[Chimera-users] Cannot open the .pdb file generated from ZDOCK

Hsih-Te Yang paulhtyang at gmail.com
Wed Jun 27 08:44:09 PDT 2012

Got it and thank you.
Happy Wed.


On 6/27/12, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Good morning,
> The file is not in standard PDB format.  In the ATOM lines, although the
> first several columns are in the correct format, the columns after the
> coordinates are not. Probably ZDOCK uses that space for other information,
> and Rasmol ignores that part while Chimera tries to read it, but then fails
> because it is not the expected format.
> The Chimera documentation includes some information on PDB format:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html>
> .... ATOM lines:
> <http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#coords>
> If you remove the columns after the x,y,z coordinates from your file (remove
> the last 4 columns) it can be read correctly.
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Jun 27, 2012, at 7:54 AM, Hsih-Te Yang wrote:
>> Good morning, all:
>> Attached is the output file generated by "ZDOCK". I couldn't open it
>> by "Chimera", but "RasMol" was working.
>> What wrong with this?
>> Any comment and reply are greatly appreciated.
>> Hsih-Te Yang
>> <complex.1.pdb>

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