Learn to Use DSV

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Visualizing FTMap and SiteMap output from an ensemble of structures on a single representative structure using DSV Visualize or VisualizeRef

Visualizing FTMap output from an ensemble of structures on a single representative structure using DSV VisFT or VisFTRef

Visualizing SiteMap output from an ensemble of structures on a single representative structure using DSV VisST or VisSTRef

Determine which receptor residues from an ensemble of structures are near FTMap sites and display them on a representative receptor using DSV SelResFT or SelResFTRef

Determine which receptor residues from an ensembleof structures are near SiteMap sites and display them on a representative receptor using DSV SelResST or SelResSTRef

Determine which receptor residues from an ensemble of structures are near both FTMap CSs and SiteMap sites and display them on a representative receptor using DSV SelResFTST or SelResFTSTRef

Visualizing FTMap and SiteMap output from an ensemble of structures on a single representative structure using DSV Visualize or VisualizeRef

This tutorial assumes that you have already generated an ensemble of receptor structures and are familiar with Visual Molecular Dynamics (VMD), FTMap, and/or SiteMap. In the example case I have five structures of LSD1/CoREST (PDB 2V1D) that were extracted from molecular dynamics simulation. An RMSD-based conformational clustering algorithm was used to cluster structures and from each cluster a representative member was extracted, referred to as the centroid. FTMap and SiteMap prediction tools were also run on each centroid and the output from each algorithm was saved in pdb file format. Please see our paper under the Reference DSV tab for experimental details and for citation information. Note that the procedure followed below is for tutorial purposes and the procedure followed in the paper differed slightly.

In this tutorial there are a total of ten output files, five from FTMap and five from SiteMap. The output files are named ftmap-1.pdb, ftmap-2.pdb etc. and sitemap-1.pdb, sitemap-2.pdb etc. There is also the reference x-ray structure file 2V1D.pdb. You can download all of the structure files here.

Let's begin.

I have the 10 output pdb files and 2V1D.pdb in my working directory.

Open VMD and then the TkConsole.

In the Tk Console type then enter: source DSV.tcl

We'll be using the DSV Visualize proc with six arguments. The six arguments are: FTstart (the number of the first FTMap output file), FTend (the number of the last FTMap output file), FTfileformat (the name of the FTMap output files not including the number), STstart (the number of the first SiteMap output file), STend (the number of the last SiteMap output file), and STfileformat (the name of the SiteMap output files not including the number).

The command to enter in the Tk Console is: Visualize 1 5 ftmap-%d.pdb 1 5 sitemap-%d.pdb

A number of things happen after entering the Visualize command. First, in the Main window all of the files are loaded. You'll notice that ftmap-1.pdb is loaded twice. This is because the first ftmap-1.pdb (mol 0) was loaded as a reference and the remaining structures were aligned to this structure. In addition, the reference structure (mol 0) appeared in the Display window as a 'ghost' surface representation of the protein components. The remaining files display the FTMap and SiteMap sites. The Main window should look like this:

Things were happening in the Tk Console as well. The reference structure was loaded and as the other stuctures loaded they were aligned to the reference structure and the RMSD was calculated. The RMSD values were reported in the Tk Console. Two RMSD values were reported for each alignement: the RMSD prior to alignment and the RMSD after alignment. There is some repetitive information here since the receptor structure in ftmap-1.pdb and sitemap-1.pdb are identical, so for example, the RMSDs reported for these molecules are identical. The alignment parameters can be edited in the DSV.tcl file and are set to 'type CA and residue 5 to 200' for no particular reason. The Tk Console should look similar to this:

Most important for visualizing the results was the appearance in the VMD Display window of the reference receptor structure (mol 0/ftmap-1.pdb) with the FTMap CSs represented as spheres and the SiteMap sites represented as surfaces. The spheres and surfaces were colored to match the centroid they originated from. The FTMap CSs and SiteMap sites from ftmap-1.pdb and sitemap-1.pdb were colored red and the CSs and sites from ftmap-5.pdb and sitemap-5.pdb were colored blue; the ones in between were colored on a spectrum from red-to-green-to-blue. The FTMap CSs were sized according to their rank as determined in the FTMap calculation. I decided to show the top three FTMap CSs from each centroid as spheres so the largest sphere is the top-ranked and smallest is third-ranked. The option to show different numbers of CSs can be changed in DSV.tcl. The SiteMap sites were merged when exported from Schrodinger's Maestro and the ranking information was not retained so the SiteMap sites were not sized according to rank but according to the area and density of the site. The iValue can be changed in DSV.tcl to change how 'thick' the SiteMap surfaces are. The Display window should look like this:

That's it for DSV Visualize!

Let's switch gears just a little and look at DSV VisualizeRef. With DSV VisuzlizeRef we can align the FTMap and SiteMap output files to a specified reference receptor such as 2V1D.pdb rather than the first centroid (ftmap-1.pdb above). This works very similarly to the above example except in the Tk Console we type: VisualizeRef 1 5 ftmap-%d.pdb 1 5 sitemap-%d.pdb 2V1D.pdb

Now we notice that RMSD values have changed and we can visualize our results on the x-ray structure rather than the first centroid. The Tk Console is shown below:

Thanks and if you have questions please feel free to contact us. Also, please inspect the DSV.tcl file to see comments in the script, which should help you customize DSV for use on your system.

Visualizing FTMap output from an ensemble of structures on a single representative structure using DSV VisFT or VisFTRef

Note: If you have already performed the above tutorial (Visualizing FTMap and SiteMap output from an ensemble of structures on a single representative structure using DSV Visualize or VisualizeRef) then all you need to know is the command for VisFT or VisFTRef. If you haven't performed the previous tutorial then continue with the next paragrah. The commands are: VisFT 1 5 ftmap-%d.pdb -or- VisFTRef 1 5 ftmap-%d.pdb 2V1D.pdb

VisFT and VisFTRef are for occasions when you have FTMap output be not SiteMap output. There is also VisST and VisSTRef for times when you have SiteMap output but not FTMap output. This tutorial assumes that you have already generated an ensemble of receptor structures and are familiar with Visual Molecular Dynamics (VMD) and FTMap. In the example case I have five structures of LSD1/CoREST (PDB 2V1D) that were extracted from molecular dynamics simulation. An RMSD-based conformational clustering algorithm was used to cluster structures and from each cluster a representative member was extracted, referred to as the centroid. FTMap prediction tool was also run on each centroid and the output from the algorithm was saved in pdb file format. Please see our paper under the Reference DSV tab for experimental details and for citation information. Note that the procedure followed below is for tutorial purposes and the procedure followed in the paper differed slightly.

In this tutorial there are a total of five output files from FTMap. The output files are named ftmap-1.pdb, ftmap-2.pdb etc. There is also the reference pdb 2V1D.pdb. You can download all of the structure files here.

Let's begin.

I have the six pdb files and the DSV.tcl file in my working directory.

Open VMD and then the Tk Console.

In the Tk Console type then enter: source DSV.tcl

We'll be using the DSV VisFT proc with three arguments. The three arguments are: FTstart (the number of the first FTMap output file), FTend (the number of the last FTMap output file), and FTfileformat (the name of the FTMap output files, not including the number).

The command to enter in the Tk Console is: VisFT 1 5 ftmap-%d.pdb

A number of things happen as a result of typing in the command. First, in the Main window all of the files are loaded. You'll notice that ftamp-1.pdb is loaded twice. This is because the first ftmap-1.pdb (mol 0) was loaded as a reference and the remaining structures were aligned to this structure. In addition, the reference (mol 0) will appear in the Display window as a 'ghost' surface representation.

Things were happening in the Tk Console as well. The reference structure was loaded and as the other structures were aligned to it the RMSD to the reference structure was calculated and all of those valued printed in the Tk Console. Two RMSD values were reported: the RMSD prior to alignment and the RMSD after alignment. The alignment parameters can be edited in the DSV.tcl file and are set to 'type CA and residue 5 to 200' for no particular reason.

Most important for visualizing the results was the appearance in the VMD Display window of the referece receptor structure (mol 0) with the FTMap CSs represented as spheres. The spheres were colored to match the centroid they originated from. The FTMap CSs from ftmap-1.pdb were colored red and the CSs from ftmap-5.pdb were colored blue, the ones in between were colored on a spectrum from red-to-green-to-blue. The FTMap CSs were sized according to their rank as determined in the FTMap calculation. Here, I decided to show the top three FTMap CSs from each centroid as spheres so the largest sphere is top-ranked and the smallest is third-ranked. The option to show different numbers of CSs can be changed in the DSV.tcl.

With DSV VisFTRef we can align FTMap pdbs to a specified reference receptor such as 2V1D rather than the first centroid (ftmap-1.pdb). This works very similarly to the above example except in the Tk Console we type: VisFTRef 1 5 ftmap-%d.pdb 2V1D.pdb

Visualizing SiteMap output from an ensemble of structures on a single representative structure using DSV VisST or VisSTRef

Note: If you have already performed any of the above tutorials then all you need to know is the command for VisST or VisSTRef. If you haven't performed the previous tutorial then continue with the next paragrah. The commands are: VisST 1 5 sitemap-%d.pdb -or- VisSTRef 1 5 sitemap-%d.pdb 2V1D.pdb

VisST and VisSTRef are for occasions when you have SiteMap output but not FTMap output. There is alos VisFT and VisFTRef for times when you have FTMap output be not SiteMap output. This tutorial assumes that you have already generated an ensemble of receptor structures and are familiar with Visual Molecular Dynamics (VMD) and SiteMap. In the example case I have five structures of LSD1/CoREST (PDB 2V1D) that were extracted from molecular dynamics simulation. An RMSD-based conformational clustering algorithm was used to cluster structures and from each cluster a representative member was extracted, referred to as the centroid. SiteMap prediction tool was also run on each centroid and the output from the algorithm was saved in pdb file format. Please see our paper under the Reference DSV tab for experimental details and for citation information. Note that the procedure followed below is for tutorial purposes and the procedure followed in the paper differed slightly.

In this tutorial there are a total of five output files from SiteMap. The output files are named sitemap-1.pdb, sitemap-2.pdb etc. There is also the reference pdb 2V1D.pdb. You can download all of the structure files here.

Let's begin.

I have the six files and the DSV.tcl file in my working directory.

Open VMD and the the Tk Console.

In the Tk Console type then enter: source DSV.tcl

We'll be using the DSV VisST proc with three arguments. The three arguments are: STstart (the number of the first SiteMap output file), STend (the number of the last SiteMap file), and STfileformat (the name of the SiteMap output files, not including the number).

The command to enter into the Tk Console is: VisSt 1 5 sitemap-%d.pdb

A number of things happen as a result of typing this command. First, in the Main window all of the files are loaded. You'll notice that sitemap-1.pdb is loaded twice. This is because the first sitemap-1.pdb (mol 0) was loaded as a reference and the remaining structures were aligned to this structure. In addition, the reference structure (mol 0) will appear in the Display window as a 'ghost' surface representation.

Things were happening in the Tk Console as well. The reference structure was loaded and as the other structures were aligned to it the RMSD to the reference structure was calculated and all of those valued printed in the Tk Console. Two RMSD values were reported: the RMSD prior to alignment and the RMSD after alignment. The alignment parameters can be edited in the DSV.tcl file and are set to 'type CA and residue 5 to 200' for no particular reason.

Most important for visualizing the results was the appearance in the VMD Display window of the reference receptor structure (mol 0) with the SiteMap sites represented as surfaces. The surfaces were colored to match the centroid they originated from. The SiteMap sites from sitemap-1.pdb were colored red and the sites from sitemap-5.pdb were colored blue, the ones in between were colored on a spectrum from red-to-green-to-blue. The SiteMap sites were merged when exported from Schrodinger's Maestro and the ranking information was not retained so the SiteMap sites were not sized according to rank (like the FTMap CS spheres) but according to the area and density of the site. The iValue can be changed in DSV.tcl to display how 'thick' the SiteMap surfaces are.

With DSV VisSTRef we can align the SiteMap pdbs to a specified receptor such as 2V1D rather than the first centroid (sitemap-1.pdb). This works very similarly to the above except in the Tk Console we type: VisSTRef 1 5 sitemap-%d.pdb 2V1D.pdb

Determine which receptor residues from an ensemble of structures are near FTMap sites and display them on a representative receptor using DSV SelResFT or SelResFTRef

Note: If you have already performed any of the above tutorials then all you need to know is the command for SelResFT or SelResFTRef. If you haven't performed the previous tutorial then continue with the next paragrah. The commands are: SelResFT 1 5 ftmap-%d.pdb -or- SelResFTRef 1 5 ftmap-%d.pdb 2V1D.pdb

SelResFT and SelResFTRef are used to determine the residues that fall within a specified distance of FTMap CSs on an ensemble of structures and displays the residues on a representative receptor structure. This tutorial assumes that you have already generated an ensemble of receptor structures and are familiar with Visual Molecular Dynamics (VMD) and FTMap. In the example case I have five structures of LSD1/CoREST (PDB 2V1D) that were extracted from molecular dynamics simulation. An RMSD-based conformational clustering algorithm was used to cluster structures and from each cluster a representative member was extracted, referred to as the centroid. FTMap prediction tool was also run on each centroid and the output from the algorithm was saved in pdb file format. Please see our paper under the Reference DSV tab for experimental details and for citation information. Note that the procedure followed below is for tutorial purposes and the procedure followed in the paper differed slightly.

In this tutorial there are a total of five output files from FTMap. The output files are named ftmap-1.pdb, ftmap-2.pdb etc. There is also the reference pdb 2V1D.pdb. You can download all of the structure files here

Let's begin.

I have the six files and the DSV.tcl file in my working directory.

Open VMD and the the Tk Console.

In the Tk Console type then enter: source DSV.tcl

We'll be using the DSV SelResFT proc with three arguments. The three arguments are: FTstart (the number of the first FTMap output file), FTend (the number of the last FTMap file), and FTfileformat (the name of the FTMap output files, not including the number).

The command to enter into the Tk Console is: SelResFT 1 5 ftmap-%d.pdb

A number of things happen as a result of typing this command. First, in the Main window all of the files are loaded. You'll notice that ftmap-1.pdb is loaded twice. This is because the first ftmap-1.pdb (mol 0) was loaded as a reference and the remaining structures were aligned to this structure. In addition, the reference structure (mol 0) will appear in the Display window as a 'NewCartoon' and as a 'ghost' surface representation.

Things were happening in the Tk Console as well. The reference structure was loaded and as the other strucutres were aligned to it the RMSD to the reference structure was calculated and all of those valued printed in the Tk Console. Two RMSD values were reported: the RMSD prior to alignment and the RMSD after alignment. The alignment parameters can be edited in the DSV.tcl file and are set to 'type CA and residue 5 to 200' for no particular reason.

Most important for visualizing the results was the appearance in the VMD Display window of the reference receptor structure (mol 0) with the residues near (3.0 Angstrom in this tutorial, the distance can be edited in DSV.tcl) FTMap CSs displayed as 'licorice' representations. All residues within 3.0 Angstrom of any FTMap CSs from any of the five output files was displayed on the reference receptor, ftmap-1.pdb in this case.

With DSV SelResFTRef we can display the residues near FTMap CSs on a specified receptor such as 2V1D rather than the first centroid (ftmap-1.pdb). This works very similarly to the above except in the Tk Console we type: SelResFTRef 1 5 ftmap-%d.pdb 2V1D.pdb

Determine which receptor residues from an ensemble of structures are near SiteMap sites and display them on a representative receptor using DSV SelResST or SelResSTRef

Note: If you have already performed any of the above tutorials then all you need to know is the command for SelResST or SelResSTRef. If you haven't performed the previous tutorial then continue with the next paragrah. The commands are: SelResST 1 5 sitemap-%d.pdb -or- SelResSTRef 1 5 sitemap-%d.pdb 2V1D.pdb

SelResST and SelResSTRef are used to determine the residues that fall within a specified distance of SiteMap sites on an ensemble of structures and displays the residues on a representative receptor structure. This tutorial assumes that you have already generated an ensemble of receptor structures and are familiar with Visual Molecular Dynamics (VMD) and SiteMap. In the example case I have five structures of LSD1/CoREST (PDB 2V1D) that were extracted from molecular dynamics simulation. An RMSD-based conformational clustering algorithm was used to cluster structures and from each cluster a representative member was extracted, referred to as the centroid. SiteMap prediction tool was also run on each centroid and the output from the algorithm was saved in pdb file format. Please see our paper under the Reference DSV tab for experimental details and for citation information. Note that the procedure followed below is for tutorial purposes and the procedure followed in the paper differed slightly.

In this tutorial there are a total of five output files from SiteMap. The output files are named sitemap-1.pdb, sitemap-2.pdb etc. There is also the reference pdb 2V1D.pdb. You can download all of the structure files here

Let's begin.

I have the six files and the DSV.tcl file in my working directory.

Open VMD and the the Tk Console.

In the Tk Console type then enter: source DSV.tcl

We'll be using the DSV SelResST proc with three arguments. The three arguments are: STstart (the number of the first SiteMap output file), STend (the number of the last SiteMap file), and STfileformat (the name of the SiteMap output files, not including the number).

The command to enter into the Tk Console is: SelResST 1 5 sitemap-%d.pdb

A number of things happen as a result of typing this command. First, in the Main window all of the files are loaded. You'll notice that sitemap-1.pdb is loaded twice. This is because the first sitemap-1.pdb (mol 0) was loaded as a reference and the remaining structures were aligned to this structure. In addition, the reference structure (mol 0) will appear in the Display window as a 'NewCartoon' and as a 'ghost' surface representation.

Things were happening in the Tk Console as well. The reference structure was loaded and as the other strucutres were aligned to it the RMSD to the reference structure was calculated and all of those valued printed in the Tk Console. Two RMSD values were reported: the RMSD prior to alignment and the RMSD after alignment. The alignment parameters can be edited in the DSV.tcl file and are set to 'type CA and residue 5 to 200' for no particular reason.

Most important for visualizing the results was the appearance in the VMD Display window of the reference receptor structure (mol 0) with the residues near (3.0 Angstrom in this tutorial, the distance can be edited in DSV.tcl) SiteMap sites displayed as 'licorice' representations. All residues within 3.0 Angstrom of any SiteMap sites from any of the five output files was displayed on the reference receptor, sitemap-1.pdb in this case.

With DSV SelResSTRef we can display the residues near SiteMap sites on a specified receptor such as 2V1D rather than the first centroid (sitemap-1.pdb). This works very similarly to the above except in the Tk Console we type: SelResSTRef 1 5 sitemap-%d.pdb 2V1D.pdb

Determine which receptor residues from an ensemble of structures are near both FTMap CSs and SiteMap sites and display them on a representative receptor using DSV SelResFTST or SelResFTSTRef

Note: If you have already performed any of the above tutorials then all you need to know is the command for SelResFTST or SelResFTSTRef. If you haven't performed the previous tutorial then continue with the next paragrah. The commands are: SelResFTST 1 5 ftmap-%d.pdb 1 5 sitemap-%d.pdb -or- SelResFTSTRef 1 5 ftmap-%d.pdb 1 5 sitemap-%d.pdb 2V1D.pdb

SelResFTST and SelResFTSTRef are used to determine the residues that fall within a specified distance of both FTMap CSs and SiteMap sites on an ensemble of structures and displays the residues on a representative receptor structure. Only residues that are near both FTMap and SiteMap sites will be displayed. This tutorial assumes that you have already generated an ensemble of receptor structures and are familiar with Visual Molecular Dynamics (VMD), FTMap, and SiteMap. In the example case I have five structures of LSD1/CoREST (PDB 2V1D) that were extracted from molecular dynamics simulation. An RMSD-based conformational clustering algorithm was used to cluster structures and from each cluster a representative member was extracted, referred to as the centroid. FTMap and SiteMap prediction tools were also run on each centroid and the output from the algorithms was saved in pdb file format. Please see our paper under the Reference DSV tab for experimental details and for citation information. Note that the procedure followed below is for tutorial purposes and the procedure followed in the paper differed slightly.

In this tutorial there are a total of five output files from FTMap and five from SiteMap. The output files are named ftmap-1.pdb, ftmap-2.pdb etc. and sitemap-1.pdb, sitemap-2.pdb etc. There is also the reference pdb 2V1D.pdb. You can download all of the structure files here

Let's begin.

I have the ten output files and the DSV.tcl file in my working directory.

Open VMD and the the Tk Console.

In the Tk Console type then enter: source DSV.tcl

We'll be using the DSV SelResFTST proc with six arguments. The six arguments are: FTstart (the number of the first FTMap output file), FTend (the number of the last FTMap output file), FTfileformat (the name of the FTMap output files not including the number), STstart (the number of the first SiteMap output file), STend (the number of the last SiteMap file), and STfileformat (the name of the SiteMap output files, not including the number).

The command to enter into the Tk Console is: SelResFTST 1 5 ftmap-%d.pdb 1 5 sitemap-%d.pdb

A number of things happen as a result of typing this command. First, in the Main window all of the files are loaded. You'll notice that ftmap-1.pdb is loaded twice. This is because the first ftmap-1.pdb (mol 0) was loaded as a reference and the remaining structures were aligned to this structure. In addition, the reference structure (mol 0) will appear in the Display window as a 'NewCartoon' and as a 'ghost' surface representation.

Things were happening in the Tk Console as well. The reference structure was loaded and as the other strucutres were aligned to it the RMSD to the reference structure was calculated and all of those valued printed in the Tk Console. Two RMSD values were reported: the RMSD prior to alignment and the RMSD after alignment. The alignment parameters can be edited in the DSV.tcl file and are set to 'type CA and residue 5 to 200' for no particular reason.

Most important for visualizing the results was the appearance in the VMD Display window of the reference receptor structure (mol 0) with the residues near (3.0 Angstrom in this tutorial, the distance can be edited in DSV.tcl) FTMap and SiteMap sites displayed as 'licorice' representations. All residues within 3.0 Angstrom of both FTMap and SiteMap sites from any of the five output files were displayed on the reference receptor, ftmap-1.pdb in this case.

With DSV SelResFTSTRef we can display the residues near both FTMap and SiteMap sites on a specified receptor such as 2V1D rather than the first centroid (ftmap-1.pdb). This works very similarly to the above except in the Tk Console we type: SelResFTSTRef 1 5 ftmap-%d.pdb 1 5 sitemap-%d.pdb 2V1D.pdb