General concerns

Setting the parameters

Dealing with output results

Q: How to cite the server?

- When using the images generated by POLYVIEW-3D, it is highly recommended to cite also the respective program (PyMol or RasMol) used for the rendering of a protein structure.

Q: How to cross-link the server?

- First of all, never bookmark or post at your web-site a hyperlink to the resulting page with the image, as POLYVIEW-2D does not contain necessary information in the address line of the browser to retrieve the same page, whereas POLYVIEW-3D automatically deletes generated files after two weeks.

- For simple link to the submission form with PDB ID as a parameter, include the following hyperlink into your electronic document:

<a href="http://polyview.cchmc.org?PDBName=XXXX">POLYVIEW</a>
or
<a href="http://polyview.cchmc.org/polyview3d.html?PDBName=XXXX">POLYVIEW-3D</a>

for POLYVIEW and POLYVIEW-3D, respectively. XXXX is a PDB ID represented by a 4-letter code. Example of this cross-link can be found in the PDBwiki pages.

- For advanced link with specific requirements, especially when requesting the visualization of custom coordinate files in the PDB format, contact the developers of the server in order to set up an automated way for data exchange. Example of this cross-link can be found in the MolMovDB resulting pages.

- To have POLYVIEW handy on your own web-page, you can use the following code to include the POLYVIEW widget:

<script type="text/javascript">
  <!-- width of the widget (px or %) -->
  var pw_width = '200px';
  <!-- background color of widget header -->
  var pw_color_header = '#404040';
  <!-- background color of widget body -->
  var pw_color_body = '#808080';
  <!-- delay between examples (seconds), 0=hide examples, -1=no examples -->
  var pw_time_period = 15;
</script>
<script type="text/javascript" src="http://polyview.cchmc.org/pwidget.js"></script>

Q: Is stand-alone version of POLYVIEW-3D available?

POLYVIEW-3D is a set of perl scripts combining the rendering programs with the protein structure analysis tools and databases. In order to work locally, please use the respective software and databases freely available for download from their home sites.

Q: How is the privacy of requests and results maintained?

- For the servers usage statistics, we keep track of the user`s ip address, type of request and time of submission. These data are logged in addition to the standard access log generated by Apache.

- When submitted a protein not deposited to PDB, its structure is kept at our local drive for two weeks only. It is used to generate images and obtain structural annotations during this period without asking the user to re-submit the structure upon each next request.

- All temporary files including submitted protein structures, calculations, images, and other results to be retrieved to user are stored in the directories directly inaccessible from internet and can only be retrieved using CGI-scripts by following the links provided personally to user. File names comprise of two parts and formed by using the time function combined with random number generator yielding unique and big numbers of different digit length. Thus, files can not be scanned by internet crawlers, neither file names can be guessed by the simple number enumeration. After two weeks since initial request, all related files are automatically deleted from the disk.

- E-mail addresses, if optionally specified for the POLYVIEW-3D requests, are used solely for sending the links to user in order to retrieve results when they are ready.

- Developers of the POLYVIEW server reserve the right to periodically look through generated results and images randomly chosen among available in order to check the proper server functioning and to detect the possible bugs in the server-related software.

Q: Why is the status of my request shown as "waiting in the queue" for long time?

All our servers run on the cluster of more than 100 compute nodes. However, as these services are free, they do not have any separate queue or high priority while sharing computational resources with local users. Occasionally, cluster is full of requests from both local and internet users. Just be patient, or specify your email address to receive a notice once your request has been processed.

Q: PyMol (or RasMol) provides the option that I can't find at the POLYVIEW-3D request form. What should I do?

POLYVIEW-3D never was conceived as a complete web-interface to any of the protein structure rendering programs used in it. Instead, it is focused on combining the easy access to high quality and animated images with the automated protein structure and function annotations. For advanced rendering and more custom images, please consider using the stand-alone versions of respective rendering software. However, scripts provided along with images generated by POLYVIEW-3D can serve as a starting point in practical learning the command syntax of PyMol or RasMol.

Q: How can I get bigger images than those available from options?

We restricted the maximal image size to 1000x1000 pixels in order to avoid creating the huge files when animations requested. However, one still can get bigger static images (2000x2000 pixels) by requesting the animations and checking the HD slides checkbox at the Animation Settings field set.

Q: When I request an animation from POLYVIEW-3D, I see some static slides of the fixed size below the animation. Why?

Along with animated image of requested size, we provide the user with all slides of maximal size (1000x1000 pixels) that were used during the preparation of animation. So one can download the high-quality static image of the desired protein structure projection in PNG or TIFF format, with 300 DPI resolution in latter case, to be used for publication.

Q: Why is the image no longer animated, when I copy and paste an animation from POLYVIEW-3D to PowerPoint?

When in the slide designing mode, PowerPoint shows all animations as static images. Just start your presentation, and the corresponding images will be shown animated.

Q: I submitted a request to POLYVIEW-3D but obtained a blank image. What is wrong?

- First, make sure that you requested at least one protein chain to be rendered, as some combinations of options can make all chains become hidden.

- Second and most typical case, the requested protein is represented by low resolution model or crystal structure, i.e. alpha-carbons are available only. Default rendering option, Cartoon, fails to generate any image of such a structure. Try to change the chain rendering to the CPK spacefill or Surface options. See example below.

Changing the rendering options for low resolution protein structure (PDB code 2lzh)
Rendering with default Cartoon option	Rendering with CPK spacefill option	Rendering with Surface option

Q: I requested a protein structure to be rendered with transparent surface. Why did the color of the chain change to the darker tint?

It is a part of PyMol rendering. When transparency requested along with black or, in general, dark background, all colors used for surface renderings become shaded. To avoid this effect, change the background of the image to white or other light color. See example below.

Changing the image background to keep the original colors of protein structure rendered with transparent elements (PDB code 1mba)
Rendering with default Black background	Rendering with White background