PRT+instructions

=Building proteins in SL= Author: Graham Mills


 * (UNDER DEVELOPMENT;** Proteins Home**)**

The process involves three phases:
 * 1) Parsing the PDB file to get coordinates.
 * 2) Rezzing the protein.
 * 3) Packaging the protein.

To date the packaging of proteins has used Lex Neva's commercial Rez-Faux (L$600). This can be obtained in-world from his (fake) p0rn shop in the dystopian Suffugium ([|SLURL]). However, preliminary experiments suggest that the free Builder's Buddy also works for small molecules and we will use that ([|http://wiki.secondlife.com/wiki/Builders_Buddy]).

> code Add avatar name. Add species from which molecule was derived. Add location if molecule is currently on display. Add molecule, e.g. lysozyme. Add structure, e.g. 1rez. Add model, i.e. the structure you created. code > > If you want an existing molecule, the best approach currently is simply to IM the avatar concerned. Graham Mills has compiled a vendor of some of the proteins he has rezzed and this is available from him and will shortly be available from onrez.com under the OpenSLedware tag. Do, however, check the prim count as some models are much larger than others. It may make more sense to visit the deployed model using the SLURL on SiSL rather than rez your own copy.
 * 1) You are provided with a protein rezzing toolkit contained in a plywood prim. Take a copy by rightclicking it and choosing Buy.
 * 2) Rez your copy of the prim by dragging it from inventory to the ground before you. Open it and take its contents into inventory. Note that it contains: a notecard with this text, a protein rezzer prim (black), a BB packaging base prim (white), a BB positioner script.
 * 3) You need to choose a pdb file, e.g. from [|http://www.rcsb.org/] You can use the search field at the top of the page. Go for a small monomeric protein, e.g. 1rez or the even smaller 1t0c (NB 0 is the number zero). The script we use is not smart enough to parse anywhere near the entire pdb file. The proteins in this case comprise just the backbone (N, CA, C atoms) of the polypeptide chain. At the moment the script handles just the ATOM, HELIX and SHEET data and generates its own CONECT data on the assumption that it is a linear molecule. If you have multiple subunits, these can typically be identified by the abnormally long bond (which, of course, you delete) or a shouted error.
 * 4) Go to http://biolsci.webfactional.com/sisl/sisl1.ks/selectPdb/ . Select option 1, enter the pdb id (1t0c or 1rez), select OK and the webpage will retrieve the pdb file and generate a page of unformatted text in two sections (ignore the first two lines). The first section is the ATOM data, the second the CONECT data augmented where appropriate with the secondary structure info.
 * 5) Go to a sim where there is a sandbox with a good prim allocation. Move to a location at least 10 m away from any other avatar rezzing proteins. Rez a copy of the protein rezzer prim. Right-click the prim and choose edit. You should see .sn1 and .sn2 files. Double-click the .sn1 file, and replace the contents with the augmented ATOM data from the previous step. Save. Likewise, replace the contents of the .sn2 file with the augmented CONECT data. Again, save.
 * 6) Type '/42 rezatoms'. You should see the atoms of the molecule rez above the rezzer. The completion of this step will be reported in chat. Then type '/42 rezbonds' and allow the bonds to be rezzed to completion. Don't attempt to do both at the same time.
 * 7) DON'T DO THIS WHILE SOMEONE ELSE IS REZZING NEARBY UNTIL THEY HAVE FINISHED: You can now remove the building scripts by shouting '/121 remscript' and '/137 remscript'.
 * 8) The final step is to package the molecule. This is the typically the most labour-intensive operation and can require serious amounts of concentration. Rez a copy of the BB controller prim and move it so that it is fairly close beneath the molecule. Now edit a prim in the molecule and with the editor still open, select a group of adjacent prims (remember that you can use Shift-click-drag to extend the selection). There should not be >256 prims in a group and they must be reasonably close to one another (e.g. within 10 m). Press Ctrl-L to group them. All but the root prim should turn light blue. If this doesn't happen, try a smaller group and/or cam round to check that the selected prims are indeed adjacent. In my experience most alpha-helix structures can be grouped end-on; beta-sheet tends to be more laborious to group.
 * 9) Once you have a group linked and selected, select the Object tab in the Edit menu and give the group a name, e.g. 1t0c_1 (replace whatever default text is there). We will increment the suffix in subsequent groups so it makes sense to copy the prefix to the clipboard for subsequent reuse.
 * 10) Copy the BB Postitioner script from the BB folder in your Inventory into the group scripts tab in the Edit dialog. You may find dragging across the tab opens the tab without a click being needed.
 * 11) Once all the prims have been grouped and the positioner script added to each group, click the base prim and select Record.
 * 12) Then take all the grouped prims into inventory. (You may actually find it easier to record positions and 'take' groups incrementally if you have a large molecule).
 * 13) Open the BB base prim and add the grouped prims from inventory.
 * 14) Touch the base prim and select Build. The molecule should assemble.
 * 15) The molecule will respond to touch by displaying the residue number, type and amino acid (for the atom). You can clear this by shouting (if necessary) /747 clear. Other commands available on the /747 channel include HELIX and SHEET. You can also search for particular amino acids using the 3-letter code (the particles are color-coded) or highlight atom types, e.g. /747 :CA:. By default the particles display for about 15 s.
 * 16) You can reposition the molecule by moving or rotating the base prim in edit mode, quiting edit mode, touching the prim and selecting Position. Clean will similarly delete the molecule. There is a Save option to freeze the structure in place. Use the ordinary delete or take to remove the base prim.
 * 17) You can add new structures to the SiSL database accessed via http://biolsci.webfactional.com/sisl/sisl1.ks. This goes through six stages.