Hi
Frequently such problems arise because the resulting models
a) do not have the residues in their proper order (the patched-in piece gets
added to the end of the pdb file)
This is particularely severe in DNA, where you have to place
b) residue and chain labels do not match (duplicate labels)
c) dependent on your PyMOl setting, “TER” records are placed at the end of each
segment originating from a different structure
Solution:
-Set pymol not to introduce “TER” records where residue labels are not
sequential by "set pdb_use_ter_records, 0”
(https://pymolwiki.org/index.php/Pdb_use_ter_records
<https://pymolwiki.org/index.php/Pdb_use_ter_records>)
-Using the “alter” command (https://pymolwiki.org/index.php/Iterate
<https://pymolwiki.org/index.php/Iterate>), adjust chain, residue and atom
labels to what they should be according to their position in the combined
structure.
-Using the “sort” command (https://pymolwiki.org/index.php/Sort
<https://pymolwiki.org/index.php/Sort>), reorder the atom records in the
combint structure
____________________________________________________________
Dr. Annemarie Honegger
Dept. of Biochemistry
Zürich University
Winterthurerstrasse 190
8057 Zürich
Switzerland
e-mail: honeg...@bioc.uzh.ch
phone: +41 44 635 55 62
fax: +41 44 635 57 12
>
> Hi All,
>
> From time to time I am asked to create missing parts of proteins, DNA or RNA
> in existing structures.
>
> Often when I duplicate parts of one DNA to use it to fill in for a missing
> part of another DNA, the cartoon view of the DNA gets messed up. The sticks
> that represent the bases disappear, or the backbone tube disappears, or parts
> drop out randomly. Obviously some part of the PDB is getting messed up when
> combining these DNA parts together.
>
> Is there a way to fix this?
>
> Attached is once such DNA pdb file as both a .pdb and a .png. It is made up
> of three different pieces of DNA. I went through the pdb file and changed all
> the chains to the same identifier but it still will not render the cartoon
> view correctly.
>
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