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PubChem Web-based 3D Viewer |
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PubChem provides a viewer for 3-dimensional (3D) conformations of molecules. This enables one to visualize and interact with 3D information available within PubChem. Such information includes computed theoretical descriptions of PubChem Compounds and their neighboring relationships.
The PubChem 3D viewer comes in two forms, an application that can be downloaded and installed and an interactive web-based service. Both viewers provide the means to interact with this information. The usage of the web-based 3D viewer is described here.
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Default View |
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By default, the initial view of a 3D conformer or a conformer alignment consists of a
rocking motion to give a sense of the overall shape of the molecule or molecular similarity.
This default view excludes hydrogen atoms for clarity. For example, the default view of the
conformation of Ampicillin ( CID 6249):
You may go to the PubChem Compound Summary page of this molecule by clicking the label
CID 6249
in the middle of the display window. You may also retrieve the conformer of a different
compound through search function provided at the top right of the page
( ) by
providing a CID of interest into the text box and clicking the button
 .
Through various other task buttons on the page, you have the ability to display different
views of the conformer of interest, launch the PubChem stand-alone 3D Viewer Application (Pc3D), and download
the conformer in different file formats (see details oelow).
The default view of a 3D conformer alignment between Aspirin
(CID 2244)
and 4-Bromo-3-thenoic acid (CID 85546) looks like the one below:
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The compound CID 85546 is one of the 828 conformers that are 3D conformer neighbors to the compound
<CID 2244 with
more than 80% shape similarity (reference OEShape toolkit, see the description on the FTP site) and 50% feature similarity (reference the OEShape toolkit)
after rigid body overlay to a conformer of aspirin, as indicated by
 at the top of the
page. The conformer alignments are sorted by shape similarity first and then the feature
similarity, and listed in the order from the most to least simiar to the reference compound.
By clicking the 4 arrow buttons in the same line, you may navigate each of these similar
conformers:
 will lead to the 1st (most similar) conformer alignment,
 will display the previous conformer alignment,
 will display the next conformer alignment, and the
 will display the last (least similar) conformer alignment.
Clicking the " " button to surface
the Show alignment # of 828, inputting a number to replace the "#" and
clicking the is another way to choose a conformer alignment of interest to display:
The image of the conformer alignment is at the center of the view page, in which the carbon
atoms of the reference conformer
(CID 2244) are
in grey and where the fit conformer
(CID 85546)
is partially transparent and the carbon atoms are green. The links underneath the
label CID 2244
and CID 85546
go to PubChem Compound Summary of these 2 compounds. Clicking the 2D and 3D
tabs below these 2 links will display the 2-dimensional and 3-dimensional structure
thumbnails of these 2 conformers. The task buttons similar to those on the view page of a
3D conformer will help you to display different view of the conformer alignment, launch the
Pc3D helper application on your desktop, or download particular alignment.
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Rotation View |
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Besides the default view of a 3D conformer or a conformer alignment, the web-based 3D viewer
provides means to rotate a 3D conformer or a conformer alignment axially, equatirually and
azimuthally. The start position of a 3D conformer or a conformer aligment in all rotations is
the same as it in its default view. All the rotation operations are integrated into the
rotation icon
(  ), clicking one of the 6
arrows will rotate a 3D conformer or a conformer aligment around a selected axis clockwise or
counter-clockwise. Clicking the star button
(  ) at the center of the
rotation icon will show the default rocking motion of a 3D conformer or a conformer alignment.
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Speed Control |
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The web-based 3D viewer conveys information about a 3D conformer or a conformer alignment by displaying
a series of images to give the appearance of animation. The rate at which these images are displayed may
be altered using the speed control. The speed control for automatic image flipping is listed as a side bar
at the left of the conformer or conformer alignment image. 4 speed options are indicated by
 ,  ,  and
 , from fast to slow till, eventually, stop the image flipping.
The speed option in light grey indicates the current speed.
Clicking one of these options in the speed control is the way to modify the relative speed of image flipping.
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Task Buttons |
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Submission Page |
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Besides following the links on PubChem Compound and Substance summary pages,
you may use our
submission page
to input and view your interesting conformers and their alignments.
The 3 tabs at the top of the submission page allow you to choose to view conformer, conformer alignment, or a saved view:
- To view conformers, you need to provide information on PubChem compounds or substances
by their CIDs or SIDs. For PubChem compounds, you may input CIDs through a list or a file, or retrieve and select a list of ID from Entrez compound history.
Similarly, you may input SIDs to view their conformers.
- To view alignments, you need to provide information on the reference
compound and fit compounds by their CIDs. You should input only one CID as a
referencei, and you may have different options to input fit conformers by searching
similar ones in PubChem Compound Database, providing a CID list or a CID file, and by
retrieving an item from Entrez compound history.
- To upload a saved view file, you need to provide a XML file containing
information on conformers or conformer aligments.
You may find XML data type definiton
(DTD) at http://pubchem.ncbi.nlm.nih.gov/pug/pug.dtd,
or the equivalent XML Schema definiton at http://pubchem.ncbi.nlm.nih.gov/pug/pug.xsd.
Example 1: XML file of 5 CID conformers.
<PCT-View>
<PCT-View_conf>
<PCT-ViewConformer>
<PCT-ViewConformer_id>
<PCT-ConformerId>
<PCT-ConformerId_confid>4294967298<PCT-ConformerId_confid>
<PCT-ConformerId>
<PCT-ConformerId>
<PCT-ConformerId_confid>8589934594<PCT-ConformerId_confid>
<PCT-ConformerId>
<PCT-ConformerId>
<PCT-ConformerId_confid>12884901889<PCT-ConformerId_confid>
<PCT-ConformerId>
<PCT-ConformerId>
<PCT-ConformerId_confid>17179869185<PCT-ConformerId_confid>
<PCT-ConformerId>
<PCT-ConformerId>
<PCT-ConformerId_confid>9637906612225<PCT-ConformerId_confid>
<PCT-ConformerId>
<PCT-ViewConformer_id>
<PCT-ViewConformer_conf-idx>1<PCT-ViewConformer_conf-idx>
<PCT-ViewConformer_img-style>
<PCT-3DImgStyle>
<PCT-3DImgStyle_rotation value="default">0<PCT-3DImgStyle_rotation>
<PCT-3DImgStyle_speed value="normal">2<PCT-3DImgStyle_speed>
<PCT-3DImgStyle_hydrogen value="false"/>
<PCT-3DImgStyle_size>400<PCT-3DImgStyle_size>
<PCT-3DImgStyle>
<PCT-ViewConformer_img-style>
<PCT-ViewConformer>
<PCT-View_conf>
<PCT-View>
Example 2: XML file of alignments between CID 123 and its similar conformers.
<PCT-View>
<PCT-View_algn>
<PCT-ViewConformerAlignment>
<PCT-ViewConformerAlignment_ref>
<PCT-ConformerId>
<PCT-ConformerId_confid>528280977409<PCT-ConformerId_confid>
<PCT-ConformerId>
<PCT-ViewConformerAlignment_ref>
<PCT-ViewConformerAlignment_fit>
<PCT-ConformerId>
<PCT-ConformerId_confid>528280977409<PCT-ConformerId_confid>
<PCT-ConformerId>
<PCT-ConformerId>
<PCT-ConformerId_confid>2147483648001<PCT-ConformerId_confid>
<PCT-ConformerId>
<PCT-ConformerId>
<PCT-ConformerId_confid>81399603173261313<PCT-ConformerId_confid>
<PCT-ConformerId>
<PCT-ConformerId>
<PCT-ConformerId_confid>45965173793488897<PCT-ConformerId_confid>
<PCT-ConformerId>
<PCT-ConformerId>
<PCT-ConformerId_confid>86853198026899457<PCT-ConformerId_confid>
<PCT-ConformerId>
<PCT-ConformerId>
<PCT-ConformerId_confid>854698491905<PCT-ConformerId_confid>
<PCT-ConformerId>
<PCT-ConformerId>
<PCT-ConformerId_confid>2400886718465<PCT-ConformerId_confid>
<PCT-ConformerId>
<PCT-ConformerId>
<PCT-ConformerId_confid>19624547389014017<PCT-ConformerId_confid>
<PCT-ConformerId>
<PCT-ConformerId>
<PCT-ConformerId_confid>43706476262326273<PCT-ConformerId_confid>
<PCT-ConformerId>
<PCT-ConformerId>
<PCT-ConformerId_confid>107415328186695681<PCT-ConformerId_confid>
<PCT-ConformerId>
<PCT-ConformerId>
<PCT-ConformerId_confid>97138506534486017<PCT-ConformerId_confid>
<PCT-ConformerId>
<PCT-ConformerId>
<PCT-ConformerId_confid>84925474970533889<PCT-ConformerId_confid>
<PCT-ConformerId>
<PCT-ConformerId>
<PCT-ConformerId_confid>97719740163686401<PCT-ConformerId_confid>
<PCT-ConformerId>
<PCT-ConformerId>
<PCT-ConformerId_confid>100391162577158145<PCT-ConformerId_confid>
<PCT-ConformerId>
<PCT-ConformerId>
<PCT-ConformerId_confid>94608813746814980<PCT-ConformerId_confid>
<PCT-ConformerId>
<PCT-ConformerId>
<PCT-ConformerId_confid>97719894782509057<PCT-ConformerId_confid>
<PCT-ConformerId>
<PCT-ViewConformerAlignment_fit>
<PCT-ViewConformerAlignment_sort value="shape1feature2">0<PCT-ViewConformerAlignment_sort>
<PCT-ViewConformerAlignment_algn-idx>2<PCT-ViewConformerAlignment_algn-idx>
<PCT-ViewConformerAlignment_img-style>
<PCT-3DImgStyle>
<PCT-3DImgStyle_rotation value="default">0<PCT-3DImgStyle_rotation>
<PCT-3DImgStyle_speed value="normal">2<PCT-3DImgStyle_speed>
<PCT-3DImgStyle_hydrogen value="false"/>
<PCT-3DImgStyle_size>400<PCT-3DImgStyle_size>
<PCT-3DImgStyle>
<PCT-ViewConformerAlignment_img-style>
<PCT-ViewConformerAlignment>
<PCT-View_algn>
<PCT-View>
When a query is ready, clicking the button  will launch the viewer to produce image for that query; clicking the button  will save the query into an XML file for future reference.
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URL-based Interface |
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PubChem web-based 3D viewer can be used directly by formulating an appropriate URL with the necessary input.
The URL consists of a base (see below), being the same as that required to invoke the PubChem web-based 3D conformer viewer with a "?cmd=submit" or a "?cmd=svfile" at the end. There are a series of parameters that may be provided to indicate the structure by CID , and the image control. The parameters are described in more detail below.
Formulating the URL for a display view is rather straightforward. Each parameter may be provided in any order and must have "=" after the parameter name and a "&" character between parameters. All query data input must be properly URL-encoded to enable proper interpretation.
- Base URL for image display:
http://pubchem.ncbi.nlm.nih.gov/vw3d/vw3d.cgi?cmd=submit
- URL parameters for image display:
- Structure data: is indicated by keyword "cid" or "sid"
- Image control:
- Choose a conformer alignement: (hit_cnf=#)
- Rotation view(axis):
- Rotate counter-clockwise axially: axis=y
- Rotate clockwise axially: axis=-y
- Rotate counter-clockwise equatorially: axis=x
- Rotate clockwise equatorially: axis=-x
- Rotate counter-clockwise azimuthally: axis=z
- Rotate clockwise azimuthally: axis=-z
- Speed selection (spd):
- Flip image per 0.2 second: spd=200
- Flip image per 0.6 second: spd=600
- Flip image per 1.0 second: spd=1000
- Stop image flipping: spd=0
- Hydrogen(atm):
- Display hydrogen atoms: atm=-80
- Remove hydrogen atoms: atm=%2b80 (atm=+80)
- Image Size(size):
- Choose an image size of (# pixel)*(# pixel): size=# (# should be betwee 100 to 1000 for images with high quality)
- Enlarge image: size=inc, the image size is increased by 100 unit
- Shrink image: size=dec, the image size is decrease by 100 unit
- Base URL for view in Pc3D and file download:
http://pubchem.ncbi.nlm.nih.gov/vw3d/vw3d.cgi?cmd=svfile
- URL parameters for view in Pc3D and file download: (opt)
- Launch Pc3D and display view in it: opt=live3d
- download Asn.1 text file: opt=asnt
- download Asn.1 binary file: opt=asnb
- download XML file: opt=xml
- download SD file: opt=sdf
Examples:
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