Re: [PyMOL] separate two molecule as an object from a complex of four molecules

2023-08-03 Thread Norbert Straeter 

Dear Shreya,

one further possibility is to create a new object using the named chains:

reinitialize
fetch 6ous
create trimer1, chain A+C+E+B+D+F
disable 6ous

alternatively, you could delete all other chains:

reinitialize
fetch 6ous
remove not chain A+C+E+B+D+F

It is usually necessary (or at least preferable) to make yourself 
familiar with the PyMOL selection algebra and some basic commands to 
show selected residues.


Working only with the GUI, you could use:
Menu: Display, Sequence Mode, Chain Identifiers
Menu: Display, Sequence

Next you select the chains you want to show (CTRL or Strg and left mouse 
click)
Finally you use the command buttons next to the selection (sele): A, 
copy to object, new


Best,

Norbert

Am 03.08.2023 um 09:57 schrieb Saurabh Gayali:

Have you tried this:
https://pymolwiki.org/index.php/Split_object


*Saurabh Gayali*
Business Analyst [Excelra], Former Research Scientist [IGIB]
saurabh.gay...@gmail.com / +91 8800412916
Bangalore, India


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On Thu, Aug 3, 2023 at 8:15 AM Mukhopadhyay, Shreya via PyMOL-users 
 wrote:


Public


Hello All,

I am trying to separate out two molecules(one copy for each of
RSVF F1 and F2) from one pdb (6OUS). It’s a trimeric protein bound
to a Fab.

I want to separate out RSVF1 and F2 proteins as one object from
the bound antibody, ie create one object with only chains A,C,E
and B,D,F. If you could explain the commands to use that will be
really helpful to me.

Thanks,

Shreya

Shreya Mukhopadhyay, PhD.(She/Her)
*Post Doc Fellow (Infectious Diseases and Vaccines-Discovery)*

770 Sumneytown Pike, West Point B46, 2048-C,  PA 19486

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-
Norbert Straeter  fon +49 (0)341-97-31311
Univ.-Prof. Dr. rer. nat.
Center for Biotechnology and Biomedicine
Institute of Bioanalytical Chemistry
Faculty of Chemistry and Mineralogy
Leipzig University
Deutscher Platz 5
04103 Leipzig, germanystra...@bbz.uni-leipzig.de
 
https://www.bbz.uni-leipzig.de/en/research/structural-analysis-of-biopolymers

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Re: [PyMOL] separate two molecule as an object from a complex of four molecules

2023-08-03 Thread Saurabh Gayali 
Have you tried this:
https://pymolwiki.org/index.php/Split_object

--

*Saurabh Gayali*
Business Analyst [Excelra], Former Research Scientist [IGIB]
saurabh.gay...@gmail.com / +91 8800412916
Bangalore, India


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03/08/23,
01:27:34 pm

On Thu, Aug 3, 2023 at 8:15 AM Mukhopadhyay, Shreya via PyMOL-users <
pymol-users@lists.sourceforge.net> wrote:

> Public
>
> Hello All,
>
>
>
> I am trying to separate out two molecules(one copy for each of RSVF F1 and
> F2) from one pdb (6OUS). It’s a trimeric protein bound to a Fab.
>
>
>
> I want to separate out RSVF1 and F2 proteins as one object from the bound
> antibody, ie create one object with only chains A,C,E and B,D,F. If you
> could explain the commands to use that will be really helpful to me.
>
>
>
> Thanks,
>
> Shreya
>
>
>
>
>
> Shreya Mukhopadhyay, PhD. (She/Her)
> *Post Doc Fellow (Infectious Diseases and Vaccines-Discovery)*
>
> 770 Sumneytown Pike, West Point B46, 2048-C,  PA 19486
>
>
>
>
>
> This e-mail message, together with any attachments, contains information
> of Merck & Co., Inc. (126 East Lincoln Ave., P.O. Box 2000, Rahway, NJ USA
> 07065) and/or its affiliates, that may be confidential, proprietary
> copyrighted and/or legally privileged.   (Direct contact information for
> affiliates is available at - Contact us - MSD
> .)  It is intended solely for the use of
> the individual or entity named on this message. If you are not the intended
> recipient, and have received this message in error, please notify us
> immediately by reply e-mail and then delete it from your system.
>
> ___
> 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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