I downloaded the current version of FATCAT and ran the following command:
/bin/FATCAT -p1 1a2x.pdb -p2 1tcf.pdb -o Output -m -ac -t
Where 1a2x.pdb and 1tcf.pdb are pdb files downloaded from PDB, these two files also happen to be the default values/files on the webserver version of FATCAT ( https://fatcat.godziklab.org/fatcat/fatcat_pair.html ).
Both programs (webserver and command line) generate a pdb file with the two structures superimposed.
Command line generates a longer file (2740 lines) while the webserver generates a shorter (2484 lines), almost of the lines in the web server version are the same, except for these, which are exclusive to the command line all are just REMARK and have no structural data.
REMARK protein 1tcfA.pdb chain A with twisted protein 1a2xA.pdb in chain B
REMARK 1tcfA.pdb chain A
REMARK 1a2xA.pdb chain B
These are included in 267 lines that are unique to the command line file. By inspecting the file and rendering the files it looks like some atoms from the first block are printed out of order and with the wrong coordinates. Below I show lines 2478 to 2489, which shows how after the last aminoacid residue, it starts printing the atoms from the first block all over again.
ATOM 1241 CB GLN B 159 24.527 55.355 13.785
ATOM 1242 CG GLN B 159 25.685 55.095 12.831
ATOM 1243 CD GLN B 159 26.075 53.636 12.804
ATOM 1244 OE1 GLN B 159 26.817 53.171 13.667
ATOM 1245 NE2 GLN B 159 25.572 52.900 11.820
ATOM 1246 OXT GLN B 159 22.906 57.831 13.347
ATOM 1247 N GLU B 3 35.960 74.372 -2.047
ATOM 1248 CA GLU B 3 35.408 73.801 -3.317
ATOM 1249 C GLU B 3 34.963 72.348 -3.183
ATOM 1250 O GLU B 3 33.911 71.968 -3.681
ATOM 1251 CB GLU B 3 36.442 73.888 -4.437
ATOM 1252 CG GLU B 3 36.006 73.201 -5.723
I have 'fixed' this by creating a parser that removes positions that are out of oder in the command line output, which renders a pymol structure indistinguishable from the generated from the web server.
I understand though that the file generated from the command line output should be a final output and not additional processing should be done, can you please double check that the blocks are merging correctly in the final step?
I downloaded the current version of FATCAT and ran the following command:
/bin/FATCAT -p1 1a2x.pdb -p2 1tcf.pdb -o Output -m -ac -tWhere 1a2x.pdb and 1tcf.pdb are pdb files downloaded from PDB, these two files also happen to be the default values/files on the webserver version of FATCAT ( https://fatcat.godziklab.org/fatcat/fatcat_pair.html ).
Both programs (webserver and command line) generate a pdb file with the two structures superimposed.
Command line generates a longer file (2740 lines) while the webserver generates a shorter (2484 lines), almost of the lines in the web server version are the same, except for these, which are exclusive to the command line all are just REMARK and have no structural data.
These are included in 267 lines that are unique to the command line file. By inspecting the file and rendering the files it looks like some atoms from the first block are printed out of order and with the wrong coordinates. Below I show lines 2478 to 2489, which shows how after the last aminoacid residue, it starts printing the atoms from the first block all over again.
I have 'fixed' this by creating a parser that removes positions that are out of oder in the command line output, which renders a pymol structure indistinguishable from the generated from the web server.
I understand though that the file generated from the command line output should be a final output and not additional processing should be done, can you please double check that the blocks are merging correctly in the final step?
Thank you very much !