[Bug]: Mapping of the residues given in input failed. This can be due to a malformed residue file or a mistake in the reisdue numbering, type or chain.

[avilella]

Operating System

Unix (e.g., Ubuntu 20.04)

Version

1.0

Python Version (optional)

3.10.12

Python Virtual Environment

Not using a virtual environment

Execution Environment

Encapsulated environment from the SURFMAP Docker image

Bug Description

The command below used to work, but I think the chimera version that I now use might be introducing lines in the .pdb file that SURFACE doesn't know how to interpret.

See error below:

Running: /home/surfmap/MSMS//pdb_to_xyzr /input/0307326f3c557828716ec74b28fdf620.rf2.lcpb.mmkr.pdb > ./shells/0307326f3c557828716ec74b28fdf620.rf2.lcpb.mmkr.xyzr-tmp ...
                                                                                                                                                                                                                 surface property mapping: kyte_doolittle                                                                                                                                                                         Traceback (most recent call last):
  File "/home/surfmap/tools/SurfmapTools.py", line 177, in <module>
    main()
  File "/home/surfmap/tools/SurfmapTools.py", line 166, in main
    scalevalue = Structure.returnPropensity(dPDB[chainid][resid]["resname"], distmini, scale = "kyte_doolittle")
  File "/home/surfmap/tools/Structure.py", line 158, in returnPropensity
    kyte_doolittle = float(dkyte_doolittle[aa])
KeyError: 'UNK'

Mapping of the residues given in input failed. This can be due to a malformed residue file or a mistake in the reisdue numbering, type or chain.

Format should be the following:
chain residuenumber residuetype
example: A      5 LEU

Exiting now.

docker run --tty --rm --volume /bfx_nfs/surface/03/0307326f3c557828716ec74b28fdf620:/input/:rw --volume /bfx_nfs/surface/03/0307326f3c557828716ec74b28fdf620:/output/:rw nchenche/surfmap:v0.2 -pdb /input/0307326f3c557828716ec74b28fdf620.rf2.lcpb.mmkr.pdb -tomap all -d /output/0307326f3c557828716ec74b28fdf620.rf2.lcpb.mmkr_all.srfm

See a screenshot of the first few lines of the input file:

Should getting rid of the non-ATOM lines fix the issue?

Steps to Reproduce

see above

Relevant Log Output

Additional context (optional)

No response

Confirmation

• I confirm I have searched for duplicates and reviewed the relevant documentation.

[nchenche]

Hello @avilella,

The SURMAP pdb parsing process reads only 'ATOM' starting line so new lines will not cause an error.

From what i see however, the problem you encounter resides in an unknow residue name in your pdb:

kyte_doolittle = float(dkyte_doolittle[aa])
KeyError: 'UNK'

For properties like kyte-doolitle, wimley_white or stickiness, the 20 amino acids are assigned a specific value in a dictionary with their standard residue name as key. As a consequence, any non-standard or unknow residue names will generate a key error for those properties.

To solve your problem, you should remove this 'UNK' residues in your pdb.