Hi James,
> 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).
the "Mutagenesis Wizard" comes in handy for editing caps. However it
fails with non-standard amino acis as far as I know. Then you have to do
it manually.
These commands could be a good start for your task:
http://pymolwiki.org/index.php/Remove
http://pymolwiki.org/index.php/Fuse
> So I'd like to change FOR- > ACE and ETA-> NH2
> twisely for the 1MAG dtructure
hm, shouldn't it be the other way round? FOR is N-terminus and ETA is
C-terminus?
Cheers,
Thomas
--
Thomas Holder
MPI for Developmental Biology
Spemannstr. 35
D-72076 Tübingen
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