VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Tue Sep 12 2017 - 17:00:33 CDT

Hi Chris,

Yeah, that sounds about right. The easiest way to confirm would be to
put in a dummy segname into a loaded molecule and ask vmd to write it
out again for you. Something like:

set sel [atomselect top "index 0 to 10"]
$sel set segname DUMMY
$sel writepdb test.pdb

I *think* it only gives you two characters for the segname, but that
could just me imagining things.
-Josh

On 09/12/2017 03:50 PM, Goedde, Chris wrote:
> Hi all,
>
> Is there documentation that specifies which columns in a pdb file are interpreted as the “segname” field by vmd? It seems to be columns 73-75 in the pdb files that I’ve seen, but I wanted to make sure that’s correct. (As far as I can see it’s not part of the official pdb spec at https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.wwpdb.org%2Fdocumentation%2Ffile-format-content%2Fformat33%2Fv3.3.html&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7Cedb88a3eba62403a8b0808d4fa2847b9%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636408498296820419&sdata=26whUwu6TznGytRx5YYDsC16tek8FN2u5HWDY%2FhbN2M%3D&reserved=0.)
>
> Sorry if this is answered in some obvious place, but I don’t see it in the molfile plugin documentation that I’ve looked at.
>
> BTW, the link to the pdb format that’s in the first line of the documentation at
>
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.ks.uiuc.edu%2FResearch%2Fvmd%2Fplugins%2Fmolfile%2Fpdbplugin.html&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7Cedb88a3eba62403a8b0808d4fa2847b9%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636408498296820419&sdata=S2sCxr%2BmxWr%2Fxkad6YOlsu96pvMqB1%2BE5alrt4z5F%2FI%3D&reserved=0
>
> gives a 404.
>
> Thanks!
>
> Chris Goedde
>
>
>