[Molvis-list] no chain designation

[Frieda S. Reichsman]

On Nov 15, 2004, at 9:58 AM, Roberts, Rebecca wrote:

> Hello -
>
> I've got a molecule that has a propeptide but there are no chain 
> designations in the file to distinguish this part of the molecule from 
> the rest. So, when selecting a region (I'm trying to select only the 
> first 62 amino acids that consistitute the propiece) PE selects the 
> first 62 and also the next 62 (because the residue numbering system 
> begins again from '1' at the '63rd' amino acid). Any ideas on how to 
> get around this when no chain designations are provided?
>
>  Thanks - Rebecca

Hi Rebecca,
Your attachment did not come through (attachments are not allowed on 
this list) so I cannot be sure of the format of the file you mention, 
but I believe I have encountered this type of problem before. My 
solution has been to use a text editor to select the lines I want to 
add a chain designation to, and then use Find & Replace within the 
selected text. It's pretty fast and gets you what you need.

The Chain designator belongs at a certain position of the 80-character 
line in a pdb file. You can identify the correct position of the chain 
letter in a properly formatted pdb file. In the file you are editing, 
copy and paste all the empty character spaces where the chain 
designation should be  into both the  "Find"  and "Replace" fields. 
Then in the Replace field,  remove the relevant space character and 
enter a chain letter in its place, such as "A". Make sure only the 
lines for the propeptide are selected, and that you check the "only in 
selection" option in the find & replace dialog, otherwise everything 
will get the same chain designation.

One problem that could occur is if there is another "run" of space 
characters that is exactly the same length as the one where the chain 
should be, but I have not yet run into this, so I think it is probably 
rare. Good luck!

Frieda

Frieda S. Reichsman, PhD
Educational Multimedia Specialist

Molecules in Motion
Interactive Molecular Structures
http://www.MoleculesInMotion.com

94 Pratt Corner Road
Shutesbury, MA 01072
413-253-2405


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