Re: [PyMOL] Disable cartoon representation on load

[Thomas Holder]

Hi Petro,

Put this line in your pymolrc file (File > Edit pymolrc):

set auto_show_classified, 0

See also:
https://pymolwiki.org/index.php/pymolrc
https://pymolwiki.org/index.php/auto_show_classified
https://sourceforge.net/p/pymol/mailman/message/36155392/

Cheers,
  Thomas

On Wed, May 17, 2023 at 4:51 PM Khoroshyy Petro  wrote:
>
> Hi.
> How can I force pymol to show things in lines, not in cartoons, by default?
> Thanks.
> Petro.
>
>
> --
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[PyMOL] Disable cartoon representation on load

[Khoroshyy Petro]

Hi.
How can I force pymol to show things in lines, not in cartoons, by default?
Thanks.
Petro.


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Re: [PyMOL] on cartoon representation

[Osvaldo Martin]

Hi Smith,

There are several setting you could change to modify the way helices (and
loops and beta strands) are rendered. Try with this
 page and let us
know if you find something useful or you have further doubts.
Cheers,
Osvaldo.

On Wed, Oct 7, 2015 at 3:52 PM, Smith Liu  wrote:

Dear All,
>
> Recently I have noticed in Science and Nature paper, the author present
> the helix in cartoon as thin as that observed in VMD (and even similar in
> appearance). I do not know whether the author made the image by pymol or by
> VMD.
>
> Is any way for pymol to make helix in carton as  observed in VMD?
>
> Best regards.
>
> Smith
>
>
>
>
>
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Re: [PyMOL] Pymol: Cartoon representation for .pdb file with multible entries

[Alexander Schulz]

Hi Robert,

this solves exactly my problem and gives me the pictures I wanted.

Thank you very much for the quick answer!

Cheers,
Alexander

Am Mittwoch, den 26.10.2011, 09:48 -0400 schrieb Robert Campbell:
 Hi Alexander,
 
 On Wed, 2011-10-26 12:53  EDT,  Alexander Schulz
 sch...@dwi.rwth-aachen.de wrote:
 
  Hi Thomas,
  
  thank you very much for the answer, I'm beginning to understand the
  actual problem now. 
  
  dss state=1 
  helps, but it changes the problem: I would like to see the secondary
  structure that corresponds to the single snapshot. When I use dss
  state=1, I just see the secondary structure of the first snapshot in all
  snapshots. 
  
  Is there a way to calculate the secondary structure for each individual
  snapshot stored in this single .pdb file?
 
 Yes, simply load the pdb file with the discrete=1 flag:
 
 load md_file.pdb, discrete=1
 dss md_file
 
 Setting the discrete flag causes PyMOL to store more information
 (B-factors, secondary structure) with each atom of each state -- so it can
 also be noticeably slower to load and uses more memory.
 
 Cheers,
 Rob
 



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Re: [PyMOL] Pymol: Cartoon representation for .pdb file with multible entries

[Thomas Holder]

Hi Alexander,

by default PyMOL recognized secondary structure as the minimum consensus 
over all states. So if a residue is not recognized as helix or sheet in 
_all_ states, it will be assigned as loop. You might be happy with this:

# type after loading the file
dss state=1

For detailed explanation what values are valid for the state argument 
see the PyMOLWiki page:
http://pymolwiki.org/index.php/Dss

Cheers,
   Thomas

On 10/26/2011 11:04 AM, Alexander Schulz wrote:
 Hi everyone,

 I'm quite new to Pymol and I hope that I don't ask something that has
 been answered several times before, but I didn't find anything about
 this topic that could solve my problem.

 I've prepared a .pdb file containing one protein at different times in
 the simulation. I'd like to prepare a video from this file, which is why
 I'd like to keep everything in one .pdb file.

 When I select cartoon as a representation, the backbone is visualized
 as a tibe (as always), but no secondary strucutres are recognized. When
 I copy one of the snaphots out of the .pdb and open in seperately, the
 secondary structure is shown correctly.

 How can I make Pymol show the structure of the multible states in one
 file correctly?

 Thanks in advance for answers!

 Cheers,
 Alexander

-- 
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MPI for Developmental Biology

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Re: [PyMOL] Pymol: Cartoon representation for .pdb file with multible entries

[Alexander Schulz]

Hi Thomas,

thank you very much for the answer, I'm beginning to understand the
actual problem now. 

dss state=1 
helps, but it changes the problem: I would like to see the secondary
structure that corresponds to the single snapshot. When I use dss
state=1, I just see the secondary structure of the first snapshot in all
snapshots. 

Is there a way to calculate the secondary structure for each individual
snapshot stored in this single .pdb file?

Cheers,
Alexander

Am Mittwoch, den 26.10.2011, 12:18 +0200 schrieb Thomas Holder:
 Hi Alexander,
 
 by default PyMOL recognized secondary structure as the minimum consensus 
 over all states. So if a residue is not recognized as helix or sheet in 
 _all_ states, it will be assigned as loop. You might be happy with this:
 
 # type after loading the file
 dss state=1
 
 For detailed explanation what values are valid for the state argument 
 see the PyMOLWiki page:
 http://pymolwiki.org/index.php/Dss
 
 Cheers,
Thomas
 
 On 10/26/2011 11:04 AM, Alexander Schulz wrote:
  Hi everyone,
 
  I'm quite new to Pymol and I hope that I don't ask something that has
  been answered several times before, but I didn't find anything about
  this topic that could solve my problem.
 
  I've prepared a .pdb file containing one protein at different times in
  the simulation. I'd like to prepare a video from this file, which is why
  I'd like to keep everything in one .pdb file.
 
  When I select cartoon as a representation, the backbone is visualized
  as a tibe (as always), but no secondary strucutres are recognized. When
  I copy one of the snaphots out of the .pdb and open in seperately, the
  secondary structure is shown correctly.
 
  How can I make Pymol show the structure of the multible states in one
  file correctly?
 
  Thanks in advance for answers!
 
  Cheers,
  Alexander
 



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Re: [PyMOL] Pymol: Cartoon representation for .pdb file with multible entries

[Robert Campbell]

Hi Alexander,

On Wed, 2011-10-26 12:53  EDT,  Alexander Schulz
sch...@dwi.rwth-aachen.de wrote:

 Hi Thomas,
 
 thank you very much for the answer, I'm beginning to understand the
 actual problem now. 
 
 dss state=1 
 helps, but it changes the problem: I would like to see the secondary
 structure that corresponds to the single snapshot. When I use dss
 state=1, I just see the secondary structure of the first snapshot in all
 snapshots. 
 
 Is there a way to calculate the secondary structure for each individual
 snapshot stored in this single .pdb file?

Yes, simply load the pdb file with the discrete=1 flag:

load md_file.pdb, discrete=1
dss md_file

Setting the discrete flag causes PyMOL to store more information
(B-factors, secondary structure) with each atom of each state -- so it can
also be noticeably slower to load and uses more memory.

Cheers,
Rob

-- 
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Senior Research Associate/Adjunct Assistant Professor 
Dept. of Biomedical  Molecular Sciences, Botterell Hall Rm 644
Queen's University, 
Kingston, ON K7L 3N6  Canada
Tel: 613-533-6821
robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc

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[PyMOL] Discreet cartoon representation for overlapping secondary structure ?

[Indraneel Majumdar]

Hi,

Is changing cartoon representation a major work? My program PALSSE
defines overlapping Secondary Structural Elements and it would be nice
if I could see cartoons without having consecutive elements merged.

It is technically possible for consecutive helices or consecutive
strands or helices and strands to have upto 2 common residues.

I was wondering if the start and ends could somehow be distinguished,
eg. by changing or adding another more_fancy option to not remove
the head arrow of any SSE (also add arrow to helices) and modify the
base of all SSE so they are visible at all times (probably show the base
as a circle?). The SS merge feature would probably have to be switched
off before this though.

Which is the best place to start modifications?

An example arrow:

__  *
  ***  *
 *  **
 * *
 *  **
  * __ **  *
*

 1  2   3  4

The head should be visible even if 1-2 overlaps on 3-4.


Thanks,
Indraneel

-- 
http://prodata.swmed.edu

RE: [PyMOL] Discreet cartoon representation for overlapping secondary structure ?

[Warren DeLano]

Indraneel,

PyMOL's cartoon generation code is some of the worst production code I
have ever written in my life.  It consists of one huge 2,000 line
function with numerous one or two-letter variables and all kinds of
implicit assumptions about the linear structure of the protein and the
discrete nature of secondary structure elements.  It would requires
tremendous effort to make changes to it safely, and as such, it serves
as a classic example of how NOT to write important code.
[layer2/RepCartoon.c, RepCartoonNew()]

My only defense for that mess it is that it has performed
extraordinarily well over a period of years with all kinds of
structures, from small peptides up to million-atom virus particles.
Despite is ugliness, is fast, stable, and functional.
 
Eventually it will be overhauled and we'll probably switch over nicer
looking to Bezier curves at that point -- but until then, I am loath to
make any significant modifications to it.  Since PyMOL is open-source
you are welcome to try, but I think your time would be better spent
constructing an alternate implementation that meets your specific needs.


Cheers,
Warren

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. Biz:(650)-872-0942  Tech:(650)-872-0834 
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. mailto:war...@delsci.com  
 

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net 
 [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
 Indraneel Majumdar
 Sent: Saturday, November 05, 2005 7:29 PM
 To: pymol-users@lists.sourceforge.net
 Cc: Warren DeLano
 Subject: [PyMOL] Discreet cartoon representation for 
 overlapping secondary structure ?
 
 Hi,
 
 Is changing cartoon representation a major work? My program 
 PALSSE defines overlapping Secondary Structural Elements and 
 it would be nice if I could see cartoons without having 
 consecutive elements merged.
 
 It is technically possible for consecutive helices or 
 consecutive strands or helices and strands to have upto 2 
 common residues.
 
 I was wondering if the start and ends could somehow be 
 distinguished, eg. by changing or adding another more_fancy 
 option to not remove the head arrow of any SSE (also add 
 arrow to helices) and modify the base of all SSE so they are 
 visible at all times (probably show the base as a circle?). 
 The SS merge feature would probably have to be switched off 
 before this though.
 
 Which is the best place to start modifications?
 
 An example arrow:
 
 __  *
   ***  *
  *  **
  * *
  *  **
   * __ **  *
 *
 
  1  2   3  4
 
 The head should be visible even if 1-2 overlaps on 3-4.
 
 
 Thanks,
 Indraneel
 
 --
 http://prodata.swmed.edu
 
 
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[PyMOL] Outline cartoon representation

[Todd Geders]

Hello all,

We'd like to render some cartoon representations of protein structures
in a manner similar to the style of Jane Richardson.  Basically white,
opaque surfaces (no reflections) with black outlines at each of the
edges.  

Here's a link to give you an idea what we're looking for (Figure 1b-c):
http://www.nature.com/nsmb/journal/v7/n8/fig_tab/nsb0800_624_F1.html

Any suggestions on how to do this using PyMOL?

~Todd

RE: [PyMOL] Outline cartoon representation

[Warren DeLano]

Todd,

Unfortunately that is not a problem PyMOL was designed to solve, and off the
top of my head I can't think of any way to bend it around to do this --
you're talking about a different rendering scheme.  I think it amounts to
the following: trace every sharp edge, and outline every round surface that
is tangent to the view.  The former could be done with straight OpenGL, but
the latter would take a custom shader program.

Plus, ideally you'd want postscript or vector output for this kind of
illustration -- not a PyMOL-style raster image. Perhaps Molscript has this
capability? http://www.avatar.se  I think that's what it was originally
written to do, way back before color was invented ; ).

If not, then you might try contacting David Goodsell.  He's got some
fantasic protein illustration software...

http://www.scripps.edu/pub/goodsell/

Cheers,
Warren

 

 -Original Message-
 From: pymol-users-ad...@lists.sourceforge.net 
 [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of 
 Todd Geders
 Sent: Tuesday, February 03, 2004 8:02 AM
 To: pymol-users@lists.sourceforge.net
 Subject: [PyMOL] Outline cartoon representation
 
 Hello all,
 
 We'd like to render some cartoon representations of protein 
 structures in a manner similar to the style of Jane 
 Richardson.  Basically white, opaque surfaces (no 
 reflections) with black outlines at each of the edges.  
 
 Here's a link to give you an idea what we're looking for 
 (Figure 1b-c):
 http://www.nature.com/nsmb/journal/v7/n8/fig_tab/nsb0800_624_F1.html
 
 Any suggestions on how to do this using PyMOL?
 
 ~Todd
 
 
 
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