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Data Formats
User data must have the following formats. Please follow these formats and check your input before submitting to the server to avoid errors and wasting processor time.
Fasta 
Optional single-line description (line starts with ">"), followed by
lines of amino acid sequence data.
Example:
>1UBQ:_ UBIQUITIN - CHAIN _
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN
IQKESTLHLVLRLRGG
Accepted amino acid codes are:
A alanine P proline
B TREATED AS asparagine Q glutamine
C cystine R arginine
D aspartate S serine
E glutamate T threonine
F phenylalanine V valine
G glycine W tryptophan
H histidine Y tyrosine
I isoleucine Z TREATED AS glutamine
K lysine
L leucine ALL OTHER ALPHABETIC CHARACTERS ARE
M methionine TREATED AS alanine. NON-ALPHABETIC
N asparagine CHARACTERS ARE IGNORED.
Batch Fasta (not available to public)
Concatenated fasta sequences each requiring single-line target information (line starts with ">" followed by Target Name and Optional Notes), followed by lines of amino acid sequence data. Target Names cannot have spaces. Example: >1UBQ_ Sequence one MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYN IQKESTLHLVLRLRGG >PFAM00240 Sequence two consensus ubiquitin family MKIFVKTLDGKTITLEVDPSDTVLELKEKIEDKEGIPPEQQRLIYKGKVLEDDTTLAEYNIQDGSTLHLVLRLR See Fasta above for accepted amino acid codes.
Chemical Shifts
1 line per residue format(a3,1x,i4,7(1x,f7.2)) AA (1 letter or 3 letter), residue number, chem shifts (C,CA,CB,HA,N) any unknown shifts should be '9999.00' The sample file below also has the actual phi and psi as the last two fields on the line. These aren't read in; they can be present or absent ------- 1d3z_.chsft_in ----------- M 1 170.54 54.45 33.27 4.23 9999.00 180.00 -180.00 Q 2 175.92 55.08 30.76 5.25 123.22 -91.02 138.26 I 3 172.45 59.57 42.21 4.21 115.34 -131.09 163.04 F 4 175.32 55.21 41.48 5.63 118.11 -115.99 140.22 V 5 174.87 60.62 34.23 4.72 121.00 -118.03 114.22 (etc) ----------------------------------
NOE Constraints
current format 'NMR_v3.0' :
NMR_v3.0 (first line)
comment
comment
n_pairLines (# of lines of constraints to read)
tag,res1,atom1,res2,atom2,upperbound,lowerbound,{true distance}
format(a1,2x,i4,1x,a4,1x,i4,1x,a4,1x,f10.2,1x,f10.2)
tag: '#':ignore, ' ':score
true distance is optional and not read, any characters after lowerbound is treated
as a comment
atom1 and atom2 should follow pdb-style atom names
also allowed: ' CEN' for centroid constraints
protons: only 'HN ' and 'HA ' are currently recognized
for others, use heavy atom and pad bounds appropiately
res1 and res2 are residue numbers
atom names should be in the pdb format ie ' CA ', ' CG ' etc.
left justified names okay; Protons other than HA or HN not recognized
so use the heavy atoms and pad your bounds; 'CEN' is also a valid
atom name. This is a constraint between sidechain centroids for
use in early rosetta phases before fullatom representation of sidechains.
Also, the lower bound is specified in the input file, but
rosetta doesn't do anything with it yet. So they're all effectively zero.
-------1d3z_.cst------------------------------
NMR_v3.0
HA-HN csts, subset from 1d3z.mr PDB deposition
data set used in Bowers et al., (2000) J Biomol NMR 18:311
55
6 HN 68 HA 3.71 0.00 2.23
5 HA 67 HN 3.79 0.00 2.27
3 HA 64 HN 3.92 0.00 2.35
4 HN 66 HA 3.94 0.00 2.36
22 HA 56 HN 4.31 0.00 2.58
3 HA 65 HN 4.31 0.00 2.59
(etc)
--------------------------------------------
Dipolar Constraints
file format:
line1: version? (not yet in use)
line2: parameters? (not yet in use)
line3: comments
line4: # of lines to read (<=physical number of lines)
line5 -> beginning in 1st column
tag res1 atom1 res2 atom2 J
a1 2x i4 1x a4 ix a4 1x 4x 1x f10.2
200 format(a1,2x,i4,1x,a4,1x,i4,1x,a4,1x,f10.2)
If the first character of a line is '#', the line is read, but
the data is ignored. Otherwise, the first column of each line
contains a tag identifying the set to which the measurement belongs.
(ie different experimental conditions with different alignment
tensor) tags may be any single character other than '#'.
Also, only bb atoms (including H) are included at present.
Also, HA# for glycine not dealt with, just ignored.
-------------------------------------------------------------------------------
sample data file > everything over here is just my comments
> and shouldn't be in the file
------------------------------------------------------------------------
1d3z (662 total) comments
JACS 1998 120:12334 comments
Ottiger & Bax, HN & HA only (134) comments
134 lines to read (include '#' lines)
a 2 N 2 H -8.17
a 3 N 3 H 8.27 HN-N data, a is a tag
a 4 N 4 H 10.49
# 5 N 5 H 9.87 commented out line
a 6 N 6 H 9.15
a 7 N 7 H 3.70
.... (lots more lines)
a 2 CA 2 HA 5.60
a 3 CA 3 HA 8.98 HA-CA data, same conditions
a 4 CA 4 HA 24.27 (ie alignment tensor) as
a 5 CA 5 HA 21.73 HN data above
a 6 CA 6 HA 16.15
(etc)
---------------------------------------------------------------------
PDB Complex
Multi-chain protein complex using RCSB's PDB File Format.
Mutations List
List of alanine scan mutations to be made in a given PDB Complex.
3 space delimited columns representing:
- Column 1. The residue number as in the PDB complex.
- Column 2. Chain ID as in the PDB complex (case sensitive).
- Column 3. Experimental delta delta G values (for future use).
------------------------------------------------------------------------ sample data file ------------------------------------------------------------------------ 15 A 0.00 16 A 0.00 17 A 0.00 18 A 0.00 74 A 0.00 143 B 0.00 145 B 0.00 148 B 0.00 150 B 0.00 189 B 0.00 191 B 0.00 196 B 0.00 (etc) ------------------------------------------------------------------------
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