Using the ESPript www interface

Your browser should be separated in three frames:

The Main frame

Fill up the www form by, at least, uploading a multiple alignment file. Strings of characters in blue are hyperlinks to the manual.
PDB files and DSSP files can be uploaded. They can also be retrieved from a SRS or 3DBBROWSE server. If you do not see the buttons labelled "Get pdb file from server" or "Get dssp file from server", please ask your administrator.

The Buttons frame

When the main form is filled, click on the RUN button to start the program.
Click on A (Advanced) or E (Expert) to customize your output. In A mode, you can introduce another secondary structure file, change labels of secondary elements, fiddle with special characters and calculate similarity scores between groups of sequences. In E mode, you can also define your own colours, shift sequence numbering... You can navigate between B, A and E modes without losing information in your query.
If you are in Advanced or Expert mode, you can use the + buttons (+1, +3, -1, -3) to build a non-standard command file. If you press on '+1', the form for a new data set is created. The parameters specified for the data set 0 (i.e. the first one) are copied to the new data sets. You can switch between the different data sets by using the scroll bar or by clicking on the [01] commands, displayed at each header of the main form.
Once the PostScript is generated and if you are curious, click on the IN button to have a look to the ESPript input file. Copy and paste it if you want to use ESPript without the www form.
To read the ESPript logfile, click on the OUT button (always check warnings).
Use the SAVE button to save your session locally, so that you can use later the same parameters and files.
Use the LOAD button to load a previously saved session. Uploaded files (file.aln, file.dssp ...) are saved with the session. Use the button 'do not load data files' if these files have been modified and reenter them. Alternatively, use buttons "new" in main frame. Save your new session when completed.
Before leaving, click on the EXIT button: files are removed from server. This is important for security.

The Results frame

Error messages, security warnings, etc. appear in this frame. When ESPript has been ran, the results files are not automatically downloaded: they appear in this frame as a hypertext link. Click on the link to visualize them (if your browser is correctly configured), or click with the right button of the mouse for retrieve. Conversion of PostScript to Gif or Tiff images takes some time, specially if you use the 300 dpi option. However the result is of good quality and ready to be inserted and resized in a word processor.

Examples

Session vp7_beg.sav for beginners

The resulting PostScript shows a CLUSTAL alignment for the viral protein VP7. vp7_btv1s is the first sequence in the alignment file, vp7.aln, then comes vp7_btv10 and seven other sequences. The 3D structure of vp7_btv10 has been determined and secondary structure elements have been extracted in the DSSP file vp7_btv10.dssp. By default, ESPript aligns secondary elements with the first displayed sequence. The entry '2 all' allows to display the sequence vp7_btv10 firstly. Similarities are boxed according to physico-chemical properties (%Equivalent).

Session vp7_adv.sav for advanced users

Same CLUSTAL alignment, but now the user can play with the option Special Characters. Blue stars highlight an RGD tripeptide (S B 168-170 178-180), alpha and beta domains are colored (X B 1-126 254-349 and X G 127-253) and two red triangles separate the domains (U R 127 250). Title of the first and second sequences are in red (T R 1-2). Name of sec. str. elements is removed (button "hide names"). Three groups of sequences are defined, so as to calculate in-group and cross-group similarities with a Risler matrix (calculation by groups is not possible with a %calculation as in the first example). Relative accessibility is displayed.

Session vp7_exp.sav for experts

Same CLUSTAL alignment, but the 3D structure of vp7_btv1s has been solved and two secondary structure files are entered. The button +1 is used to show the secondary elements of the two structures. The aligned sequences are hidden in [0] and only the secondary structure elements of the first displayed sequence are shown in blue (X B 1). The first 310 helix is not labeled (h). A vertical shift of -1 is used to position the structure elements of the second sequence in [1] and to display them in red (X R 2). Labels are hidden (A S 1-2000 or button "hide labels"). Note that the same entry (2 all) is used for block definition in [0] and [1] to avoid problems with residues insertion. All sequences are numbered. The RGD tripeptide is highlighted by pink boxes.
The advanced and expert input files are also presented at the end of the manual. There is one difference though, similarity score is passed to a pdb file, vp7_btv10_bcol.pdb, in vp7_adv.inp. You must be in mode expert to have access to this option.

Emmanuel Courcelle <manu@ipbs.fr>

Last modified: Mon May 29 13:47:41 MDT 2000