Very fancy graphics; molecular pornography (PORNO)

Introduction.

The menu PORNO holds the real fancy graphics stuff and some options that were requested by users. The menus PORNO and GRAEXT are somewhat similar, so options expected here but not found could very well be found in the GRAEXT menuu. In the PORNO menu you will find an interface to the RIBBONS program by Carson and Bugg. Also the Chebyshev polynomial ribbons and arrows module written by David Thomas is accessible from this menu.

The RIBBONS program is interfaced to WHAT IF. That means that the PORNO menu creates the files needed to run the RIBBONS program,

Using the ribbons program

Ribbon plus side chains (RIBBON)

The command RIBBON allows you to use the RIBBONS program to draw a ribbon plus CPK models of side chains. You will repeatedly be prompted for a range of residues through which to draw a ribbon, and for a range of which the side chains will be represented as CPK models. If you answer both questions with 0 (zero) WHAT IF will cause RIBBONS to start. See your RIBBON writeup about how to operate the RIBBON program.

Ribbon plus full cpk model (RIBCPK)

The command RIBCPK function similar to RIBBON (see above). The difference is that RIBBON draws CPK's of only side chain atoms, whereas RIBCPK uses the whole residues for CPK representation.

Adding hydrogen bonds (HBOFIL)

The command HBOFIL will cause WHAT IF to prompt you for two ranges. The hydrogen bonds between these two ranges will be calculated and a RIBBONS cylinder file will be created that can manually be added to the RIBBONS file with cylinder file names.

Other fancy graphics options

Indicate alpha carbon trace directionallity (CARROW)

The command CARROW will cause WHAT IF to prompt you for a residue range. This range will be displayed by cones that run from alpha carbon to alpha carbon with their wide end N-terminal, and their pointed end C-terminal. The terminal residues of of molecules are not always displayed.

Indicate alpha carbons with crosses (CACROS)

The command CARROW will cause WHAT IF to prompt you for a residue range. This range will be labeled with crosses at their alpha carbon positions.

Arrow and cylinder representation (WIFRIB)

This command spline does the same as the command SPLINE in the GRAFIC menu. (See the GRAFIC menu).

Using the small molecule plotting program (PLUTON)

Calling PLUTON a small molecule plotting program is really an insult to it, because PLUTON is a very fancy program that can do very many thing, but I expect that most WHAT IF users will not do much more than this with it. You need to get the PLUTON program from T Spek (see the chapter on licenses). WHAT IF, as usual with other people's programs, only provides an interface.

Other options

Apply the view to the soup (APLVIE)

The command APLVIE will take the present graphical view matrix and apply it to the soup. Be aware that after this option old MOL-items no longer correspond with the soup, and thus are no longer pickable. This option is useful as preparation for complicated RIBBON pictures in which you want to make manual modifications.