On 2005-08-10 (19:48) Nicolas Vervelle wrote:
>Brandon Hespenheide wrote:
>
>>I’ve been looking through the archive for a way around
>>concatenating files (PDB format) in order to utilize the animation
>>command in a jmol script. We have software that can explore
>>conformational motion in proteins. Generally, 10-100 unique
>>conformations can be produced, it depends on the user input. These
>>files are then made available for download and further analysis by
>>the user. I would like to display a movie of the conformational
>>motion, but I do not want to have to create an additional PDB file
>>that is simply a cat’ed version of all the other output files, as
>>this will essentially double the amount of space each run requires.
>>
>>Does anyone know if it is possible with scripting to load each of
>>my conformers sequentially, and then display them as an animation?
>>A results similar to the anim command would be desirable.
>>Otherwise, I think we’ll need to hack something with php and rpc in
>>order to dynamically create and destroy a concatenated file for
>>viewing.
>>
>At the time being, it's not possible to load several files in Jmol
>(no script, no menu, ...). The best option available is loading a
>concatenated file.
>
if you use php and Jmol's loadinline param, you don't need any new files on
your server. something like this should work (untested!):
<?php
$struct = '';
$filelist = array();
// fill the $filelist array with your files
// loop thru each file and add contents to $struct
// uses MODEL-ENDMDL to separate individual files.
foreach ( $filelist as $model => $thisf ) {
$struct .= 'MODEL ' . $model . '\n';
$struct .= file_get_contents( $thisf );
$struct .= 'ENDMDL\n';
}
// append pipe to start of each line of $struct
// (required for loadinline param)
$struct = stripslashes( preg_replace( '/^/m','|', $struct ) );
?>
<applet...>
<param name="loadinline" value="|
<?php echo $struct ?>" />
</applet>
hth,
tim
--
Timothy Driscoll
molvisions - see, grasp, learn.
<http://www.molvisions.com/>
usa:north carolina:raleigh
"Never judge a philosophy by its abuse." - Saint Augustine
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