date:20190606

Re: [PyMOL] How to assign secondary structure as 3-10 helix in pymol?

2019-06-06 Thread h. adam steinberg

When you use the alter command, then rebuild, and then save the PyMOL session 
as a .pse file, the changes will be written into the .pse file. They will not 
be lost when you reopen the .pse file.

The alter command doesn’t do anything to the actual .pdb or .cif file. It’s my 
understanding that when you open a structure file in PyMOL, it reads the pdb or 
cif file and then assigns appropriate secondary structure based on the phi and 
psi angles of the protein backbone.

> On Jun 5, 2019, at 11:50 PM, sunyeping  wrote:
> 
> Thank you for the reply.
> 
> Do alter and rebuild commands really change the secondary structure of the 
> specific residues or they just change the display? I saved the structure 
> altered bt the alter and rebuild commands, but when I open the structure 
> agian in pymol, the residues I changes are still displayed as in the original 
> structure file.
> 
> Best regards 
> --
> From:h. adam steinberg 
> Sent At:2019 Jun. 5 (Wed.) 20:43
> To:孙业平 ; pymol-users 
> Subject:Re: [PyMOL] How to assign secondary structure as 3-10 helix in pymol?
> 
> It’s the same command but just change the “S” to an “H”. Or you can use a “L” 
> if you want a loop (unstructured).
> 
> alter 3-10/, ss=‘H’ 
> 
> You also need to enter the command: rebuild, to redraw the structure on your 
> screen. Use rebuild after you enter the alter command.
> 
> 
> On Jun 4, 2019, at 10:37 PM, sunyeping via PyMOL-users 
>  > wrote:
> 
> Dear pymol user,
> 
> I wonder why sometimes the secondary structure of a protein can not be 
> displayed incorrect in pymol. I have a structure, some residues are predicted 
> to be sheet or 3-10 helix with DSSP, but they are displayed as loop. Only 
> typing "dss" command in pymol doesn't work. I know by using the "alter" 
> commad the secondary structures can be assigned. The following command:
> 
> alter 61-63/, ss='S' 
> 
> can assign residue 61-63 as sheet. However, what is the command to assign 
> residues as 3-10 helix?
> 
> Thank you in advance.
> 
> Arthur
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Re: [PyMOL] colored secondary structure of two chains with different colors [resolved]

2019-06-06 Thread ABEL Stephane

Thank you vevry much Annemarie  it worked 

--
Stéphane Abel, Ph.D.
Commissariat à l’Energie Atomique et aux Energies Alternatives
Centre de Saclay DSV/ISVFJ/SB2SM
Bat 528, Office 138C
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60

--

Message: 1
Date: Thu, 6 Jun 2019 12:49:56 +0200
From: ahoneg 
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] colored secondary structure of two chains with
different colors
Message-ID: 
Content-Type: text/plain;   charset=utf-8

Dear St?phane,

by default, the cartoon representation takes its color from the color of the 
c-alpha atoms of your protein.
However, you can override this default and assign a specific color to the 
cartoon representation of a given selection by:

set cartoon_color, color, (selection)

e.g.

set cartoon_color, red, resi 1-60

best regards

Annemarie Honegger


Dr. Annemarie Honegger
Dept. of Biochemistry
Z?rich University
Winterthurerstrasse 190
8057 Z?rich
Switzerland

e-mail:   honeg...@bioc.uzh.ch
phone:   +41 44 635 55 62
fax:+41 44 635 57 12


>
> Message: 4
> Date: Thu, 6 Jun 2019 10:26:29 +
> From: ABEL Stephane 
> To: "h. adam steinberg" 
> Cc: "pymol-users@lists.sourceforge.net"
>   
> Subject: Re: [PyMOL] colored secondary structure of two chains with
>   different colors
> Message-ID:
>   <3e39b768bb199548ab18f7289e7534af4b042...@exdag0-b0.intra.cea.fr>
> Content-Type: text/plain; charset="Windows-1252"
>
> Hi Adam
>
> OK I can colored each chain with different colors. But it is not exactly what 
> I want. Indeed in the figure*
>
> - the AA are  in sticks with the different colors for each atom --> I can do 
> this
> - the beta sheet in the monomer are in red and blue ---> I can "not" do this 
> even if I use your suggestion
>
> I would like in two representations at the same time and the necessary 
> commands for adding them in a script.
> ript.
>
> *https://cdn.rcsb.org/images/rutgers/ma/1mag/1mag.pdb-500.jpg
>
> Thank you again.
>
> St?phane
>
>
> --
> St?phane Abel, Ph.D.
> Commissariat ? l?Energie Atomique et aux Energies Alternatives
> Centre de Saclay DSV/ISVFJ/SB2SM
> Bat 528, Office 138C
> Gif-sur-Yvette, F-91191 FRANCE
> Phone (portable) : +33 6 49 37 70 60
> 
> De : h. adam steinberg [h.adam.steinb...@gmail.com]
> Envoy? : mercredi 5 juin 2019 21:36
> ? : ABEL Stephane
> Objet : Re: [PyMOL] colored secondary structure of two chains with different 
> colors
>
> If you change your mouse / selection mode to chains, you can then click on 
> one of the monomers and choose a color for it from the (sale) in the right 
> side panel drop down menu. Then click on the other monomer and do the same.
>
> Is that what you are asking for?
>
>> On Jun 5, 2019, at 1:23 PM, ABEL Stephane  wrote:
>>
>> Hello all
>>
>> I have a pdb structure of gramicidin A dimer (PDB 1MAG) and I would like to 
>> color the  beta sheets of each monomer with different colors (for instance 
>> in red and blue colors) in Figure
>>
>> https://cdn.rcsb.org/images/rutgers/ma/1mag/1mag.pdb-500.jpg
>>
>> How to do this ?
>>
>> Thank you
>>
>> St?phane
>>
>>
>>
>> ___
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>> Unsubscribe: 
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
>
>
> --
>
>
>
> --
>
> Subject: Digest Footer
>
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> End of PyMOL-users Digest, Vol 157, Issue 5
> ***




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Re: [PyMOL] PyMOL-users Digest, Vol 157, Issue 6

2019-06-06 Thread ABEL Stephane

Dear Annemarie, 

Thank you very much it worked !!! 

Stéphane

--
Stéphane Abel, Ph.D.
Commissariat à l’Energie Atomique et aux Energies Alternatives
Centre de Saclay DSV/ISVFJ/SB2SM
Bat 528, Office 138C
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60


--

Message: 1
Date: Thu, 6 Jun 2019 12:49:56 +0200
From: ahoneg 
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] colored secondary structure of two chains with
different colors
Message-ID: 
Content-Type: text/plain;   charset=utf-8

Dear St?phane,

by default, the cartoon representation takes its color from the color of the 
c-alpha atoms of your protein.
However, you can override this default and assign a specific color to the 
cartoon representation of a given selection by:

set cartoon_color, color, (selection)

e.g.

set cartoon_color, red, resi 1-60

best regards

Annemarie Honegger


Dr. Annemarie Honegger
Dept. of Biochemistry
Z?rich University
Winterthurerstrasse 190
8057 Z?rich
Switzerland

e-mail:   honeg...@bioc.uzh.ch
phone:   +41 44 635 55 62
fax:+41 44 635 57 12


>
> Message: 4
> Date: Thu, 6 Jun 2019 10:26:29 +
> From: ABEL Stephane 
> To: "h. adam steinberg" 
> Cc: "pymol-users@lists.sourceforge.net"
>   
> Subject: Re: [PyMOL] colored secondary structure of two chains with
>   different colors
> Message-ID:
>   <3e39b768bb199548ab18f7289e7534af4b042...@exdag0-b0.intra.cea.fr>
> Content-Type: text/plain; charset="Windows-1252"
>
> Hi Adam
>
> OK I can colored each chain with different colors. But it is not exactly what 
> I want. Indeed in the figure*
>
> - the AA are  in sticks with the different colors for each atom --> I can do 
> this
> - the beta sheet in the monomer are in red and blue ---> I can "not" do this 
> even if I use your suggestion
>
> I would like in two representations at the same time and the necessary 
> commands for adding them in a script.
> ript.
>
> *https://cdn.rcsb.org/images/rutgers/ma/1mag/1mag.pdb-500.jpg
>
> Thank you again.
>
> St?phane
>
>
> --
> St?phane Abel, Ph.D.
> Commissariat ? l?Energie Atomique et aux Energies Alternatives
> Centre de Saclay DSV/ISVFJ/SB2SM
> Bat 528, Office 138C
> Gif-sur-Yvette, F-91191 FRANCE
> Phone (portable) : +33 6 49 37 70 60
> 
> De : h. adam steinberg [h.adam.steinb...@gmail.com]
> Envoy? : mercredi 5 juin 2019 21:36
> ? : ABEL Stephane
> Objet : Re: [PyMOL] colored secondary structure of two chains with different 
> colors
>
> If you change your mouse / selection mode to chains, you can then click on 
> one of the monomers and choose a color for it from the (sale) in the right 
> side panel drop down menu. Then click on the other monomer and do the same.
>
> Is that what you are asking for?
>
>> On Jun 5, 2019, at 1:23 PM, ABEL Stephane  wrote:
>>
>> Hello all
>>
>> I have a pdb structure of gramicidin A dimer (PDB 1MAG) and I would like to 
>> color the  beta sheets of each monomer with different colors (for instance 
>> in red and blue colors) in Figure
>>
>> https://cdn.rcsb.org/images/rutgers/ma/1mag/1mag.pdb-500.jpg
>>
>> How to do this ?
>>
>> Thank you
>>
>> St?phane
>>
>>
>>
>> ___
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>> Unsubscribe: 
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
>
>
>
>
> --
>
>
>
> --
>
> Subject: Digest Footer
>
> ___
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> PyMOL-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/pymol-users
> Unsubscribe: 
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> End of PyMOL-users Digest, Vol 157, Issue 5
> ***




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[PyMOL] colored secondary structure of two chains with different colors

2019-06-06 Thread ahoneg

Dear Stéphane,

by default, the cartoon representation takes its color from the color of the 
c-alpha atoms of your protein. 
However, you can override this default and assign a specific color to the 
cartoon representation of a given selection by:

set cartoon_color, color, (selection)

e.g.

set cartoon_color, red, resi 1-60

best regards

Annemarie Honegger


Dr. Annemarie Honegger
Dept. of Biochemistry
Zürich University
Winterthurerstrasse 190
8057 Zürich
Switzerland

e-mail:   honeg...@bioc.uzh.ch
phone:   +41 44 635 55 62
fax:+41 44 635 57 12 


> 
> Message: 4
> Date: Thu, 6 Jun 2019 10:26:29 +
> From: ABEL Stephane 
> To: "h. adam steinberg" 
> Cc: "pymol-users@lists.sourceforge.net"
>   
> Subject: Re: [PyMOL] colored secondary structure of two chains with
>   different colors
> Message-ID:
>   <3e39b768bb199548ab18f7289e7534af4b042...@exdag0-b0.intra.cea.fr>
> Content-Type: text/plain; charset="Windows-1252"
> 
> Hi Adam 
> 
> OK I can colored each chain with different colors. But it is not exactly what 
> I want. Indeed in the figure* 
> 
> - the AA are  in sticks with the different colors for each atom --> I can do 
> this 
> - the beta sheet in the monomer are in red and blue ---> I can "not" do this 
> even if I use your suggestion
> 
> I would like in two representations at the same time and the necessary 
> commands for adding them in a script. 
> ript. 
> 
> *https://cdn.rcsb.org/images/rutgers/ma/1mag/1mag.pdb-500.jpg
> 
> Thank you again. 
> 
> St?phane
> 
> 
> --
> St?phane Abel, Ph.D.
> Commissariat ? l?Energie Atomique et aux Energies Alternatives
> Centre de Saclay DSV/ISVFJ/SB2SM
> Bat 528, Office 138C
> Gif-sur-Yvette, F-91191 FRANCE
> Phone (portable) : +33 6 49 37 70 60
> 
> De : h. adam steinberg [h.adam.steinb...@gmail.com]
> Envoy? : mercredi 5 juin 2019 21:36
> ? : ABEL Stephane
> Objet : Re: [PyMOL] colored secondary structure of two chains with different 
> colors
> 
> If you change your mouse / selection mode to chains, you can then click on 
> one of the monomers and choose a color for it from the (sale) in the right 
> side panel drop down menu. Then click on the other monomer and do the same.
> 
> Is that what you are asking for?
> 
>> On Jun 5, 2019, at 1:23 PM, ABEL Stephane  wrote:
>> 
>> Hello all
>> 
>> I have a pdb structure of gramicidin A dimer (PDB 1MAG) and I would like to 
>> color the  beta sheets of each monomer with different colors (for instance 
>> in red and blue colors) in Figure
>> 
>> https://cdn.rcsb.org/images/rutgers/ma/1mag/1mag.pdb-500.jpg
>> 
>> How to do this ?
>> 
>> Thank you
>> 
>> St?phane
>> 
>> 
>> 
>> ___
>> PyMOL-users mailing list
>> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
>> Unsubscribe: 
>> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe
> 
> 
> 
> 
> --
> 
> 
> 
> --
> 
> Subject: Digest Footer
> 
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Re: [PyMOL] colored secondary structure of two chains with different colors

2019-06-06 Thread ABEL Stephane

Hi Adam 

OK I can colored each chain with different colors. But it is not exactly what I 
want. Indeed in the figure* 

- the AA are  in sticks with the different colors for each atom --> I can do 
this 
- the beta sheet in the monomer are in red and blue ---> I can "not" do this 
even if I use your suggestion

I would like in two representations at the same time and the necessary commands 
for adding them in a script. 
ript. 

*https://cdn.rcsb.org/images/rutgers/ma/1mag/1mag.pdb-500.jpg

Thank you again. 

Stéphane

--
Stéphane Abel, Ph.D.
Commissariat à l’Energie Atomique et aux Energies Alternatives
Centre de Saclay DSV/ISVFJ/SB2SM
Bat 528, Office 138C
Gif-sur-Yvette, F-91191 FRANCE
Phone (portable) : +33 6 49 37 70 60

De : h. adam steinberg [h.adam.steinb...@gmail.com]
Envoyé : mercredi 5 juin 2019 21:36
À : ABEL Stephane
Objet : Re: [PyMOL] colored secondary structure of two chains with different 
colors

If you change your mouse / selection mode to chains, you can then click on one 
of the monomers and choose a color for it from the (sale) in the right side 
panel drop down menu. Then click on the other monomer and do the same.

Is that what you are asking for?

> On Jun 5, 2019, at 1:23 PM, ABEL Stephane  wrote:
>
> Hello all
>
> I have a pdb structure of gramicidin A dimer (PDB 1MAG) and I would like to 
> color the  beta sheets of each monomer with different colors (for instance in 
> red and blue colors) in Figure
>
> https://cdn.rcsb.org/images/rutgers/ma/1mag/1mag.pdb-500.jpg
>
> How to do this ?
>
> Thank you
>
> Stéphane
>
>
>
> ___
> PyMOL-users mailing list
> Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
> Unsubscribe: 
> https://sourceforge.net/projects/pymol/lists/pymol-users/unsubscribe

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Re: [PyMOL] How to assign secondary structure as 3-10 helix in pymol?

Re: [PyMOL] colored secondary structure of two chains with different colors [resolved]

Re: [PyMOL] PyMOL-users Digest, Vol 157, Issue 6

[PyMOL] colored secondary structure of two chains with different colors

Re: [PyMOL] colored secondary structure of two chains with different colors

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