Re: [PyMOL] how to get an atom coordinates information

[Thomas Holder]

Hi Carsten & Albert,

There actually is a function for getting the coordinates of a single atom. 
Example:

PyMOL>print cmd.get_atom_coords('first (elem O)')

Cheers,
  Thomas

On 25 Feb 2016, at 09:54, Schubert, Carsten [JRDUS]  
wrote:

> Albert,
> 
> there is no command line tool for that purpose per se, however you can use 
> the iterate command for that purpose. 
> http://pymolwiki.org/index.php/Iterate#Example:_Get_coordinates
> 
> 
> There are other ways to do this but this will get you going more quickly.
> 
> -Original Message-
> From: Albert [mailto:mailmd2...@gmail.com] 
> Sent: Thursday, February 25, 2016 12:48 PM
> To: pymol-users@lists.sourceforge.net
> Subject: [PyMOL] how to get an atom coordinates information
> 
> Hello:
> 
> I would like to know the XYZ information of a specific atom. I am just 
> wondering how can we do this? Is there any command line?
> 
> thank you very much
> 
> Albert

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] how to get an atom coordinates information

[Schubert, Carsten [JRDUS]]

Albert,

there is no command line tool for that purpose per se, however you can use the 
iterate command for that purpose. 
http://pymolwiki.org/index.php/Iterate#Example:_Get_coordinates


There are other ways to do this but this will get you going more quickly.

-Original Message-
From: Albert [mailto:mailmd2...@gmail.com] 
Sent: Thursday, February 25, 2016 12:48 PM
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] how to get an atom coordinates information

Hello:

I would like to know the XYZ information of a specific atom. I am just 
wondering how can we do this? Is there any command line?

thank you very much

Albert

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[PyMOL] how to get an atom coordinates information

[Albert]

Hello:

I would like to know the XYZ information of a specific atom. I am just 
wondering how can we do this? Is there any command line?

thank you very much

Albert

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[PyMOL] Electrostatic Map for a molecule containing a citrulline

[Andreas Warnecke]

Dear all,

a colleague is interested in generating an electrostatic map of a protein
containing a citrulline. Does anybody have any experience with this and
could recommend any approach?

Cheers,

Andreas
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Re: [PyMOL] Alignment of two proteins

[Mohsen Chitsaz]

Hi Amin,

It worked. Many Thanks

Cheers
Mohsen

From: a...@imtech.res.in [mailto:a...@imtech.res.in]
Sent: Thursday, 25 February 2016 10:24 PM
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Alignment of two proteins


Hi. I think

align 4mt1 & chain A, 3aob & chain B

should work.

Amin.

On 2016-02-25 17:02, Mohsen Chitsaz wrote:
Hi Julian,

I have two homotrimer proteins, i.e. 3aob and 4mt1. I want to align chain A of 
4mt1 to chain B of 3aob. How to tell Pymol to align a specific chain or part of 
a protein, in my case chain A of 4mt1, to a specific chain or part of another 
protein, in my case chain B of 3aob?

Cheers
Mohsen

From: Mohsen Chitsaz
Sent: Wednesday, 24 February 2016 11:17 PM
To: 'Julian Heinrich' mailto:jul...@joules.de>>
Cc: pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] Appending a pdb file

Hi Julian,

Many Thanks for your help. It worked.

Cheers
Mohsen

From: julian.heinr...@gmail.com 
[mailto:julian.heinr...@gmail.com] On Behalf Of Julian Heinrich
Sent: Monday, 22 February 2016 8:24 PM
To: Mohsen Chitsaz 
mailto:mohsen.chit...@flinders.edu.au>>
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Appending a pdb file

Hi Mohsen,

if you want to superimpose structures, have a look at the align command:
http://pymolwiki.org/index.php/Align

Cheers,
Julian

On Thu, Feb 18, 2016 at 10:47 PM, Mohsen Chitsaz 
mailto:mohsen.chit...@flinders.edu.au>> wrote:
Hi

In order to superimpose two protein sequences, I am trying to append a pdb file 
to an existing protein sequence, which I have already opened in PyMol. The 
append function is not working in my PyMol. Could someone help me with this 
please.

Cheers
Mohsen

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Re: [PyMOL] Alignment of two proteins

[amin]

 

Hi. I think 

align 4mt1 & chain A, 3aob & chain B 

should work. 

Amin. 

On 2016-02-25 17:02, Mohsen Chitsaz wrote: 

> Hi Julian, 
> 
> I have two homotrimer proteins, i.e. 3aob and 4mt1. I want to align chain A 
> of 4mt1 to chain B of 3aob. How to tell Pymol to align a specific chain or 
> part of a protein, in my case chain A of 4mt1, to a specific chain or part of 
> another protein, in my case chain B of 3aob? 
> 
> Cheers 
> 
> Mohsen 
> 
> FROM: Mohsen Chitsaz 
> SENT: Wednesday, 24 February 2016 11:17 PM
> TO: 'Julian Heinrich' 
> CC: pymol-users@lists.sourceforge.net
> SUBJECT: RE: [PyMOL] Appending a pdb file 
> 
> Hi Julian, 
> 
> Many Thanks for your help. It worked. 
> 
> Cheers 
> 
> Mohsen 
> 
> FROM: julian.heinr...@gmail.com [mailto:julian.heinr...@gmail.com] ON BEHALF 
> OF Julian Heinrich
> SENT: Monday, 22 February 2016 8:24 PM
> TO: Mohsen Chitsaz 
> CC: pymol-users@lists.sourceforge.net
> SUBJECT: Re: [PyMOL] Appending a pdb file 
> 
> Hi Mohsen, 
> 
> if you want to superimpose structures, have a look at the align command: 
> 
> http://pymolwiki.org/index.php/Align [4] 
> 
> Cheers, 
> 
> Julian 
> 
> On Thu, Feb 18, 2016 at 10:47 PM, Mohsen Chitsaz 
>  wrote: 
> 
>> Hi 
>> 
>> In order to superimpose two protein sequences, I am trying to append a pdb 
>> file to an existing protein sequence, which I have already opened in PyMol. 
>> The append function is not working in my PyMol. Could someone help me with 
>> this please. 
>> 
>> Cheers 
>> 
>> Mohsen 
>> 
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> 
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Re: [PyMOL] Alignment of two proteins

[Mohsen Chitsaz]

Hi Julian,

I have two homotrimer proteins, i.e. 3aob and 4mt1. I want to align chain A of 
4mt1 to chain B of 3aob. How to tell Pymol to align a specific chain or part of 
a protein, in my case chain A of 4mt1, to a specific chain or part of another 
protein, in my case chain B of 3aob?

Cheers
Mohsen

From: Mohsen Chitsaz
Sent: Wednesday, 24 February 2016 11:17 PM
To: 'Julian Heinrich' 
Cc: pymol-users@lists.sourceforge.net
Subject: RE: [PyMOL] Appending a pdb file

Hi Julian,

Many Thanks for your help. It worked.

Cheers
Mohsen

From: julian.heinr...@gmail.com 
[mailto:julian.heinr...@gmail.com] On Behalf Of Julian Heinrich
Sent: Monday, 22 February 2016 8:24 PM
To: Mohsen Chitsaz 
mailto:mohsen.chit...@flinders.edu.au>>
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] Appending a pdb file

Hi Mohsen,

if you want to superimpose structures, have a look at the align command:
http://pymolwiki.org/index.php/Align

Cheers,
Julian

On Thu, Feb 18, 2016 at 10:47 PM, Mohsen Chitsaz 
mailto:mohsen.chit...@flinders.edu.au>> wrote:
Hi

In order to superimpose two protein sequences, I am trying to append a pdb file 
to an existing protein sequence, which I have already opened in PyMol. The 
append function is not working in my PyMol. Could someone help me with this 
please.

Cheers
Mohsen

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