O With Hydrogens Home Page: Richardsons' Laboratory 2/2000

Using Explicit Hydrogens Within O


The OwithHydrogens package contains files we have developed to allow the use of hydrogens within the program O. We no longer recommend the display of explicit hydrogens as the best way to display contact surfaces in O. Instead we suggest you use the 'ProbewithO' package.

Files in the O With Hydrogens Package

README.txt  — how to use small probe contact dots within O
acolor.omac  — an O macro to recolor atoms (makes hydrogens white)
allH.dat  — modified O connectivity table
dict_ehH.dat  — modified O hydrogen parameters
dict_pdbH.dat  — modified O hydrogen parameters
hparms.omac  — O macro to load data files for use with hydrogens
pdbcns  — executable UNIX shell script to convert hydrogen names
pdbcns.awk  — awk program for pdbcns (usually put in /usr/local)
README.pdbcns  — description of pdbcns
residue_dictH.o  — modified O residue dictionary
refi_aaH.o  — (refi_aa dictionary file for O v6.2.2 with hydrogens)
(12/7/98  The refi_aaH.o file was added to support v6.2.2 You can use it by putting the command "read refi_aaH.o" in the new on_startup macro.)
rscH.o  — modified O rotamer dictionary
torsionH.o  — modified O torsion parameters
torsionHshort.o  — modified O torsion parameters, sidechain only
The following files are considered obsolete
probe.macro  — O macro to run probe around the current center point
centerprobe  — executable UNIX shell script to run probe
renameH  — executable UNIX shell script to fix O output hydrogen names

Additional Software You Will Need

Reduce can be used to add hydrogens (with PDB standard names) to PDB format files. It is written in C++, originally on the SGI and ported to linux.

The unpacked executables may need to be renamed, and the permissions changed to add the execute bit. Rename to 'reduce' and move it to one of the directories in your UNIX command path. The command 'rehash' can then be used in each operating system window to make the programs immediately available.

Getting Hydrogens In O

  1. Reduce should be downloaded (see above), and installed in one of the directories in your UNIX command path.
  2. in your $ODAT directory rename rsc.o to rsc.o.orig (save old rotamers)
  3. copy rscH.o to $ODAT/rsc.o to install the rotamers with hydrogens
  4. add hydrogens to your coordinate file with reduce using the command:

    reduce -build -penalty1 xxx.pdb >xxxH.pdb

    where xxx.pdb is your PDB format coordinate file.

    There are lots of parameters to Reduce, most of which you should not need, but if you are curious, "reduce -help" will list them.

    When it is trying to add hydrogens to groups like serine and theonine OH groups or asparagine and glutamine sidechains, Reduce tries to rotate the OH group or flip the sidechain amides to best effect. This is a combinatorial process but usually only a few groups interact, we call this a "clique", and so it can enumerate and test each possible configuration pretty quickly. In pathological cases, these groups can be larger than Reduce can handle and it will not optimize the positions of these hydrogens, giving you a warning message instead. We are working to improve Reduce's ability to handle large cliques but in practice it often works quite well.

    You can make cliques smaller and speed up reduce by skipping the step that tries to flip Asn,Gln and His sidechains. To to this just leave off the flags:

    reduce xxx.pdb >xxxH.pdb

    Reduce works with PDB format atom names and XPLOR is particularly cavalier about generating non-standard atom names such as _HB1 instead of the correct 2HB_ (the numbers are in different columns and the stereochemistry is backwards too). If you are starting with hydrogens generated by XPLOR (e.g., polar hydrogens) you may want to run pdbcns to convert them to pdb format:

    pdbcns cnsinput=sega,a,segb,b xplorfile.pdb > pdbfile.pdb

    (also converts the segid "sega" to chainid "a", etc.)

    Or you could trim the existing hydrogens from the file with:

    reduce -t xxx.pdb >xxx.noH.pdb

    before rebuilding them as described above.

  5. after you start up O, run @hparms.omac to install the files- allH.dat, torsionH.o, residue_dictH.o, and dict_pdbH.dat
  6. load xxxH.pdb and then run @acolor.omac to fix the colors

Now you can modify torsion angles or dial through rotamers and the hydrogens should move too. There are a couple of bugs which we can't completely fix without Alwyn's help so we note them here.

David C. Richardson
URL: http://kinemage.biochem.duke.edu
Biochemistry Department
Duke University
Durham, NC USA 27710