dssp: unknown option -c

[Lars Skjærven]

Downloaded DSSP-2 from http://www.cmbi.ru.nl/dssp.html today, and it seems that the option "-c" has been removed:

slars@dhc$ dssp -c file7a07932d257
DSSP could not be created due to an error:
unknown option -c

slars@dhc$ dssp --version
mkdssp version 2.0.4

I got the following error message when calling it from R:

> dssp(pdb)
Error in file(con, "r") : cannot open the connection
In addition: Warning message:
In file(con, "r") :
  cannot open file '/tmp/Rtmp4bFt0p/file7a019893276': No such file or directory

and if I remove '-c' from function dssp():

dssp(pdb)
Warning messages:
1: In dssp(pdb) : NAs introduced by coercion
2: In dssp(pdb) : NAs introduced by coercion

($phi and $psi seems to be NA with this version of dssp)

[Xinqiu Yao]

I also tested the old and new versions of DSSP program. Without "-c" option, the two versions generated consistent format, which is shiftted to the right by two spaces compared to the one with "-c" option. So, probably we could remove the "-c" and a little bit adjust the columns numbers to read, then both versions should work properly. Do you have any comment, Barry? Is there any particular reason that we should keep the old format (with "-c" option)?

The two versions I used:

$ dssp -V
==== Secondary Structure Definition by the program DSSP, updated CMBI version by ElmK / April 1,2000 ====
$ dssp2 --version
mkdssp version 2.2.0

[Barry Grant]

I think I used the -c option to preserve the old classic format that predated the CMBI 2006 version. I think its time to move on and not worry about the very old versions. So lets drop the -c and change the parsing slightly to cope with the extra spaces. Thanks for reporting! Barry