[Molvis-list] no chain designation

Annemarie Honegger honegger at bioc.unizh.ch
Wed Nov 17 02:27:47 EST 2004

On Nov 16, 2004, at 4:57 PM, Frieda S. Reichsman wrote:

> 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
Amongst a series of Excel Macros I provide on the Antibody website 
(http://www.biochem.unizh.ch), Tab "Macros", there is a Macro 
"PDB_GetFiles" and "PDB_PutFiles",
which will load one or more PDB Files into Microsoft Excel worksheets, 
each field of the records in their own data column, where it is easy to 
add a chain identifier. The Macro will remove the header of the PDB 
file, but this can easely be  replaced afterwards, if you don't 
overwrite the original file when you export the Excel table to a PDB 
file using  "PDB_PutFiles". You find the Documentation for these Macros 
under the Link for "renumbering Macros" .


Dr. Annemarie Honegger, Ph.D.
Zürich University, Dept. of Biochemistry
CH-8057 Zürich

e-mail: honegger at bioc.unizh.ch
Tel. 41-44-635 55 62
Fax 41-44-635 57 12
www: http://www.biochem.unizh.ch/antibody

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