Dear all! :)

I need to merge two chains in one pdb ( object) into one united chain. How I could do it?



2011/11/18 Joel Tyndall <>



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.




From: James Starlight []
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 ?


2011/11/15 James Starlight <>

Thanks Joel, it's clear now :)


2011/11/14 Joel Tyndall <>

See attached.


To switch to editing mode click on 3 button viewing or use the menu


Mouse > 3 button editing






From: James Starlight []
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 :)


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?


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


2011/11/11 Joel Tyndall <>

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




From: James Starlight []
Sent: Friday, 11 November 2011 1:44 a.m.
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?