Re: [PyMOL] post-processing of pdb ensemble

[Thomas Holder]

or simply:

alter bound_combined, chain = chr(ord(chain) - 1)

Cheers,
  Thomas

On 25 May 2016, at 11:06, Tsjerk Wassenaar  wrote:

> Hi James,
> 
> This should do:
> 
> for i in range(65:78): cmd.alter("bound_combined and chain 
> %s"%chr(i+1),'chain="%s"'%chr(i))
> 
> Cheers,
> 
> Tsjerk
> 
> 
> On Wed, May 25, 2016 at 5:00 PM, James Starlight  
> wrote:
> More precisely I would like to know how to script in pymol the
> following alteration fo the chains for the multi-chain pdb
> 
> 
> PyMOL>alter (bound_combined and chain B), chain="A"
>  Alter: modified 5157 atoms.
> PyMOL>alter (bound_combined and chain C), chain="B"
>  Alter: modified 2285 atoms.
> PyMOL>alter (bound_combined and chain D), chain="C"
>  Alter: modified 2778 atoms.
> PyMOL>alter (bound_combined and chain E), chain="D"
>  Alter: modified 1560 atoms.
> PyMOL>alter (bound_combined and chain F), chain="E"
>  Alter: modified 1114 atoms.
> PyMOL>alter (bound_combined and chain G), chain="F"
>  Alter: modified 950 atoms.
> PyMOL>alter (bound_combined and chain H), chain="G"
>  Alter: modified 895 atoms.
> PyMOL>alter (bound_combined and chain I), chain="H"
>  Alter: modified 843 atoms.
> PyMOL>alter (bound_combined and chain J), chain="I"
>  Alter: modified 806 atoms.
> PyMOL>alter (bound_combined and chain K), chain="J"
>  Alter: modified 574 atoms.
> PyMOL>alter (bound_combined and chain L), chain="K"
>  Alter: modified 501 atoms.
> PyMOL>alter (bound_combined and chain M), chain="L"
>  Alter: modified 511 atoms.
> PyMOL>alter (bound_combined and chain N), chain="M"
>  Alter: modified 433 atoms.
> 
> 
> So each step we rename chain i to the i-1 name within given model :)
> 
> Thanks!
> 
> J.
> 
> 2016-05-23 19:11 GMT+02:00 James Starlight :
> > Dear Pymol users!
> >
> > After some post-processing of MD simulation I have extracted from the
> > traejctory several snapshots as individual pdbs which I need to
> > 1-  to re-assign information regarding chain letters (which was lost
> > after some operations on pdbs)  for all of those structures assuming
> > that within each of these pdbs residues are ordered correctly e.g from
> > (1-104 which
> > should be chain A) than from 1-100 (it should be chain B), than 1-70
> > (in should be chain C) etc.
> >
> > 2- superimpose and combine all of the pdbs within one model in nmr-like 
> > format.
> >
> > Thanks for help!
> >
> > James
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


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Re: [PyMOL] post-processing of pdb ensemble

[Tsjerk Wassenaar]

Hi James,

This should do:

for i in range(65:78): cmd.alter("bound_combined and chain
%s"%chr(i+1),'chain="%s"'%chr(i))

Cheers,

Tsjerk


On Wed, May 25, 2016 at 5:00 PM, James Starlight 
wrote:

> More precisely I would like to know how to script in pymol the
> following alteration fo the chains for the multi-chain pdb
>
>
> PyMOL>alter (bound_combined and chain B), chain="A"
>  Alter: modified 5157 atoms.
> PyMOL>alter (bound_combined and chain C), chain="B"
>  Alter: modified 2285 atoms.
> PyMOL>alter (bound_combined and chain D), chain="C"
>  Alter: modified 2778 atoms.
> PyMOL>alter (bound_combined and chain E), chain="D"
>  Alter: modified 1560 atoms.
> PyMOL>alter (bound_combined and chain F), chain="E"
>  Alter: modified 1114 atoms.
> PyMOL>alter (bound_combined and chain G), chain="F"
>  Alter: modified 950 atoms.
> PyMOL>alter (bound_combined and chain H), chain="G"
>  Alter: modified 895 atoms.
> PyMOL>alter (bound_combined and chain I), chain="H"
>  Alter: modified 843 atoms.
> PyMOL>alter (bound_combined and chain J), chain="I"
>  Alter: modified 806 atoms.
> PyMOL>alter (bound_combined and chain K), chain="J"
>  Alter: modified 574 atoms.
> PyMOL>alter (bound_combined and chain L), chain="K"
>  Alter: modified 501 atoms.
> PyMOL>alter (bound_combined and chain M), chain="L"
>  Alter: modified 511 atoms.
> PyMOL>alter (bound_combined and chain N), chain="M"
>  Alter: modified 433 atoms.
>
>
> So each step we rename chain i to the i-1 name within given model :)
>
> Thanks!
>
> J.
>
> 2016-05-23 19:11 GMT+02:00 James Starlight :
> > Dear Pymol users!
> >
> > After some post-processing of MD simulation I have extracted from the
> > traejctory several snapshots as individual pdbs which I need to
> > 1-  to re-assign information regarding chain letters (which was lost
> > after some operations on pdbs)  for all of those structures assuming
> > that within each of these pdbs residues are ordered correctly e.g from
> > (1-104 which
> > should be chain A) than from 1-100 (it should be chain B), than 1-70
> > (in should be chain C) etc.
> >
> > 2- superimpose and combine all of the pdbs within one model in nmr-like
> format.
> >
> > Thanks for help!
> >
> > James
>
>
> --
> Mobile security can be enabling, not merely restricting. Employees who
> bring their own devices (BYOD) to work are irked by the imposition of MDM
> restrictions. Mobile Device Manager Plus allows you to control only the
> apps on BYO-devices by containerizing them, leaving personal data
> untouched!
> https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
> ___
> 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
>



-- 
Tsjerk A. Wassenaar, Ph.D.
--
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j___
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Re: [PyMOL] post-processing of pdb ensemble

[James Starlight]

More precisely I would like to know how to script in pymol the
following alteration fo the chains for the multi-chain pdb


PyMOL>alter (bound_combined and chain B), chain="A"
 Alter: modified 5157 atoms.
PyMOL>alter (bound_combined and chain C), chain="B"
 Alter: modified 2285 atoms.
PyMOL>alter (bound_combined and chain D), chain="C"
 Alter: modified 2778 atoms.
PyMOL>alter (bound_combined and chain E), chain="D"
 Alter: modified 1560 atoms.
PyMOL>alter (bound_combined and chain F), chain="E"
 Alter: modified 1114 atoms.
PyMOL>alter (bound_combined and chain G), chain="F"
 Alter: modified 950 atoms.
PyMOL>alter (bound_combined and chain H), chain="G"
 Alter: modified 895 atoms.
PyMOL>alter (bound_combined and chain I), chain="H"
 Alter: modified 843 atoms.
PyMOL>alter (bound_combined and chain J), chain="I"
 Alter: modified 806 atoms.
PyMOL>alter (bound_combined and chain K), chain="J"
 Alter: modified 574 atoms.
PyMOL>alter (bound_combined and chain L), chain="K"
 Alter: modified 501 atoms.
PyMOL>alter (bound_combined and chain M), chain="L"
 Alter: modified 511 atoms.
PyMOL>alter (bound_combined and chain N), chain="M"
 Alter: modified 433 atoms.


So each step we rename chain i to the i-1 name within given model :)

Thanks!

J.

2016-05-23 19:11 GMT+02:00 James Starlight :
> Dear Pymol users!
>
> After some post-processing of MD simulation I have extracted from the
> traejctory several snapshots as individual pdbs which I need to
> 1-  to re-assign information regarding chain letters (which was lost
> after some operations on pdbs)  for all of those structures assuming
> that within each of these pdbs residues are ordered correctly e.g from
> (1-104 which
> should be chain A) than from 1-100 (it should be chain B), than 1-70
> (in should be chain C) etc.
>
> 2- superimpose and combine all of the pdbs within one model in nmr-like 
> format.
>
> Thanks for help!
>
> James

--
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
___
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[PyMOL] post-processing of pdb ensemble

[James Starlight]

Dear Pymol users!

After some post-processing of MD simulation I have extracted from the
traejctory several snapshots as individual pdbs which I need to
1-  to re-assign information regarding chain letters (which was lost
after some operations on pdbs)  for all of those structures assuming
that within each of these pdbs residues are ordered correctly e.g from
(1-104 which
should be chain A) than from 1-100 (it should be chain B), than 1-70
(in should be chain C) etc.

2- superimpose and combine all of the pdbs within one model in nmr-like format.

Thanks for help!

James

--
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
___
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