pymol-users — Collaborative support and tips for PyMOL users

[PyMOL] Mac installation error: clang++, segmentation fault 11

[Sumudu L. <sum...@gm...>]

Hi,

I was trying to get open source pymol installed on my Mac but was unable to
do so. I tried brew and macports. I'm on Mojave 10.14.6. I attached the
error I get with brew. With Macports, when I try to open Pymol it returns a
segmentation fault 11 error.

Has anybody seen this before? Any suggestions?

Thank you!

brew install brewsci/bio/pymol




Updating Homebrew...

==> *Auto-updated Homebrew!*

Updated 4 taps (homebrew/core, homebrew/cask, homebrew/services and
caskroom/cask).

==> *Updated Formulae*

*cmake **✔*           deno              ffsend            go@1.12
gspell            haproxy           iso-codes         node              rke
            roswell           rust


==> *Installing pymol from brewsci/bio*

==> *Downloading
https://github.com/schrodinger/pymol-open-source/archive/v2.3.0.tar.gz
<https://github.com/schrodinger/pymol-open-source/archive/v2.3.0.tar.gz>*

Already downloaded:
/Users/sumudu/Library/Caches/Homebrew/downloads/a51d46dea90ae24d275dac1d9efa7cf70025ab5fed71dc210ce3000d5d65219c--pymol-open-source-2.3.0.tar.gz

==> *Downloading
https://files.pythonhosted.org/packages/11/74/2c151a13ef41ab9fb43b3c4ff9e788e0496ed7923b2078d42cab30622bdf/virtualenv-16.7.4.tar.gz
<https://files.pythonhosted.org/packages/11/74/2c151a13ef41ab9fb43b3c4ff9e788e0496ed7923b2078d42cab30622bdf/virtualenv-16.7.4.tar.gz>*

Already downloaded:
/Users/sumudu/Library/Caches/Homebrew/downloads/507d2087bf24df82641b681a5fe4da778ef50ebe819a86ea1b584f70788f0f63--virtualenv-16.7.4.tar.gz

==> *python3 -c import setuptools... --no-user-cfg install
--prefix=/usr/local/Cellar/pymol/2.3.0/libexec
--install-scripts=/usr/local/Cellar/pymol/2.3.0/libexec/bin
--single-version-externally-man*

==> *Downloading
https://files.pythonhosted.org/packages/3a/20/c81632328b1a4e1db65f45c0a1350a9c5341fd4bbb8ea66cdd98da56fe2e/numpy-1.15.0.zip
<https://files.pythonhosted.org/packages/3a/20/c81632328b1a4e1db65f45c0a1350a9c5341fd4bbb8ea66cdd98da56fe2e/numpy-1.15.0.zip>*

Already downloaded:
/Users/sumudu/Library/Caches/Homebrew/downloads/c3591902b12abd9354b52438f4e5aa07974b9e83cf502a778095fd0fd6a1cc46--numpy-1.15.0.zip

==> *python3 -c import setuptools... --no-user-cfg install
--prefix=/usr/local/Cellar/pymol/2.3.0/libexec
--install-scripts=/usr/local/Cellar/pymol/2.3.0/libexec/bin
--single-version-externally-man*

==> *Downloading
https://files.pythonhosted.org/packages/13/ea/c6a302ccdfdcc1ab200bd2b7561e574329055d2974b1fb7939a7aa374da3/mmtf-python-1.1.2.tar.gz
<https://files.pythonhosted.org/packages/13/ea/c6a302ccdfdcc1ab200bd2b7561e574329055d2974b1fb7939a7aa374da3/mmtf-python-1.1.2.tar.gz>*

Already downloaded:
/Users/sumudu/Library/Caches/Homebrew/downloads/8184cd2975ddc6f5276f8aca6273b4b0e2e98a69ae60a94e8f087e2bf4f7fbc2--mmtf-python-1.1.2.tar.gz

==> *python3 -c import setuptools... --no-user-cfg install
--prefix=/usr/local/Cellar/pymol/2.3.0/libexec
--install-scripts=/usr/local/Cellar/pymol/2.3.0/libexec/bin
--single-version-externally-man*

==> *Downloading
https://files.pythonhosted.org/packages/81/9c/0036c66234482044070836cc622266839e2412f8108849ab0bfdeaab8578/msgpack-0.6.1.tar.gz
<https://files.pythonhosted.org/packages/81/9c/0036c66234482044070836cc622266839e2412f8108849ab0bfdeaab8578/msgpack-0.6.1.tar.gz>*

Already downloaded:
/Users/sumudu/Library/Caches/Homebrew/downloads/432b50d5f899f052d91eb12c17bb4fe7686828cd77a7f5d3b6e4f646b09eabf6--msgpack-0.6.1.tar.gz

==> *python3 -c import setuptools... --no-user-cfg install
--prefix=/usr/local/Cellar/pymol/2.3.0/libexec
--install-scripts=/usr/local/Cellar/pymol/2.3.0/libexec/bin
--single-version-externally-man*

==> *Downloading
https://files.pythonhosted.org/packages/8a/20/6eca772d1a5830336f84aca1d8198e5a3f4715cd1c7fc36d3cc7f7185091/msgpack-python-0.5.6.tar.gz
<https://files.pythonhosted.org/packages/8a/20/6eca772d1a5830336f84aca1d8198e5a3f4715cd1c7fc36d3cc7f7185091/msgpack-python-0.5.6.tar.gz>*

Already downloaded:
/Users/sumudu/Library/Caches/Homebrew/downloads/49c4120b43aa86620eaebc552b359f6d897f72f59d979634a803f54088ea44d8--msgpack-python-0.5.6.tar.gz

==> *python3 -c import setuptools... --no-user-cfg install
--prefix=/usr/local/Cellar/pymol/2.3.0/libexec
--install-scripts=/usr/local/Cellar/pymol/2.3.0/libexec/bin
--single-version-externally-man*

==> *Downloading
https://files.pythonhosted.org/packages/73/0c/55e4294143ba6781936c799ff13181db9109b161a8d8fc9b50eec45e1134/msgpack-tool-0.0.1.tar.gz
<https://files.pythonhosted.org/packages/73/0c/55e4294143ba6781936c799ff13181db9109b161a8d8fc9b50eec45e1134/msgpack-tool-0.0.1.tar.gz>*

Already downloaded:
/Users/sumudu/Library/Caches/Homebrew/downloads/cc8ecf250035cd7b706c464cf5a1be6cfdd1a92482350d209d6900918ec93b34--msgpack-tool-0.0.1.tar.gz

==> *python3 -c import setuptools... --no-user-cfg install
--prefix=/usr/local/Cellar/pymol/2.3.0/libexec
--install-scripts=/usr/local/Cellar/pymol/2.3.0/libexec/bin
--single-version-externally-man*

==> *Downloading
https://files.pythonhosted.org/packages/e7/20/8d0c4ba96a5fe62e1bcf2b8a212ccfecd67ad951e8f3e89cf147d63952aa/Pmw-2.0.1.tar.gz
<https://files.pythonhosted.org/packages/e7/20/8d0c4ba96a5fe62e1bcf2b8a212ccfecd67ad951e8f3e89cf147d63952aa/Pmw-2.0.1.tar.gz>*

Already downloaded:
/Users/sumudu/Library/Caches/Homebrew/downloads/50fbcfa2c8f747eb0d10f58fb92b1405935cdbeb84b675b4a28b0235409fa10b--Pmw-2.0.1.tar.gz

==> *python3 -c import setuptools... --no-user-cfg install
--prefix=/usr/local/Cellar/pymol/2.3.0/libexec
--install-scripts=/usr/local/Cellar/pymol/2.3.0/libexec/bin
--single-version-externally-man*

==> *python3 setup.py install
--install-scripts=/usr/local/Cellar/pymol/2.3.0/libexec/bin
--install-lib=/usr/local/Cellar/pymol/2.3.0/libexec/lib/python3.7/site-packages
--glut --use-msgpackc=c++11*

Last 15 lines from /Users/sumudu/Library/Logs/Homebrew/pymol/08.python3:

            ^

contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:1097:13: warning: unused
function 'whereami' [-Wunused-function]

static void whereami(FILE *file) {

            ^

contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:490:13: warning: unused
function 'replace_wavefunction' [-Wunused-function]

static void replace_wavefunction(qm_timestep_t *ts, int n) {

            ^

contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:507:13: warning: unused
function 'del_wavefunction' [-Wunused-function]

static void del_wavefunction(qm_timestep_t *ts) {

            ^

contrib/uiuc/plugins/molfile_plugin/src/qmplugin.h:585:13: warning: unused
function 'print_matrix4' [-Wunused-function]

static void print_matrix4(const float mat[16]) {

            ^

12 warnings generated.

error: command 'clang++' failed with exit status 1

Re: [PyMOL] feature request

[Jared S. <jar...@co...>]

Hi Thomas - 

When I said it's easy to implement, I was only thinking of object color. Among the various cases you describe, the "dominant color" is probably the most important one, as it might not be obvious to the user that object color can be different from atom colors.
Indeed, I was among those for whom "it might not be obvious" that there are separate object and atom colors!  I had thought all coloring was done at the atom level (as you show using the selection), and didn't realize there is a separate object-level color, nor did I know about the `set_object_color` command.

Thanks for the explanation, Thomas!

Cheers,

Jared

Re: [PyMOL] feature request

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

Hi Jared and Vaheh -

Jared, you've put way more thought into this than I did :-) When I said it's easy to implement, I was only thinking of object color. Among the various cases you describe, the "dominant color" is probably the most important one, as it might not be obvious to the user that object color can be different from atom colors.

color blue, (obj)                    ;# only changes atom colors
color blue, obj                      ;# changes object and atom colors
cmd.set_object_color("obj", "blue")  ;# only changes object color

More complex situations like spectrum or per-representation colors can be neglected I think - I wouldn't know how to map those to a label color in a useful way.

As a first step, I can add internal_gui_name_color_mode=1 with object colors.

Cheers,
  Thomas


> On Oct 1, 2019, at 9:31 PM, Oganesyan, Vaheh <vah...@as...> wrote:
> 
> Thomas and Jared,
> I’m not sure what will be the best solution, but as a start, color of the object name may stay white if more than one color is used. Because you both found this as an interesting idea allows me to ask similar question now regarding labels. What if we can get label_color match the residue color. I vaguely remember something like this discussed x number of years ago, but do not remember why not. Could label become property of the object and not just a property of a session?
>  
> Thank you.
>  
>  
> From: Jared Sampson <jar...@co...> 
> Sent: Tuesday, October 1, 2019 2:45 PM
> To: Oganesyan, Vaheh <vah...@as...>; Thomas Holder <tho...@sc...>
> Cc: pymol-users <pym...@li...>
> Subject: Re: [PyMOL] feature request
>  
> Hi Thomas and Vaheh - 
>  
> This is indeed an interesting idea.  I was thinking about this in terms of implementation, and what the edge cases might be.  I wonder what would be the mechanism for assigning the color if the object is not just a single color.  Would it be the color that is the dominant color of the object over all (visible) representations?
>  
> What about a spectrum-colored object?  Would it be possible to color the object name according to the colors in the spectrum (like the "spectrum" and "rainbow" menu items already in the OpenGL menu)?
>  
> And what if there are different coloring schemes for the different representations—would there be a hierarchy in terms of choosing , e.g. surface > cartoon > stick > line, etc.?
>  
> I definitely like Thomas' idea of a global `internal_gui_name_color_mode` setting to turn the menu object name coloring on/off.  (Perhaps different modes could correspond to different ways of choosing the displayed color.)  It might also be useful to include object-level (or named-selection-level) settings to override the global setting and specify the color or spectrum directly, e.g.:
>  
>     set internal_gui_name_color, red, obj1
>     set internal_gui_name_spectrum, rainbow, obj1
>  
> Really interesting suggestion, Vaheh.  Looking forward to seeing how it might work!
>  
> Cheers,
> Jared
>  
> On October 1, 2019 at 5:13:07 AM, Thomas Holder (tho...@sc...) wrote:
> 
> Hi Vaheh,
> 
> I see that this can be useful, and it's fairly easy to implement. We can add a new setting to turn this on and off, like "internal_gui_name_color_mode" (or do you have a suggestion for a better name?).
> 
> Cheers,
> Thomas
> 
> 
> > On Sep 26, 2019, at 4:34 PM, Oganesyan, Vaheh <vah...@as...> wrote:
> > 
> > Thomas and other PyMOL developers,
> > 
> > It looks as if we color the object name similar to the object color it will be easier to distinguish which structure am I manipulating now. While models can be colored, the names of the models can't.
> > Anybody else think it might be helpful?
> > 
> > Thank you.
> > Regards,
> > 
> > Vaheh Oganesyan, Ph.D.
> > Scientist, Biologic Therapeutics
> > ____________________________________________________________________
> > AstraZeneca
> > R&D | Antibody Discovery and Protein Engineering
> > One Medimmune Way, Gaithersburg, MD 20878
> > T: 301-398-4640 M: 240-398-0046 
> > Vah...@as...
> 
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
> 
> 
> 
> _______________________________________________
> PyMOL-users mailing list
> Archives: https://clicktime.symantec.com/3UV6BFZxvbLGNd6ZnGajdMx6H2?u=http%3A%2F%2Fwww.mail-archive.com%2Fpymol-users%40lists.sourceforge.net
> Unsubscribe: https://clicktime.symantec.com/3E9dosvp4WJ7Ck38g9VwWNV6H2?u=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fpymol%2Flists%2Fpymol-users%2Funsubscribe

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] feature request

[Jared S. <jar...@co...>]

Hi Vaheh - 

Fortunately, `label_color` is an atom-level setting already.  For example:

```
PyMOL>fab AAAAA, ala_pep
PyMOL>label n. CA, f"{resn} {resi}"
 Label: labelled 5 atoms.
PyMOL>color white
 Executive: Colored 50 atoms.
PyMOL>set label_color, red, resi 1
 Setting: label_color set for 10 atoms in object "pep1".
PyMOL>set label_color, orange, resi 2
 Setting: label_color set for 10 atoms in object "pep1".
PyMOL>set label_color, yellow, resi 3
 Setting: label_color set for 10 atoms in object "pep1".
PyMOL>set label_color, green, resi 4
 Setting: label_color set for 10 atoms in object "pep1".
PyMOL>set label_color, blue, resi 5
 Setting: label_color set for 10 atoms in object "pep1".
```

Hope that helps.

Cheers,
Jared


On October 1, 2019 at 3:31:54 PM, Oganesyan, Vaheh (vah...@as...) wrote:

Thomas and Jared,

I’m not sure what will be the best solution, but as a start, color of the object name may stay white if more than one color is used. Because you both found this as an interesting idea allows me to ask similar question now regarding labels. What if we can get label_color match the residue color. I vaguely remember something like this discussed x number of years ago, but do not remember why not. Could label become property of the object and not just a property of a session?

 

Thank you.

 

 

From: Jared Sampson <jar...@co...>  
Sent: Tuesday, October 1, 2019 2:45 PM
To: Oganesyan, Vaheh <vah...@as...>; Thomas Holder <tho...@sc...>
Cc: pymol-users <pym...@li...>
Subject: Re: [PyMOL] feature request

 

Hi Thomas and Vaheh - 

 

This is indeed an interesting idea.  I was thinking about this in terms of implementation, and what the edge cases might be.  I wonder what would be the mechanism for assigning the color if the object is not just a single color.  Would it be the color that is the dominant color of the object over all (visible) representations?

 

What about a spectrum-colored object?  Would it be possible to color the object name according to the colors in the spectrum (like the "spectrum" and "rainbow" menu items already in the OpenGL menu)?

 

And what if there are different coloring schemes for the different representations—would there be a hierarchy in terms of choosing , e.g. surface > cartoon > stick > line, etc.?

 

I definitely like Thomas' idea of a global `internal_gui_name_color_mode` setting to turn the menu object name coloring on/off.  (Perhaps different modes could correspond to different ways of choosing the displayed color.)  It might also be useful to include object-level (or named-selection-level) settings to override the global setting and specify the color or spectrum directly, e.g.:

 

    set internal_gui_name_color, red, obj1

    set internal_gui_name_spectrum, rainbow, obj1

 

Really interesting suggestion, Vaheh.  Looking forward to seeing how it might work!

 

Cheers,

Jared

 

On October 1, 2019 at 5:13:07 AM, Thomas Holder (tho...@sc...) wrote:

Hi Vaheh,

I see that this can be useful, and it's fairly easy to implement. We can add a new setting to turn this on and off, like "internal_gui_name_color_mode" (or do you have a suggestion for a better name?).

Cheers,
Thomas


> On Sep 26, 2019, at 4:34 PM, Oganesyan, Vaheh <vah...@as...> wrote:
>  
> Thomas and other PyMOL developers,
>  
> It looks as if we color the object name similar to the object color it will be easier to distinguish which structure am I manipulating now. While models can be colored, the names of the models can't.
> Anybody else think it might be helpful?
>  
> Thank you.
> Regards,
>  
> Vaheh Oganesyan, Ph.D.
> Scientist, Biologic Therapeutics
> ____________________________________________________________________
> AstraZeneca
> R&D | Antibody Discovery and Protein Engineering
> One Medimmune Way, Gaithersburg, MD 20878
> T: 301-398-4640 M: 240-398-0046  
> Vah...@as...

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.



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Re: [PyMOL] feature request

[Oganesyan, V. <vah...@as...>]

Thomas and Jared,
I’m not sure what will be the best solution, but as a start, color of the object name may stay white if more than one color is used. Because you both found this as an interesting idea allows me to ask similar question now regarding labels. What if we can get label_color match the residue color. I vaguely remember something like this discussed x number of years ago, but do not remember why not. Could label become property of the object and not just a property of a session?

Thank you.


From: Jared Sampson <jar...@co...>
Sent: Tuesday, October 1, 2019 2:45 PM
To: Oganesyan, Vaheh <vah...@as...>; Thomas Holder <tho...@sc...>
Cc: pymol-users <pym...@li...>
Subject: Re: [PyMOL] feature request

Hi Thomas and Vaheh -

This is indeed an interesting idea.  I was thinking about this in terms of implementation, and what the edge cases might be.  I wonder what would be the mechanism for assigning the color if the object is not just a single color.  Would it be the color that is the dominant color of the object over all (visible) representations?

What about a spectrum-colored object?  Would it be possible to color the object name according to the colors in the spectrum (like the "spectrum" and "rainbow" menu items already in the OpenGL menu)?

And what if there are different coloring schemes for the different representations—would there be a hierarchy in terms of choosing , e.g. surface > cartoon > stick > line, etc.?

I definitely like Thomas' idea of a global `internal_gui_name_color_mode` setting to turn the menu object name coloring on/off.  (Perhaps different modes could correspond to different ways of choosing the displayed color.)  It might also be useful to include object-level (or named-selection-level) settings to override the global setting and specify the color or spectrum directly, e.g.:

    set internal_gui_name_color, red, obj1
    set internal_gui_name_spectrum, rainbow, obj1

Really interesting suggestion, Vaheh.  Looking forward to seeing how it might work!

Cheers,
Jared


On October 1, 2019 at 5:13:07 AM, Thomas Holder (tho...@sc...<mailto:tho...@sc...>) wrote:
Hi Vaheh,

I see that this can be useful, and it's fairly easy to implement. We can add a new setting to turn this on and off, like "internal_gui_name_color_mode" (or do you have a suggestion for a better name?).

Cheers,
Thomas


> On Sep 26, 2019, at 4:34 PM, Oganesyan, Vaheh <vah...@as...<mailto:vah...@as...>> wrote:
>
> Thomas and other PyMOL developers,
>
> It looks as if we color the object name similar to the object color it will be easier to distinguish which structure am I manipulating now. While models can be colored, the names of the models can't.
> Anybody else think it might be helpful?
>
> Thank you.
> Regards,
>
> Vaheh Oganesyan, Ph.D.
> Scientist, Biologic Therapeutics
> ____________________________________________________________________
> AstraZeneca
> R&D | Antibody Discovery and Protein Engineering
> One Medimmune Way, Gaithersburg, MD 20878
> T: 301-398-4640 M: 240-398-0046
> Vah...@as...<mailto:Vah...@as...>

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.



_______________________________________________
PyMOL-users mailing list
Archives: https://clicktime.symantec.com/3UV6BFZxvbLGNd6ZnGajdMx6H2?u=http%3A%2F%2Fwww.mail-archive.com%2Fpymol-users%40lists.sourceforge.net
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Re: [PyMOL] feature request

[Jared S. <jar...@co...>]

Hi Thomas and Vaheh - 

This is indeed an interesting idea.  I was thinking about this in terms of implementation, and what the edge cases might be.  I wonder what would be the mechanism for assigning the color if the object is not just a single color.  Would it be the color that is the dominant color of the object over all (visible) representations?

What about a spectrum-colored object?  Would it be possible to color the object name according to the colors in the spectrum (like the "spectrum" and "rainbow" menu items already in the OpenGL menu)?

And what if there are different coloring schemes for the different representations—would there be a hierarchy in terms of choosing , e.g. surface > cartoon > stick > line, etc.?

I definitely like Thomas' idea of a global `internal_gui_name_color_mode` setting to turn the menu object name coloring on/off.  (Perhaps different modes could correspond to different ways of choosing the displayed color.)  It might also be useful to include object-level (or named-selection-level) settings to override the global setting and specify the color or spectrum directly, e.g.:

    set internal_gui_name_color, red, obj1
    set internal_gui_name_spectrum, rainbow, obj1

Really interesting suggestion, Vaheh.  Looking forward to seeing how it might work!

Cheers,
Jared

On October 1, 2019 at 5:13:07 AM, Thomas Holder (tho...@sc...) wrote:

Hi Vaheh,

I see that this can be useful, and it's fairly easy to implement. We can add a new setting to turn this on and off, like "internal_gui_name_color_mode" (or do you have a suggestion for a better name?).

Cheers,
Thomas


> On Sep 26, 2019, at 4:34 PM, Oganesyan, Vaheh <vah...@as...> wrote:
>  
> Thomas and other PyMOL developers,
>  
> It looks as if we color the object name similar to the object color it will be easier to distinguish which structure am I manipulating now. While models can be colored, the names of the models can't.
> Anybody else think it might be helpful?
>  
> Thank you.
> Regards,
>  
> Vaheh Oganesyan, Ph.D.
> Scientist, Biologic Therapeutics
> ____________________________________________________________________
> AstraZeneca
> R&D | Antibody Discovery and Protein Engineering
> One Medimmune Way, Gaithersburg, MD 20878
> T: 301-398-4640 M: 240-398-0046  
> Vah...@as...

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.



_______________________________________________
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pym...@li...
Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

Re: [PyMOL] feature request

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

Hi Vaheh,

I see that this can be useful, and it's fairly easy to implement. We can add a new setting to turn this on and off, like "internal_gui_name_color_mode" (or do you have a suggestion for a better name?).

Cheers,
  Thomas


> On Sep 26, 2019, at 4:34 PM, Oganesyan, Vaheh <vah...@as...> wrote:
> 
> Thomas and other PyMOL developers,
> 
> It looks as if we color the object name similar to the object color it will be easier to distinguish which structure am I manipulating now. While models can be colored, the names of the models can't.
> Anybody else think it might be helpful?
> 
> Thank you.
> Regards,
> 
> Vaheh Oganesyan, Ph.D.
> Scientist, Biologic Therapeutics
> ____________________________________________________________________
> AstraZeneca
> R&D | Antibody Discovery and Protein Engineering
> One Medimmune Way, Gaithersburg, MD 20878
> T:  301-398-4640  M:  240-398-0046 
> Vah...@as...

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

[PyMOL] feature request

[Oganesyan, V. <vah...@as...>]

Thomas and other PyMOL developers,

It looks as if we color the object name similar to the object color it will be easier to distinguish which structure am I manipulating now. While models can be colored, the names of the models can't.
Anybody else think it might be helpful?

Thank you.
Regards,

Vaheh Oganesyan, Ph.D.
Scientist, Biologic Therapeutics
____________________________________________________________________
AstraZeneca
R&D | Antibody Discovery and Protein Engineering
One Medimmune Way, Gaithersburg, MD 20878
T:  301-398-4640  M:  240-398-0046 
Vah...@as...

[PyMOL] Schedule Up - 26th Annual Tcl/Tk Conference (Tcl'2019)

[<con...@tc...>]

Hello pymol-users, fyi ...

26th Annual Tcl/Tk Conference (Tcl'2019)
https://www.tcl-lang.org/community/tcl2019/

November 05 - 08, 2019
Crowne Plaza Houston River Oaks
2712 Southwest Freeway, 77098
Houston, Texas, USA

[ NEWS
  * Our keynote speaker is [Will Duquette](https://github.com/wduquette)
    talking about "Tcl, Rust, and the Death of Rube Goldberg"

  * Registration is open. Please have a look at

    https://www.tcl-lang.org/community/tcl2019/register.html

  * The tutorials are known. See

    https://www.tcl-lang.org/community/tcl2019/tutorials.html
]

And our schedule for this year is now available at

    https://www.tcl-lang.org/community/tcl2019/schedule.html

This is the last general mail for the year.

Conference Committee

   * Andreas Kupries
   * Arjen Markus    Deltares
   * Brian Griffin   Mentor - A Siemens Business
   * Gerald Lester   KnG Consulting LLC
   * Joe Mistachkin  Mistachkin Systems
   * Ronald Fox      CAEN Technologies
                     NSCL @ Michigan State University

Contact Information     tcl...@go...

Tcl'2019 would like to thank those who are sponsoring the conference:

   * FlightAware
   * Mentor - A Siemens Business
   * Noumena Corp

Re: [PyMOL] "Qt not available" error from compilation with python2 but not python3

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

> On Sep 14, 2019, at 8:46 AM, sunyeping via PyMOL-users <pym...@li...> wrote:
> 
> Even if I re-compile with --glut:
>     python2 setup.py install --prefix=~/pymol-install-py2
> the same error occurs.

Remove the "build" directory before you re-compile with --glut:

  rm -rf build
  python2 setup.py --glut install --prefix=~/pymol-install-py2

Hope that helps.

Cheers,
  Thomas

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

[PyMOL] "Qt not available" error from compilation with python2 but not python3

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

dear all, 

I am trying to compile pymol from source (https://github.com/schrodinger/pymol-open-source.git). Python 3 and python 2 both have been installed in my system. I first tried compile pymol with python 3
    python3 setup.py install --prefix=~/pymol-install-py3
It can work.
  python3 setup.py install --prefix=~/pymol-install-py2

However, when I try to compile pymol with python2:
 python2 setup.py install --prefix=~/pymol-install-py2
lauching pymol gives the following error:

Qt not available, using GLUT/Tk interface
Traceback (most recent call last):
  File "__init__.py", line 65, in <module>
    pymol.launch(args)
  File "/home/sunyp/pymol-install-py2/lib64/python2.7/site-packages/pymol/__init__.py", line 436, in launch
    _cmd.runpymol(_cmd._get_global_C_object(), block_input_hook)
NotImplementedError: compile with --glut

Even if I re-compile with --glut:
python2 setup.py install --prefix=~/pymol-install-py2
the same error occurs.

PyQt4 has been install in my system with yum install. I am very confused and wish to know why qt cannot be fould by pymol comoled with python2. 

Could you help me with that?

Thank you in advacne.
Yeping Sun

[PyMOL] APBS TOOLS 2.1 does not work

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

Dear all, 

I am trying to use APBS TOOLs 2.1 to calculate electrostatic potential of proteins. After I finish "set grid", I press the "set grid" button, I get the following error,

(<type 'exceptions.ImportError'>, ImportError('No module named pdb2pqr',), <traceback object at 0x7fed3cf46c68>)
In show error 2

Could you tell what is the cause of the error and how to fix it?

Best regards.

Re: [PyMOL] PyMol: incomplete replacement of b- and q-factors

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

Hi Joe,

There can be atoms without coordinates. In particular, when loading mmCIF files, PyMOL fills in dummy-CA atoms for missing residues, to provide a complete sequence display in the sequence viewer.

"alter" iterates over all atoms, including those without coordinates. "iterate_state" only includes those *with* coordinates.

Your issue can be handled in several ways:

1) Make a selection on the atoms with coordinates in state 1:
   select mysele, state 1, enable=0
   alter mysele, b = next(di)
   spectrum b, selection=mysele

2) Or just remove atoms which don't have coordinates in state 1:
   remove not state 1
   alter all, b = next(di)
   spectrum b

See "Coordinates" section here:
https://pymolwiki.org/index.php/Selection_Algebra

Cheers,
  Thomas

> On Sep 12, 2019, at 6:09 PM, Heffron, Joseph <jos...@ma...> wrote:
> 
> Hello all, 
> 
> I am trying to color several proteins by different factors, e.g., distance from a given point (here the origin). To do this, I replace the q-factor (or b-factor) with my variable of choice. However, most of my files have one or a few residues that are for some reason not affected by the alter_state (e.g., pdb = 1ihm). I can't see any distinction in these residues compared to the others.  
> 
> example code: 
> 
>     fetch 1ihm
>     alldist = []
>     iterate_state 1, all, alldist.append((x**2+y**2+z**2)**0.5)
>     di = iter(alldist)
>     alter all, b = next(di)
>     spectrum b
> 
> Thank you, 
> Joe 
> _______________________________________________
> 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] How to manually define the lower and upper limit of vacuum electrostatics?

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

Hello, Marko,

Think you for your reply. I can use the bar object "Action" > "Levels" to set the levels/scales to -100~100, but could you tell me what are the units for the values?

Best regards
------------------------------------------------------------------
From:Marko Hyvonen <mh...@ca...>
Sent At:2019 Sep. 12 (Thu.) 15:58
To:pymol-users <pym...@li...>
Subject:Re: [PyMOL] How to manually define the lower and upper limit of vacuum electrostatics?

 Hi Yeping, 

 Click on the bar object "Action" > "Levels" for a few preset levels/scales.

 hth, Marko 

On 12/09/2019 08:03, sunyeping via PyMOL-users wrote:
Dear all,

I am trying to compare the vacuum electrostatics of three related proteins. I loaded them in pymol and use "Action>generate>vacuum electrostatics menu to generate the vacuum electrostatics of the three proteins. I find that the lower and upper limit of the gradient bars generated with the  vacuum electrostatics of the three proteins are different. They are -64.1~64.1, -72.2~72.2 and -82.2~82.2, respectively.  

I wonder whether I could define the lower and upper limit of the gradients to the same values so that the vacuum electrostatics of the three proteins can be better compared?

Best regards.
Yeping 

_______________________________________________
PyMOL-users mailing list
Archives: http://www.mail-archive.com/pym...@li...
Unsubscribe: https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe 
-- 

Marko Hyvonen
Department of Biochemistry, University of Cambridge
mh...@ca...
+44 (0)1223 766 044
@HyvonenGroup
http://hyvonen.bioc.cam.ac.uk
 

[PyMOL] PyMol: incomplete replacement of b- and q-factors

[Heffron, J. <jos...@ma...>]

Hello all,

I am trying to color several proteins by different factors, e.g., distance from a given point (here the origin). To do this, I replace the q-factor (or b-factor) with my variable of choice. However, most of my files have one or a few residues that are for some reason not affected by the alter_state (e.g., pdb = 1ihm). I can't see any distinction in these residues compared to the others.

example code:

    fetch 1ihm
    alldist = []
    iterate_state 1, all, alldist.append((x**2+y**2+z**2)**0.5)
    di = iter(alldist)
    alter all, b = next(di)
    spectrum b

Thank you,
Joe

Re: [PyMOL] How to manually define the lower and upper limit of vacuum electrostatics?

[Marko H. <mh...@ca...>]

<html>
  <head>
    <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
  </head>
  <body text="#000000" bgcolor="#FFFFFF">
    <tt>Hi Yeping, <br>
      <br>
      Click on the bar object "Action" &gt; "Levels" for a few preset
      levels/scales.<br>
      <br>
      hth, Marko </tt><br>
    <br>
    <div class="moz-cite-prefix">On 12/09/2019 08:03, sunyeping via
      PyMOL-users wrote:<br>
    </div>
    <blockquote type="cite"
      cite="mid:506...@al...">
      <meta http-equiv="content-type" content="text/html; charset=UTF-8">
      <div class="__aliyun_email_body_block">
        <div style="clear:both;"><span
style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;">Dear
            all,</span></div>
        <div style="clear:both;"><span
style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;"><br>
          </span></div>
        <div style="clear:both;"><span
style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;">I
            am trying to compare the vacuum electrostatics of three
            related proteins. I loaded them in pymol and use
            "Action&gt;generate&gt;vacuum electrostatics menu to
            generate the <span
style="color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;background-color:#ffffff;text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline;">vacuum </span><span
style="color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;background-color:#ffffff;text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline;">electrostatics
              of the three proteins. I find that the lower and upper
              limit of the gradient bars generated with the <span
style="color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;background-color:#ffffff;text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline;"> </span><span
style="margin:.0px;padding:.0px;border:.0px;outline:.0px;color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;text-decoration-style:initial;text-decoration-color:initial;background-color:#ffffff;float:none;display:inline;">vacuum </span><span
style="margin:.0px;padding:.0px;border:.0px;outline:.0px;color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;text-decoration-style:initial;text-decoration-color:initial;background-color:#ffffff;float:none;display:inline;">electrostatics
                of the three proteins are different. They are
                -64.1~64.1, -72.2~72.2 and -82.2~82.2, respectively.  </span></span></span></div>
        <div style="clear:both;"><span
style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;"><span
style="color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;background-color:#ffffff;text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline;"><span
style="margin:.0px;padding:.0px;border:.0px;outline:.0px;color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;text-decoration-style:initial;text-decoration-color:initial;background-color:#ffffff;float:none;display:inline;"><br>
              </span></span></span></div>
        <div style="clear:both;"><span
style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;"><span
style="color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;background-color:#ffffff;text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline;"><span
style="margin:.0px;padding:.0px;border:.0px;outline:.0px;color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;text-decoration-style:initial;text-decoration-color:initial;background-color:#ffffff;float:none;display:inline;">I
                wonder whether I could define the lower and upper limit
                of the gradients to the same values so that the <span
style="margin:.0px;padding:.0px;border:.0px;outline:.0px;color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;text-decoration-style:initial;text-decoration-color:initial;background-color:#ffffff;float:none;display:inline;">vacuum </span><span
style="margin:.0px;padding:.0px;border:.0px;outline:.0px;color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;text-decoration-style:initial;text-decoration-color:initial;background-color:#ffffff;float:none;display:inline;">electrostatics
                  of the three proteins can be better compared?</span></span></span></span></div>
        <div style="clear:both;"><span
style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;"><span
style="color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;background-color:#ffffff;text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline;"><span
style="margin:.0px;padding:.0px;border:.0px;outline:.0px;color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;text-decoration-style:initial;text-decoration-color:initial;background-color:#ffffff;float:none;display:inline;"><span
style="margin:.0px;padding:.0px;border:.0px;outline:.0px;color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;text-decoration-style:initial;text-decoration-color:initial;background-color:#ffffff;float:none;display:inline;"><br>
                </span></span></span></span></div>
        <div style="clear:both;"><span
style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;"><span
style="color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;background-color:#ffffff;text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline;"><span
style="margin:.0px;padding:.0px;border:.0px;outline:.0px;color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;text-decoration-style:initial;text-decoration-color:initial;background-color:#ffffff;float:none;display:inline;"><span
style="margin:.0px;padding:.0px;border:.0px;outline:.0px;color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;text-decoration-style:initial;text-decoration-color:initial;background-color:#ffffff;float:none;display:inline;">Best
                  regards.</span></span></span></span></div>
        <div style="clear:both;"><span
style="font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;color:#000000;"><span
style="color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;background-color:#ffffff;text-decoration-style:initial;text-decoration-color:initial;float:none;display:inline;"><span
style="margin:.0px;padding:.0px;border:.0px;outline:.0px;color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;text-decoration-style:initial;text-decoration-color:initial;background-color:#ffffff;float:none;display:inline;"><span
style="margin:.0px;padding:.0px;border:.0px;outline:.0px;color:#000000;font-family:Tahoma,Arial,STHeiti,SimSun;font-size:14.0px;font-style:normal;font-variant-ligatures:normal;font-variant-caps:normal;font-weight:400;text-align:start;text-indent:.0px;text-transform:none;widows:2;text-decoration-style:initial;text-decoration-color:initial;background-color:#ffffff;float:none;display:inline;">Yeping</span></span></span></span></div>
      </div>
      <br>
      <fieldset class="mimeAttachmentHeader"></fieldset>
      <br>
      <fieldset class="mimeAttachmentHeader"></fieldset>
      <pre class="moz-quote-pre" wrap="">_______________________________________________
PyMOL-users mailing list
Archives: <a class="moz-txt-link-freetext" href="http://www.mail-archive.com/pym...@li...">http://www.mail-archive.com/pym...@li...</a>
Unsubscribe: <a class="moz-txt-link-freetext" href="https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe">https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe</a></pre>
    </blockquote>
    <br>
    <pre class="moz-signature" cols="72">-- 

Marko Hyvonen
Department of Biochemistry, University of Cambridge
<a class="moz-txt-link-abbreviated" href="mailto:mh...@ca...">mh...@ca...</a>
+44 (0)1223 766 044
@HyvonenGroup
<a class="moz-txt-link-freetext" href="http://hyvonen.bioc.cam.ac.uk">http://hyvonen.bioc.cam.ac.uk</a>
 

</pre>
  </body>
</html>

[PyMOL] How to manually define the lower and upper limit of vacuum electrostatics?

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

Dear all,

I am trying to compare the vacuum electrostatics of three related proteins. I loaded them in pymol and use "Action>generate>vacuum electrostatics menu to generate the vacuum electrostatics of the three proteins. I find that the lower and upper limit of the gradient bars generated with the  vacuum electrostatics of the three proteins are different. They are -64.1~64.1, -72.2~72.2 and -82.2~82.2, respectively.  

I wonder whether I could define the lower and upper limit of the gradients to the same values so that the vacuum electrostatics of the three proteins can be better compared?

Best regards.
Yeping

[PyMOL] MacOS install

[Enrique O. <en....@gm...>]

Hi!
I'm having problems installing compiling and installing the open source version of pymol on MacOS High Sierra; specifically I need the 1.8.4 or 1.8.6. I don't have much experience compiling and installing it and I haven't found clear instructions on how to install previous versions of pymol on Mac.

Hope someone can give me some guidance.
Best regards
E. Ordaz

[PyMOL] Membrane protein view according to X/Y axis and to Z=0 with Pymol

[ABEL S. <Ste...@ce...>]

Hello Pymol users 

I have a snapshot of a membrane protein embedded in a model of bilayer. And I would like to have a picture of the protein according to X/Y axis and at z=0 

It is possible with a script. If yes how ?

Thank you 

Stéphane

Re: [PyMOL] Amber trajectories

[Piter_ <x....@gm...>]

Hi Hira.

I have  had similar experience.
The trick is that you have to load them into the same object.
load file.top, protein
load file.rst, protein
where protein, is the object name.
Best.
Petro


*[PyMOL] Amber trajectories
<https://sourceforge.net/p/pymol/mailman/message/36759912/>*
From: Hira Jabeen <hira.jabeen@br...> - 2019-09-09 14:25:14
*Attachments:* Message as HTML
<https://sourceforge.net/p/pymol/mailman/attachment/DB6PR0601MB2533A27E104F51F50EAB7CF5A0B70%40DB6PR0601MB2533.eurprd06.prod.outlook.com/1/>

Hi everyone,

I am trying to load Amber trajectories in pymol.
I have loaded prmtop file but on loading rst its giving error:
CmdLoad-Error: must load object topology before loading restart file!

please guide about this error.

Thanks,
Hira

[PyMOL] 4th Call For Papers - Extended Deadline - 26th Annual Tcl/Tk Conference (Tcl'2019)

[<con...@tc...>]

Today is the original deadline for paper submissions. We are __extending__
this deadline_by one week, to __Sep 16, 2019, i.e. next Monday__.

Hello pymol-users, fyi ...

26th Annual Tcl/Tk Conference (Tcl'2019)
https://www.tcl-lang.org/community/tcl2019/

November 05 - 08, 2019
Crowne Plaza Houston River Oaks
2712 Southwest Freeway, 77098
Houston, Texas, USA

[ NEWS
  * Our keynote speaker is [Will Duquette](https://github.com/wduquette)
    talking about "Tcl, Rust, and the Death of Rube Goldberg"

  * [Submission is open](https://www.tcl-lang.org/community/tcl2019/cfp.html)

    We are at the original deadline for submissions. It has been extended
    by one week.

  * Registration is open. Please have a look at

    https://www.tcl-lang.org/community/tcl2019/register.html

  * The tutorials are known. See

    https://www.tcl-lang.org/community/tcl2019/tutorials.html
]

Important Dates:

Abstracts and proposals due   September 09, 2019  ** Extended by a week **
Notification to authors       September 16, 2019
WIP and BOF reservations open August 12, 2019
Registration opens            September 09, 2019     ** open already **
Author materials due          October 14, 2019
Tutorials Start               November 04, 2019
Conference starts             November 06, 2019

Email Contact:                tcl...@go...

Submission of Summaries

Tcl/Tk 2019 will be held in Houston, Texas, USA from November 05, 2019 to November 08, 2019.

The program committee is asking for papers and presentation proposals
from anyone using or developing with Tcl/Tk (and extensions). Past
conferences (Proceedings: https://www.tcl-lang.org/community/conferences.html)
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 tcl...@go... no later than September 09, 2019. Authors of accepted
abstracts will have until October 14, 2019 to submit their final
paper for the inclusion in the conference proceedings. The proceedings
will be made available on digital media, so extra materials such as
presentation slides, code examples, code for extensions etc. are
encouraged.

Printed proceedings will be produced as an on-demand book at lulu.com
Online proceedings will appear via
	https://www.tcl-lang.org/community/conferences.html

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 12, 2019. Specific instructions for reserving WIP
and BOF time slots will be provided in the registration information
available in August 12, 2019. 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 (https://www.tcl-lang.org/community/tcl2019/) and will be
published on various Tcl/Tk-related information channels.

To keep in touch with news regarding the conference, subscribe to the
tcl...@go... list. See:
https://groups.google.com/forum/#!forum/tclconference for list
information, archive, and subscription.

To keep in touch with Tcl events in general, subscribe to the
tcl-announce list. See: https://code.activestate.com/lists/tcl-announce
for list information, archive, and subscription.

Conference Committee

   * Andreas Kupries
   * Arjen Markus    Deltares
   * Brian Griffin   Mentor - A Siemens Business
   * Gerald Lester   KnG Consulting LLC
   * Joe Mistachkin  Mistachkin Systems
   * Ronald Fox      CAEN Technologies
                     NSCL @ Michigan State University

Contact Information     tcl...@go...

Tcl'2019 would like to thank those who are sponsoring the conference:

   * FlightAware
   * Mentor - A Siemens Business
   * Noumena Corp

[PyMOL] Amber trajectories

[Hira J. <hir...@br...>]

Hi everyone,

I am trying to load Amber trajectories in pymol.
I have loaded prmtop file but on loading rst its giving error: CmdLoad-Error: must load object topology before loading restart file!

please guide about this error.

Thanks,
Hira

Re: [PyMOL] amino acids displayed for mutagenesis. Hyp? PTMs? (Bruce Onisko)

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

Hi Bruce,

Worked for me without issues, on all platforms (Windows, Linux, Mac).

Installation:
1) Open PyMOL
2) Plugin > Plugin Manager > Install New Plugin
3) Install from PyMOLWiki or any URL
   URL: https://pymolwiki.org/index.php/Pytms
4) Click "Fetch"

Test Usage:
1) Load something:
    fetch 1ubq
    as lines
2) Plugin > Legacy Plugins > PyTMs
3) Click "Acetylation" on the left
4) Click "Modify: Acetylation!" in the bottom right

Cheers,
  Thomas

> On Sep 5, 2019, at 6:22 AM, Bruce Onisko <bco...@gm...> wrote:
> 
> Dear all,
> 
> I just read "PyTMs: a useful PyMol plugin for modelling common post-translational modifications" and it looks great for my needs.
> 
> However after an hour of frustration I have not been able to download and install the plugin.  (I had no trouble downloading, installing and using the SwissModel plugin.......)
> 
> Has anyone done this recently?  If so maybe point me to a working link, or step me through the process please?
> 
> Thanks!
> 
> Bruce

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Re: [PyMOL] amino acids displayed for mutagenesis. Hyp? PTMs? (Bruce Onisko)

[Bruce O. <bco...@gm...>]

Dear all,

I just read "PyTMs: a useful PyMol plugin for modelling common
post-translational modifications" and it looks great for my needs.

However after an hour of frustration I have not been able to download and
install the plugin.  (I had no trouble downloading, installing and using
the SwissModel plugin.......)

Has anyone done this recently?  If so maybe point me to a working link, or
step me through the process please?

Thanks!

Bruce

On Mon, Jul 22, 2019 at 5:19 AM ahoneg <ann...@uz...> wrote:

> Dear Bruce
>
> Try the SwissSidechain PyMOL plugin and database
>
> https://www.swisssidechain.ch/visualization/pymol.php
>
> Annemarie
> ____________________________________________________________
>
> Dr. Annemarie Honegger
> Dept. of Biochemistry
> Zürich University
> Winterthurerstrasse 190
> 8057 Zürich
> Switzerland
>
> e-mail:   hon...@bi...
> phone:   +41 44 635 55 62
> fax:        +41 44 635 57 12
>
>
>
> > On 22 Jul 2019, at 14:02, pym...@li...
> wrote:
> >
> > Send PyMOL-users mailing list submissions to
> >       pym...@li...
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >       https://lists.sourceforge.net/lists/listinfo/pymol-users
> > or, via email, send a message with subject or body 'help' to
> >       pym...@li...
> >
> > You can reach the person managing the list at
> >       pym...@li...
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of PyMOL-users digest..."
> >
> >
> > Today's Topics:
> >
> >   1. amino acids displayed for mutagenesis. Hyp? PTMs? (Bruce Onisko)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Sun, 21 Jul 2019 22:02:08 -0700
> > From: Bruce Onisko <bco...@gm...>
> > To: pym...@li...
> > Subject: [PyMOL] amino acids displayed for mutagenesis. Hyp? PTMs?
> > Message-ID:
> >       <CANFKuAo=
> JQw...@ma...>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hi all,
> >
> > I need to 'mutate" a residue of a protein to a hydroxyproline, aka HYP.
> >
> > In Wizard|Mutagenesis, I see how to choose 1 of about 20 other amino
> acids,
> > but I hydroxyproline is not in the list.
> >
> > Does anyone know how I create such an entry?
> >
> > Or should I learn how to edit a proline?  (Using Builder I assume?)
> >
> > Anyone creating post-translational modifications (eg SER-O-phosphate)
> would
> > have a similar question........
> >
> > Thanks!
> >
> > Bruce
> >
> > PS \PyMOL\share\pymol\data\chempy\fragments\ has all the amino acids, but
> > not what i need.
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> >
> > ------------------------------
> >
> >
> >
> > ------------------------------
> >
> > Subject: Digest Footer
> >
> > _______________________________________________
> > PyMOL-users mailing list
> > PyM...@li...
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> > Unsubscribe:
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> > End of PyMOL-users Digest, Vol 158, Issue 17
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>
>
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Re: [PyMOL] label color

[Dyda <dy...@ul...>]

Try setting 
set spec_direct=0.0

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