Re: [PyMOL] how can quickly make a fractional atoms into one

[lina <lin...@gm...>]

On Tue, Oct 11, 2011 at 4:41 PM, Marius Retegan
<mar...@gm...>wrote:

> Dear Lina,
>
> I don't want to be rude, but you should read this part of a document
> on how to ask questions on a mailing list
> http://catb.org/~esr/faqs/smart-questions.html#before.
> Some of the question that you posted on this mailing list could have
> been solved by a simple Google search.
>

Sorry. But I did a very rough search about how to add chain identifier.

did not notice the one for adding to some one like,

with the same resn and resi,

I have 7 moleculars shared the same resn and resi,

Actually I am kinda of unconsciously self-blame myself,
for lots of things unable not dive into it, so far it's a great pity to me.


Thanks for your advice,

Best regards,

>
> Best regards,
> Marius
>
> --
> Département de Chimie Moléculaire
> Université Joseph Fourier
> 301 Rue de la Chimie
> BP 53, 38041 Grenoble Cedex 9, France
> Tel: +33 (0) 4 76 63 44 03
>
> GnuPG http://db.tt/rr7Hd0Y
>
>
>
> On Tue, Oct 11, 2011 at 10:37 AM, Tsjerk Wassenaar <ts...@gm...>
> wrote:
> > Hi Lina,
> >
> > That's best done following Thomas' approach, but using chain="X" in
> > stead of segi=''
> >
> > set pdb_retain_ids
> > load input.pdb
> > alter selection, chain='X'
> > save output.pdb
> >
> > Cheers,
> >
> > Tsjerk
> >
> > On Tue, Oct 11, 2011 at 10:33 AM, lina <lin...@gm...> wrote:
> >>
> >>
> >> On Tue, Oct 11, 2011 at 4:24 PM, Thomas Holder
> >> <sp...@us...> wrote:
> >>>
> >>> On 10/11/2011 10:16 AM, Tsjerk Wassenaar wrote:
> >>>>
> >>>> Not really a Pymol question, is it?
> >>>
> >>> well, it's the segment identifier column, so you can do with PyMOL:
> >>>
> >>> set pdb_retain_ids
> >>> load input.pdb
> >>> alter all, segi=''
> >>> save output.pdb
> >>
> >> Thanks,
> >>
> >> a bit further question, how to add chain identifier in pymol?
> >>
> >> Here the situation is the 6 small ligands shared the same resn and even
> same
> >> resi,
> >>
> >>
> >>>
> >>> Cheers,
> >>>  Thomas
> >>>
> >>>> On linux you can use sed:
> >>>>
> >>>> sed '/^\(ATOM\|HETA\)/s/^\(.\{72\}\)..../\1    /' filein.pdb>
> >>>>  fileout.pdb
> >>>>
> >>>> That means:
> >>>>
> >>>> /^\(ATOM\|HETA\)/ :: Match lines starting with ATOM or with HETA, and
> >>>> on those lines execute:
> >>>> s/^\(.\{72\}\)..../\1    / :: Subsitute the first 72 characters and
> >>>> the following four by the first 72 and four spaces. '\1' refers to the
> >>>> 72 stored characters: \(.\{72\}\}
> >>>>
> >>>> Hope it helps,
> >>>>
> >>>> Tsjerk
> >>>>
> >>>>
> >>>> On Tue, Oct 11, 2011 at 9:59 AM, lina<lin...@gm...>
>  wrote:
> >>>>>
> >>>>> Hi,
> >>>>>
> >>>>> I wish to change
> >>>>>
> >>>>> ATOM    822  H01 PDB     1      32.103  36.531  -0.203 -0.11  0.02
> >>>>>  .296
> >>>>> H
> >>>>> ATOM    823  C12 PDB     1      34.140  35.147  -0.218 -0.18 -0.01
> >>>>>  .122
> >>>>> C
> >>>>>
> >>>>> to:
> >>>>>
> >>>>> ATOM    822  H01 PDB     1      32.103  36.531  -0.203 -0.11
> >>>>> 0.02             H
> >>>>> ATOM    823  C12 PDB     1      34.140  35.147  -0.218 -0.18
> >>>>> -0.01             C
> >>>>>
> >>>>> only the last field.
> >>>>>
> >>>>> How can I quickly achieve it.
> >>>>>
> >>>>> Thanks,
> >>>
> >>> --
> >>> Thomas Holder
> >>> MPI for Developmental Biology
> >>
> >>
> >>
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> >
> >
> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> >
> > post-doctoral researcher
> > Molecular Dynamics Group
> > * Groningen Institute for Biomolecular Research and Biotechnology
> > * Zernike Institute for Advanced Materials
> > University of Groningen
> > The Netherlands
> >
> >
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