pdb.dssp fails with dssp 4.0

[c]

On bio3d 2.4.4 and dssp 4.0.5, I’m having an issue running pdb.dssp. It looks like they're more strict about pdb formatting now (see this issue here: https://github.com/PDB-REDO/dssp/issues/49)

simple test:

test <- read.pdb("2NAJ")
test_sse <- dssp(test, exefile = "dssp", verbose=TRUE)

output:

test <- read.pdb("2NAJ")
Note: Accessing on-line PDB file
test_sse <- dssp(test, exefile = "dssp", verbose=TRUE)
/usr/local/bin/mkdssp

.. 00000132 atom(s) from 'string' selection
.. 00000132 atom(s) in final combined selection

.. 00000483 atom(s) from 'string' selection
.. 00000483 atom(s) in final combined selection
.. 00000000 atom(s) in inversed selection

Running command:
/usr/local/bin/mkdssp /var/folders/zj/k43ry_057vx4214xn9zvm7180000gn/T//RtmpeOj62t/file10936740e8b84 /var/folders/zj/k43ry_057vx4214xn9zvm7180000gn/T//RtmpeOj62t/file1093666e9c2a2
Error parsing PDB at line 1
Error trying to load file "/var/folders/zj/k43ry_057vx4214xn9zvm7180000gn/T//RtmpeOj62t/file10936740e8b84"
Expected record CRYST1 but found ATOM
Warning: cannot open file '/var/folders/zj/k43ry_057vx4214xn9zvm7180000gn/T//RtmpeOj62t/file1093666e9c2a2': No such file or directoryError in file(con, "r") : cannot open the connection

Checking the output file shows the pdb generated by bio3d indeed doesn’t include a CRYST1 header. I can run mkdssp from CLI on the input pdb fine. This seems like it should be a simple fix: just make sure temporary pdbs have a CRYST1 record at the start.

[c]

Works with dssp 3 - changing this issue to requested enhancement for dssp 4.0 compatibility, I guess

[Xinqiu Yao]

Thanks. This seems a reasonable request.

[George Tzotzos]

I have encountered the same problem on a Mac running on M1 processor (see below). No such problem on Macs running on Intel processors. Any ideas how to obtain dssp 3?

sse <- dssp(pdb, exefile='/Users/george/myPrograms/anaconda3/bin/mkdssp', verbose=TRUE)
/Users/george/myPrograms/anaconda3/bin/mkdssp

.. 00001292 atom(s) from 'string' selection
.. 00001292 atom(s) in final combined selection

.. 00002527 atom(s) from 'string' selection
.. 00002527 atom(s) in final combined selection
.. 00000206 atom(s) in inversed selection

Running command:
/Users/george/myPrograms/anaconda3/bin/mkdssp /var/folders/x1/wdn20q097_x2ft2897npfjvr0000gn/T//RtmpTrM407/file25f0f7e083b /var/folders/x1/wdn20q097_x2ft2897npfjvr0000gn/T//RtmpTrM407/file25f01b4e616f
Error parsing PDB at line 1
Error trying to load file "/var/folders/x1/wdn20q097_x2ft2897npfjvr0000gn/T//RtmpTrM407/file25f0f7e083b"
Expected record CRYST1 but found ATOM
Error in file(con, "r") : cannot open the connection
In addition: Warning messages:
1: In dssp.pdb(pdb, exefile = "/Users/george/myPrograms/anaconda3/bin/mkdssp", :
Non-protein residues detected in input PDB: MG, ACT, ADP, HOH
2: In file(con, "r") :
cannot open file '/var/folders/x1/wdn20q097_x2ft2897npfjvr0000gn/T//RtmpTrM407/file25f01b4e616f': No such file or directory