
zoom

The "assembly" setting replaces the use of type=pdb1. It works with type=cif and type=mmtf.

https://pymolwiki.org/index.php/Assembly

Hope that helps.

Cheers,
  Thomas




> On Jan 20, 2020, at 7:21 AM, Ting Hu via PyMOL-users <pym...@li...> wrote:
> 
> Dear Pymol-users support,
> 
> I want to compare the sizes of different virus and IgG in Pymol. But they are exhibiting similar sizes. how can i change that?
> 
> the commands I enter are as below:
> fetch 1igt, type=pdb1
> fetch 1s58, type=pdb1 set all_states, on
> fetch 3j3i, type=pdb1 set all_states, on
> fetch 2ztn, type=pdb1 set all_states, on
> fetch 6ui6, type=pdb1 set all_states, on
> fetch 5wtf, type=pdb1 set all_states, on
> fetch 3iyo, type=pdb1 set all_states, on
> fetch 1s58, type=pdb1 set all_states, on
> 
> Best regrds
> Ting
>  
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

[PyMOL] diaplay actural sizes in Pymol

[Ting Hu <ti...@mo...>]

Dear Pymol-users support,

I want to compare the sizes of different virus and IgG in Pymol. But they
are exhibiting similar sizes. how can i change that?

the commands I enter are as below:
fetch 1igt, type=pdb1
fetch 1s58, type=pdb1 set all_states, on
fetch 3j3i, type=pdb1 set all_states, on
fetch 2ztn, type=pdb1 set all_states, on
fetch 6ui6, type=pdb1 set all_states, on
fetch 5wtf, type=pdb1 set all_states, on
fetch 3iyo, type=pdb1 set all_states, on
fetch 1s58, type=pdb1 set all_states, on

Best regrds
Ting

[PyMOL] Does Pymol perform protein folding to get from a amino acid

[Edward M. <sci...@gm...>]

sequence to the structure of the protein.

 What version of Python is Pymol written in.

Re: [PyMOL] click and select bug in 2.2

[Tamas H. <bio...@gm...>]

Hi Thomas,

Thanks a lot.

In the last 15 years I tried to compile pymol several times without 
success. Now installing from the source was like a charm. Till now I did 
not find that bug in the github version.

(6 months were not enough to get used to the new interface. I am trying 
to use it with decoupled windows, but somehow the two windows are pretty 
inconvenient in this version.)

Cheers,
Thomas

-- 
Tamas Hegedus, PhD
Senior Research Fellow
Department of Biophysics and Radiation Biology
Semmelweis University     | phone: (36) 1-459 1500/60233
Tuzolto utca 37-47        | mailto:ta...@he...
Budapest, 1094, Hungary   | http://www.hegelab.org

On 1/10/20 5:35 PM, Thomas Holder wrote:
> Hi Tamas,
> 
> Sounds like one of these bugs:
> 
> https://github.com/schrodinger/pymol-open-source/issues/11
> https://github.com/schrodinger/pymol-open-source/issues/35
> 
> Can you install the latest version from source, like described here?
> 
> https://pymolwiki.org/index.php/Linux_Install#Install_from_source
> 
> Cheers,
>    Thomas
> 
>> On Jan 10, 2020, at 4:15 PM, Tamas Hegedus <bio...@gm...> wrote:
>>
>> Hi,
>>
>> I use pymol 2.2 (debian stable release).
>> Sometimes pymol starts to behave in a strange way. Clicking to an amino acid select a residue somewhere else in the protein.
>> (This is not caused by me missing the click in the 3D)
>>
>> I would be happy not to downgrade pymol if you have a solution to get around this bug.
>>
>> Thanks,
>> Tamas
>>
>>
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
> 
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
> 

[PyMOL] How to print the time stample on each frame of the movie for molecular dynamics trajectory in Pymol?

[sunyeping <sun...@al...>]

Dear All,

I load a molecular dynamics (gromacs) trajectory into Pymol and wish to make a movie with it. The trajectory contains 2500 frames, corresponding to 200 ns simulation time, so each frame represents 80 ps. I wish to print time stample on each stample. For example, on the first frame, " 0 ns" is printed; on the second frame, "80 ps" is printed; on the third frame, "160 ps" is printed. How I cannot find any clue how to do this. Could you have any clue how to finish this task? 

Best regards,
Yeping Sun

Re: [PyMOL] How to see a homotetramer

[Roger R. <rro...@co...>]

fetch 6h07, type=pdb1

Roger Rowlett
Gordon & Dorothy Kline Professor, Emeritus
Department of Chemistry
Colgate University


On Tue, Jan 14, 2020, 3:42 AM Clelia Canova <cle...@gm...> wrote:

> Hi!
>
> I’m studying the file *6H07. pdb *for a project, download for rcsb.com.
> How can I see the Biological Assembly on Pymol like in PDB, instead of
> seeing only the monomer (asymmetric unit).
>
> In the screen I see 6h07 1/4 and not 4/4.
>
> In the commander zone it’s written:
>  ” Detected 4 cpu cores. Enable multithreaded rendering.”
> If I push the key PLAY the protein start to move fast from 1 to 4 of 4
> positions.
>
> How can I see the 4 position together??
>
> Thank you very much,
>
> Clelia Canova
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] How to see a homotetramer

[Ali K. <aku...@un...>]

Hi Clelia,

You can use the split_states command on 6h07 to make each frame an object,

If you want to combine them into a single object, use the following to make the chains unique:
alter 6h07_0002 and chain A, chain = 'C'
alter 6h07_0002 and chain B, chain = 'D'

Then combine using:
create 6h07_assembly, 6h07_*

Cheers,

Ali

Ali Kusay | BPharm (Hons) | PhD Candidate
The University of Sydney School of Pharmacy | Faculty of Medicine and Health
424, Brain and Mind Centre | The University of Sydney | NSW 2050

From: Clelia Canova <cle...@gm...>
Date: Tuesday, 14 January 2020 at 7:45 pm
To: "pym...@li..." <pym...@li...>
Subject: [PyMOL] How to see a homotetramer

Hi!

I’m studying the file 6H07. pdb for a project, download for rcsb.com.
How can I see the Biological Assembly on Pymol like in PDB, instead of seeing only the monomer (asymmetric unit).

In the screen I see 6h07 1/4 and not 4/4.

In the commander zone it’s written:
 ” Detected 4 cpu cores. Enable multithreaded rendering.”
If I push the key PLAY the protein start to move fast from 1 to 4 of 4 positions.

How can I see the 4 position together??

Thank you very much,
Clelia Canova

[PyMOL] How to see a homotetramer

[Clelia C. <cle...@gm...>]

Hi!

I’m studying the file 6H07. pdb for a project, download for rcsb.com.
How can I see the Biological Assembly on Pymol like in PDB, instead of seeing only the monomer (asymmetric unit).

In the screen I see 6h07 1/4 and not 4/4.

In the commander zone it’s written:
 ” Detected 4 cpu cores. Enable multithreaded rendering.”
If I push the key PLAY the protein start to move fast from 1 to 4 of 4 positions.

How can I see the 4 position together??

Thank you very much,

Clelia Canova

Re: [PyMOL] click and select bug in 2.2

[Thomas H. <tho...@sc...>]

Hi Tamas,

Sounds like one of these bugs:

https://github.com/schrodinger/pymol-open-source/issues/11
https://github.com/schrodinger/pymol-open-source/issues/35

Can you install the latest version from source, like described here?

https://pymolwiki.org/index.php/Linux_Install#Install_from_source

Cheers,
  Thomas

> On Jan 10, 2020, at 4:15 PM, Tamas Hegedus <bio...@gm...> wrote:
> 
> Hi,
> 
> I use pymol 2.2 (debian stable release).
> Sometimes pymol starts to behave in a strange way. Clicking to an amino acid select a residue somewhere else in the protein.
> (This is not caused by me missing the click in the 3D)
> 
> I would be happy not to downgrade pymol if you have a solution to get around this bug.
> 
> Thanks,
> Tamas
> 
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

[PyMOL] click and select bug in 2.2

[Tamas H. <bio...@gm...>]

Hi,

I use pymol 2.2 (debian stable release).
Sometimes pymol starts to behave in a strange way. Clicking to an amino 
acid select a residue somewhere else in the protein.
(This is not caused by me missing the click in the 3D)

I would be happy not to downgrade pymol if you have a solution to get 
around this bug.

Thanks,
Tamas

Re: [PyMOL] Protonated aspartic acid

[Neena S. E. <nee...@gm...>]

Thank you Pedro!

On Tue, 7 Jan 2020 at 20:17, Pedro Lacerda <psl...@gm...> wrote:

> Hi Neena,
>
> Check the builder. You can change the charge of a atom adding or removing
> H.
>
> Cheers,
>
> [image: image.png]
>
> Em ter., 7 de jan. de 2020 às 20:29, Neena Susan Eappen <
> nee...@gm...> escreveu:
>
>> Hello PyMOL users,
>>
>> How to change the protonation state of aminoacid in Pymol? Say from
>> aspartic acid at deprotonated state to protonated state?
>>
>> Thank you,
>> Neena
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
>
> --
> Pedro Sousa Lacerda
>
> Laboratório de Bioinformática e Modelagem Molecular
> Faculdade de Farmácia / UFBA
>
> @pslacerda
> +55 71 9 9981-1856
> http://lattes.cnpq.br/8338596525330907
>

[PyMOL] Display Slabbing and Ray Tracing Mode with Exported Movies

[Cowan, R. H. (Dr.) <rc...@le...>]

Hi All,

I'm wondering if you can help me with a problem that I've come across whilst generating a movie in pymol.

I've generated a morph, which i've then used the movie menu in version 2.3.2 to loop through the morp and go back to the start state with a pause at each end.

When I output the movie, using the draw rendering, the render does not appear to respect the existing slab settings for the display, and instead uses what appears to be the default settings. This does not appear to be the case with ray traced frames.

However, when ray tracing frames, the ray tracing mode setting is not respected, and only mode 1 is utilised, resulting in heavy borders around the protein in cartoon display mode.

I have not been able to find any details online about this behaviour, or any reference to changing display settings for movie rendering, so I assume it is supposed to follow the current selected options?

I am afraid that I cannot upload or attach a sample.

Any assistance with this odd behaviour would be appreciated.

Thanks,

Dr Richard Cowan
Research Associate

HWLSB 1/05
Department of Biochemistry
University of Leicester
Lancaster Road
Leicester, LE1 9HN, U.K.

Phone +44 (0) 116 229 7077

Re: [PyMOL] Protonated aspartic acid

[Pedro L. <psl...@gm...>]

Hi Neena,

Check the builder. You can change the charge of a atom adding or removing H.

Cheers,

[image: image.png]

Em ter., 7 de jan. de 2020 às 20:29, Neena Susan Eappen <
nee...@gm...> escreveu:

> Hello PyMOL users,
>
> How to change the protonation state of aminoacid in Pymol? Say from
> aspartic acid at deprotonated state to protonated state?
>
> Thank you,
> Neena
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 
Pedro Sousa Lacerda

Laboratório de Bioinformática e Modelagem Molecular
Faculdade de Farmácia / UFBA

@pslacerda
+55 71 9 9981-1856
http://lattes.cnpq.br/8338596525330907

[PyMOL] Protonated aspartic acid

[Neena S. E. <nee...@gm...>]

Hello PyMOL users,

How to change the protonation state of aminoacid in Pymol? Say from
aspartic acid at deprotonated state to protonated state?

Thank you,
Neena

[PyMOL] Open source build on Windows, watch out for the default path

[David M. <ma...@ca...>]

This is a FYI about avoiding a gotcha which shows up on some Windows 
systems.

When setting up a bat file to run the open source pymol on windows be 
sure to reduce the path to just the top of the pymol directory and 
C:\Windows\System32 and C:\Windows.  Typically other installed software 
has patched this so that it includes many more directories.

I ran into one machine which had "zlib1.dll" in an Intel wifi driver on 
the system's default path.  This was used instead of the "zlib1.dll" in 
the pymol ./bin directory which resulted in a mysterious crash part way 
through pymol starting up.

Regards,

David Mathog
ma...@ca...
Manager, Sequence Analysis Facility, Biology Division, Caltech

[PyMOL] Pymol, qt organization question

[David M. <ma...@ca...>]

Greetings,

I built Pymol 2.4.0.0a from the open source under mingw64 on W10(64 bit) 
and also have another variant from Christoph Gohlke's site here:

   https://www.lfd.uci.edu/~gohlke/pythonlibs/

When run in cmd.exe and access to the mingw64 directories is allowed 
mine starts right up
in qt mode and looks just like CG's version.  If access to mingw64 is 
blocked by renaming the top directory for that then mine does not start. 
  Apparently qt has hard coded paths.  The directory structure under the 
mingw64 directory for Qt parts is:

   ./bin/Qt*dll
   ./share/qt5/plugins/PyQt5/Qt
      ./plugins
          ./platforms
      ./qml
      ./translations
      (and many other directories not shown)


My mingw64 build reproduced the pieces shown above in the same 
organization, with also

   ./lib
      ./python38
      ./tcl8.6
      ./tk8.6


but it would not start when access the mingw64 directory structure was 
blocked.  By copying the "platforms" directory into "bin" mine would 
start without access to the mingw64 directories, but there were subtle 
differences in the interface.  Examples:

1. icon in upper left corner: CG small image of molecule, Mine small 
window icon.
2. Menu names: CG black on white, Mine black on gray
3. top pane border:  CG single blue line, mine narrow grey bar with thin 
black line on outside and thicker black line on inside etc.

As far as I can tell the program works OK otherwise (other than that 
that APBS plugin won't load, which is discussed in other threads on this 
list).  There were no warnings.

My assumption is that Qt is not finding configuration, plugins, etc. it 
needs to start.

The organization in CG's is quite different, with the plugins, qml, 
translations and a bin
directory under: Python37/lib/site-packages/PyQt5/Qt.  When  my 
"share/PyQt5/Qt" is
moved to "./lib/Python3.8/site-packages/PyQt5/Qt" then mine starts up 
even without access to
mingw64 and looks again like CG's.

This is what I want to understand:

1. Why would the Qt directory tree from mingw64 work under 
site-packages/PyQt5 when it does not work under its original (relative) 
position?  (I read a lot about qt.conf and did not find anything 
describing this.)

2. Is there some way to get qt5 to log "could not find whatever" 
messages?  When it was running not quite right with just a "platform" 
directory under ./bin it was clearly not finding things, but it wasn't 
giving any indications that there was a problem.

(Note, be sure to remove the _many_ *d.dll libraries, these debug 
libraries are huge and not needed for normal use of the program.)


Thanks,

David Mathog
ma...@ca...
Manager, Sequence Analysis Facility, Biology Division, Caltech