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.
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 >> >> >> ------------------------------------------------------------------------------ >> 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 >> _______________________________________________ >> 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. > > 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 > _______________________________________________ > 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 > ------------------------------------------------------------------------------ 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 _______________________________________________ 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
