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This document covers some of the more common questions concerning using MidasPlus for molecular visualization. For questions regarding licensing MidasPlus, send email to midasplus@cgl.ucsf.edu.

 

Layout

The questions are organized according to whether they relate to MidasPlus itself, or to a delegate or auxiliary program (i.e. those programs documented in Appendix 6 of the MidasPlus manual). The questions related to MidasPlus itself are further broken down by the specific MidasPlus command they refer to.

 

The Questions

 

MidasPlus

 

How can I use the match command to superimpose more than 2 models?

The match command will move the first model named on the match command line so that it overlays the second model. Therefore if you have three model structures (opened in model numbers 1, 2, and 3) you would overlay them with:

match #1 #2 (will move model 1 on top of model 2)
match #3 #2 (moves model 3 onto model 2)

Additional models would be handled in an analogous manner. There is no direct method for simultaneously superimposing multiple models.

 

I want to create a PDB file that contains just what's displayed on the screen. The write and save commands create a PDB file with everything in it. How can I get what I want?

Try pdbrun cat > filename to save just what is displayed on the screen. Note that the pdbrun command includes USER records to describe atom color, etc. If the application you intend to use the pdb file with cannot handle USER records, then use the nouser keyword to pdbrun, like so:

	pdbrun nouser cat > filename

 

When I open my PDB file in midas the waters are connected to each other with very long bonds. How can I fix this?

The problem is that your water residues are in PDB ATOM records instead of HETATM records. Midas always connects consecutive residues in a PDB file unless there TERcards between the residues or unless the residues are in HETATM records. One possibility is to fix your PDB file so that the ATOM records for the waters are changed to HETATM records, being careful to preserve the column positions. Another alternative is to use the longbond command in midas to break the bonds. Check the MidasPlus manual for details.

 

Ribbonjr

 

Can conic and ribbonjr images be combined?

Conic and ribbonjr use very different methods for computing images and there is no easy way to combine them. However ribbonjr can be ``duped'' into displaying space-filling atoms (though without shadows) if that is what is desired.

The simplest way to do this is to invoke ribbonjr with the command line flag "-A 1". This causes all "balls" to be displayed at their full VDW radii (the sticks will still be displayed also, but will be buried inside the balls and therefore not visible).

However, if you require both space-filling atoms and balls and sticks in the same image, a more elaborate procedure is necessary. Also, a requirement of the procedure is that the residues that are to be space-filled have names unique from the residues to be depicted normally. This is frequently the case anyway since one of the more common uses of the mixed space-filling/ball-and-stick representation is to show a space-filled ligand with a ball-and-sticked/ribboned receptor.

The trick is to make ribbonjr believe that the VDW radii of the ``space-filling'' atoms are larger than normal so that when ribbonjr reduces their size in order to depict them as balls and sticks, the net effect is to show them at their proper VDW radii. This is done by using the vdwopt radii command to specify a file of VDW radii for MidasPlus to use. The main task is to construct the file of VDW radii. The radii files that MidasPlus uses are in /usr/local/midas/resource/midas. They are called vdw.hydrogen (used if the the model has explicit hydrogen atoms) and vdw.default (used otherwise). Each line in these files has two or three fields: atom name, radius, and (optionally) residue name. You would want to copy the appropriate Midas radius file and tack radii for your ligand residue(s) on the end just before the wildcard line. The ligand radii would need to be increased by a factor of 5 to compensate for ribbonjr "shrinkage."

As an example, the standard PDB file 1FMP has a ligand whose residue name is FMP. There are no explicit hydrogens in 1FMP. The FMP residue is composed of carbons, nitrogens, oxygens, and a phosphorus. So, the proper file to copy would be /usr/local/midas/resource/midas/vdw.default and it would be modified to look as follows:


C       1.8
N       1.8
O       1.5
S       1.85
P       1.9
F       1.35
I       2.15
B       1.8
CL      1.8
FE      0.64
CU      1.28
ZN      1.38
BR      1.95
H       1.0
0       1.0
1       1.0
2       1.0
3       1.0
4       1.0
5       1.0
6       1.0
7       1.0
8       1.0
9       1.0
C       9.0     FMP
N       9.0     FMP
O       7.5     FMP
P       9.5     FMP
*       1.8

With the VDW radii file created, the procedure to render the desired image is actually fairly simple:

  1. Set up the desired view in Midas
  2. Read in the modified radii file:
  3. vdwopt radii modified_radii_file
  4. Render the scene with ribbonjr:
  5. ribbonjr -B 0.1

 

Can I change the width of strands or helices?

Yes, by using the -x option. Read the "CROSS-SECTION FILE" section of the manual page. You need to copy the default cross-section file (/usr/local/midas/resource/ribbonjr/xs.default) and modify the specification for the secondary structure type you want to change. In particular, modify the X values to change the width. For example, to make a strand 50% wider, change the X values for "strand": -1.0's to -1.5, and 1.0's to 1.5.

 

I'd like to color my helices one color, my strands another, and leave the sidechain colors as is. How can I do this?

Assuming that your PDB file has proper HELIX and SHEET records in it, then

	color magenta mainchain /helix

from within MidasPlus before running ribbonjrshould color the backbone atoms of the helix magenta. Mainchain is an alias defined in the system midasrc file (which expands to: "@CA,C,O,N"). Use /sheet instead of /helix for beta sheets.

 

I want to show certain atoms in the main chain, but ribbonjr hides all main chain atoms as part of the ribbon. How can I show them?

It can't be done directly; you have to resort to dirty tricks. However, the "dirty trick" isn't hard to pull off. Essentially, you save a file containing just the main chain atoms you want shown to a new file, then open the new file in Midas along with the original file and display them both in ribbonjr. The procedure is as follows:

  1. Use the standard Midas display commands (e.g. display, show) to show only those main chain atoms you want shown with the ribbon.
  2. Save them to a file using pdbrun: pdbrun nouser cat > filename
  3. Edit the file to change the atom names so that they are no longer the names of main chain atoms (e.g. "CA" to "CX" or "N " to "NX"). Remember to keep all other columns aligned.
  4. Read the edited file back into Midas, aligned as it was originally, with: open original filename
  5. Display both the original and new files as you want them to look, and run ribbonjr.

 

My helices look like corkscrews (and/or my beta sheets look like tubes) What's wrong?

Your PDB file lacks HELIX and SHEET records describing where secondary structure exists. Ribbonjr doesn't determine the position of secondary structure motifs; it relies on these records. You don't have to create them by hand though; check the ksdssp command in the manual. From within Midas it can be used to add HELIX and SHEET information to the open model(s). From the UNIX command line (see Appendix 6) it can be used to create a file of HELIX and SHEET records which can be added to your PDB file permanently.

 

Conic/Neon

 

Can conic draw in orthographic rather than perspective view?

Not without a hack. What you would have to do is save the input to conic into a file, edit the file, then run conic. In detail:

  1. In Midas, set up the desired view, then run "pdbrun cat > filename".
  2. Outside Midas, edit the file you named "filename". What you will be doing is changing the annotations in the PDB file so that the observer position is an extreme distance from the molecule, resulting in an essentially orthographic projection. The information in Appendix 1 of the manual describes the format of the file you'll be editing.
    • Change the second line of the file (the "USER EYEPOS" record) by adding 9000 to the last number on the line. This increases the distance from the observer to the molecule by 9000 angstroms.
    • Change the fourth line of the file (the "USER WINDOW" record) by adding 9000 to the last and next-to-last values on the line. This increases the distance of the hither and yon clipping planes to the observer by 9000 angstoms, keeping them in the same relative position with respect to the molecule.
  3. Run conic with "conic filename" (outside Midas) or "system conic filename" (inside Midas).

 

How do you change the lighting direction in conic and/or neon?

Changing the light direction is done by using a configuration file in conjunction with conic/neon. This is described in the "Configuration File" section of the conic manual page. In particular, the light keyword is used to add light sources to a scene, and to override the default light source. Also, conic adds some weak illumination to spheres that would otherwise be completely in shadow. You can override this by using the eye keyword to make that light source black, though most likely you don't want to do this (the resulting image rarely looks good).

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