pymol-users — Collaborative support and tips for PyMOL users

Re: [PyMOL] User defined variable or property

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

Didn't found the module `pymol.properties.set_property` as stated by
https://pymol.org/pymol-command-ref.html#set_property.

Em seg., 6 de jan. de 2020 às 15:40, Pedro Lacerda <psl...@gm...>
escreveu:

> Hi,
>
> How can I store custom object properties.
>
> I didn't found `set_property` or `get_property` in my PyMOL version.
> Neither found a way to store arbitrary session data. I even tried to encode
> data in the label to parse it back, but found no way to read a label value.
>
> How can I have the `set_property` and `get_property` feature?
>
> --
> Pedro Sousa Lacerda
>
> Laboratório de Bioinformática e Modelagem Molecular
> Faculdade de Farmácia / UFBA
>
> @pslacerda
> +55 71 9 9981-1856
> http://lattes.cnpq.br/8338596525330907
>


-- 
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] User defined variable or property

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

Hi,

How can I store custom object properties.

I didn't found `set_property` or `get_property` in my PyMOL version.
Neither found a way to store arbitrary session data. I even tried to encode
data in the label to parse it back, but found no way to read a label value.

How can I have the `set_property` and `get_property` feature?

-- 
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] 13th CCP4/APS Crystallographic School in the US

[Xu, Q. <qx...@an...>]

Dear Colleagues,

We are pleased to announce the 13th annual CCP4/APS crystallographic school “From data collection to structure refinement and beyond” will be held on June 15-22, 2020 at the Advanced Photon Source (APS), Argonne National Laboratory (ANL), near Chicago, Illinois, USA. All details can be found at the school website: http://www.ccp4.ac.uk/schools/APS-2020/index.php.

Dates: June 15 through 22, 2020

Location: Advanced Photon Source, Argonne National Laboratory, Argonne (Near Chicago), Illinois, USA

The school comprises two parts: data collection workshop and crystallographic computing workshop. Data collection workshop includes beamline training, data collection on GM/CA@APS beamlines 23ID-D and 23ID-B equipped with Pilatus3 6M and Eiger 16M detectors respectively, and data processing. For data collection, only the participants' crystals will be used. Crystallographic computation workshop will feature many modern crystallographic software packages taught by authors and other experts. The daily schedule will be organized in three sections – lectures, tutorials, and hands-on (interactive trouble-shooting of the technical difficulties the participants face in their projects). We have had considerable success resolving these problems in past years, attested by resulting publications (see http://www.ccp4.ac.uk/schools/APS-school/publications.php). A sample program, contact info and other details can be found at the School website.

Applicants: Graduate students, postdoctoral researchers and early-career faculty, along with commercial/industrial researchers are encouraged to apply. Only about 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops.

Application: Application deadline is April 1th, 2020. To apply, visit https://www.ccp4.ac.uk/schools/APS-2020/application.php<https://www.ccp4.ac.uk/schools/APS-2019/application.php>.

Fees: The registration for application is free but there is $500 participation fee for the selected academic students and $950 for industrial researchers. A valid credit card is required for registration, however, it will be charged only for students selected to participate. The students will be responsible for their transportation and lodging. The workshop organizers can assist in making lodging reservations at the Argonne Guest House. The workshop will cover all other expenses (including meals).


We hope to see you at the school.


Charles, Garib and Qingping

Re: [PyMOL] SOLVED Re: PyMOL 2.3.2 - GUI not printing/returning values when running get, count_atoms etc

[Aureliano G. <gue...@gm...>]

Thank you for the feedback

On Sun, Jan 5, 2020 at 12:30 AM Joe Kaczmarski <kac...@gm...>
wrote:

> Thanks Aureliano,
>
> I have just worked out what the issue was: I was using a new .pymolrc file
> that I had got from someone else which had a line to limit the pymol
> feedback:
>
> _ feedback disable,all,everything
>
> Removing this line has got rid of this problem.
>
> Joe
>
> On 5 Jan 2020, at 4:18 pm, Aureliano Guedes <gue...@gm...>
> wrote:
>
> Did you try: ` print(cmd.get("light_count"))`?
>
> On Sun, Jan 5, 2020 at 12:02 AM Joe Kaczmarski <kac...@gm...>
> wrote:
>
>> Hi all,
>>
>> Pymol is not returning/printing values in the GUI command line window
>> after I run any command that is supposed to return/print a value (e.g. get,
>> count_atoms, get_viewport).
>>
>> For example, if I run >get light_count, nothing is returned.
>> However, I can get the value to print by running >print
>> cmd.get(“light_count”), but I find this a bit annoying..
>>
>> Any ideas why this may be happening? I am using Pymol 2.3.2 (MacOS),
>> education license.
>>
>> Regards,
>>
>> Joe
>>
>> <Screen Shot 2020-01-05 at 3.54.02 pm.png>
>>
>>
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
>
> --
> Aureliano Guedes
> skype: aureliano.guedes
> contato:  (11) 94292-6110
> whatsapp +5511942926110
>
>
>

-- 
Aureliano Guedes
skype: aureliano.guedes
contato:  (11) 94292-6110
whatsapp +5511942926110

[PyMOL] SOLVED Re: PyMOL 2.3.2 - GUI not printing/returning values when running get, count_atoms etc

[Joe K. <kac...@gm...>]

Thanks Aureliano, 

I have just worked out what the issue was: I was using a new .pymolrc file that I had got from someone else which had a line to limit the pymol feedback: 

_ feedback disable,all,everything

Removing this line has got rid of this problem. 

Joe

> On 5 Jan 2020, at 4:18 pm, Aureliano Guedes <gue...@gm...> wrote:
> 
> Did you try: ` print(cmd.get("light_count"))`?
> 
> On Sun, Jan 5, 2020 at 12:02 AM Joe Kaczmarski <kac...@gm... <mailto:kac...@gm...>> wrote:
> Hi all, 
> 
> Pymol is not returning/printing values in the GUI command line window after I run any command that is supposed to return/print a value (e.g. get, count_atoms, get_viewport).  
> 
> For example, if I run >get light_count, nothing is returned. 
> However, I can get the value to print by running >print cmd.get(“light_count”), but I find this a bit annoying.. 
> 
> Any ideas why this may be happening? I am using Pymol 2.3.2 (MacOS), education license. 
> 
> Regards, 
> 
> Joe
> 
> <Screen Shot 2020-01-05 at 3.54.02 pm.png>
> 
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li... <http://www.mail-archive.com/pym...@li...>
> Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe <https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe>
> 
> -- 
> Aureliano Guedes
> skype: aureliano.guedes
> contato:  (11) 94292-6110
> whatsapp +5511942926110

Re: [PyMOL] PyMOL 2.3.2 - GUI not printing/returning values when running get, count_atoms etc

[Aureliano G. <gue...@gm...>]

Did you try: ` print(cmd.get("light_count"))`?

On Sun, Jan 5, 2020 at 12:02 AM Joe Kaczmarski <kac...@gm...>
wrote:

> Hi all,
>
> Pymol is not returning/printing values in the GUI command line window
> after I run any command that is supposed to return/print a value (e.g. get,
> count_atoms, get_viewport).
>
> For example, if I run >get light_count, nothing is returned.
> However, I can get the value to print by running >print
> cmd.get(“light_count”), but I find this a bit annoying..
>
> Any ideas why this may be happening? I am using Pymol 2.3.2 (MacOS),
> education license.
>
> Regards,
>
> Joe
>
>
>
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe



-- 
Aureliano Guedes
skype: aureliano.guedes
contato:  (11) 94292-6110
whatsapp +5511942926110

[PyMOL] PyMOL 2.3.2 - GUI not printing/returning values when running get, count_atoms etc

[Joe K. <kac...@gm...>]

Hi all, 

Pymol is not returning/printing values in the GUI command line window after I run any command that is supposed to return/print a value (e.g. get, count_atoms, get_viewport).  

For example, if I run >get light_count, nothing is returned. 
However, I can get the value to print by running >print cmd.get(“light_count”), but I find this a bit annoying.. 

Any ideas why this may be happening? I am using Pymol 2.3.2 (MacOS), education license. 

Regards, 

Joe

[PyMOL] 2.4.0.0a oddness when building on Windows.

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

 From time to time I have been building pymol-open-source in one of two 
environments:

   WA:  Windows 7 32 bit, mingw32
   WB:  Windows 10 64 bit, mingw64

Christoph Gohlke does the same (and much more) using Visual Studio.  So 
two more environments:

   WC:  Windows 32 bit, Visual Studio
   WD:  Windows 64 bit, Visual studio

In previous versions I have never managed to make Qt work in WA, WB (it 
always fell back to tkinter because the qt5 import would fail), but Qt 
works in WC, WD.  Going forward I hope to figure out where the Qt 
problem is in WA,WB.

In any case, for 2.4.0.0a mine and his have exactly the same two bugs in 
tkinter mode in these environments.  I could not test this in a licensed 
version in these environments, perhaps somebody as Schrodinger will do 
that.

The issues are:

WA-BUG/WC-BUG:  Mouse scroll button often does not work.  (Also present 
at 2.3.0).  To demonstrate in either version do something like this:

    cd C:\progs\Python37\Lib\site-packages\pymol
    c:\progs\Python37\python.exe __init__.py -w pmg_tk
    #two separate windows will appear, as is normal
    #  for tkinter versions.
    #Load a molecule (I have been using 1du0.cif)
    #rotate the mouse scroll wheel - nothing happens
    #hold CONTROL and rotate the mouse scroll wheel -
    #  nothing happens
    #click several times on "3-button editing"/"3-button viewing",
    #  after a while the scroll wheel will start to work.
    #change focus to some other program's window by clicking on its frame
    #change focus back to lower Pymol window by clicking on its frame.
    #Scrolling will (usually) be broken again, repair as before.

WB-BUG/WD-BUG:  Tkinter larger window is blank.  To demonstrate start
either version in pmg_tk mode, as for WA-BUG above.  Two windows will 
appear but the larger one (where the molecule should appear once loaded) 
is solid black.  The upper window appears to be working normally.  There 
are no warning or error messages at launch and the program is still 
responsive in the upper window.  File->open->1duo.cif seems to complete, 
as the  program does not hang, and there are no warnings or errors, but 
the lower window is still solid black. To be more specific, the window 
frame appears to be normal, with a "Pymol Viewer   - [] X" header and a 
1 pixel border on the sides and bottom, but the interior is always just 
black.  This bug was NOT present in 2.3.0.

The mingw32/64 build install instructions are way too long to post here. 
  This is how I installed C. Gohlke's version (WD):

1. Download and install Pymol 3.7.5 from
   https://www.python.org/ftp/python/3.7.5/python-3.7.5-amd64.exe
Install into
   C:\progs\Python37
then delete the installer.


2.  From C. Gohlke's site
   https://www.lfd.uci.edu/~gohlke/pythonlibs/
download into C:\temp\gohlke_pieces:

numpy-1.17.4+mkl-cp37-cp37m-win_amd64.whl
pymol-2.4.0a0-cp37-cp37m-win_amd64.whl
pymol_launcher-2.1-cp37-cp37m-win_amd64.whl
pip-19.3.1-py2.py3-none-any.whl
Pmw-2.0.1-py3-none-any.whl

3. CMD window, do:
cd .. #to top
cd progs
cd Python37
cd Scripts
pip3 install pyQt5

cd C:\temp\gohlke_pieces
C:\progs\Python37\python.exe pip-19.3.1-py2.py3-none-any.whl/pip install 
--no-index --find-links="%CD%" pymol_launcher

Regards,

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

Re: [PyMOL] Performance of extended commands vs python function

[Lorenzo G. <br...@gm...>]

Hi Thomas,

I'm not sure I get it. Does that mean that `cmd.sync()` is actually not
doing anything at all if called outside of `cmd.do()`?

Cheers,
Lorenzo

Il giorno mer 18 dic 2019 alle ore 10:49 Thomas Holder <
tho...@sc...> ha scritto:

> Hi Lorenzo,
>
> Thanks for the script, and great that you could identify cmd.sync() as the
> culprit. I looked at the code, cmd.do("cmd.sync()") literally blocks itself
> until it times out after 1 second. cmd.do() puts commands in a queue, and
> cmd.sync() tries to ensure that all queued commands have been executed.
> PyMOL calls cmd.sync() in a few places right before capturing an image for
> example.
>
> Not sure how this could be improved. Maybe cmd.sync() should print a
> warning if it times out, that would help to notice a self-lock.
>
> Cheers,
>   Thomas
>
>
> > On Dec 17, 2019, at 11:42 AM, Lorenzo Gaifas <br...@gm...> wrote:
> >
> > After playing around with it a bit longer, it's clear that I
> misunderstood. The issue was not with `cmd.alter` nor with `cmd.show_as`,
> but with `cmd.sync`.
> >
> > I was calling many times a smaller function that contained `cmd.sync()`,
> which resulted - it seems - in all these calls piling up.
> >
> > Still, I don't know if it's intended behaviour for `sync` to be so much
> slower if it's called as a pymol function. Attached you will find a minimal
> working example to show the difference.
> >
> >
> > Il giorno lun 16 dic 2019 alle ore 17:52 Thomas Holder <
> tho...@sc...> ha scritto:
> > OK thanks. I haven't seen such performance differences before and
> couldn't reproduce it so far. Could you share your script (and data files
> if possible) with me?
> >
> > Thanks,
> >   Thomas
> >
> >
> > > On Dec 16, 2019, at 5:42 PM, Lorenzo Gaifas <br...@gm...> wrote:
> > >
> > > Yes, it does. Both cases are with the GUI and ewual graphical
> representation.
> > >
> > > On Mon, Dec 16, 2019, 17:37 Thomas Holder <
> tho...@sc...> wrote:
> > > Hi Lorenzo,
> > >
> > > When you say "run from a python script", is that with the graphical
> GUI? That "instant update", does that include instant update of visual
> representations?
> > >
> > > Thanks,
> > >   Thomas
> > >
> > >
> > > > On Dec 13, 2019, at 12:55 PM, Lorenzo Gaifas <br...@gm...>
> wrote:
> > > >
> > > > Dear Pymol users,
> > > >
> > > > I just discovered something I did not expect: the same python
> function can have extremely different performance when called as a python
> function or using the pymol api.
> > > >
> > > > To be more specific: I have a function func that (among other
> things) uses cmd.alter several times over a big system to change the
> properties and representation.
> > > >
> > > > If I run it calling func() from a python script, its effects are
> almost instant. If I call it with cmd.do('func') (or directly from within
> pymol with func), it’s extremely slow (up to 10 seconds) and Pymol freezes
> completely during this time.
> > > >
> > > > I expected this to be due to an overhead of the api itself, but when
> I do the same thing with a simpler function, I see no noticeable difference.
> > > >
> > > > Why exactly is this happening? And more importantly, how can I get
> the performance of func even when I call it from within pymol?
> > > >
> > > > Thank you,
> > > > Lorenzo
> > > >
> > > > _______________________________________________
> > > > 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.
> > >
> >
> > --
> > Thomas Holder
> > PyMOL Principal Developer
> > Schrödinger, Inc.
> >
> > <slow.py>
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

Re: [PyMOL] Performance of extended commands vs python function

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

Hi Lorenzo,

Thanks for the script, and great that you could identify cmd.sync() as the culprit. I looked at the code, cmd.do("cmd.sync()") literally blocks itself until it times out after 1 second. cmd.do() puts commands in a queue, and cmd.sync() tries to ensure that all queued commands have been executed. PyMOL calls cmd.sync() in a few places right before capturing an image for example.

Not sure how this could be improved. Maybe cmd.sync() should print a warning if it times out, that would help to notice a self-lock.

Cheers,
  Thomas


> On Dec 17, 2019, at 11:42 AM, Lorenzo Gaifas <br...@gm...> wrote:
> 
> After playing around with it a bit longer, it's clear that I misunderstood. The issue was not with `cmd.alter` nor with `cmd.show_as`, but with `cmd.sync`.
> 
> I was calling many times a smaller function that contained `cmd.sync()`, which resulted - it seems - in all these calls piling up.
> 
> Still, I don't know if it's intended behaviour for `sync` to be so much slower if it's called as a pymol function. Attached you will find a minimal working example to show the difference.
> 
> 
> Il giorno lun 16 dic 2019 alle ore 17:52 Thomas Holder <tho...@sc...> ha scritto:
> OK thanks. I haven't seen such performance differences before and couldn't reproduce it so far. Could you share your script (and data files if possible) with me?
> 
> Thanks,
>   Thomas
> 
> 
> > On Dec 16, 2019, at 5:42 PM, Lorenzo Gaifas <br...@gm...> wrote:
> > 
> > Yes, it does. Both cases are with the GUI and ewual graphical representation.
> > 
> > On Mon, Dec 16, 2019, 17:37 Thomas Holder <tho...@sc...> wrote:
> > Hi Lorenzo,
> > 
> > When you say "run from a python script", is that with the graphical GUI? That "instant update", does that include instant update of visual representations?
> > 
> > Thanks,
> >   Thomas
> > 
> > 
> > > On Dec 13, 2019, at 12:55 PM, Lorenzo Gaifas <br...@gm...> wrote:
> > > 
> > > Dear Pymol users,
> > > 
> > > I just discovered something I did not expect: the same python function can have extremely different performance when called as a python function or using the pymol api.
> > > 
> > > To be more specific: I have a function func that (among other things) uses cmd.alter several times over a big system to change the properties and representation.
> > > 
> > > If I run it calling func() from a python script, its effects are almost instant. If I call it with cmd.do('func') (or directly from within pymol with func), it’s extremely slow (up to 10 seconds) and Pymol freezes completely during this time.
> > > 
> > > I expected this to be due to an overhead of the api itself, but when I do the same thing with a simpler function, I see no noticeable difference.
> > > 
> > > Why exactly is this happening? And more importantly, how can I get the performance of func even when I call it from within pymol?
> > > 
> > > Thank you,
> > > Lorenzo
> > > 
> > > _______________________________________________
> > > 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.
> > 
> 
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
> 
> <slow.py>

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] Performance of extended commands vs python function

[Lorenzo G. <br...@gm...>]

After playing around with it a bit longer, it's clear that I misunderstood.
The issue was not with `cmd.alter` nor with `cmd.show_as`, but with
`cmd.sync`.

I was calling many times a smaller function that contained `cmd.sync()`,
which resulted - it seems - in all these calls piling up.

Still, I don't know if it's intended behaviour for `sync` to be so much
slower if it's called as a pymol function. Attached you will find a minimal
working example to show the difference.


Il giorno lun 16 dic 2019 alle ore 17:52 Thomas Holder <
tho...@sc...> ha scritto:

> OK thanks. I haven't seen such performance differences before and couldn't
> reproduce it so far. Could you share your script (and data files if
> possible) with me?
>
> Thanks,
>   Thomas
>
>
> > On Dec 16, 2019, at 5:42 PM, Lorenzo Gaifas <br...@gm...> wrote:
> >
> > Yes, it does. Both cases are with the GUI and ewual graphical
> representation.
> >
> > On Mon, Dec 16, 2019, 17:37 Thomas Holder <tho...@sc...>
> wrote:
> > Hi Lorenzo,
> >
> > When you say "run from a python script", is that with the graphical GUI?
> That "instant update", does that include instant update of visual
> representations?
> >
> > Thanks,
> >   Thomas
> >
> >
> > > On Dec 13, 2019, at 12:55 PM, Lorenzo Gaifas <br...@gm...>
> wrote:
> > >
> > > Dear Pymol users,
> > >
> > > I just discovered something I did not expect: the same python function
> can have extremely different performance when called as a python function
> or using the pymol api.
> > >
> > > To be more specific: I have a function func that (among other things)
> uses cmd.alter several times over a big system to change the properties and
> representation.
> > >
> > > If I run it calling func() from a python script, its effects are
> almost instant. If I call it with cmd.do('func') (or directly from within
> pymol with func), it’s extremely slow (up to 10 seconds) and Pymol freezes
> completely during this time.
> > >
> > > I expected this to be due to an overhead of the api itself, but when I
> do the same thing with a simpler function, I see no noticeable difference.
> > >
> > > Why exactly is this happening? And more importantly, how can I get the
> performance of func even when I call it from within pymol?
> > >
> > > Thank you,
> > > Lorenzo
> > >
> > > _______________________________________________
> > > 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.
> >
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

Re: [PyMOL] Performance of extended commands vs python function

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

OK thanks. I haven't seen such performance differences before and couldn't reproduce it so far. Could you share your script (and data files if possible) with me?

Thanks,
  Thomas


> On Dec 16, 2019, at 5:42 PM, Lorenzo Gaifas <br...@gm...> wrote:
> 
> Yes, it does. Both cases are with the GUI and ewual graphical representation.
> 
> On Mon, Dec 16, 2019, 17:37 Thomas Holder <tho...@sc...> wrote:
> Hi Lorenzo,
> 
> When you say "run from a python script", is that with the graphical GUI? That "instant update", does that include instant update of visual representations?
> 
> Thanks,
>   Thomas
> 
> 
> > On Dec 13, 2019, at 12:55 PM, Lorenzo Gaifas <br...@gm...> wrote:
> > 
> > Dear Pymol users,
> > 
> > I just discovered something I did not expect: the same python function can have extremely different performance when called as a python function or using the pymol api.
> > 
> > To be more specific: I have a function func that (among other things) uses cmd.alter several times over a big system to change the properties and representation.
> > 
> > If I run it calling func() from a python script, its effects are almost instant. If I call it with cmd.do('func') (or directly from within pymol with func), it’s extremely slow (up to 10 seconds) and Pymol freezes completely during this time.
> > 
> > I expected this to be due to an overhead of the api itself, but when I do the same thing with a simpler function, I see no noticeable difference.
> > 
> > Why exactly is this happening? And more importantly, how can I get the performance of func even when I call it from within pymol?
> > 
> > Thank you,
> > Lorenzo
> > 
> > _______________________________________________
> > 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.
> 

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] Performance of extended commands vs python function

[Lorenzo G. <br...@gm...>]

Yes, it does. Both cases are with the GUI and ewual graphical
representation.

On Mon, Dec 16, 2019, 17:37 Thomas Holder <tho...@sc...>
wrote:

> Hi Lorenzo,
>
> When you say "run from a python script", is that with the graphical GUI?
> That "instant update", does that include instant update of visual
> representations?
>
> Thanks,
>   Thomas
>
>
> > On Dec 13, 2019, at 12:55 PM, Lorenzo Gaifas <br...@gm...> wrote:
> >
> > Dear Pymol users,
> >
> > I just discovered something I did not expect: the same python function
> can have extremely different performance when called as a python function
> or using the pymol api.
> >
> > To be more specific: I have a function func that (among other things)
> uses cmd.alter several times over a big system to change the properties and
> representation.
> >
> > If I run it calling func() from a python script, its effects are almost
> instant. If I call it with cmd.do('func') (or directly from within pymol
> with func), it’s extremely slow (up to 10 seconds) and Pymol freezes
> completely during this time.
> >
> > I expected this to be due to an overhead of the api itself, but when I
> do the same thing with a simpler function, I see no noticeable difference.
> >
> > Why exactly is this happening? And more importantly, how can I get the
> performance of func even when I call it from within pymol?
> >
> > Thank you,
> > Lorenzo
> >
> > _______________________________________________
> > 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] Performance of extended commands vs python function

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

Hi Lorenzo,

When you say "run from a python script", is that with the graphical GUI? That "instant update", does that include instant update of visual representations?

Thanks,
  Thomas


> On Dec 13, 2019, at 12:55 PM, Lorenzo Gaifas <br...@gm...> wrote:
> 
> Dear Pymol users,
> 
> I just discovered something I did not expect: the same python function can have extremely different performance when called as a python function or using the pymol api.
> 
> To be more specific: I have a function func that (among other things) uses cmd.alter several times over a big system to change the properties and representation.
> 
> If I run it calling func() from a python script, its effects are almost instant. If I call it with cmd.do('func') (or directly from within pymol with func), it’s extremely slow (up to 10 seconds) and Pymol freezes completely during this time.
> 
> I expected this to be due to an overhead of the api itself, but when I do the same thing with a simpler function, I see no noticeable difference.
> 
> Why exactly is this happening? And more importantly, how can I get the performance of func even when I call it from within pymol?
> 
> Thank you,
> Lorenzo
> 
> _______________________________________________
> 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] Performance of extended commands vs python function

[Lorenzo G. <br...@gm...>]

Dear Pymol users,

I just discovered something I did not expect: the same python function can
have extremely different performance when called as a python function or
using the pymol api.

To be more specific: I have a function func that (among other things) uses
cmd.alter several times over a big system to change the properties and
representation.

If I run it calling func() from a python script, its effects are almost
instant. If I call it with cmd.do('func') (or directly from within pymol
with func), it’s extremely slow (up to 10 seconds) and Pymol freezes
completely during this time.

I expected this to be due to an overhead of the api itself, but when I do
the same thing with a simpler function, I see no noticeable difference.

Why exactly is this happening? And more importantly, how can I get the
performance of func even when I call it from within pymol?

Thank you,
Lorenzo

Re: [PyMOL] [EXTERNAL] Differentiate between bond types by color and representation

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

Hi Lorenzo and Blaine,

There is a "set_bond" command which can set (some) settings for individual bonds.

To change stick color and radius for the bond between atom 2 and 3:

set_bond stick_color, yellow, index 2, index 3
set_bond stick_radius, 0.2, index 2, index 3

Cheers,
  Thomas


> On Dec 11, 2019, at 4:57 PM, Mooers, Blaine H.M. (HSC) <Bla...@ou...> wrote:
> 
> Hi Lorenzo,
> 
> The use the lines instead of sticks may reduce the anticipated hit on performance. 
> There is a line_color setting that use you can.
> 
> Best regards,
> 
> Blaine
> 
> ________________________________________
> From: Lorenzo Gaifas [br...@gm...]
> Sent: Wednesday, December 11, 2019 9:48 AM
> To: Mooers, Blaine H.M.  (HSC)
> Cc: pymol-users
> Subject: Re: [EXTERNAL] [PyMOL] Differentiate between bond types by color and representation
> 
> Hi Blaine,
> 
> Yes, that's essentially what I'm doing. My worry is that since this doubles the amount of coordinates to keep track of, it will be detrimental to how long a trajectory I can load. Is there any other way to do this?
> 
> On Wed, Dec 11, 2019, 16:31 Mooers, Blaine H.M. (HSC) <Bla...@ou...<mailto:Bla...@ou...>> wrote:
> Hi Lorenzo,
> 
> You could make an object out of the elastic bonds with the 'create' command, show it as sticks, and use the stick_color setting to color the sticks only.
> You could make different objects for different subsets of the elastic bonds and color them differently.
> 
> Here is an example of the 'create' command that I used to make an object out of six coordinate covalent bonds between a sodium, a N7 nitrogen of an adenine, and five waters.
> 
> cmd.create('coorCov', '(3nd4_0001 and (resi 19 or resi 119 or resi 219 or resi 319 or resi 419 or resi 519 or (resi 3 and name N7)))')
> cmd.set('stick_color','magenta','coorCov')
> cmd.show('sticks','coorCov')
> 
> The color of the atoms, if shown as spheres, will remain the same.
> Although the above two commands are in the Python form, you can paste them onto the top command line in PyMOL.
> 
> By specifying the object as your selection in the argument to the set command, you can also change the thickness of the sticks in only than object so
> you can have sticks of different thickness in the same scene.
> 
> Best regards,
> 
> Blaine
> 
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
> 
> ________________________________________
> From: Lorenzo Gaifas [br...@gm...<mailto:br...@gm...>]
> Sent: Wednesday, December 11, 2019 8:38 AM
> To: pymol-users
> Subject: [EXTERNAL] [PyMOL] Differentiate between bond types by color and representation
> 
> Dear pymol users,
> 
> I'm trying to properly represent a coarse-grained protein model that has an elastic network.
> 
> I would like to show the bonds that are part of the elastic network with a different color (and possibly representation) from the normal bonds between atoms. However, as far as I know, color settings are atom-based, so I wasn't able to do what I wanted, because all bonds that lead to an atom will always share the same color.
> 
> The only solution I found was to create a copy of the protein with pseudoatoms and draw the elastic network there. However, I expect this has a negative effect on the performance, which is relevant since I plan to use this for molecular dynamics trajectories.
> 
> Am I trying to do this the wrong way? Is it just unfeasible?
> 
> 
> _______________________________________________
> 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] [EXTERNAL] Differentiate between bond types by color and representation

[Mooers, B. H.M. (HSC) <Bla...@ou...>]

Hi Lorenzo,

The use the lines instead of sticks may reduce the anticipated hit on performance. 
There is a line_color setting that use you can.

Best regards,

Blaine

________________________________________
From: Lorenzo Gaifas [br...@gm...]
Sent: Wednesday, December 11, 2019 9:48 AM
To: Mooers, Blaine H.M.  (HSC)
Cc: pymol-users
Subject: Re: [EXTERNAL] [PyMOL] Differentiate between bond types by color and representation

Hi Blaine,

Yes, that's essentially what I'm doing. My worry is that since this doubles the amount of coordinates to keep track of, it will be detrimental to how long a trajectory I can load. Is there any other way to do this?

On Wed, Dec 11, 2019, 16:31 Mooers, Blaine H.M. (HSC) <Bla...@ou...<mailto:Bla...@ou...>> wrote:
Hi Lorenzo,

You could make an object out of the elastic bonds with the 'create' command, show it as sticks, and use the stick_color setting to color the sticks only.
You could make different objects for different subsets of the elastic bonds and color them differently.

Here is an example of the 'create' command that I used to make an object out of six coordinate covalent bonds between a sodium, a N7 nitrogen of an adenine, and five waters.

cmd.create('coorCov', '(3nd4_0001 and (resi 19 or resi 119 or resi 219 or resi 319 or resi 419 or resi 519 or (resi 3 and name N7)))')
cmd.set('stick_color','magenta','coorCov')
cmd.show('sticks','coorCov')

The color of the atoms, if shown as spheres, will remain the same.
Although the above two commands are in the Python form, you can paste them onto the top command line in PyMOL.

By specifying the object as your selection in the argument to the set command, you can also change the thickness of the sticks in only than object so
you can have sticks of different thickness in the same scene.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

________________________________________
From: Lorenzo Gaifas [br...@gm...<mailto:br...@gm...>]
Sent: Wednesday, December 11, 2019 8:38 AM
To: pymol-users
Subject: [EXTERNAL] [PyMOL] Differentiate between bond types by color and representation

Dear pymol users,

I'm trying to properly represent a coarse-grained protein model that has an elastic network.

I would like to show the bonds that are part of the elastic network with a different color (and possibly representation) from the normal bonds between atoms. However, as far as I know, color settings are atom-based, so I wasn't able to do what I wanted, because all bonds that lead to an atom will always share the same color.

The only solution I found was to create a copy of the protein with pseudoatoms and draw the elastic network there. However, I expect this has a negative effect on the performance, which is relevant since I plan to use this for molecular dynamics trajectories.

Am I trying to do this the wrong way? Is it just unfeasible?

Re: [PyMOL] [EXTERNAL] Differentiate between bond types by color and representation

[Mooers, B. H.M. (HSC) <Bla...@ou...>]

Hi Lorenzo,

You could make an object out of the elastic bonds with the 'create' command, show it as sticks, and use the stick_color setting to color the sticks only.
You could make different objects for different subsets of the elastic bonds and color them differently.

Here is an example of the 'create' command that I used to make an object out of six coordinate covalent bonds between a sodium, a N7 nitrogen of an adenine, and five waters.

cmd.create('coorCov', '(3nd4_0001 and (resi 19 or resi 119 or resi 219 or resi 319 or resi 419 or resi 519 or (resi 3 and name N7)))')
cmd.set('stick_color','magenta','coorCov')
cmd.show('sticks','coorCov')

The color of the atoms, if shown as spheres, will remain the same.
Although the above two commands are in the Python form, you can paste them onto the top command line in PyMOL. 

By specifying the object as your selection in the argument to the set command, you can also change the thickness of the sticks in only than object so 
you can have sticks of different thickness in the same scene.

Best regards,

Blaine

Blaine Mooers, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
College of Medicine
University of Oklahoma Health Sciences Center
S.L. Young Biomedical Research Center (BRC) Rm. 466
975 NE 10th Street, BRC 466
Oklahoma City, OK 73104-5419

________________________________________
From: Lorenzo Gaifas [br...@gm...]
Sent: Wednesday, December 11, 2019 8:38 AM
To: pymol-users
Subject: [EXTERNAL] [PyMOL] Differentiate between bond types by color and representation

Dear pymol users,

I'm trying to properly represent a coarse-grained protein model that has an elastic network.

I would like to show the bonds that are part of the elastic network with a different color (and possibly representation) from the normal bonds between atoms. However, as far as I know, color settings are atom-based, so I wasn't able to do what I wanted, because all bonds that lead to an atom will always share the same color.

The only solution I found was to create a copy of the protein with pseudoatoms and draw the elastic network there. However, I expect this has a negative effect on the performance, which is relevant since I plan to use this for molecular dynamics trajectories.

Am I trying to do this the wrong way? Is it just unfeasible?

Re: [PyMOL] [EXTERNAL] Differentiate between bond types by color and representation

[Lorenzo G. <br...@gm...>]

Hi Blaine,

Yes, that's essentially what I'm doing. My worry is that since this doubles
the amount of coordinates to keep track of, it will be detrimental to how
long a trajectory I can load. Is there any other way to do this?

On Wed, Dec 11, 2019, 16:31 Mooers, Blaine H.M. (HSC) <
Bla...@ou...> wrote:

> Hi Lorenzo,
>
> You could make an object out of the elastic bonds with the 'create'
> command, show it as sticks, and use the stick_color setting to color the
> sticks only.
> You could make different objects for different subsets of the elastic
> bonds and color them differently.
>
> Here is an example of the 'create' command that I used to make an object
> out of six coordinate covalent bonds between a sodium, a N7 nitrogen of an
> adenine, and five waters.
>
> cmd.create('coorCov', '(3nd4_0001 and (resi 19 or resi 119 or resi 219 or
> resi 319 or resi 419 or resi 519 or (resi 3 and name N7)))')
> cmd.set('stick_color','magenta','coorCov')
> cmd.show('sticks','coorCov')
>
> The color of the atoms, if shown as spheres, will remain the same.
> Although the above two commands are in the Python form, you can paste them
> onto the top command line in PyMOL.
>
> By specifying the object as your selection in the argument to the set
> command, you can also change the thickness of the sticks in only than
> object so
> you can have sticks of different thickness in the same scene.
>
> Best regards,
>
> Blaine
>
> Blaine Mooers, Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Oklahoma Health Sciences Center
> S.L. Young Biomedical Research Center (BRC) Rm. 466
> 975 NE 10th Street, BRC 466
> Oklahoma City, OK 73104-5419
>
> ________________________________________
> From: Lorenzo Gaifas [br...@gm...]
> Sent: Wednesday, December 11, 2019 8:38 AM
> To: pymol-users
> Subject: [EXTERNAL] [PyMOL] Differentiate between bond types by color and
> representation
>
> Dear pymol users,
>
> I'm trying to properly represent a coarse-grained protein model that has
> an elastic network.
>
> I would like to show the bonds that are part of the elastic network with a
> different color (and possibly representation) from the normal bonds between
> atoms. However, as far as I know, color settings are atom-based, so I
> wasn't able to do what I wanted, because all bonds that lead to an atom
> will always share the same color.
>
> The only solution I found was to create a copy of the protein with
> pseudoatoms and draw the elastic network there. However, I expect this has
> a negative effect on the performance, which is relevant since I plan to use
> this for molecular dynamics trajectories.
>
> Am I trying to do this the wrong way? Is it just unfeasible?
>

[PyMOL] Differentiate between bond types by color and representation

[Lorenzo G. <br...@gm...>]

Dear pymol users,

I'm trying to properly represent a coarse-grained protein model that has an
elastic network.

I would like to show the bonds that are part of the elastic network with a
different color (and possibly representation) from the normal bonds between
atoms. However, as far as I know, color settings are atom-based, so I
wasn't able to do what I wanted, because all bonds that lead to an atom
will always share the same color.

The only solution I found was to create a copy of the protein with
pseudoatoms and draw the elastic network there. However, I expect this has
a negative effect on the performance, which is relevant since I plan to use
this for molecular dynamics trajectories.

Am I trying to do this the wrong way? Is it just unfeasible?

[PyMOL] Conference Announcement: Molecular Modeling Workshop, Feb 17-19, 2020 in Erlangen, Germany

[Harald L. <har...@fa...>]

Dear list subscribers,

we are very delighted to announce this year’s

“34th Molecular Modelling Workshop (MMWS)” (http://mmws2020.mgms-ds.de)

that takes place on Monday 17th to Wednesday 19th February 2020
at the Friedrich-Alexander-University in Erlangen, Germany.

The MMWS has a long history of giving young scientists (especially
graduate students) the opportunity to present their work and dive into
discussions with each other and the "older experts" of the field to gain
valuable feedback from academic as well as industrial colleagues. Oral
and poster contributions are welcome from all areas of molecular
modelling – from the life sciences, computational biology and chemistry,
cheminformatics, to materials sciences.

Starting with the scientific program on Monday after lunch should allow
to avoid travelling on weekend keeping the expenses at a minimum. Once
again the location changed - back to the roots we are now back again
in the Organic Chemistry building at Henkestrasse 42.
A hearty workshop dinner and a traditional joint evening in Erlangen’s
Steinbach-Bräu brewery complement the scientific program. The workshop
is organised by the German Section of the Molecular Graphics and
Modelling Society (MGMS-DS e.V.).

####### Pre-conference Schrödinger workshop #######
For the third time at our Molecular Modeling Workshop, Schrödinger is
offering a pre-conference workshop entiteled "Structure-based Drug
Design using the Schrödinger Suite". If you are interested in
participating at the software session, please checkmark the
corresponding field upon filling the registration form. Please note that
this event is taking place at the CCC in Naegelsbachstrasse 25.

####### Plenary Speakers #######
We are very happy to announce that five outstanding researchers accepted
our invitation to present a plenary lecture at the Modeling workshop:

Petra Imhof, Berlin
“Recognition and specificity in protein-DNA interactions - insight from
molecular simulations”

Pavel Jungwirth, Prague
"Electrons in Liquid Ammonia and in Water: From Blue Electrolytes to
Bronze Colored Metallic Solutions"

Barbara Kirchner, Bonn
"Insights into ionic and molecular liquids and their interfaces from
computational chemistry"

Charles Laughton, Nottingham
"Enhancing conformational sampling with machine learning"

Birgit Strodel, Jülich
"Modelling peptide aggregation influenced by in vivo conditions"


####### Poster and Lecture Awards #######
As in the past years, there will be two poster awards of EUR 100 each
and three lecture awards for the best contributed oral presentations:

1st winner: Travel bursary to attend the Young Modeller's Forum in
London, UK, plus a speaker slot option at YMF (travel expenses are
reimbursed up to EUR 500)
2nd winner: EUR 200 travel expenses reimbursement
3rd winner: EUR 100 travel expenses reimbursement

Only undergraduate and graduate research students qualify for the poster
and lecture awards.

####### Registration and poster/talk submission #######
Submit talks and/or poster titles via the registration form accessible
on the workshop website https://mmws2020.mgms-ds.de/index.php?m=register
The deadline for all submissions is January 24th, 2020.

####### General information #######
Website http://mmws2020.mgms-ds.de will provide all necessary
information about the meeting.

We are looking forward to meeting you in Erlangen!
- Christof Jäger, Scientific Committee Workshop Organisation 2020
- Harald Lanig, Chairman of the MGMS-DS e.V. (http://www.mgms-ds.de)


-- 
--------------------------------------------------------
  PD Dr. Harald Lanig     Universitaet Erlangen/Nuernberg
  Zentralinstitut fuer Scientific Computing        (ZISC)
  Forschungsdatenmanagement          SFB 814 und SFB 1411
  Martensstrasse 5a                        91058 Erlangen
  +49 9131-85 20781                   har...@fa...
--------------------------------------------------------

[PyMOL] Movie showing a slice-through a cryo-EM map

[Tomas M. <tom...@gm...>]

Dear PyMOL users,

I would like to make a movie showing a slice-through a cryo-EM map.
Something similar to Video 1s (produced using Chimera) in PMIDs
30602789 and 30602790:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6364807/PMC6364807/bin/NIHMS80767-supplement-Supplementary_Video_1.mp4

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6370056/bin/NIHMS80639-supplement-Video_1.mp4

I am using PyMOL 2.3.2 which can handle cryo-EM maps (in MRC format).
I would be very grateful if anyone could please direct me to a
relevant tutorial or a PyMOL script if possible.

I thank you for your help.

Best wishes,
Tomas

Re: [PyMOL] Pymol APBS plugin error

[Jack H. <how...@gm...>]

Also, keep in mind that pdb2pqr isn't python3 friendly so you will have to
use an externally generated pqr file. The current mechanism for calling
pdb2pqr from within the APBS Tool results in pdb2pqr running under the same
python as pymol.
        Jack

On Mon, Dec 2, 2019 at 5:58 PM Jack Howarth <how...@gm...>
wrote:

> You need more patches in your installed Pmw 2.0.0. On MacPorts, we use...
>
>
> https://github.com/macports/macports-ports/blob/master/python/py-pmw/files/patch-pmw2-py36.diff
>
> and
>
>
> https://github.com/macports/macports-ports/blob/master/python/py-pmw/files/patch-pmw2.diff
>
> applied over Pmw_2_0_0.
> Jack
>
> On Mon, Dec 2, 2019 at 2:43 PM RDirective <rdi...@gm...> wrote:
>
>> Dear all,
>>
>>
>> I get the following errors when trying to launch the APBS plugin from the
>> plugins menu
>>
>>
>> Traceback (most recent call last):
>>
>>   File "/home/quyen/Pymol/install/lib64/python/pmg_tk/startup/apbs_tools.py", line 322, in <lambda>
>>     command = lambda s=self: APBSTools2(s))
>>
>>   File "/home/quyen/Pymol/install/lib64/python/pmg_tk/startup/apbs_tools.py", line 617, in __init__
>>     self.notebook = Pmw.NoteBook(self.dialog.interior())
>>
>>   File "/usr/lib/python3.7/site-packages/Pmw/Pmw_2_0_0/lib/PmwNoteBook.py", line 60, in __init__
>>     Pmw.Color.bordercolors(self, self['hull_background'])
>>
>>   File "/usr/lib/python3.7/site-packages/Pmw/Pmw_2_0_0/lib/PmwColor.py", line 359, in bordercolors
>>     '#%04x%04x%04x' % (lightRGB[0], lightRGB[1], lightRGB[2]),
>> TypeError: %x format: an integer is required, not float
>>
>>
>> Pymol source Version 2.4.0a0
>>
>>
>> Best,
>>
>> Quyen
>> _______________________________________________
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pym...@li...
>> Unsubscribe:
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>

Re: [PyMOL] Pymol APBS plugin error

[Jack H. <how...@gm...>]

You need more patches in your installed Pmw 2.0.0. On MacPorts, we use...

https://github.com/macports/macports-ports/blob/master/python/py-pmw/files/patch-pmw2-py36.diff

and

https://github.com/macports/macports-ports/blob/master/python/py-pmw/files/patch-pmw2.diff

applied over Pmw_2_0_0.
Jack

On Mon, Dec 2, 2019 at 2:43 PM RDirective <rdi...@gm...> wrote:

> Dear all,
>
>
> I get the following errors when trying to launch the APBS plugin from the
> plugins menu
>
>
> Traceback (most recent call last):
>
>   File "/home/quyen/Pymol/install/lib64/python/pmg_tk/startup/apbs_tools.py", line 322, in <lambda>
>     command = lambda s=self: APBSTools2(s))
>
>   File "/home/quyen/Pymol/install/lib64/python/pmg_tk/startup/apbs_tools.py", line 617, in __init__
>     self.notebook = Pmw.NoteBook(self.dialog.interior())
>
>   File "/usr/lib/python3.7/site-packages/Pmw/Pmw_2_0_0/lib/PmwNoteBook.py", line 60, in __init__
>     Pmw.Color.bordercolors(self, self['hull_background'])
>
>   File "/usr/lib/python3.7/site-packages/Pmw/Pmw_2_0_0/lib/PmwColor.py", line 359, in bordercolors
>     '#%04x%04x%04x' % (lightRGB[0], lightRGB[1], lightRGB[2]),
> TypeError: %x format: an integer is required, not float
>
>
> Pymol source Version 2.4.0a0
>
>
> Best,
>
> Quyen
> _______________________________________________
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pym...@li...
> Unsubscribe:
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

[PyMOL] Pymol APBS plugin error

[RDirective <rdi...@gm...>]

Dear all,


I get the following errors when trying to launch the APBS plugin from the
plugins menu


Traceback (most recent call last):
  File "/home/quyen/Pymol/install/lib64/python/pmg_tk/startup/apbs_tools.py",
line 322, in <lambda>
    command = lambda s=self: APBSTools2(s))
  File "/home/quyen/Pymol/install/lib64/python/pmg_tk/startup/apbs_tools.py",
line 617, in __init__
    self.notebook = Pmw.NoteBook(self.dialog.interior())
  File "/usr/lib/python3.7/site-packages/Pmw/Pmw_2_0_0/lib/PmwNoteBook.py",
line 60, in __init__
    Pmw.Color.bordercolors(self, self['hull_background'])
  File "/usr/lib/python3.7/site-packages/Pmw/Pmw_2_0_0/lib/PmwColor.py",
line 359, in bordercolors
    '#%04x%04x%04x' % (lightRGB[0], lightRGB[1], lightRGB[2]),
TypeError: %x format: an integer is required, not float


Pymol source Version 2.4.0a0


Best,

Quyen