Well, for me at least it is a good think Lina asked, because there were two different answers from the experts and i learned from each. I don't think we want to discourage or intimidate new users from asking questions. It is very easy to ignore or delete a silly email.
Marius Retegan 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. > > 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 > ------------------------------------------------------------------------------ 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
