For reference, here is a note about
.par file from SNAP.
>> Following our Monday meeting, I have updated the SNAP program to do what we
>> have discussed. Specifically,
>>
>> [1] I have added a command line option -frame=NUMBER. By default, it now
>> uses the CA-CB-N based reference frame for AA as used by Pabo and
>> Siggers/Honig. The ls-fitting scheme applies equally well to GLYCINE
>> since FOUR atoms (N/CA/C/CB) are used by default. For glycine, where
>> CB is missing, the other three are used.
>>
>> With -frame=1, the previous peptide based reference frame is used.
>>
>> [2] When deciding the contacts, only heavy atoms (i.e., non-Hs) are
>> considered.
>>
>> [3] SNAP now ouputs 4 types of AA-bp interactions, controlled by the new
>> command line option -type=NUMBER, as follows:
>> 0: with any atom -- EITHER base OR backbone atom
>> 1: with base atom (could also contact backbone, default)
>> 2: with backbone atom (could also contact base)
>> 3: must contact BOTH base AND backbone atom
>> The output files are now named like
>> AT-ALA_1.par, AT-ALA_1.pdb etc for type=1, i.e., contacting base
>> for -type=2, it would be AT-ALA_2.par etc, and so on.
>> Note the interaction type info is now in the file name, and is NOT
>> included in the .par file (see below).
>>
>> [4] The format of the .par file is now as follows:
>>
>> C4.A-D19.T:A55.ALA 1a73.pdb + 8.6310 -99.8367
>> # identifier, PDB file name, '+' or '-' as defined by dot(dz1, dz2)
>> # followed by "translational distance" and "rotational distance", as in #
>> Pabo, except that "translational distance" is NEGATIVE if it is below # the
>> base-pair mean plane. "rotational distance" is within [-180 to +180]
>>
>> -3.6380 7.5388 2.1037 0.2592 38.5504 -93.9814
>> # six rigid body parameters: tx, ty, tz, rx, ry, rz
>>
>> 3.6415 7.1395 3.2034 # AA frame origin
>> -0.1708 -0.8874 -0.4282 # x-axis
>> 0.8903 0.0471 -0.4529 # y-axis
>> 0.4220 -0.4586 0.7821 # z-axis
>> # The above 4 lines define the AA reference frame w.r.t. the bp frame, and
>> # can be *rigorously* deduced from the 6 rigid parameters. They are #
>> redundant, and can be safely ignored. They are included here for info #
>> purpose only.
>>
>> 3.6277 7.1391 3.1907 # CA atom coordinates
>>
>> [5] In processing all the PDB files in batch mode, you need to first run
>> "snap -c" to initialize all the files. Then each run will "append" to
>> the corresponding files to get the compilation of the whole set.
>>
Topic: general questions about SNAP- rotation parameters (Read 32545 times)