pymol-users Mailing List for PyMOL Molecular Graphics System

Just a friendly reminder that the deadline for applying the upcoming 
CCP4 school at APS is next Wednesday (5/2/2018), please apply or finish 
your application (if you have already applied) if you wish to 
participate in the school. Please let us know if you have any 
questions/concerns.

Qingping Xu
GMCA/APS
Argonne National Laboratory

===========

Dear Colleagues,

We are pleased to announce the *11th annual CCP4 crystallographic school 
*“From data collection to structure refinement and beyond” will be held 
on June 18-25, 2018 at Advanced Photon Source (APS), Argonne National 
Laboratory (ANL), near Chicago, Illinois, USA. All details can be found 
at http://www.ccp4.ac.uk/schools/APS-2018/index.php.

*Dates*: June 18 through 25, 2018

*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).

*Applicants*: Graduate students, postdoctoral researchers and young 
scientists at the assistant professor level, along with 
commercial/industrial researchers are encouraged to apply. Only 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 *Wednesday May 2nd, 2018*. The 
application form, the program, contact info and other details can be 
found at http://www.ccp4.ac.uk/schools/APS-2018/index.php

*Registration fees*: The registration for application is free but there 
is $500 participation fee for the selected academic students and $950 
for the industrial researchers. The link for the on-line payments and 
instructions will be provided once the selection process is completed. 
The students will be responsible for their transportation and lodging. 
The workshop organizers can assist in making the 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

Hi Thomas,

Fantastic! I can confirm that this works on my end. Thanks everyone.

Cody

On 4/25/18, 5:07 PM, "Thomas Holder" <tho...@sc...> wrote:

    Hi Cody,
    
    I found a simple workaround to get stereo working in batch mode. Just set the "stereo" setting to 1 after switching to anaglyph, like this:
    
    stereo anaglyph
    set stereo
    
    Cheers,
      Thomas
    
    > On Apr 24, 2018, at 8:29 AM, Thomas Holder <tho...@sc...> wrote:
    > 
    > Thanks Jared and Cody! There is not much I can add, yes this looks like a bug and we should fix it.
    > 
    > Cheers,
    >  Thomas
    > 
    >> On Apr 23, 2018, at 11:51 PM, Jared Sampson <jar...@co...> wrote:
    >> 
    >> Hi Cody - 
    >> 
    >> I can confirm that I see similar behavior on 2.1.0 (stereo rendered properly from the GUI but not in batch mode) but the issue is not limited to just anaglyph stereo.  Rather, (admittedly not having tested all stereo_mode options) it seems stereo in general doesn't get rendered as expected in batch mode.  I imagine Thomas will chime in as well, but I would file a bug report with pym...@sc... and/or via https://sourceforge.net/p/pymol/bugs/.
    >> 
    >> Cheers,
    >> Jared
    >> 
    >> On April 23, 2018 at 6:59:03 PM, Cody Jackson (cja...@sc...) wrote:
    >> 
    >>> Hi Everyone, 
    >>> 
    >>> I'm trying to make anaglyph 3D figures and movies in command line mode and I'm having some trouble - using incentive version 2.1.1 right now. 
    >>> 
    >>> It seems like anaglyph stereo is only ray traced when the GUI is open. Here's a quick example adapted from the wiki, it saves the desired red-cyan png when I run it with @script.pml in the GUI, but I only get the 2D output when I run pymol -c script.pml. Is there a trick to getting stereo images in the command line/batch mode? Is it not possible? 
    >>> 
    >>> -- 
    >>> fetch 1ESR, async=0 
    >>> as cartoon 
    >>> set cartoon_smooth_loops 
    >>> spectrum 
    >>> bg white 
    >>> stereo anaglyph 
    >>> ray 640,480 
    >>> png demo.png 
    >>> -- 
    >>> 
    >>> Thank you for any input. 
    >>> 
    >>> Best, 
    >>> Cody Jackson
    
    --
    Thomas Holder
    PyMOL Principal Developer
    Schrödinger, Inc.
    
    

Hi Cody,

I found a simple workaround to get stereo working in batch mode. Just set the "stereo" setting to 1 after switching to anaglyph, like this:

stereo anaglyph
set stereo

Cheers,
  Thomas

> On Apr 24, 2018, at 8:29 AM, Thomas Holder <tho...@sc...> wrote:
> 
> Thanks Jared and Cody! There is not much I can add, yes this looks like a bug and we should fix it.
> 
> Cheers,
>  Thomas
> 
>> On Apr 23, 2018, at 11:51 PM, Jared Sampson <jar...@co...> wrote:
>> 
>> Hi Cody - 
>> 
>> I can confirm that I see similar behavior on 2.1.0 (stereo rendered properly from the GUI but not in batch mode) but the issue is not limited to just anaglyph stereo.  Rather, (admittedly not having tested all stereo_mode options) it seems stereo in general doesn't get rendered as expected in batch mode.  I imagine Thomas will chime in as well, but I would file a bug report with pym...@sc... and/or via https://sourceforge.net/p/pymol/bugs/.
>> 
>> Cheers,
>> Jared
>> 
>> On April 23, 2018 at 6:59:03 PM, Cody Jackson (cja...@sc...) wrote:
>> 
>>> Hi Everyone, 
>>> 
>>> I'm trying to make anaglyph 3D figures and movies in command line mode and I'm having some trouble - using incentive version 2.1.1 right now. 
>>> 
>>> It seems like anaglyph stereo is only ray traced when the GUI is open. Here's a quick example adapted from the wiki, it saves the desired red-cyan png when I run it with @script.pml in the GUI, but I only get the 2D output when I run pymol -c script.pml. Is there a trick to getting stereo images in the command line/batch mode? Is it not possible? 
>>> 
>>> -- 
>>> fetch 1ESR, async=0 
>>> as cartoon 
>>> set cartoon_smooth_loops 
>>> spectrum 
>>> bg white 
>>> stereo anaglyph 
>>> ray 640,480 
>>> png demo.png 
>>> -- 
>>> 
>>> Thank you for any input. 
>>> 
>>> Best, 
>>> Cody Jackson

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

> On Apr 24, 2018, at 7:17 PM, Yang Su <su...@cr...> wrote:
> 
> OK, thanks. If you don't mind, I can add it to the wiki: https://pymolwiki.org/index.php/Launching_From_a_Script

Sure, that would be great. Thanks a lot!

Cheers,
  Thomas

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

OK, thanks. If you don't mind, I can add it to the wiki:
https://pymolwiki.org/index.php/Launching_From_a_Script

Best,
Yang


On Tue, Apr 24, 2018 at 6:47 PM, Thomas Holder <
tho...@sc...> wrote:

> Hi Yang,
>
> Very good questions. I don't think that it's documented anywhere.
> Reference counting is maintained, I fixed that up as best as I could before
> the PyMOL 2.0 release (in PyMOL 1.x it leaks references). Looks like there
> is no way to introspect whether start() has been called already.
>
> Cheers,
>   Thomas
>
> > On Apr 24, 2018, at 6:16 PM, Yang Su <su...@cr...> wrote:
> >
> > Thanks Thomas. The code snippet works. Does start(), stop() maintain
> reference counting? Is there a way to know if it's already started/stopped?
> Is this API documented somewhere?
> >
> > Thanks,
> > Yang
> >
> >
> > On Mon, Apr 23, 2018 at 1:15 PM, Thomas Holder <
> tho...@sc...> wrote:
> > Hi Yang,
> >
> > Yes it's possible to have independent instances. The API has actually
> been around for a long time. For some reason it was never widely adopted
> and thus is not very thoroughly tested. Please report any bugs you
> encounter.
> >
> > Example:
> >
> > import pymol2
> > p = pymol2.PyMOL()
> > p.start()
> > p.cmd.fragment('ala')
> > p.cmd.show_as('sticks')
> > p.cmd.zoom()
> > p.cmd.png('/tmp/ala.png', 1000, 800, dpi=150, ray=1)
> > p.stop()
> >
> > Cheers,
> >   Thomas
> >
> > > On Apr 19, 2018, at 3:33 PM, Yang Su <su...@cr...> wrote:
> > >
> > > Hi,
> > >
> > > Is it possible to start multiple independent pymol backend processes
> in a python script/jupyter notebook? Now with PyMOL 2.1 I can 'import
> pymol' and call a pymol.cmd function to start a backend process, but this
> is kind of 'global'. I'm looking for a way to manage multiple PyMOL
> sessions in parallel, each manipulating its own structures.
> > >
> > > Thanks,
> > > Yang
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

Hi Yang,

Very good questions. I don't think that it's documented anywhere. Reference counting is maintained, I fixed that up as best as I could before the PyMOL 2.0 release (in PyMOL 1.x it leaks references). Looks like there is no way to introspect whether start() has been called already.

Cheers,
  Thomas

> On Apr 24, 2018, at 6:16 PM, Yang Su <su...@cr...> wrote:
> 
> Thanks Thomas. The code snippet works. Does start(), stop() maintain reference counting? Is there a way to know if it's already started/stopped? Is this API documented somewhere?
> 
> Thanks,
> Yang
> 
> 
> On Mon, Apr 23, 2018 at 1:15 PM, Thomas Holder <tho...@sc...> wrote:
> Hi Yang,
> 
> Yes it's possible to have independent instances. The API has actually been around for a long time. For some reason it was never widely adopted and thus is not very thoroughly tested. Please report any bugs you encounter.
> 
> Example:
> 
> import pymol2
> p = pymol2.PyMOL()
> p.start()
> p.cmd.fragment('ala')
> p.cmd.show_as('sticks')
> p.cmd.zoom()
> p.cmd.png('/tmp/ala.png', 1000, 800, dpi=150, ray=1)
> p.stop()
> 
> Cheers,
>   Thomas
> 
> > On Apr 19, 2018, at 3:33 PM, Yang Su <su...@cr...> wrote:
> > 
> > Hi,
> > 
> > Is it possible to start multiple independent pymol backend processes in a python script/jupyter notebook? Now with PyMOL 2.1 I can 'import pymol' and call a pymol.cmd function to start a backend process, but this is kind of 'global'. I'm looking for a way to manage multiple PyMOL sessions in parallel, each manipulating its own structures.
> > 
> > Thanks,
> > Yang

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Thanks Thomas. The code snippet works. Does start(), stop() maintain
reference counting? Is there a way to know if it's already started/stopped?
Is this API documented somewhere?

Thanks,
Yang


On Mon, Apr 23, 2018 at 1:15 PM, Thomas Holder <
tho...@sc...> wrote:

> Hi Yang,
>
> Yes it's possible to have independent instances. The API has actually been
> around for a long time. For some reason it was never widely adopted and
> thus is not very thoroughly tested. Please report any bugs you encounter.
>
> Example:
>
> import pymol2
> p = pymol2.PyMOL()
> p.start()
> p.cmd.fragment('ala')
> p.cmd.show_as('sticks')
> p.cmd.zoom()
> p.cmd.png('/tmp/ala.png', 1000, 800, dpi=150, ray=1)
> p.stop()
>
> Cheers,
>   Thomas
>
> > On Apr 19, 2018, at 3:33 PM, Yang Su <su...@cr...> wrote:
> >
> > Hi,
> >
> > Is it possible to start multiple independent pymol backend processes in
> a python script/jupyter notebook? Now with PyMOL 2.1 I can 'import pymol'
> and call a pymol.cmd function to start a backend process, but this is kind
> of 'global'. I'm looking for a way to manage multiple PyMOL sessions in
> parallel, each manipulating its own structures.
> >
> > Thanks,
> > Yang
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

Thanks Jared and Cody! There is not much I can add, yes this looks like a bug and we should fix it.

Cheers,
  Thomas

> On Apr 23, 2018, at 11:51 PM, Jared Sampson <jar...@co...> wrote:
> 
> Hi Cody - 
> 
> I can confirm that I see similar behavior on 2.1.0 (stereo rendered properly from the GUI but not in batch mode) but the issue is not limited to just anaglyph stereo.  Rather, (admittedly not having tested all stereo_mode options) it seems stereo in general doesn't get rendered as expected in batch mode.  I imagine Thomas will chime in as well, but I would file a bug report with pym...@sc... and/or via https://sourceforge.net/p/pymol/bugs/.
> 
> Cheers,
> Jared
> 
> On April 23, 2018 at 6:59:03 PM, Cody Jackson (cja...@sc...) wrote:
> 
>> Hi Everyone, 
>> 
>> I'm trying to make anaglyph 3D figures and movies in command line mode and I'm having some trouble - using incentive version 2.1.1 right now. 
>> 
>> It seems like anaglyph stereo is only ray traced when the GUI is open. Here's a quick example adapted from the wiki, it saves the desired red-cyan png when I run it with @script.pml in the GUI, but I only get the 2D output when I run pymol -c script.pml. Is there a trick to getting stereo images in the command line/batch mode? Is it not possible? 
>> 
>> -- 
>> fetch 1ESR, async=0 
>> as cartoon 
>> set cartoon_smooth_loops 
>> spectrum 
>> bg white 
>> stereo anaglyph 
>> ray 640,480 
>> png demo.png 
>> -- 
>> 
>> Thank you for any input. 
>> 
>> Best, 
>> Cody Jackson

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi Cody - 

I can confirm that I see similar behavior on 2.1.0 (stereo rendered properly from the GUI but not in batch mode) but the issue is not limited to just anaglyph stereo.  Rather, (admittedly not having tested all stereo_mode options) it seems stereo in general doesn't get rendered as expected in batch mode.  I imagine Thomas will chime in as well, but I would file a bug report with pym...@sc... and/or via https://sourceforge.net/p/pymol/bugs/.

Cheers,
Jared

On April 23, 2018 at 6:59:03 PM, Cody Jackson (cja...@sc...) wrote:

Hi Everyone,  

I'm trying to make anaglyph 3D figures and movies in command line mode and I'm having some trouble - using incentive version 2.1.1 right now.  

It seems like anaglyph stereo is only ray traced when the GUI is open. Here's a quick example adapted from the wiki, it saves the desired red-cyan png when I run it with @script.pml in the GUI, but I only get the 2D output when I run pymol -c script.pml. Is there a trick to getting stereo images in the command line/batch mode? Is it not possible?  

--  
fetch 1ESR, async=0  
as cartoon  
set cartoon_smooth_loops  
spectrum  
bg white  
stereo anaglyph  
ray 640,480  
png demo.png  
--  

Thank you for any input.  

Best,  
Cody Jackson  

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Hi Everyone,

I'm trying to make anaglyph 3D figures and movies in command line mode and I'm having some trouble - using incentive version 2.1.1 right now.

It seems like anaglyph stereo is only ray traced when the GUI is open. Here's a quick example adapted from the wiki, it saves the desired red-cyan png when I run it with @script.pml in the GUI, but I only get the 2D output when I run pymol -c script.pml. Is there a trick to getting stereo images in the command line/batch mode? Is it not possible?

--
fetch 1ESR, async=0
as cartoon
set cartoon_smooth_loops
spectrum
bg white
stereo anaglyph
ray 640,480
png demo.png
--

Thank you for any input.

Best,
Cody Jackson

Hi Yang,

Yes it's possible to have independent instances. The API has actually been around for a long time. For some reason it was never widely adopted and thus is not very thoroughly tested. Please report any bugs you encounter.

Example:

import pymol2
p = pymol2.PyMOL()
p.start()
p.cmd.fragment('ala')
p.cmd.show_as('sticks')
p.cmd.zoom()
p.cmd.png('/tmp/ala.png', 1000, 800, dpi=150, ray=1)
p.stop()

Cheers,
  Thomas

> On Apr 19, 2018, at 3:33 PM, Yang Su <su...@cr...> wrote:
> 
> Hi,
> 
> Is it possible to start multiple independent pymol backend processes in a python script/jupyter notebook? Now with PyMOL 2.1 I can 'import pymol' and call a pymol.cmd function to start a backend process, but this is kind of 'global'. I'm looking for a way to manage multiple PyMOL sessions in parallel, each manipulating its own structures.
> 
> Thanks,
> Yang

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

I see. It would be nice to have the cartoon_flat_sheets effect on the loop
and tube variants, too. I like the looks of it. Maybe in a future version
:-)

Thanks,
Yang

On Thu, Apr 19, 2018 at 4:30 PM, Thomas Holder <
tho...@sc...> wrote:

> Hi Yang,
>
> That's an interesting observation, I wasn't aware that cartoon dash and
> loop may be traced differently. Apparently the "cartoon_flat_sheets"
> setting only applies to dash, not loop. Turning it off will make them
> follow the same path:
>
> set cartoon_flat_sheets, 0
>
> Cheers,
>   Thomas
>
> > On Apr 19, 2018, at 4:15 PM, Yang Su <su...@cr...> wrote:
> >
> > Also, 'cartoon dash' and 'cartoon loop' render beta-strands differently,
> so I can't combine the two and get a consistent look and feel. The use case
> is to show regions of the structure as dashed line to indicate 'not covered
> in study'. I can't use different colors for this purpose because color
> coding is already used to represent other properties.
> >
> > Best,
> > Yang
> >
> > On Thu, Apr 19, 2018 at 3:56 PM, Yang Su <su...@cr...> wrote:
> > Thanks for the tip, Thomas. 'cartoon dash' works with cartoon
> representation, but doesn't seem to affect the ribbon representation. For
> some use cases I like the 'cornered' ribbon representation better than the
> smooth cartoon representation, but cartoon is still a good alternative if
> it is not possible to show ribbon as dashed/dotted lines.
> >
> > Thanks,
> > Yang
> >
> >
> > On Thu, Apr 19, 2018 at 1:54 PM, Thomas Holder <
> tho...@sc...> wrote:
> > Hi Yang,
> >
> > Yes, since PyMOL 1.8.2 there is "cartoon dash". e.g.:
> >
> > fetch 1ubq, async=0
> > as cartoon
> > cartoon dash
> >
> > See also:
> > https://pymolwiki.org/index.php/Cartoon#USAGE
> >
> > Cheers,
> >   Thomas
> >
> > > On Apr 19, 2018, at 12:54 PM, Yang Su <su...@cr...> wrote:
> > >
> > > Hi,
> > >
> > > Is there an option to show the ribbon as dashed or dotted lines in
> pymol?
> > >
> > > Thanks,
> > >
> > > Yang
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

Hi Yang,

That's an interesting observation, I wasn't aware that cartoon dash and loop may be traced differently. Apparently the "cartoon_flat_sheets" setting only applies to dash, not loop. Turning it off will make them follow the same path:

set cartoon_flat_sheets, 0

Cheers,
  Thomas

> On Apr 19, 2018, at 4:15 PM, Yang Su <su...@cr...> wrote:
> 
> Also, 'cartoon dash' and 'cartoon loop' render beta-strands differently, so I can't combine the two and get a consistent look and feel. The use case is to show regions of the structure as dashed line to indicate 'not covered in study'. I can't use different colors for this purpose because color coding is already used to represent other properties.
> 
> Best,
> Yang
> 
> On Thu, Apr 19, 2018 at 3:56 PM, Yang Su <su...@cr...> wrote:
> Thanks for the tip, Thomas. 'cartoon dash' works with cartoon representation, but doesn't seem to affect the ribbon representation. For some use cases I like the 'cornered' ribbon representation better than the smooth cartoon representation, but cartoon is still a good alternative if it is not possible to show ribbon as dashed/dotted lines.
> 
> Thanks,
> Yang
> 
> 
> On Thu, Apr 19, 2018 at 1:54 PM, Thomas Holder <tho...@sc...> wrote:
> Hi Yang,
> 
> Yes, since PyMOL 1.8.2 there is "cartoon dash". e.g.:
> 
> fetch 1ubq, async=0
> as cartoon
> cartoon dash
> 
> See also:
> https://pymolwiki.org/index.php/Cartoon#USAGE
> 
> Cheers,
>   Thomas
> 
> > On Apr 19, 2018, at 12:54 PM, Yang Su <su...@cr...> wrote:
> > 
> > Hi,
> > 
> > Is there an option to show the ribbon as dashed or dotted lines in pymol?
> > 
> > Thanks,
> > 
> > Yang

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Also, 'cartoon dash' and 'cartoon loop' render beta-strands differently, so
I can't combine the two and get a consistent look and feel. The use case is
to show regions of the structure as dashed line to indicate 'not covered in
study'. I can't use different colors for this purpose because color coding
is already used to represent other properties.

Best,
Yang

On Thu, Apr 19, 2018 at 3:56 PM, Yang Su <su...@cr...> wrote:

> Thanks for the tip, Thomas. 'cartoon dash' works with cartoon
> representation, but doesn't seem to affect the ribbon representation. For
> some use cases I like the 'cornered' ribbon representation better than the
> smooth cartoon representation, but cartoon is still a good alternative if
> it is not possible to show ribbon as dashed/dotted lines.
>
> Thanks,
> Yang
>
>
> On Thu, Apr 19, 2018 at 1:54 PM, Thomas Holder <
> tho...@sc...> wrote:
>
>> Hi Yang,
>>
>> Yes, since PyMOL 1.8.2 there is "cartoon dash". e.g.:
>>
>> fetch 1ubq, async=0
>> as cartoon
>> cartoon dash
>>
>> See also:
>> https://pymolwiki.org/index.php/Cartoon#USAGE
>>
>> Cheers,
>>   Thomas
>>
>> > On Apr 19, 2018, at 12:54 PM, Yang Su <su...@cr...> wrote:
>> >
>> > Hi,
>> >
>> > Is there an option to show the ribbon as dashed or dotted lines in
>> pymol?
>> >
>> > Thanks,
>> >
>> > Yang
>>
>> --
>> Thomas Holder
>> PyMOL Principal Developer
>> Schrödinger, Inc.
>>
>>
>

Thanks for the tip, Thomas. 'cartoon dash' works with cartoon
representation, but doesn't seem to affect the ribbon representation. For
some use cases I like the 'cornered' ribbon representation better than the
smooth cartoon representation, but cartoon is still a good alternative if
it is not possible to show ribbon as dashed/dotted lines.

Thanks,
Yang


On Thu, Apr 19, 2018 at 1:54 PM, Thomas Holder <
tho...@sc...> wrote:

> Hi Yang,
>
> Yes, since PyMOL 1.8.2 there is "cartoon dash". e.g.:
>
> fetch 1ubq, async=0
> as cartoon
> cartoon dash
>
> See also:
> https://pymolwiki.org/index.php/Cartoon#USAGE
>
> Cheers,
>   Thomas
>
> > On Apr 19, 2018, at 12:54 PM, Yang Su <su...@cr...> wrote:
> >
> > Hi,
> >
> > Is there an option to show the ribbon as dashed or dotted lines in pymol?
> >
> > Thanks,
> >
> > Yang
>
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
>
>

Hi,

Is it possible to start multiple independent pymol backend processes in a
python script/jupyter notebook? Now with PyMOL 2.1 I can 'import pymol' and
call a pymol.cmd function to start a backend process, but this is kind of
'global'. I'm looking for a way to manage multiple PyMOL sessions in
parallel, each manipulating its own structures.

Thanks,
Yang

Hi Yang,

Yes, since PyMOL 1.8.2 there is "cartoon dash". e.g.:

fetch 1ubq, async=0
as cartoon
cartoon dash

See also:
https://pymolwiki.org/index.php/Cartoon#USAGE

Cheers,
  Thomas

> On Apr 19, 2018, at 12:54 PM, Yang Su <su...@cr...> wrote:
> 
> Hi,
> 
> Is there an option to show the ribbon as dashed or dotted lines in pymol?
> 
> Thanks,
> 
> Yang

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Hi,

Is there an option to show the ribbon as dashed or dotted lines in pymol?

Thanks,

Yang

Hi, I have found that with this settings the rendering keeps always white
the interior color.

fetch 1c0k, async=0
as spheres,
clip near , -50
set ray_interior_color, pink
set direct,off
set spec_direct,1
set light_count, 1
ray

If you change the light_count to 2 or try to shut down spec_direct, the
problem disappears.

Is this normal?

Found It:
Display->External GUI->Toggle Floating or Ctrl E


Thanks,
Abhinav


________________________________
From: Kumar, Abhinav
Sent: Tuesday, April 17, 2018 8:24 AM
To: Pymol User list
Subject: Menu and view windows

Hi,
Can someone please remind me how to detach the menu window from the main viewer window?

Thanks,
Abhinav

Abhinav Kumar, PhD
Principal Scientist, Data Science & Computational Biology
Intrexon, Inc.
329 Oyster Point Blvd., South San Francisco, CA 94080
(650) 597-4072 | ak...@in...


________________________________

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Hi,
Can someone please remind me how to detach the menu window from the main viewer window?

Thanks,
Abhinav

Abhinav Kumar, PhD
Principal Scientist, Data Science & Computational Biology
Intrexon, Inc.
329 Oyster Point Blvd., South San Francisco, CA 94080
(650) 597-4072 | ak...@in...


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CONFIDENTIAL TRANSMISSION - To the extent this electronic communication or any of its attachments contain information that is not in the public domain, such information is considered by Intrexon Corporation to be confidential and proprietary. This communication is expected to be read and/or used only by the individual(s) for whom it is intended. If you have received this electronic communication in error, please reply to the sender advising of the error in transmission and delete the original message and any accompanying documents from your system immediately, without copying, reviewing or otherwise using them for any purpose. Thank you for your cooperation.

Hi Paul,

After loading the MTZ file, did any objects show up in the panel on the right? If PyMOL detects columns for 2fofc and/or fofc maps, and the file is named "foo.mtz", then you should get "foo.2fofc" and "foo.fofc" maps. Use one of these maps as the second argument to volume (or isomesh). If automatic column detection fails, use a loading option with manual column selection.

Summary of MTZ loading options:

1) Command line with column auto detection for 2fofc and fofc:
   load file.mtz
2) Command line with manual column selections:
   load_mtz file.mtz, mapname, FP, PHIC
3) GUI, opens MTZ import dialog:
   File > Open ...

In each case you should get one or more map objects, which you can use with volume or isomesh in the next step to get a visualization.

Cheers,
  Thomas

> On Apr 16, 2018, at 11:18 AM, Paul Miller <pa...@st...> wrote:
> 
> Hi
> 
> I'm using Windows Pymol 2.0 and would like to show mtz (NOT ccp4!) file 2fofc density around a ligand. Can anyone tell me how to do this?
> 
> I found info on a website (below), which I modified in various ways but it didn't work. Kept saying the some.2fofc file was not found.
> volume abc, some.2fofc, 0, organic, 4., 1, 4
> 
> Cheers, Paul
> 
> Paul Steven Miller (PhD) 
> Postdoctoral Researcher 
> University of Oxford 
> Wellcome Trust Centre for Human Genetics 
> Division of Structural Biology 
> Roosevelt Drive 
> Oxford 
> OX3 7BN

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.

Dear Colleagues,

This is a reminder for the upcoming CCP4/APS school. The deadline for 
registering is coming up soon, please register if you plan to attend.

Thanks.

Charles, Garib and Qingping

====original announcement ====

Dear Colleagues,

We are pleased to announce the *11th annual CCP4 crystallographic school 
*“From data collection to structure refinement and beyond” will be held 
on June 18-25, 2018 at Advanced Photon Source (APS), Argonne National 
Laboratory (ANL), near Chicago, Illinois, USA. All details can be found 
at http://www.ccp4.ac.uk/schools/APS-2018/index.php.

*Dates*: June 18 through 25, 2018

*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).

*Applicants*: Graduate students, postdoctoral researchers and young 
scientists at the assistant professor level, along with 
commercial/industrial researchers are encouraged to apply. Only 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 *Wednesday May 2nd, 2018*. The 
application form, the program, contact info and other details can be 
found at http://www.ccp4.ac.uk/schools/APS-2018/index.php

*Registration fees*: The registration for application is free but there 
is $500 participation fee for the selected academic students and $950 
for the industrial researchers. The link for the on-line payments and 
instructions will be provided once the selection process is completed. 
The students will be responsible for their transportation and lodging. 
The workshop organizers can assist in making the 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

Hi

I'm using Windows Pymol 2.0 and would like to show mtz (NOT ccp4!) file 2fofc density around a ligand. Can anyone tell me how to do this?

I found info on a website (below), which I modified in various ways but it didn't work. Kept saying the some.2fofc file was not found.

volume abc, some.2fofc, 0, organic, 4., 1, 4
Cheers, Paul


Paul Steven Miller (PhD)
Postdoctoral Researcher
University of Oxford
Wellcome Trust Centre for Human Genetics
Division of Structural Biology
Roosevelt Drive
Oxford
OX3 7BN
 

Hi Gary -

In the session you want to record, before performing the actions or commands, type:

```
log_open log.pml
```

You can also optionally provide the full path to the log file.  

Then to replay the recorded instructinos in the new session (here assuming the same working directory):

```
@log.pml
```

This is a great way to learn how to automate PyMOL with scripts based on actions performed in the GUI.  One caveat is that the various wizards that involve picking atoms (measurement, mutagenesis, etc) generally don't work so well.  But normal GUI operations (changing view, representation, color, etc.) get logged fine.

Hope that helps.

Cheers,
Jared


On April 14, 2018 at 9:30:20 AM, Gary Oberbrunner (ga...@da...) wrote:

Is there a way in pymol to record all the typed commands as well as the menu actions (select, show, hide, etc.) so they can be replayed in a script?

--
Gary Oberbrunner -- CEO -- Dark Star Systems, Inc.
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