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.