VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Thu Jan 23 2020 - 05:13:57 CST

A quick look shows tabs in your PDB file, suggesting that you probably just
copy pasted. The PDB (ATOM record) is a 80 column record. Each column or
group of columns is reserved for something.

Details here:
https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM

Instead of doing things in excel (which is definitely not the correct way)
you can do your change in VMD.
Load a structure, make a selection and then use the

get

keywords to ensure you have selected the thing. The use the

set

keyword to make changes you want.
Once all changes have been made use "writepdb" to write out the new
structure with the changes you have made.

If you are not OK with using the VMD PDB parser you can use many others
available out there for example the parser included in Biopython.

Hope this helps.

On Thu, Jan 23, 2020 at 5:21 PM Yogesh Sharma <yogesh.rma13_at_gmail.com>
wrote:

> Hi everyone,
> I was trying to reformat rows of my PDB file in excel sheet. I am not
> able to load generated output file to VMD. Is there any specific formatting
> required?That i probably messed with.
> * with regards*
> *Yogesh Sharma*
>
> 

-- 
Best,
/A