Documentation for the HOLE: 7.0 Ancillary programs

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7.0 Ancillary programs

All the programs described in this section are designed to be run interactively. If you followed the setup instruction you should be able to start the programs by typing the command at you normal unix prompt. All the programs ask a series of questions to which you can type a reply. Wherever possible a default option is provided, this is indicated in angle brackets <>. For example when a program wants a quanta plot file name (which already exists) it will ask:

       Please enter input binary quanta plot (old) filename
       defaults <example.qpt>ext:<.qpt> (abort by EXIT or ^D):

where example.qpt is the newest file with extension .qpt in the current directory. If you just hit enter then the filename shown will be used. However, if a reply of "file1" is given the program will try to open a file with the name "file1.qpt" and if that fails will try just "file1" but if a reply of "file2.dat" is given an attempt will be made to open file2.dat. Note that you can now use ~'s in filenames to refer to peoples home directories (e.g., ~mary/hello.txt refers to a file hello.txt in user mary's home directory). If you wish to abort the question enter "exit" (either case) or hit ctrl_D. Normally "abort" stops the execution of a program completely but sometimes I use this to jump out of a loop e.g. in asking for multiple input files. Generally you can get any of these programs to abort by entering ctrl_D at any question (if you have setup HOLE on a non-unix machine then the EOF character is often ctrl-Z).

7.1 qpt_conv

This is a utility program which converts the .qpt (quanta plot file format program) into another format. Start it by typing qpt_conv. You should see the following menu:

 *** Program qpt_conv ***
 Version H2alpha0
 (c) 1996 Oliver Smart & Birkbeck College, All rights reserved.
 Program linked at Tue Feb 20 16:57:02 GMT 1996  
 Last modified .f files: 
        8477 Feb 20 16:56 qptsyb.f       
         158 Feb 20 14:37 qpto.f         
        3392 Feb 20 14:36 qpt_conv.f     
 
 This program converts a .qpt file (as produced by hole) 
  to something else.
 Output options
 'A' to/from ascii version of original .qpt (can then edit)
 'C' A .qpt file in which dots are replaced by 3D crosses
 'L' A .qpt file with long lines split into smaller sections
       (useful for proper depth queueing in qplot)
 'I' InsightII format
 'S' Sybyl format
 'K' to David C. Richardson's kinemage format
 'O' for use with O program
  Enter conversion option character :

Type the conversion type you want and the program will then give appropriate prompts.

Note for release 1 users: qpt_conv incorporates and replaces programs hydasc, qptdot and qpt_insight.

Short description of the options

'A' to/from ascii version of original .qpt (can then edit)

This simply converts the binary qpt into an ascii version this can then be edited (e.g., to change the colour number of a particular object). Once the ascii version has be edited it should be converted back using this option. Also useful when you wish to use a qpt file created on one machine on another with a different architecture - which stores binary files in a different order. This option replaces hydasc program of original HOLE.

'C' outputs another .qpt file in which small 3D crosses replace all dots.

As mentioned in section 6.2 dots do not show up very well when displayed in quanta, and a number of other molecular graphics programs. You can use this option to convert all the dot records in a quanta 3D binary plot file (.qpt) to 3D crosses (like a cross in 2D but with a third cross bar). These should then be quite visable. Note the sensible default for the output .qpt filename. You are prompted for the size of the cross bar to be used - the default of 0.1 angs gives small crosses which show up well in quanta. Note that using this option will considerably increase the size of the graphics file (it take 6 records to draw a 3d cross cf to one for a dot). Also note that qplot has some nice drawing options for dots when doing hardcopy.

'L' A .qpt file with long lines split into smaller sections

Program qplot use a crude depth queueing method in which lines are drawn in order from the lowest Z value to the highest. The centre point of the line is used in the comparison. This can sometimes lead to errors where long lines cross one another. if this occurs then use this option which splits the line up into smaller sections and try again.

'S' converts to sybyl format.

This produces a .plt2 format file which can be read into sybyl.
For details of how to get sybyl to display the file see section 6.2.

'O' produces a file for use with O.

For details of how to get O to display the file see section 6.2.

'K' produces a kinemage for use with mage.

For details of mage and how to display the file see section 6.2.

'I' produces a file for use with InsightII.

The output is two .usr files
for details and how to display the file see section 6.2.

7.2 sphqpt

Occasionally you may wish to add the result of two or more HOLE runs together and view the overall surface (as done for annexin V in Smart, Wallace and Goodfellow, 1993). You can use program sphqpt to do this. It can also be used to change the dot density of a result without rerunning the whole procedure or edit out unwanted parts of a run. The program reads a '.sph' file. This is a file containing information about the sphere centres determined in HOLE which is in pdb format (with the radius determined lurking as an occupancy. The file is output by HOLE if a 'sphpdb' card is present (see section 3.0). sphqpt asks for and reads in a '.sph' file and opens a QUANTA format 3D binary plot file (.qpt). The program asks the user to supply a dot density (as explain in 'dotden' section 3.0). The program then proceeds to produce an overall dot surface for all the sphere centres read. Optionally the sphere centre line is also written.

When editing the .sph file (or files) bear in mind that the sphqpt needs to known when an 'end' sphere centre has been reached. It does this by detecting breaks in the residue numbering in the pseudo-pdb file. If you are doing something relatively sophisticated you may have to play about a bit to achieve your desired aim.

7.3 qplot

This is a very much larger program than the previous two. It is intended to allow the production of publication quality stereo diagrams of QUANTA plot files, in particular the results of HOLE. The program outputs postscript files suitable for printing on a postscript printer. The initial version was written in collaboration with Valeriu Niculae, a student doing a vocational course in computing with work experience at Birkbeck. Subsequently it has been substantially rewritten with support for colour postscript printers and simple depth queuing. The program is a bit of a mess and unfortunately I do not have the time to revise it. I hope that you find it useful and not too much of a pain. If you find things difficult persevere as the output is quite pretty.

The program asks a series of questions which you answer to produce an output file. The first question sets the level of complication of the questions to be asked. There are three levels: "amateur" gives very little control (defaults are used for practically everything), "normal" gives more control (for instance allowing the image to be rotated and "expert" level allows you to control everything. To produce output of the form shown in Smart, Goodfellow and Wallace (1993) follow this brief outline. Before running qplot you must have the following files ready: (i) the .qpt file output from HOLE preferably before it has been put through qptdot. (ii) A QUANTA plot file of the part of your ion channel you wish to display. Generate this using the "generate plots" option under the file menu in QUANTA. Make sure you select the "stick plot" option from the "identity matrix" view. If you wish all the molecule to appear as one line type make sure that you are displaying it as one colour before this. (iii) If you wish to have a hard copy from a view other than the identity then use QUANTA to select a view and write it to a view file (using the option "save view" under the "view" menu the default extension is .vew). At present only the rotation matrix in the view file is used. In the future I may introduce a feature to read the other data so clipping and scaling could also be used. (iv) Prepare any labels you wish to place on the picture by using program qptlab (see section 7.4). Then run qplot by typing qplot at the command line. As you want to read two .qpt files (the stick plot and the HOLE output) you must select the "expert" level. Enter the filename for the stick plot and hit return, answer the subsequent question until asked for the next filename when you should enter the name for the HOLE output .qpt file). When asked for yet another filename enter ctrl_D to jump out of the loop. I hope that the rest of the questions asked should be fairly self explanatory. Please also refer to the example_doc.* in the example directory for an example of the programs use.

The stereo output option produces a picture of reasonable size to be view through normal stereo glasses (with lenses) and for publication. I have produced pretty stereo pictures for a poster on an A3 colour postscript printer by editing the output postscript file and adding the line "1.7 1.7 scale -50 -50 translate" to the top of the file. If you want to scale the picture try something along this line.

7.4 labqpt

This little program allows the user to produce a quanta 3D binary plot file containing labels for chosen atoms. It was called qptlab in the previous release but labqpt seems more logical! The program reads in a .pdb co-ordinate file and ask for the user to name an atom (giving atom name and residue number). It then asks the user to enter a label to be written at the atom's position (with the default of the atom name and residue number). Furthermore the user is asked for a "positioning integer". This is integer is written to the quanta plot file and is interpreted by program qplot - if the integer is: 1 the label is placed below the atom to the left 2 the label is centred below the atom ... 5 the label is centred on the atom ... 9 the label is placed above the atom to the right. An easy way to remember what the integer means is to look at the keypad of any keyboard. Note that this control integer is an extension to the QUANTA format so that other programs will not recognize it. For an example of the use of the program see example_doc.*.

7.5 vdwdot

This program calculates the "internal" van der Waals dot surface for a given molecule. The technique used is to consider a number of dots isotropically distributed around each atom at the van der Waals radii for the atom. A dot is only output if it lies outside the van der Waals radius of every other atom. In addition a test is made to see whether the dot is "internal". A dot is defined as internal if it meets the following test. Extend the dot to a line pointing from the centre of the atom to infinity. If this line crosses any atom then the dot is "internal". Simply put a dot is internal if it opposes some other atom's surface. (In fact the test is slightly different to this but very difficult to explain in words!).

vdwdot is intended to complement HOLE by allowing the visualization of the full internal van der Waals surface without the outer surface complicating things. It could be used before HOLE to gain a broad idea of the shape of the inside of a pore before starting detailed analysis. Alternatively it can be used in conjunction with the surface produced by HOLE to see parts of the internal cavity not revealed by the HOLE process. The same values of van der Waals radii can (and should!) be used in vdwdot and HOLE.

Unlike the other ancillary programs in the HOLE suite, vdwdot can be quite cpu intensive. It is therefore controlled like HOLE with a keyworded entry - so that it can easily be run in the background. A number of the cards are in common:

COORD fname: The file containing the co-ordinates of the molecule in Brookhaven protein databank format. MUST be specified.
RADIUS fname: The van der Waals radius filename to be used. MUST be specified.
PLTOUT fname: The filename for graphical (.qpt) output of the dots. The dots will be assigned to colour 6. MUST be specified.
DOTDEN integer: The control integer for the density of dots to be used by the program. See section 3.2 above for more details. For large molecules avoid using high values as this will result in very slow execution and large files. Default value is 10.

One new card has been introduced in the program:

DCUT real_no: This card can be used to save time in the program. The program will only check to see whether a dot overlaps/opposes a given atom if the distance between atom centres is less than the sum of the van der Waals radii and dcut. When the maximum radius of a channel is known from HOLE dcut should be set to over twice this value. The default value is 10 angstroms. A special feature is that if dcut is set to zero then the full van der Waals surface is produced - i.e. no check is made to see whether a dot is internal.

7.6 sph2vrml

to be written.

7.7 make_post_map, bln2gnu, capost2gnu, grd2gnu, make_post2gnu

All these programs are used when making 2D Maps of the internal surface of a pore. See section 6.5 for details of use.

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Back to previous section 6.0 Visualization of HOLE results

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