Cannot open the .pdb file generated from ZDOCK
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
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>
Got it and thank you. Happy Wed. HTY On 6/27/12, Elaine Meng <meng@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>
participants (2)
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Elaine Meng -
Hsih-Te Yang