| Home | About | Applications | Entries | Search | DIAL | Help |
|
|
|
|||||
Help page
Help for Search and Online Programs :
Sequence search at domain level
Rasmol
Search by PDB code
Search engine is provided in all DDBASE pages.
To search by PDB code
Enter Valid PDB code (4 letter code starts with number - 5th letter Chain identifier (optional)).
Choose the "PDB Code" option from radio button given
Submit the form
The results will be given for the PDB code provided
Since database entries are on protein chain level even Chain identifier is not provided along with PDB code it will give results on chain level
Search by Keyword
Search engine is provided in all DDBASE pages.
To search by Keyword
Enter Keyword
Choose the "Key word" option from radio button given (by default this search engine will go for keyword search)
Submit the form
The results contain PDB code (with link) and Protein name
User can reach the choosen entry by using link provided in PDB code
Sequence search at Domain level
To search by Sequence or to run BLAST or PSI BLAST againt DDBASE domains
Choose the program to run (BLAST or PSI BLAST)
Paste query sequence in FASTA format
Choose the E value (ranges from 10 to 0.0001)
Submit the form
The results contain PDB code (with link), alignment and corresponding scores (Blast output)
User can reach the choosen entry by using link provided in PDB code
|| Back to top || || Blast page ||
DIAL online
User has the provision to run DIAL online.
Requirements to run DIAL
1. Upload or Paste the Coordinates file in PDB format
2. PDB file should be single chain chain.
3. C-alpha proteins are not useful for running DIAL.
4. Minimum 35 residues are required to run DIAL
|| Back to top || || DIAL online ||
Output file
DIAL Online gives a output which gives following Information:
Best domain definition from DANAL
Table of possible Domain definition
Cluster of segments
Matrix of Segment proximity
Sequence in PIR format
SSTRUC output
Possible trouble shootings:
No output (Problem in running DIAL):
Check input for format
Check the residue number ( more than 35)
If input file is very big then possibility of exceeding the declared dimension
Partial output :
one of the above problem may accur.
If you have any other problem please contact: mini@ncbs.res.in - with the details about your input file
|| Back to top || || DIAL online ||
Rasmol
RasMol2 is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images. RasMol runs on Microsoft Windows, Apple Macintosh, UNIX and VMS systems. The UNIX and VMS systems require an 8, 24 or 32 bit colour X Windows display (X11R4 or later). The program reads in a molecule co-ordinate file and interactively displays the molecule on the screen in a variety of colour schemes and molecule representations. Currently available representations include depth-cued wireframes, 'Dreiding' sticks, spacefilling (CPK) spheres, ball and stick, solid and strand biomolecular ribbons, atom labels and dot surfaces.
Get a complete source code of rasmol and instal it in your system
Configure your browser as follows :
(In netscape) Edit --> Preferences --> Navigator --> Applications --> New
Fill the following :
Description : PDB file
MIME Type : chemical/x-pdb
Activate the option Application
Application :"rasmol_path"
"rasmol_path" = Rasmol path in your system.
| Home | About | Applications | Entries | Search | DIAL | Help |