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****
>
> ****
>
> ** **
>
> ** **
>
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