Problem opening pdb file

[gtzotzos@…]

Hi,

I have problems opening the attached file. I get the following warning messages (see screenshot) but unfortunately I cannot immediately see what’s wrong and therefore unable to find a fix.

The first 5 lines of my pdb file are:
1    ATOM   N  N     MET A  1    1  -11.290  21.482 -48.152 1.00  52.81  1   MET A  N    1 
2    ATOM   C  CA   MET A  1    1  -10.569  20.974 -46.961 1.00  52.81  1   MET A  CA   1 
3    ATOM   C  C     MET A  1    1   -9.758  19.707 -47.247 1.00  52.81  1   MET A  C    1 
4    ATOM   C  CB    MET A  1    1  -11.484  20.837 -45.734 1.00  52.81  1   MET A  CB   1 
5    ATOM   O  O     MET A  1    1   -8.587  19.687 -46.902 1.00  52.81  1   MET A  O    1 

I’d be grateful for your help

George

[gtzotzos@…]

Added by email2trac

[Eric Pettersen]

Hi George,

The first five columns of each line in your file are a number followed by whitespace -- then the remainder of the line looks like a legal PDB record. You need to get rid of those first 5 columns.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[gtzotzos@…]

Eric, many thanks for the prompt reply.

I got rid of the first five columns. I still get errors.

My pdb file now looks like:

ATOM   N  N    MET A  1    1  -11.290  21.482 -48.152 1.00  52.81  1   MET A  N    1 
ATOM   C  CA   MET A  1    1  -10.569  20.974 -46.961 1.00  52.81  1   MET A  CA   1 
ATOM   C  C    MET A  1    1   -9.758  19.707 -47.247 1.00  52.81  1   MET A  C    1 
ATOM   C  CB   MET A  1    1  -11.484  20.837 -45.734 1.00  52.81  1   MET A  CB   1 
ATOM   O  O    MET A  1    1   -8.587  19.687 -46.902 1.00  52.81  1   MET A  O    1 
ATOM   C  CG   MET A  1    1  -10.981  21.771 -44.629 1.00  52.81  1   MET A  CG   1 
ATOM   S  SD   MET A  1    1  -11.969  21.700 -43.119 1.00  52.81  1   MET A  SD   1 
ATOM   C  CE   MET A  1    1  -10.949  22.729 -42.026 1.00  52.81  1   MET A  CE   1 
ATOM   N  N    LEU A  1    2  -10.309  18.685 -47.918 1.00  54.72  2   LEU A  N    1 
ATOM   C  CA   LEU A  1    2   -9.550  17.472 -48.287 1.00  54.72  2   LEU A  CA   1 

And the error warnings are in the attached snapshot

Apologies for this

George

[gtzotzos@…]

Added by email2trac

[Eric Pettersen]

Hi George,
	The PDB is a column-oriented format, so column position matters.  The definition/format of an ATOM record is here: wwPDB Format version 3.3: Coordinate Section <https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM>.  I guess the first five columns you had before were supposed to be the serial numbers.  As per the ATOM definition, the serial number comes after "ATOM  ".  You can see the difference between your ATOM record (first line) and an ATOM record from 1gcn (second line):

ATOM   N  N    MET A  1    1  -11.290  21.482 -48.152 1.00  52.81  1   MET A  N    1
ATOM      1  N   HIS A   1      49.668  24.248  10.436  1.00 25.00           N

The columns in your file need to line up with the columns in specified in the PDB format.

--Eric

[gtzotzos@…]

Thank you Eric. Have a good day

George