From: James S. <jms...@gm...> - 2011-11-26 11:18:01
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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 <joe...@ot...> > 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:jms...@gm...] > *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 <jms...@gm...>**** > > Thanks Joel, it's clear now :)**** > > ** ** > > 2011/11/14 Joel Tyndall <joe...@ot...>**** > > See attached.**** > > **** > > To switch to editing mode click on 3 button viewing or use the menu**** > > **** > > Mouse > 3 button editing**** > > **** > > **** > > **** > > **** > > **** > > *From:* James Starlight [mailto:jms...@gm...] > *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 <joe...@ot...>**** > > 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:jms...@gm...] > *Sent:* Friday, 11 November 2011 1:44 a.m. > *To:* pym...@li... > *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**** > > **** > > ** ** > > ** ** > |