HELP for SOCKET server at The Centre for Biomolecular Design, University of Sussex
SOCKET, Woolfson Group, University of Bristol Author: John Walshaw (john.walshaw@bbsrc.ac.uk) Maintenance: Thomas Vincent (Thomas.Vincent@bristol.ac.uk) The SOCKET program identifies knobs-into-holes packing in protein structures (Walshaw & Woolfson, 2001). Input The required input is a PDB-format atomic coordinate file (which can be compressed e.g. have the .gz or .Z extension), and optional parameters: packing-cutoff This parameter in Ångstroms essentially represents the tightness of the knobs-into-holes interactions; the smaller it is, the more ideal the packing. The SOCKET program looks for knobs (single side chains of one helix) fitting into a hole formed by four side chains of a different single helix. The 'packing-cutoff' parameter specifies how close the knob side chain must be to all of the four hole side chains. The four distances (between knob and each hole residue) must all be within this cutoff for the interaction to be considered as a knob in a hole (the distances are calculated using the centre of volume of each side chain). A sensible packing-cutoff proved to be 7.0Å. Helix extension Only residues in alpha-helices are examined by SOCKET to determine if they are part of knobs-into-holes interactions. The DSSP (Kabsch & Sander, 1983) definition of secondary structure is used. However, some helices have small kinks (eg GreA 1grj; Stebbins et al., 1995) of a couple of residues not within the alpha-helical conformation, while others may have residues just beyond the end of a helix which take part in Knobs-into-Holes packing. Some coiled coil structures might therefore be missed by SOCKET if the DSSP definition were strictly observed. The option is given to extend all alpha helical regions by E residues at each end. For example the two DSSP helices either side of the kink in 1grj are joined if E=1, giving a single helix and a positive SOCKET result. All helices separated by no more than 2E residues will be joined, meaning that E should always be <= 2; otherwise 2 helices either side of a hairpin bend could be joined, so that no interactions between them would be evaluated (a helix cannot pack against itself). Output There are three types of output: the standard output describing each coiled coil (if any) a long output (optional) which gives more details of each knobs-into-hole interaction an optional RasMol (Sayle & Milner-White, 1995) script (should work with RasMol-derivatives such as Protein Explorer), which highlights the coiled coils (if any). The RasMol script is available in two formats: the script on its own, which must be used in conjunction with the original file you uploaded; and a standalone script, which includes the structure 'inline', as well as the script commands. It is possible to configure your Web-browser so that you can automatically invoke the standalone script by clicking on the hyperlink that this server provides. 1. standard output The features are described here. 2. long output (optional) (example) All residues in alpha-helices are listed, one residue per line. The residue number and chain-identifier (if any) are given. Residues which are part of knobs-into-holes packing regions have the following additional information: the register(s) (preceded by 'R') and topology(s) (in square brackets); the knobtype (preceded by 'T'); and details of the hole into which the knob fits: the helix (preceded by 'H'), the core-packing angle; the register of the 4 hole residues; the chain identifier (if any); the residue name and number of the 4 hole residues; and the dimensions of the hole, i.e. the length of the 4 'sides' (distances between centres-of-mass of each adjacent hole sidechain). N.B. in some unusual helical assemblies based on knobs-into-holes packing, a residue can have several different registers. 3. RasMol (Sayle & Milner-White, 1995) script (optional) The basic script should work with any version of RasMol, or RasMol-derivatives worth their salt (e.g. Protein Explorer) - but let me know if they don't. Simply download the script file, and run it locally on RasMol after you have loaded the structure. The standalone script contains the structure itself, encapsulated within the RasMol commands. This works with RasMol 2.6 - remember to load the file as a script, not a structure. To use this script, either: download the script file, and run it locally on RasMol, OR configure your browser so you can just point and click; you might want to do this if you wish to use the server many times Configuring your Web-browser to run standalone scripts automatically This SOCKET server will provide a hyperlink to the standalone script. It is possible to configure a WWW-browser so that by simply clicking on this link, RasMol will be automatically run, the structure loaded and the script run to highlight the coiled-coils (if any). THE FOLLOWING APPLIES TO UNIX AND PCs - I assume its possible with Macs, so please tell me how, if you know The tricky bit is letting your WWW-browser know that it must treat an inline-RasMol script differently to a PDB file. Usually, if a WWW server is to deliver a PDB file for use with a graphical renderer like RasMol, it sends you the file with the MIME-type 'chemical/x-pdb' (a de-facto, unofficial standard, though others are sometimes used). So for example my UNIX Netscape is configured to handle the chemical/x-pdb MIME-type with this command: xterm -e rasmol %s (UNIX; in practice the full path of the executable file might be specified) -i.e., an X-terminal is run which executes the command 'rasmol %s' , where the %s represents the file which gets delivered over the web. (Configuration is done in Edit -> Preferences -> Navigator -> Applications, then select the correct file type and click Edit, in the case of Netscape; or by hacking the ~/.mailcap file.) The MS-Windows equivalent is simply the path of the RasMol executable. Again, Netscape configuration is achieved by Edit -> Preferences -> Navigator -> Applications . However, the command to run a RasMol script is different, namely 'rasmol -script %s' - note the '-script', ie treat %s as a script, not a structure file. To get Netscape to behave correctly, a different MIME-type must also be used. This Web-server delivers these inline-RasMol script files with the MIME-type chemical/x-ras which is a total non-standard that I just made up - if there is some pseudo-standard that I ought to be using, please let me know. So all you need to do is to make sure that your browser applies the right command to files it receives with MIME-type chemical/x-ras, e.g. on UNIX: xterm -e rasmol -script %s and on MS-Windows (the name of the executable should be preceded by the full path e.g. C:\...): raswin.exe -script - and it should work; a single click and you'll get the SOCKET results for your structure rendered visually by RasMol. References Kabsch, W. & Sander, C. (1983) Biopolymers 22 2577-2637 Sayle, R. & Milner-White E.J. Trends in Biochemical Sciences 20 (9) 374 Stebbins, C.E., Borukhov, S., Orlova, M., Polyakov, A., Goldfarb, A. & Darst, S.A. (1995) Nature 373 636-640 Walshaw, J. & Woolfson, D.N. (2001) J. Mol. Biol., 307 (5), 1427-1450 If you haven't already done so, please read the Socket Server
