PDBeFold Links
PDBeFold may run queries launched from any Web site. Simply make a hyperlink
with the following URL:
http://www.ebi.ac.uk/msd-srv/ssm/cgi-bin/ssmserver?query_string
where
query_string gives details
of your query. It should represent a sequence of statements
token=value separated by
semicolon, no spaces or escape symbols are allowed. Each token corresponds
to a parameter from the PDBeFold
Submission Form. If ambiguous or repeated parameters are specified,
the last one prevails. All parameters have default values, which are
exactly those specified in the PDBeFold
Submission Form displayed at PDBeFold start-up. The tokens are
case-insensitive.
List of tokens:
Token |
Default value |
Description |
q
|
1sar |
4-letter PDB code of the
query
structure. PDBeFold cannot upload structures in "link" regime.
|
t
|
|
4-letter PDB code of the
taget
structure.
|
qs
|
d1sara_ |
SCOP domain name or SCOP sunid of the
query
structure, when it is represented by a SCOP domain.
|
ts
|
|
SCOP domain name or SCOP sunid of the
taget
structure, when it is represented by a SCOP domain.
|
qf
|
|
full path to the file containing the query structure. The file
must be in found the server's file system, visible to PDBeFold. This
option can only be used on in-house installations.
|
tf
|
|
full path to the file containing the target structure. The file
must be in found the server's file system, visible to PDBeFold. This
option can only be used on in-house installations.
|
mafs
|
|
full path to the file containing a (possibly gzipped or compressed)
tarball of structures to be submitted for multiple alignment. The file
must be found in the server's file system, visible to PDBeFold. This
option can only be used on in-house installations. Note that
once this option is specified, regardless to its position in
the string, PDBeFold switches to multiple alignment submission and
all other options, except view, are ignored.
|
a
|
PDB |
specifies the archive of target structures. The value may be
PDB
| |
whole PDB archive |
SCOP
| |
whole SCOP archive |
subset
| |
a SCOP subset. See subset
selection syntax
here.
|
|
c
|
*(all) |
list of
chains of the query structure to be selected
|
d
|
*(all) |
list of secondary structure elements forming a domain
to be selected from the query structure
|
r
|
*(all) |
range of residues to be selected from the query structure
|
ct
|
*(all) |
list of
chains of the target structure to be selected
|
dt
|
*(all) |
list of secondary structure elements forming a domain
to be selected from the target structure
|
rt
|
*(all) |
range of residues to be selected from the target structure
|
qp
|
70 |
the minimum percent of secondary structure elements of the
query
structure to be mapped onto those of
target
structure(s). See details
here.
|
tp
|
70 |
the minimum percent of secondary structure elements of the
target
structure(s) to be mapped onto those of
query
structure. See details
here.
|
ic
|
ON |
match structures chain-by-chain ("on"), or as a whole
("off", without splitting into chains). See details
here.
|
cn
|
ON |
match SSE connectivity ("on") or allow for the change in the
PDBeFold ordering ("off"). See details
here.
|
bm
|
ON |
output best matches found ("on") or all of them ("off"). See details
here.
|
um
|
ON |
output unique matches only ("on") or all of them ("off"). See details
here.
|
prec
|
3 |
precision, or specificity level. Ranges from 1 (highet) to 5
(lowest). See details
here.
|
sort
|
R |
sorting of results. The possible values are:
R
| |
by increasing RMSD |
P
| |
by increasing the P-score |
Z
| |
by increasing the Z-score |
L
| |
by decreasing the
alignment length |
S
| |
by decreasing the number
of matched SSEs |
G
| |
by increasing the number
of gaps |
See details
here.
|
scopf
|
OFF |
If set ON, the results will be arranged by SCOP families (only
when matching against PDB or SCOP archives). Sorting order is
kept within the families and between them basing on the family's
leading match.
|
view
|
cartoons |
viewing mode in Rasmol scripts. The possible values are:
cartoons
| |
cartoons |
backbone
| |
backbone |
ribbons
| |
ribbons |
|
EXAMPLE:
The following links:
http://www.ebi.ac.uk/msd-srv/ssm/cgi-bin/ssmserver?q=1sar
http://www.ebi.ac.uk/msd-srv/ssm/cgi-bin/ssmserver?q=1sar;a=PDB;c=A,B
http://www.ebi.ac.uk/msd-srv/ssm/cgi-bin/ssmserver?c=*;qp=70;ic=on
are all equivalent and correspond to launching PDBeFold with default settings.
The following link:
http://www.ebi.ac.uk/msd-srv/ssm/cgi-bin/ssmserver?q=1sar;a=PDB;r=A:,B:
is different as token r=A:,B:
instructs PDBeFold to select a range consisting of chain A and chain
B. This range will be matched as a sole structure to all chains
in PDB.
Link
http://www.ebi.ac.uk/msd-srv/ssm/cgi-bin/ssmserver?mafs=/path/mystruct.tar.gz
submits structures packed in file mystruct.tar.gz for multiple alignment. Appending
the link with ;view=backbone
switches PDBeFold's visualisation in Rasmol to backbone representation of
protein chains.
NOTE:
PDBeFold does not issue warnings or error messages on the violation of the
query string syntax.