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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 experimental 3D coordinate sets provided by PubChem data depositors (via deposited PubChem Substances). It also 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
at the left top of the display window followed by its 2D thumbnail. Below them are buttons to fulfill various tasks.
At the middle of the display window, information on currently shown comformer and the total number of conformer of a compound, together with the navigation buttons to reach each conformer sequentially is provided:
A default conformer of a compound is the conformer with the minimal calculated energy. Conformers of a compound are sorted by their shape similarities and listed in the order from the most to least diverse on shape to the default conformer.
 leads to the first conformer of the compound in a displayed order;  displays the previous one;  displays the next one, and the  displays the last conformer. By default, the conformers of a compound are in the ascending order of their energies. Conformers can also be displayed in the order of the diversity of their geometry to the default conformer of theClicking the " " button to surface the Show conformer # of 30, inputting a number to replace the "#" and clicking the  is another way to choose a conformer of interest to display:
Below is the view of the 3rd conformer of CID 6246 in the order of the most diverse conformer:
The current conformer are displayed at the center of the page. At the lower left corner, a superposition of the current conformer against the default one is provided. In both images, the carbon atoms of the current conformer are in gray and while in the thumbnail, the carbon atoms of the default conformer are in green. Clicking this thumbmail will lead to the detailed view of this superposition.
The conformers of multiple compounds can be requested to view in a single query. Here is an example of the conformer view of such a query which consists of CID 2244, 666 and 123:
The combination of 2 navigation groups allows each conformer of each compound to be reachable conveniently. First, the compound navigation assisits to find the compound of interest by clicking the 4 arrow buttons in the same line or input a number to replace the "#" in the text box in the line of Show compound:
Then using the conformer nagivation as described previously, a conformer of interest can be viewed.
The conformers of a different compound may also be retrieved through the search function provided at the top right of the page:
by providing a compound ID of interest in one of the 3 formats 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 superposition between Aspirin
(CID 2244)
and 2-(1-chloropropyl)benzoic acid(CID 21691644) looks like the one below:
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The compound CID 21691644 is one of the 1593 unique compounds that are structural similar 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 (LID 1) of aspirin, as indicated by
at the top of the page. The conformer superpositions 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 conformer.
By clicking the 4 arrow buttons in the same line, you may navigate each of these similar conformers in a similar way as being introduced before. Clicking the ""
button to float up the alternative to choose a conformer superposition of interest to disaply, as well as the various options for sorting:
The image of the conformer superposition 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 21691644)
is partially transparent and the carbon atoms are green. The links underneath the
label CID 2244, LID 1
and CID 21691644, LID 1
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 superposition, or a saved view:
- To view conformers, you need to provide information on PubChem compounds or substances
by their CIDs, SIDs, or on particular conformers by their conformer IDs.
A conformer ID is 64-bit hex code to represent a conformer:
 .
The high 32-bit of such an Id represents the corresponding CID or SID. For a conformer of a CID, the lowerest 16-bit of its conformer ID represents a local identification (LID) of this conformer. Simply, a conformer ID of a CID's conformer may also be represented in the format of "CID.LID". For e.g., "2244.1" refers to the conformer of CID 2244 whose LID is 1. PubChem accpets these 2 formats when a CID's conformer is refered.
To present a SID's conformer, the high 16-bit in the lowerest 32-bit of a conformer ID is used for the version of the SID, and the lowerest 16-bit is for a LID of the conformer. Such a 64-bit hex code is the unique way for PubChem to refer to a SID's conformer.
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.
You may choose to display all the conformers of a compound by selecting the "All" from the pull-down menu in the line of "Options" below the CID input session:
If you choose "First" from the above menu, and input a count N to replace the "#" in the textbox as seen below, then the first N conforemers that are most diverse on shape from the default conformer will be displayed:
Similarly, you may input SIDs to view their conformers:
You may also input conformer IDs in the conformer ID input session to view conformers of PubChem compounds or substances:
- To view conformer superposition, you need to provide information on a reference compound and fit compounds by their CIDs; or on the reference and fit conformers by their conformer IDs. You should input only one CID or conformer ID as a
reference, and you may have different options to input fit conformers by searching
similar ones in PubChem Compound Database, providing a CID or conformer ID list or a file, and by retrieving an item from Entrez compound history:
However when a reference, represented by a conformer Id, is a conformer of SID, there is no way to search the PubChem Compound to get its similar conformers, becaue such data is unavailable now.
You may also request to view the superpositions of conformer pairs of interest by proving the pairwise conformers in the conformer pair input session:
Input each pair per line, and separate each element in a pair by a space. When a CID pair is provided, the default conformers of both CIDs will be used to make the superposition.
- 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 conformers of CID 2244.
<PCT-View>
<PCT-View_conf>
<PCT-ViewConformer>
<PCT-ViewConformer_id>
<PCT-QueryUids>
<PCT-QueryUids_conformer-ids>
<PCT-QueryUids_conformer-ids_E>8c400000001</PCT-QueryUids_conformer-ids_E>
<PCT-QueryUids_conformer-ids_E>8c40000000b</PCT-QueryUids_conformer-ids_E>
<PCT-QueryUids_conformer-ids_E>8c40000000a</PCT-QueryUids_conformer-ids_E>
<PCT-QueryUids_conformer-ids_E>8c400000003</PCT-QueryUids_conformer-ids_E>
<PCT-QueryUids_conformer-ids_E>8c40000000f</PCT-QueryUids_conformer-ids_E>
</PCT-QueryUids_conformer-ids>
</PCT-QueryUids>
<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_optimization value="shape-based">0</PCT-ViewConformerAlignment_optimization>
<PCT-ViewConformerAlignment_sort value="input-order">0</PCT-ViewConformerAlignment_sort>
<PCT-ViewConformerAlignment_algn>
<PCT-ViewConformerAlignment_algn_ref-fits>
<PCT-RefFitSuperposition>
<PCT-RefFitSuperposition_ref-idx>0</PCT-RefFitSuperposition_ref-idx>
<PCT-RefFitSuperposition_fit-idx>9</PCT-RefFitSuperposition_fit-idx>
<PCT-RefFitSuperposition_confpair-idx>0</PCT-RefFitSuperposition_confpair-idx>
<PCT-RefFitSuperposition_algn-idx>9</PCT-RefFitSuperposition_algn-idx>
</PCT-RefFitSuperposition>
</PCT-ViewConformerAlignment_algn_ref-fits>
<PCT-ViewConformerAlignment_algn>
<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_matrix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iewConformerAlignment_matrix>
<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:
- 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=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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