On Tue, Oct 11, 2011 at 4:41 PM, Marius Retegan
<marius.s.rete...@gmail.com>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 <tsje...@gmail.com>
> 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 <lina.lastn...@gmail.com> wrote:
> >>
> >>
> >> On Tue, Oct 11, 2011 at 4:24 PM, Thomas Holder
> >> <spel...@users.sourceforge.net> 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<lina.lastn...@gmail.com>
> 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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> >> _______________________________________________
> >> PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net)
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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
> >
> >
> ------------------------------------------------------------------------------
> > All the data continuously generated in your IT infrastructure contains a
> > definitive record of customers, application performance, security
> > threats, fraudulent activity and more. Splunk takes this data and makes
> > sense of it. Business sense. IT sense. Common sense.
> > http://p.sf.net/sfu/splunk-d2d-oct
> > _______________________________________________
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> >
>
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threats, fraudulent activity and more. Splunk takes this data and makes
sense of it. Business sense. IT sense. Common sense.
http://p.sf.net/sfu/splunk-d2d-oct
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