James, Please look up the 'create' (http://www.pymolwiki.org/index.php/Create) comand.
Cheers, -- Jason On Sat, Nov 26, 2011 at 6:17 AM, James Starlight <jmsstarli...@gmail.com> wrote: > Dear all! :) > > I need to merge two chains in one pdb ( object) into one united chain. How I > could do it? > > Thanks > > James > > 2011/11/18 Joel Tyndall <joel.tynd...@otago.ac.nz> >> >> James, >> >> >> >> Please post this to the bulletin board. You can try to click on the word >> (residues usually default) at the bottom right of the viewer. >> >> >> >> Joel >> >> >> >> From: James Starlight [mailto:jmsstarli...@gmail.com] >> Sent: Thursday, 17 November 2011 7:52 a.m. >> >> To: Joel Tyndall >> Subject: Re: [PyMOL] Editing of the pdb structure >> >> >> >> Another question about working with the structure. >> >> >> I have structure of the fulerene molecule wich consist of 60 carbon atoms >> >> I switch to the Sequence mode-> Atoms and try to select individual carbon >> atoms ( e.g I want to find where this atom situated in my molecule). But >> instead of selection of the individual carbons the whole molecule was >> selected. How I can work with individual atoms of my structure ? >> >> James >> >> 2011/11/15 James Starlight <jmsstarli...@gmail.com> >> >> Thanks Joel, it's clear now :) >> >> >> >> 2011/11/14 Joel Tyndall <joel.tynd...@otago.ac.nz> >> >> See attached. >> >> >> >> To switch to editing mode click on 3 button viewing or use the menu >> >> >> >> Mouse > 3 button editing >> >> >> >> >> >> >> >> >> >> >> >> From: James Starlight [mailto:jmsstarli...@gmail.com] >> Sent: Monday, 14 November 2011 8:44 p.m. >> To: Joel Tyndall >> Subject: Re: [PyMOL] Editing of the pdb structure >> >> >> >> Dear all, thank you for the advises :) >> >> Thomas, >> >> when I've tried to add ACE cap to the N-tem of the first residue of my >> peptide I've obtain >> >> Error: unable to load fragment ''. >> >> So how I should define dirr from wich those caps groups will be loaded? >> >> >> Joel, >> >> I could not find such buiilder button :o >> >> when I've tried to select individual atoms from my FOR residue ( from >> sequence panell), the overal residue with all atoms was selected instead :o >> >> James >> >> 2011/11/11 Joel Tyndall <joel.tynd...@otago.ac.nz> >> >> Hi James, >> >> >> >> If I am correct in reading what you want you wish to change the FOR group >> to an ACE. >> >> >> >> I am using a PC version 1.3. Click on the builder button (right hand side >> of grey GUI) >> >> Make sure you are in Mouse mode: 3 button editing. >> >> >> >> Click on the carbon of the FOR group and also the oxygen ( a white ball >> will appear on each atom) >> >> Then in the GUI click on the || icon adjacent to “bonds create”. This will >> give you the carbonyl. >> >> Now click on the hydrogen attached to the carbonyl carbon and then click >> in the GUI, the carbon atom C. >> >> This has now created your Acetylated nitrogen. >> >> >> >> Then save molecule as: and you can edit the text file to change For to >> ACE. >> >> >> >> Given this is some sort of dimer, I have just noticed that the second >> chain will overlap with the first. >> >> >> >> Hope this helps >> >> >> >> Joel >> >> >> >> From: James Starlight [mailto:jmsstarli...@gmail.com] >> Sent: Friday, 11 November 2011 1:44 a.m. >> To: pymol-users@lists.sourceforge.net >> Subject: [PyMOL] Editing of the pdb structure >> >> >> >> Dear PyMol Users! >> >> >> >> Recently I've opened such topic but I didnt obtain answer on this question >> so I try to paraphrase my task. Also I want to specify this topic on >> questions lincked with the processing of pdbs. >> >> 1) I need to remove some elements fron my structure described as the >> individual residue and place another element of the same size on the place >> of the first element. >> >> In particular I have two different peptides both of wich have small cap >> groups on C and N termi. ( attached) >> >> I need to remove all caps ( two caps FOR and ETA because there are two >> identical chains in that structure) from the 1MAG structure and build >> exactly on this place another cap groups wich I'd like to copy from the >> second peptide ( KALP). So I'd like to change FOR- > ACE and ETA-> NH2 >> twisely for the 1MAG dtructure >> >> How I can perform such task in PyMol? >> >> James >> >> >> >> >> >> > > ------------------------------------------------------------------------------ > 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. IT sense. And common sense. > http://p.sf.net/sfu/splunk-novd2d > _______________________________________________ > 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 > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ 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. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d _______________________________________________ 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
