Re: [PyMOL] Visualize Sheets from C-alpha Only Structure

[Hurt, Darrell (NIH/NIAID) [E]]

Hi Sean,

If you're doing this for illustrative purposes, why not just build the inferred 
backbone? You could use BBQ, among many others:

http://biocomp.chem.uw.edu.pl/tools/bbq

FWIW,
Darrell

--
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Section Head, Computational Biology
Bioinformatics and Computational Biosciences Branch (BCBB)
OCICB/OSMO/OD/NIAID/NIH

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From: Sean Law mailto:magic...@hotmail.com>>
Date: Wednesday, June 4, 2014 4:17 PM
To: "Sampson, Jared" mailto:jared.samp...@nyumc.org>>
Cc: 
"pymol-users@lists.sourceforge.net" 
mailto:pymol-users@lists.sourceforge.net>>
Subject: Re: [PyMOL] Visualize Sheets from C-alpha Only Structure

Jared,

For now, we are using different colors to indicate the SS assignments but it's 
not pretty. We would prefer to show the SS for both sheets and helices.

Can you elaborate on what you mean by "radially symmetric". Are there other 
cartoon modes where I would be able to get both helices and sheets after 
altering the residue's SS assignment by hand? I see what you mean by not being 
able to define the flat plane though.

Best,

Sean


From: jared.samp...@nyumc.org
To: magic...@hotmail.com
CC: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Visualize Sheets from C-alpha Only Structure
Date: Wed, 4 Jun 2014 20:03:54 +

Hi Sean -

I can confirm this behavior, but I’m not sure it’s unintentional on PyMOL’s 
part.  Rather, I think it may have something to do with two facts: 1) unlike 
loops, sheets represented in automatic mode are not radially symmetric; and 2) 
unlike helices, the orientation of the sheet at a particular CA atom cannot be 
determined by its immediate neighbors.  I haven’t had a chance to look at the 
relevant source, so I can’t confirm this at the moment, but it seems likely to 
me that PyMOL uses the other (non-CA) backbone atoms to define the “flat” plane 
of a sheet, and without this information, instead of guessing at its 
orientation, it omits the sheet entirely.  (This also appears to be the case 
for other non-radially symmetric modes, including dumbbell, rectangle, and 
oval.)

Could you get by using different colors to indicate your SS assignments in 
another cartoon mode?

Cheers,
Jared

Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Jun 4, 2014, at 1:50 PM, Sean Law 
mailto:magic...@hotmail.com>> wrote:

Hi PyMOLers,

I have a c-alpha only model and I would like to visualize both helices and 
sheets based on my own custom SS assignments (via "alter"). Altering a 
residue's SS assignment to helix or loop (ss="H" or ss="L") is fine and can be 
visualized. However, altering a residue's SS assignment to sheet (ss="S") 
causes that residue to disappear. Again, this is c-alpha only and I am 
visualizing in "cartoon automatic" mode.

Any suggestions for visualizing the sheets in this case would be greatly 
appreciated.

Best,

Sean
--
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech___
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Re: [PyMOL] Visualize Sheets from C-alpha Only Structure

[Sampson, Jared]

Hi Sean -

By “radially symmetric” I mean that a particular representation (e.g. anything 
in cartoon tube or putty modes, or loops in automatic mode) is drawn as a 
series of truncated cylinders or cones, so for PyMOL to draw them, basically 
all it needs for each short section are two end points and a radius (or start 
and end radii, in the case of the cones).  If you zoom in really close, you can 
actually see the boundaries between individual sections.

This differs from sheets in automatic, oval, rectangle, and dumbbell modes, 
because those require extra information to define the orientation of the 
“width” and “height” dimensions of the section with respect to the “length” 
axis (the one along the trace of the cartoon).

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Jun 4, 2014, at 4:17 PM, Sean Law 
mailto:magic...@hotmail.com>> wrote:

Jared,

For now, we are using different colors to indicate the SS assignments but it's 
not pretty. We would prefer to show the SS for both sheets and helices.

Can you elaborate on what you mean by "radially symmetric". Are there other 
cartoon modes where I would be able to get both helices and sheets after 
altering the residue's SS assignment by hand? I see what you mean by not being 
able to define the flat plane though.

Best,

Sean


From: jared.samp...@nyumc.org
To: magic...@hotmail.com
CC: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Visualize Sheets from C-alpha Only Structure
Date: Wed, 4 Jun 2014 20:03:54 +

Hi Sean -

I can confirm this behavior, but I’m not sure it’s unintentional on PyMOL’s 
part.  Rather, I think it may have something to do with two facts: 1) unlike 
loops, sheets represented in automatic mode are not radially symmetric; and 2) 
unlike helices, the orientation of the sheet at a particular CA atom cannot be 
determined by its immediate neighbors.  I haven’t had a chance to look at the 
relevant source, so I can’t confirm this at the moment, but it seems likely to 
me that PyMOL uses the other (non-CA) backbone atoms to define the “flat” plane 
of a sheet, and without this information, instead of guessing at its 
orientation, it omits the sheet entirely.  (This also appears to be the case 
for other non-radially symmetric modes, including dumbbell, rectangle, and 
oval.)

Could you get by using different colors to indicate your SS assignments in 
another cartoon mode?

Cheers,
Jared

Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Jun 4, 2014, at 1:50 PM, Sean Law 
mailto:magic...@hotmail.com>> wrote:

Hi PyMOLers,

I have a c-alpha only model and I would like to visualize both helices and 
sheets based on my own custom SS assignments (via "alter"). Altering a 
residue's SS assignment to helix or loop (ss="H" or ss="L") is fine and can be 
visualized. However, altering a residue's SS assignment to sheet (ss="S") 
causes that residue to disappear. Again, this is c-alpha only and I am 
visualizing in "cartoon automatic" mode.

Any suggestions for visualizing the sheets in this case would be greatly 
appreciated.

Best,

Sean
--
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech___
PyMOL-users mailing list 
(PyMOL-users@lists.sourceforge.net)
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Re: [PyMOL] Visualize Sheets from C-alpha Only Structure

[Tsjerk Wassenaar]

Hi Sean,

Maybe this is useful:

http://sourceforge.net/p/pymol/mailman/message/31618301/

Cheers,

Tsjerk



On Wed, Jun 4, 2014 at 10:17 PM, Sean Law  wrote:

> Jared,
>
> For now, we are using different colors to indicate the SS assignments but
> it's not pretty. We would prefer to show the SS for both sheets and helices.
>
> Can you elaborate on what you mean by "radially symmetric". Are there
> other cartoon modes where I would be able to get both helices and sheets
> after altering the residue's SS assignment by hand? I see what you mean by
> not being able to define the flat plane though.
>
> Best,
>
> Sean
>
> --
> From: jared.samp...@nyumc.org
> To: magic...@hotmail.com
> CC: pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] Visualize Sheets from C-alpha Only Structure
> Date: Wed, 4 Jun 2014 20:03:54 +
>
>
> Hi Sean -
>
>   I can confirm this behavior, but I’m not sure it’s unintentional on
> PyMOL’s part.  Rather, I think it may have something to do with two facts:
> 1) unlike loops, sheets represented in automatic mode are not radially
> symmetric; and 2) unlike helices, the orientation of the sheet at a
> particular CA atom cannot be determined by its immediate neighbors.  I
> haven’t had a chance to look at the relevant source, so I can’t confirm
> this at the moment, but it seems likely to me that PyMOL uses the other
> (non-CA) backbone atoms to define the “flat” plane of a sheet, and without
> this information, instead of guessing at its orientation, it omits the
> sheet entirely.  (This also appears to be the case for other non-radially
> symmetric modes, including dumbbell, rectangle, and oval.)
>
>  Could you get by using different colors to indicate your SS assignments
> in another cartoon mode?
>
>  Cheers,
>  Jared
>
> Jared Sampson
> Xiangpeng Kong Lab
> NYU Langone Medical Center
> http://kong.med.nyu.edu/
>
>
>
>
>
>
>  On Jun 4, 2014, at 1:50 PM, Sean Law  wrote:
>
>   Hi PyMOLers,
>
>  I have a c-alpha only model and I would like to visualize both helices
> and sheets based on my own custom SS assignments (via "alter"). Altering a
> residue's SS assignment to helix or loop (ss="H" or ss="L") is fine and can
> be visualized. However, altering a residue's SS assignment to sheet
> (ss="S") causes that residue to disappear. Again, this is c-alpha only and
> I am visualizing in "cartoon automatic" mode.
>
>  Any suggestions for visualizing the sheets in this case would be greatly
> appreciated.
>
>  Best,
>
>  Sean
>
> --
> Learn Graph Databases - Download FREE O'Reilly Book
> "Graph Databases" is the definitive new guide to graph databases and their
>
> applications. Written by three acclaimed leaders in the field,
> this first edition is now available. Download your free book today!
> http://p.sf.net/sfu/NeoTech___
> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>
>
>  
> This email message, including any attachments, is for the sole use of the
> intended recipient(s) and may contain information that is proprietary,
> confidential, and exempt from disclosure under applicable law. Any
> unauthorized review, use, disclosure, or distribution is prohibited. If you
> have received this email in error please notify the sender by return email
> and delete the original message. Please note, the recipient should check
> this email and any attachments for the presence of viruses. The
> organization accepts no liability for any damage caused by any virus
> transmitted by this email.
> =
>
>
> --
> Learn Graph Databases - Download FREE O'Reilly Book
> "Graph Databases" is the definitive new guide to graph databases and their
> applications. Written by three acclaimed leaders in the field,
> this first edition is now available. Download your free book today!
> http://p.sf.net/sfu/NeoTech
> ___
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> Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
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>



-- 
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--
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their 
applications. Written by three acclaimed leaders in the field, 
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech___
PyMOL-users mailing list (PyMOL-users

Re: [PyMOL] Visualize Sheets from C-alpha Only Structure

[Sean Law]

Jared,
For now, we are using different colors to indicate the SS assignments but it's 
not pretty. We would prefer to show the SS for both sheets and helices.
Can you elaborate on what you mean by "radially symmetric". Are there other 
cartoon modes where I would be able to get both helices and sheets after 
altering the residue's SS assignment by hand? I see what you mean by not being 
able to define the flat plane though.
Best,
Sean

From: jared.samp...@nyumc.org
To: magic...@hotmail.com
CC: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Visualize Sheets from C-alpha Only Structure
Date: Wed, 4 Jun 2014 20:03:54 +






Hi Sean - 






I can confirm this behavior, but I’m not sure it’s unintentional on PyMOL’s 
part.  Rather, I think it may have something to do with two facts: 1) unlike 
loops, sheets represented in automatic mode are not radially symmetric; and 2) 
unlike helices, the orientation
 of the sheet at a particular CA atom cannot be determined by its immediate 
neighbors.  I haven’t had a chance to look at the relevant source, so I can’t 
confirm this at the moment, but it seems likely to me that PyMOL uses the other 
(non-CA) backbone atoms
 to define the “flat” plane of a sheet, and without this information, instead 
of guessing at its orientation, it omits the sheet entirely.  (This also 
appears to be the case for other non-radially symmetric modes, including 
dumbbell, rectangle, and oval.)





Could you get by using different colors to indicate your SS assignments in 
another cartoon mode?





Cheers,

Jared



Jared Sampson

Xiangpeng Kong Lab

NYU Langone Medical Center

http://kong.med.nyu.edu/
















On Jun 4, 2014, at 1:50 PM, Sean Law  wrote:




Hi PyMOLers,



I have a c-alpha only model and I would like to visualize both helices and 
sheets based on my own custom SS assignments (via "alter"). Altering a 
residue's SS assignment to helix or loop (ss="H" or ss="L") is fine and can be 
visualized. However, altering
 a residue's SS assignment to sheet (ss="S") causes that residue to disappear. 
Again, this is c-alpha only and I am visualizing in "cartoon automatic" mode.



Any suggestions for visualizing the sheets in this case would be greatly 
appreciated.



Best,



Sean

--

Learn Graph Databases - Download FREE O'Reilly Book

"Graph Databases" is the definitive new guide to graph databases and their 

applications. Written by three acclaimed leaders in the field, 

this first edition is now available. Download your free book today!

http://p.sf.net/sfu/NeoTech___

PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)

Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users

Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net










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applications. Written by three acclaimed leaders in the field, 
this first edition is now available. Download your free book today!
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Re: [PyMOL] Visualize Sheets from C-alpha Only Structure

[Sampson, Jared]

Hi Sean -

I can confirm this behavior, but I’m not sure it’s unintentional on PyMOL’s 
part.  Rather, I think it may have something to do with two facts: 1) unlike 
loops, sheets represented in automatic mode are not radially symmetric; and 2) 
unlike helices, the orientation of the sheet at a particular CA atom cannot be 
determined by its immediate neighbors.  I haven’t had a chance to look at the 
relevant source, so I can’t confirm this at the moment, but it seems likely to 
me that PyMOL uses the other (non-CA) backbone atoms to define the “flat” plane 
of a sheet, and without this information, instead of guessing at its 
orientation, it omits the sheet entirely.  (This also appears to be the case 
for other non-radially symmetric modes, including dumbbell, rectangle, and 
oval.)

Could you get by using different colors to indicate your SS assignments in 
another cartoon mode?

Cheers,
Jared

Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/






On Jun 4, 2014, at 1:50 PM, Sean Law 
mailto:magic...@hotmail.com>> wrote:

Hi PyMOLers,

I have a c-alpha only model and I would like to visualize both helices and 
sheets based on my own custom SS assignments (via "alter"). Altering a 
residue's SS assignment to helix or loop (ss="H" or ss="L") is fine and can be 
visualized. However, altering a residue's SS assignment to sheet (ss="S") 
causes that residue to disappear. Again, this is c-alpha only and I am 
visualizing in "cartoon automatic" mode.

Any suggestions for visualizing the sheets in this case would be greatly 
appreciated.

Best,

Sean
--
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech___
PyMOL-users mailing list 
(PyMOL-users@lists.sourceforge.net)
Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users
Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net


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review, use, disclosure, or distribution is prohibited. If you have received 
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original message. Please note, the recipient should check this email and any 
attachments for the presence of viruses. The organization accepts no liability 
for any damage caused by any virus transmitted by this email.
=
--
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applications. Written by three acclaimed leaders in the field, 
this first edition is now available. Download your free book today!
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[PyMOL] Visualize Sheets from C-alpha Only Structure

[Sean Law]

Hi PyMOLers,
I have a c-alpha only model and I would like to visualize both helices and 
sheets based on my own custom SS assignments (via "alter"). Altering a 
residue's SS assignment to helix or loop (ss="H" or ss="L") is fine and can be 
visualized. However, altering a residue's SS assignment to sheet (ss="S") 
causes that residue to disappear. Again, this is c-alpha only and I am 
visualizing in "cartoon automatic" mode.
Any suggestions for visualizing the sheets in this case would be greatly 
appreciated.
Best,
Sean  --
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their 
applications. Written by three acclaimed leaders in the field, 
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech___
PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
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Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net

Re: [PyMOL] Text in main windows missing with bg_color = white

[Thomas Holder]

Hi Folmer,

> I'm using the latest opensource version of PyMOL (r4077) on Ubuntu 12.04 
> (reported as 1.7.1.3 with get_version, but 1.7.0.0 on the first text line 
> after startup).

looks like you should do a clean rebuild (remove the "build" directory).

> When the bg_color is set to white (also gray, it seems) the text in the main 
> window of PyMOL is missing (revealed when pressing ESC).
> 
> The text looks just fine if bg_color is black.
> 
> Does anyone know if this is a feature or a bug?

it's not a feature, for sure. We'll fix that.

Cheers,
  Thomas

-- 
Thomas Holder
PyMOL Developer
Schrödinger, Inc.


--
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their 
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this first edition is now available. Download your free book today!
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Re: [PyMOL] Text in main windows missing with bg_color = white

[Folmer Fredslund]

Hi Thomas,



2014-06-04 18:02 GMT+02:00 Thomas Holder :

> Hi Folmer,
>
> > I'm using the latest opensource version of PyMOL (r4077) on Ubuntu 12.04
> (reported as 1.7.1.3 with get_version, but 1.7.0.0 on the first text line
> after startup).
>
> looks like you should do a clean rebuild (remove the "build" directory).
>
>
Yes, that changed the version number.


> > When the bg_color is set to white (also gray, it seems) the text in the
> main window of PyMOL is missing (revealed when pressing ESC).
> >
> > The text looks just fine if bg_color is black.
> >
> > Does anyone know if this is a feature or a bug?
>
> it's not a feature, for sure. We'll fix that.
>
>
OK, sounds great!


> Cheers,
>   Thomas
>
> --
> Thomas Holder
> PyMOL Developer
> Schrödinger, Inc.
>
>


-- 
Folmer Fredslund
--
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their 
applications. Written by three acclaimed leaders in the field, 
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[PyMOL] Text in main windows missing with bg_color = white

[Folmer Fredslund]

Hi all,

I'm using the latest opensource version of PyMOL (r4077) on Ubuntu 12.04
(reported as 1.7.1.3 with get_version, but 1.7.0.0 on the first text line
after startup).

When the bg_color is set to white (also gray, it seems) the text in the
main window of PyMOL is missing (revealed when pressing ESC).

The text looks just fine if bg_color is black.

Does anyone know if this is a feature or a bug?

Best regards,
Folmer

-- 
Folmer Fredslund
--
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their 
applications. Written by three acclaimed leaders in the field, 
this first edition is now available. Download your free book today!
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