| version 1.18 | version 1.19 |
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| % | % |
| % $RCSfile: ug_savestate.tex,v $ | % $RCSfile: ug_savestate.tex,v $ |
| % $Author: mbach $ $Locker: $ $State: Exp $ | % $Author: mbach $ $Locker: $ $State: Exp $ |
| % $Revision: 1.18 $ $Date: 2002/10/29 16:00:45 $ | % $Revision: 1.19 $ $Date: 2002/10/31 19:54:35 $ |
| % | % |
| %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% |
| % DESCRIPTION: | % DESCRIPTION: |
| |
| \index{Saved state!Loading} | \index{Saved state!Loading} |
| | |
| \section{Loading and saving in BioCoRE} | \section{Loading and saving in BioCoRE} |
| BioCoRE, (\htmladdnormallink{{\tt http://www.ks.uiuc.edu/Research/biocore/}}{http://www.ks.uiuc.edu/Research/biocore/}), also uses JMV files. When in BioCoRE, you can open a PDB file in the Filesystem with JMV by clicking the ``Properties'' link on the right side of the file's entry. From the window that is displayed, select the ``View this molecule in JMV'' link. This will open the PDB file with JMV. To save a session to BioCoRE, select ``Save session to BioCoRE'' from the ``File'' menu. This will save the session to the Filesystem and to your local filesystem. If you selected the ``Save a JPEG of the JMV image?'' box, then a JPEG file of the molecule window will also be saved to the Filesystem and to your local filesystem. You can view saved JMV files in the same way as PDB files, by selecting the ``Properties'' link, and the ``View this molecule in JMV'' link in the pop-up window that is displayed. | |
| \index{Saved state!in BioCoRE} | \index{Saved state!in BioCoRE} |
| | |
| \section{JMV saved state file format} | \begin{rawhtml} |
| The format of the JMV saved-state file, with extension ``.jmv'', follows an XML-style format. The following tags may be used: | <CENTER> |
| \begin{itemize} | \end{rawhtml} |
| \index{Saved state!File format} | \myfigure{BioCoRE-collage.eps}{JMV in BioCoRE}{fig:ug:BioCoRE} |
| | \begin{rawhtml} |
| \BOLDLISTITEM{$<$JMVSAVEDSTATE$>${\em ...}$<$JMVSAVEDSTATE$>$}These are the tags that enclose the entire saved state file. Each of the following tags will be within these tags. | </CENTER> |
| | \end{rawhtml} |
| \BOLDLISTITEM{$<$BACKGROUND$>${\em red green blue}$<$/BACKGROUND$>$}Here, ``red'', ``green'' and ``blue'' are floats in the range 0-1 that represent the red, green, and blue components of the background color. | BioCoRE, (\htmladdnormallink{{\tt http://www.ks.uiuc.edu/Research/biocore/}}{http://www.ks.uiuc.edu/Research/biocore/}), also uses JMV files. In BioCoRE, you can open a PDB file in the Filesystem with JMV by clicking the ``Properties'' link on the right side of the file's entry. From the window that is displayed, select the ``View this molecule in JMV'' link. This will open the PDB file with JMV. To save a session to BioCoRE, select ``Save session to BioCoRE'' from the ``File'' menu. This will save the session to the Filesystem and to your local filesystem. If you selected the ``Save a JPEG of the JMV image?'' box, then a JPEG file of the molecule window will also be saved to the Filesystem and to your local filesystem. You can view saved JMV files in the same way as PDB files, by selecting the ``Properties'' link, and the ``View this molecule in JMV'' link in the pop-up window that is displayed. |
| | |
| \BOLDLISTITEM{$<$VERSION$>${\em version-number}$<$/VERSION$>$}Here, ``version-number'' is the version of the file format used. | |
| | |
| \BOLDLISTITEM{$<$MOLECULE$>$...$<$/MOLECULE$>$}The MOLECULE tag encloses information for a specific molecule. Please note that JMV can only load one molecule at a time for now. The following items are found within the MOLECULE tags: | |
| | |
| \begin{itemize} | |
| \BOLDLISTITEM{$<$FILENAME$>${\em filename}$<$/FILENAME$>$}Here, ``filename'' is the name of the file to be loaded. | |
| | |
| \BOLDLISTITEM{$<$TRANSFORMATION$>$...$<$/TRANSFORMATION$>$} This gives the transformation matrix for rotating, translating, and scaling the molecule. In between the $<$TRANSFORMATION$>$ and $<$/TRANSFORMATION$>$ tags are 16 floating point numbers that represent the 4 by 4 transformation matrix. | |
| | |
| \BOLDLISTITEM{$<$MOLECULEITEM$>$...$<$/MOLECULEITEM$>$}These tags indicate a group of atoms to be drawn in a certain way. In between the $<$MOLECULEITEM$>$ and $<$/MOLECULEITEM$>$ tags, the following tags are found: | |
| \begin{itemize} | |
| | |
| \pagebreak | |
| \BOLDLISTITEM{$<$REPRESENTATION$>${\em representation}$<$/REPRESENTATION$>$}Here, ``representation'' is the name of a specific representation in which to draw the specified atoms. The possible values are: {\em LINES, VDW, BONDS, CPK, TRACE, TUBE, LICORICE | |
| %%, VRML | |
| }. | |
| | |
| \BOLDLISTITEM{$<$COLORSCHEME$>${\em colorscheme}$<$/COLORSCHEME$>$}Here, ``colorscheme'' is the colorization method for the specified atoms. The possible values are listed below. RESNAME refers to the residue name, and SEGNAME refers to coloring by segment name. The rest of the possible values are the name of the coloring scheme in capital letters. | |
| They are: {\em NAME, INDEX, RESNAME, CHAIN, SEGNAME, STRUCTURE}. | |
| | |
| \BOLDLISTITEM{$<$GRADIENT$>${\em gradient}$<$/GRADIENT$>$}Here, ``gradient'' is the color gradient to be used. The value can be any of the values listed in the following table. The gradient that the value represents is also listed in the table. Please note that color schemes NAME and STRUCTURE use their own color gradients, and will not use the gradient specified here. | |
| | |
| \begin{table*}[htb] | |
| \hspace{.1in} | |
| \begin{tabular}{|l|p{3in}|} \hline | |
| {\em Name} & {\em Description} \\ \hline | |
| RGB & Red$\rightarrow$Green$\rightarrow$Blue\\ \hline | |
| BGR & Blue$\rightarrow$Green$\rightarrow$Red\\ \hline | |
| RWB & Red$\rightarrow$White$\rightarrow$Blue\\ \hline | |
| BWR & Blue$\rightarrow$White$\rightarrow$Red\\ \hline | |
| BW & Black$\rightarrow$White\\ \hline | |
| WB & White$\rightarrow$Black\\ \hline | |
| CUSTOM\_COLOR & If the CUSTOM\_COLOR value is specified, the next 9 tokens \newline are floats in the range 0-1 that represent the RGB colors for the Start, Middle, and End colors. \\ \hline | |
| \end{tabular} | |
| \caption{Color gradients} | |
| \end{table*} | |
| | |
| \BOLDLISTITEM{$<$ATOMLIST$>$...$<$/ATOMLIST$>$}This gives the atom indeces to be drawn. | |
| In between these tags, a series of numbers should appear. These numbers indicate the atom indeces that are to be drawn with the given representation, color scheme, and color gradient. Please note that the atom indeces listed start from zero, so they are actually one less than the corresponding atom id's in the PDB file. | |
| \end{itemize} | |
| \end{itemize} | |
| \end{itemize} | |
| | |
| An example file might look something like this: | |
| \begin{verbatim} | |
| | |
| <?xml version=``1.0'' encoding=``utf-8''?> | |
| | |
| <JMVSAVESTATE> | |
| | |
| <VERSION>1.00</VERSION> | |
| | |
| <BACKGROUND>0.0 0.0 0.0</BACKGROUND> | |
| | |
| <MOLECULE> | |
| | |
| <FILENAME>http://www.ks.uiuc.edu/Research/jmv/demo/proteins/brH.pdb </FILENAME> | |
| | |
| <TRANSFORMATION>1.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 0.0 0.0 1.0 0.0 0.0 | |
| 0.0 0.0 1.0</TRANSFORMATION> | |
| | |
| <MOLECULEITEM> | |
| <REPRESENTATION>LINES</REPRESENTATION> | |
| <COLORSCHEME>RESNAME</COLORSCHEME> | |
| <GRADIENT>CUSTOM_COLOR 1.0 1.0 0.0 0.0 1.0 1.0 1.0 0.0 1.0</GRADIENT> | |
| <ATOMLIST>0 1 2 3 4 5</ATOMLIST> | |
| </MOLECULEITEM> | |
| | |
| <MOLECULEITEM> | |
| <REPRESENTATION>TUBE</REPRESENTATION> | |
| <COLORSCHEME>INDEX</COLORSCHEME> | |
| <GRADIENT>RGB</GRADIENT> | |
| <ATOMLIST>6 7 8 9 10 | |
| 11 12 13 14 15 | |
| </ATOMLIST> | |
| </MOLECULEITEM> | |
| | |
| </MOLECULE> | |
| | |
| </JMVSAVESTATE> | |
| \end{verbatim} | |
| | |
| The first line identifies this file as an XML file. This JMV file was written with the version 2.0 file protocol, and it loads the brH file from the web, and transforms it with the identity matrix. It draws the first five molecules in Lines representation colored by residue name, with a customized gradient, and the next ten molecules in Tube representation, colored by Index, with a Red$\rightarrow$Green$\rightarrow$Blue gradient. By writing files in this way, you can draw different representations of different atoms in the molecule. An atom may be listed more than once, in which case it will be drawn in each representation that it is listed under. If a molecule index is not listed in the file, it will not be drawn. | |