date:20160208

Re: [PyMOL] Ray tracing max_threads

2016-02-08 Thread Thomas Holder

Hi all,

Quick summary after off-line discussion with Jesper: The max of 32 threads was 
hard coded in PyMOL. The latest SVN update increases this limit to 125.

If you ever need a higher limit, look for PYMOL_MAX_THREADS in the code.

Cheers,
  Thomas

On 22 Jan 2016, at 03:27, Jesper Lykkegaard Karlsen  wrote:

> Hi,
> 
> I am doing some heavy duty ray tracing in PyMOL.
> 
> I realize spreading the job over multiple nodes in a PBS requires MPI 
> integration in PyMOL, but this is run on a single machine with 36 
> physical CPU cores and 72 logical threads.
> Although, during PyMOL ray tracing CPU usage maxes-out at 32 treads.
> 
> I have even tried setting max_treads to 72, but PyMOL refuses to use any 
> more than 32 threads.
> 
> Why this limitation? and is the a way to overcome it?
> 
> Thanks
> 
> Jesper
> 
> -- 
> Jesper Lykkegaard Karlsen
> Scientific Computing
> Centre for Structural Biology
> Department of Molecular Biology and Genetics
> Aarhus University
> Gustav Wieds Vej 10C
> 8000 Aarhus C
> 
> E-mail: je...@mbg.au.dk

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] auto_show_cartoon or similar

2016-02-08 Thread Thomas Holder

Hi Ivan and Carsten,

I can take "auto_show_cartoon" as a feature request. It's trivial to implement.

What also would be nice: automatically showing sticks for ligands. e.g. 
corresponding to the "not polymer" or the "organic" selection. Thoughts?

Cheers,
  Thomas

On 08 Feb 2016, at 09:07, Schubert, Carsten [JRDUS]  
wrote:

> Hi Ivan,
>  
> you could either try to overload the “load” function in Pymol (not sure this 
> is supported) or write your own custom load function under a different name, 
> which loads the protein, assigns the name of the object, hides lines and 
> shows the cartoon.
>  
> Sorry, this is a rather generic answer but should point you in the right 
> direction.
>  
> Cheers,
>  
> Carsten
>  
> From: Ivan Vulovic [mailto:i...@uw.edu] 
> Sent: Saturday, February 06, 2016 8:18 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] auto_show_cartoon or similar
>  
> Hello 
>  
> Is there a way to make cartoon the default representation, something akin to 
> "auto_show_lines", but for cartoon? There was some dicussion of this in 2010 
> (link below) but I haven't found anything more recent that does what I'd like.
>  
> http://www.mail-archive.com/pymol-users%40lists.sourceforge.net/msg07734.html
>  
> Thanks
> Ivan

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] auto_show_cartoon or similar

2016-02-08 Thread Schubert, Carsten [JRDUS]

Hi Ivan,

you could either try to overload the “load” function in Pymol (not sure this is 
supported) or write your own custom load function under a different name, which 
loads the protein, assigns the name of the object, hides lines and shows the 
cartoon.

Sorry, this is a rather generic answer but should point you in the right 
direction.

Cheers,

Carsten

From: Ivan Vulovic [mailto:i...@uw.edu]
Sent: Saturday, February 06, 2016 8:18 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] auto_show_cartoon or similar

Hello

Is there a way to make cartoon the default representation, something akin to 
"auto_show_lines", but for cartoon? There was some dicussion of this in 2010 
(link below) but I haven't found anything more recent that does what I'd like.

http://www.mail-archive.com/pymol-users%40lists.sourceforge.net/msg07734.html

Thanks
Ivan
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[PyMOL] auto_show_cartoon or similar

2016-02-08 Thread Ivan Vulovic

Hello

Is there a way to make cartoon the default representation, something akin
to "auto_show_lines", but for cartoon? There was some dicussion of this in
2010 (link below) but I haven't found anything more recent that does what
I'd like.

http://www.mail-archive.com/pymol-users%40lists.sourceforge.net/msg07734.html

Thanks
Ivan
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Re: [PyMOL] auto_show_cartoon or similar

2016-02-08 Thread Kumar, Abhinav

Showing metal ions  (and FES clusters etc) as spheres would also be useful.

Thanks,
Abhinav

Abhinav Kumar, PhD
Senior Scientist, Bioinformatics
Intrexon, Inc.
329 Oyster Point Blvd., South San Francisco, CA 94080
(650) 597-4072 | aku...@intrexon.com



From: Thomas Holder [thomas.hol...@schrodinger.com]
Sent: Monday, February 08, 2016 8:51 AM
To: Ivan Vulovic; Schubert, Carsten [JRDUS]
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] auto_show_cartoon or similar

Hi Ivan and Carsten,

I can take "auto_show_cartoon" as a feature request. It's trivial to implement.

What also would be nice: automatically showing sticks for ligands. e.g. 
corresponding to the "not polymer" or the "organic" selection. Thoughts?

Cheers,
  Thomas

On 08 Feb 2016, at 09:07, Schubert, Carsten [JRDUS]  
wrote:

> Hi Ivan,
>
> you could either try to overload the “load” function in Pymol (not sure this 
> is supported) or write your own custom load function under a different name, 
> which loads the protein, assigns the name of the object, hides lines and 
> shows the cartoon.
>
> Sorry, this is a rather generic answer but should point you in the right 
> direction.
>
> Cheers,
>
> Carsten
>
> From: Ivan Vulovic [mailto:i...@uw.edu]
> Sent: Saturday, February 06, 2016 8:18 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] auto_show_cartoon or similar
>
> Hello
>
> Is there a way to make cartoon the default representation, something akin to 
> "auto_show_lines", but for cartoon? There was some dicussion of this in 2010 
> (link below) but I haven't found anything more recent that does what I'd like.
>
> http://www.mail-archive.com/pymol-users%40lists.sourceforge.net/msg07734.html
>
> Thanks
> Ivan

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] auto_show_cartoon or similar

2016-02-08 Thread H. Adam Steinberg

Every year I teach students PyMOL, and the look on their faces when they first 
open a pdb in PyMOL and get a cluster of green sticks… yikes!

YES!!! to the default being secondary structure, ligands as sticks, and metal 
ions as spheres! Add - nucleic acids as cartoon. 

> On Feb 8, 2016, at 10:57 AM, Kumar, Abhinav  wrote:
> 
> Showing metal ions  (and FES clusters etc) as spheres would also be useful.
> 
> Thanks,
> Abhinav
> 
> Abhinav Kumar, PhD
> Senior Scientist, Bioinformatics
> Intrexon, Inc.
> 329 Oyster Point Blvd., South San Francisco, CA 94080
> (650) 597-4072 | aku...@intrexon.com
> 
> 
> 
> From: Thomas Holder [thomas.hol...@schrodinger.com]
> Sent: Monday, February 08, 2016 8:51 AM
> To: Ivan Vulovic; Schubert, Carsten [JRDUS]
> Cc: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] auto_show_cartoon or similar
> 
> Hi Ivan and Carsten,
> 
> I can take "auto_show_cartoon" as a feature request. It's trivial to 
> implement.
> 
> What also would be nice: automatically showing sticks for ligands. e.g. 
> corresponding to the "not polymer" or the "organic" selection. Thoughts?
> 
> Cheers,
>  Thomas
> 
> On 08 Feb 2016, at 09:07, Schubert, Carsten [JRDUS]  
> wrote:
> 
>> Hi Ivan,
>> 
>> you could either try to overload the “load” function in Pymol (not sure this 
>> is supported) or write your own custom load function under a different name, 
>> which loads the protein, assigns the name of the object, hides lines and 
>> shows the cartoon.
>> 
>> Sorry, this is a rather generic answer but should point you in the right 
>> direction.
>> 
>> Cheers,
>> 
>>Carsten
>> 
>> From: Ivan Vulovic [mailto:i...@uw.edu]
>> Sent: Saturday, February 06, 2016 8:18 PM
>> To: pymol-users@lists.sourceforge.net
>> Subject: [PyMOL] auto_show_cartoon or similar
>> 
>> Hello
>> 
>> Is there a way to make cartoon the default representation, something akin to 
>> "auto_show_lines", but for cartoon? There was some dicussion of this in 2010 
>> (link below) but I haven't found anything more recent that does what I'd 
>> like.
>> 
>> http://www.mail-archive.com/pymol-users%40lists.sourceforge.net/msg07734.html
>> 
>> Thanks
>> Ivan
> 
> --
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
> 
> 
> --
> Site24x7 APM Insight: Get Deep Visibility into Application Performance
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> 
> 
> 
> CONFIDENTIAL TRANSMISSION - This message, including any attachments, is 
> confidential and may be privileged. If you are not the intended recipient, 
> please delete it without further distribution and reply to the sender that 
> you have received the message in error.
> 
> --
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H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366


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Re: [PyMOL] auto_show_cartoon or similar

2016-02-08 Thread Bourgaize David

My thoughts exactly!

Dave Bourgaize

On 2/8/16, 9:54 AM, "H. Adam Steinberg"  wrote:

>Every year I teach students PyMOL, and the look on their faces when they
>first open a pdb in PyMOL and get a cluster of green sticksŠ yikes!
>
>YES!!! to the default being secondary structure, ligands as sticks, and
>metal ions as spheres! Add - nucleic acids as cartoon.
>
>> On Feb 8, 2016, at 10:57 AM, Kumar, Abhinav  wrote:
>> 
>> Showing metal ions  (and FES clusters etc) as spheres would also be
>>useful.
>> 
>> Thanks,
>> Abhinav
>> 
>> Abhinav Kumar, PhD
>> Senior Scientist, Bioinformatics
>> Intrexon, Inc.
>> 329 Oyster Point Blvd., South San Francisco, CA 94080
>> (650) 597-4072 | aku...@intrexon.com
>> 
>> 
>> 
>> From: Thomas Holder [thomas.hol...@schrodinger.com]
>> Sent: Monday, February 08, 2016 8:51 AM
>> To: Ivan Vulovic; Schubert, Carsten [JRDUS]
>> Cc: pymol-users@lists.sourceforge.net
>> Subject: Re: [PyMOL] auto_show_cartoon or similar
>> 
>> Hi Ivan and Carsten,
>> 
>> I can take "auto_show_cartoon" as a feature request. It's trivial to
>>implement.
>> 
>> What also would be nice: automatically showing sticks for ligands. e.g.
>>corresponding to the "not polymer" or the "organic" selection. Thoughts?
>> 
>> Cheers,
>>  Thomas
>> 
>> On 08 Feb 2016, at 09:07, Schubert, Carsten [JRDUS]
>> wrote:
>> 
>>> Hi Ivan,
>>> 
>>> you could either try to overload the ³load² function in Pymol (not
>>>sure this is supported) or write your own custom load function under a
>>>different name, which loads the protein, assigns the name of the
>>>object, hides lines and shows the cartoon.
>>> 
>>> Sorry, this is a rather generic answer but should point you in the
>>>right direction.
>>> 
>>> Cheers,
>>> 
>>>Carsten
>>> 
>>> From: Ivan Vulovic [mailto:i...@uw.edu]
>>> Sent: Saturday, February 06, 2016 8:18 PM
>>> To: pymol-users@lists.sourceforge.net
>>> Subject: [PyMOL] auto_show_cartoon or similar
>>> 
>>> Hello
>>> 
>>> Is there a way to make cartoon the default representation, something
>>>akin to "auto_show_lines", but for cartoon? There was some dicussion of
>>>this in 2010 (link below) but I haven't found anything more recent that
>>>does what I'd like.
>>> 
>>> 
>>>http://www.mail-archive.com/pymol-users%40lists.sourceforge.net/msg07734
>>>.html
>>> 
>>> Thanks
>>> Ivan
>> 
>> --
>> Thomas Holder
>> PyMOL Principal Developer
>> Schrödinger, Inc.
>> 
>> 
>> 
>>-
>>-
>> Site24x7 APM Insight: Get Deep Visibility into Application Performance
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>> 
>> 
>> 
>> CONFIDENTIAL TRANSMISSION - This message, including any attachments, is
>>confidential and may be privileged. If you are not the intended
>>recipient, please delete it without further distribution and reply to
>>the sender that you have received the message in error.
>> 
>> 
>>-
>>-
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>
>H. Adam Steinberg
>7904 Bowman Rd
>Lodi, WI 53555
>608/592-2366
>
>
>--
>
>Site24x7 APM Insight: Get Deep Visibility into Application Performance
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Re: [PyMOL] auto_show_cartoon or similar

2016-02-08 Thread Joel Tyndall

That would be great, my standard is open file, cartoon, ligand sticks

Great idea

-Original Message-
From: Thomas Holder [mailto:thomas.hol...@schrodinger.com] 
Sent: Tuesday, 9 February 2016 5:52 AM
To: Ivan Vulovic ; Schubert, Carsten [JRDUS] 
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] auto_show_cartoon or similar

Hi Ivan and Carsten,

I can take "auto_show_cartoon" as a feature request. It's trivial to implement.

What also would be nice: automatically showing sticks for ligands. e.g. 
corresponding to the "not polymer" or the "organic" selection. Thoughts?

Cheers,
  Thomas

On 08 Feb 2016, at 09:07, Schubert, Carsten [JRDUS]  
wrote:

> Hi Ivan,
>  
> you could either try to overload the "load" function in Pymol (not sure this 
> is supported) or write your own custom load function under a different name, 
> which loads the protein, assigns the name of the object, hides lines and 
> shows the cartoon.
>  
> Sorry, this is a rather generic answer but should point you in the right 
> direction.
>  
> Cheers,
>  
> Carsten
>  
> From: Ivan Vulovic [mailto:i...@uw.edu] 
> Sent: Saturday, February 06, 2016 8:18 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] auto_show_cartoon or similar
>  
> Hello 
>  
> Is there a way to make cartoon the default representation, something akin to 
> "auto_show_lines", but for cartoon? There was some dicussion of this in 2010 
> (link below) but I haven't found anything more recent that does what I'd like.
>  
> http://www.mail-archive.com/pymol-users%40lists.sourceforge.net/msg07734.html
>  
> Thanks
> Ivan

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] Ray tracing max_threads

Re: [PyMOL] auto_show_cartoon or similar

Re: [PyMOL] auto_show_cartoon or similar

[PyMOL] auto_show_cartoon or similar

Re: [PyMOL] auto_show_cartoon or similar

Re: [PyMOL] auto_show_cartoon or similar

Re: [PyMOL] auto_show_cartoon or similar

Re: [PyMOL] auto_show_cartoon or similar

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