| <html> |
| <head> |
| <title>dms</title> |
| </head> |
| <body> |
| <h4>NAME</h4> |
| <h3>dms - calculate a molecular surface</h3> |
|
|
| <h4>SYNOPSIS</h4> |
| <h3><b>dms</b> <i>pdbfile</i> [ -a ] [ -d <i>density</i>] [ -g <i>logfile</i> ] |
| [ -i <i>sitefile</i> ] [-n] [-w <i>radius</i> ] [-v] -o <i>outfile</i> |
| </h3> |
|
|
| <h4>DESCRIPTION</h4> |
| <p> |
| <b>Dms</b> calculates the molecular surface of a molecule. |
| The molecular surface |
| resembles the van der Waals surface of a molecule, except that crevices |
| between atoms are smoothed over and interstices too small to accommodate |
| the probe are eliminated. The surface includes cavities in the interior of |
| the molecule, even if they are not accessible to a solvent molecule coming |
| from the outside. |
| </p><p> |
| The molecular surface calculated is that defined by Richards (see |
| the <a href="#ref">reference</a> below). |
| In particular, the calculated molecular surface is that traced out by |
| the surface of the probe sphere rather that the |
| probe sphere's center. According to Richards' definition, the molecular |
| surface consists of two parts: contact surface and reentrant surface. The |
| contact surface is made up of "those parts of the molecular van der Waals |
| surface that can actually be in contact with the surface of the probe." |
| The reentrant surface is defined by "the interior-facing part of the probe |
| when it is simultaneously in contact with more than one atom." <b>Dms</b> |
| reports the amounts of contact and reentrant surface area, and the combined |
| total surface area on the standard error output (see <a href="#gflag"> |
| <b>-g</b></a>). |
| </p><p> |
| <i>Pdbfile</i> is an input file of coordinates. |
| The input file must be in the Protein Data Bank format. |
| The first part of each atom |
| name is used to determine the element type. By default, implicit hydrogens |
| are included for carbon, nitrogen and oxygen atoms; thus, aromatic carbons |
| and nitrogens will have van der Waals radii that are somewhat too big. |
| Note that only amino acid and nucleic acid residues will be included unless |
| <a href="#aflag"><b>-a</b></a> is also specified. |
| </p> |
|
|
| <h4>COMMAND-LINE ARGUMENTS</h4> |
|
|
| <blockquote> |
| <a name="aflag"> |
| <tt><b>-a</b></tt> |
| </a> |
| <br>Include all atoms, not just those in amino acid and nucleic acid residues. |
| </blockquote> |
|
|
| <blockquote> |
| <tt><b>-d</b> <i>density</i></tt> |
| <br> <i>Density</i> is a factor affecting the density of points |
| on the surface; the default of <b>1.0</b> |
| produces about 5 points per square angstrom. Only values between |
| <b>0.1</b> and <b>10.0</b> are permitted. |
| A density of <b>0.5</b> is recommended for large molecules. |
| </blockquote> |
|
|
| <blockquote> |
| <a name="gflag"> |
| <tt><b>-g</b> <i>logfile</i></tt> |
| </a> |
| <br> Write all the informative messages to <i>logfile</i> instead of the |
| standard error output. Genuine errors still go to the standard error |
| output. New log information is appended to <i>logfile</i> rather than |
| overwriting it, and thus messages from several runs may be accumulated. |
| </blockquote> |
|
|
| <blockquote> |
| <a name="iflag"> |
| <tt><b>-i</b> <i>sitefile</i></tt> |
| </a> |
| <br> Calculate the molecular surface only for those residues and atoms |
| specified in <i>sitefile</i>, |
| keeping the rest of the molecule for collision checks. |
| <i>Sitefile</i> consists of lines such as the following: |
| <blockquote><tt> |
| <table> |
| <tr> |
| <td>ASP</td> <td align="right">205</td> <td>CA</td> |
| </tr><tr> |
| <td>TYR</td> <td align="right">13</td> <td>*</td> |
| </tr><tr> |
| <td>GLY</td> <td align="right">116</td> <td>FRM</td> |
| </tr><tr> |
| <td>HIS</td> <td align="right">178</td> <td>TO</td> |
| </tr> |
| </table> |
| </tt></blockquote> |
| The asterisk, <b>*</b>, means all atoms of the residue, and the |
| "FRM" and "TO" lines mean all residues from 116 to 178 inclusive. |
| The sequence number may |
| contain letters, and if the PDB input file contains chain identifiers, |
| then those should be appended on the right of the sequence number. |
| Residue insertion codes (if any) should be placed between the sequence |
| number and any chain identifier. Residues contained in HETATM records |
| should have an asterisk appended to the end of the residue identifier. |
| The surface generated using <a href="#iflag"><b>-i</b></a> |
| is not always the same as the |
| surface generated by running the entire molecule and afterwards |
| selecting the desired atoms. The first surface will not include |
| reentrant surface lying between an atom in <i>sitefile</i> and atoms not |
| in the file. |
| </blockquote> |
|
|
| <blockquote> |
| <a name="nflag"> |
| <tt><b>-n</b></tt> |
| </a> |
| <br> Include the unit normals to the surface with each surface point record. |
| </blockquote> |
|
|
| <blockquote> |
| <tt><b>-w</b> <i>radius</i></tt> |
| <br> Change the "water" probe <i>radius</i> from the default of <b>1.4</b> |
| angstroms. <i>Radius</i> must be between <b>1.0</b> and <b>201.0</b>. |
| </blockquote> |
|
|
| <blockquote> |
| <tt><b>-v</b></tt> |
| <br> Produce more verbose output. <b>Dms</b> |
| will announce each computation phase |
| as it is entered as well as a count of the atom types in the molecule |
| and the number of computation requests handled by each host that |
| participated in the calculation. |
| </blockquote> |
|
|
| <blockquote> |
| <tt><b>-o</b> <i>outfile</i></tt> |
| <br> The output surface is written to <i>outfile</i>. |
| This flag is not optional. |
| </blockquote> |
|
|
| <p> |
| The output consists of a series of atom and surface point records, with the |
| same format for the first six fields. Each atom is followed by the surface |
| points (if any) which belong to it. These first six fields are in the |
| following format: residue name, sequence number, atom name, x coordinate, |
| y coordinate, z coordinate. For an atom record, the seventh field is "A." |
| For a surface point record, the seventh field begins with an "S," |
| followed by a "C," "R," or "S" according to whether the point is part of |
| contact, reentrant, or saddle surface (saddle is a type of reentrant |
| surface where the probe is in contact with exactly two atoms). This |
| is followed a digit used for depicting different density levels. The |
| eighth field is the molecular surface area associated with the point in |
| square angstroms. If <a href="#nflag"><b>-n</b></a> is specified, the |
| next three fields are |
| the unit normal vector pointing outward from the surface. |
| Messages and errors are written to the standard error output |
| unless a separate log file has been |
| specified with <a href="#gflag"><b>-g</b></a>. |
| </p><p> |
| <b>Dms</b> reads the elements and radii from a file named <b>radii</b>. |
| If there is a file in the current |
| directory called <b>radii</b>, then <b>dms</b> will use that file instead. |
| To add uncommon elements or use different radii, one should copy the |
| default radii file from the distribution and modify it. |
| The file format is documented in the file itself. |
| </p> |
|
|
| <h4>SEE ALSO</h4> |
| <p> |
| <a name="ref"> |
| Richards, F.M.,</a> |
| "Areas, volumes, packing and protein structure," |
| <i>Ann. Rev. Biophys. Bioeng.</i> <b>6</b>, 151-176 (1977). |
| </p> |
|
|
| <h4>AUTHOR</h4> |
| Conrad Huang |
| <br>University of California, San Francisco |
|
|
| <h4>DIAGNOSTICS</h4> |
| Many and varied. Be sure to examine the output messages (standard error |
| or <i>logfile</i>, if specified) before leaving a background job running. |
| </body></html> |
|
|
