Mole 2.5 Command Line Output Help - Revision history

Dave: /* PyMol */

2013-11-12T17:24:05Z

PyMol

← Older revision		Revision as of 17:24, 12 November 2013
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	There are two types of the PyMol output:		There are two types of the PyMol output:
	* Standard: Contains Channels and Cavities.		* Standard: Contains Channels and Cavities.
	* Charges: Contains Channel surfaces colored by charge (min charge = red, 0 charge = white, max charge = blue).		* Charges: Contains Channel surfaces colored by charge potential (min charge = red, 0 charge = white, max charge = blue) and surfaces colored by centerline potential.

	To run the PyMol output, use the "File -> Run..." option in PyMol.		To run the PyMol output, use the "File -> Run..." option in PyMol.

Dave: /* Output Types */

2013-11-12T17:23:25Z

Output Types

← Older revision		Revision as of 17:23, 12 November 2013
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	* PDB for Channel profiles and lining residues.		* PDB for Channel profiles and lining residues.
	* CSV for Channel profiles and "centerline charges".		* CSV for Channel profiles and "centerline charges".
	* PyMol for Channels, Cavities, and Charges.		* PyMol for Channels, Cavities, and Charges (surface and centerline potential).
	* Mesh for Channel surfaces, Cavities (can be loaded by JMol), and Start Points.		* Mesh for Channel surfaces, Cavities (can be loaded by JMol), and Start Points.

Dave at 19:32, 6 November 2013

2013-11-06T19:32:16Z

← Older revision		Revision as of 19:32, 6 November 2013
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	</pre>		</pre>

	==== Start Points ====		=== Start Points ===

	Contains the XML description of automatically computed and user added start points.		Contains the XML description of automatically computed and user added start points.

Dave at 19:32, 6 November 2013

2013-11-06T19:32:00Z

← Older revision		Revision as of 19:32, 6 November 2013
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	* Profile: This is roughly equivalent to <code><Node></code> elements in the XML output. The shape of the file looks like this:		* Profile: This is roughly equivalent to <code><Node></code> elements in the XML output. The shape of the file looks like this:
	<pre>		<pre>
	REMARK ATOM NAM RES TUNID X Y Z Distnm RadiusA		REMARK ATOM NAM RES TUNID X Y Z Distnm RadiusA
	HETATM 1 X TUN H 1 -25.007 -25.093 -14.627 0.00 1.56		HETATM 1 X TUN H 1 -25.007 -25.093 -14.627 0.00 1.56
	HETATM 2 X TUN H 1 -24.999 -25.066 -14.700 0.08 1.60		HETATM 2 X TUN H 1 -24.999 -25.066 -14.700 0.08 1.60
	HETATM 3 X TUN H 1 -24.992 -25.038 -14.773 0.16 1.65		HETATM 3 X TUN H 1 -24.992 -25.038 -14.773 0.16 1.65
	</pre>		</pre>
	Each channel has its individual PDB file + a single PDB file for each channel type containing all of them.		Each channel has its individual PDB file + a single PDB file for each channel type containing all of them.
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	* Standard: Contains Channels and Cavities.		* Standard: Contains Channels and Cavities.
	* Charges: Contains Channel surfaces colored by charge (min charge = red, 0 charge = white, max charge = blue).		* Charges: Contains Channel surfaces colored by charge (min charge = red, 0 charge = white, max charge = blue).

			To run the PyMol output, use the "File -> Run..." option in PyMol.

	=== Mesh ===		=== Mesh ===

Dave at 19:27, 6 November 2013

2013-11-06T19:27:55Z

@@ Line 7: / Line 7: @@
 * CSV for Channel profiles and "centerline charges".
 * PyMol for Channels, Cavities, and Charges.
-* Mesh for Channel surfaces and Cavities (can be loaded by JMol).
+* Mesh for Channel surfaces, Cavities (can be loaded by JMol), and Start Points.
-== Output Specs ==
+Note on Pores: There are 3 types of pores - Auto (computed automatically from openings inside the proteins), Merged (created from merging two tunnels) and User (created from custom specified end points).
 === XML ===
 ==== Residue Format ====
@@ Line 101: / Line 115: @@
    </Triangles>
 </Surface>
 </pre>

Dave: Created page with "== Output Types == Mole 2.5 Command Line generates these types of output: * XML for Channels (Tunnels, Pores, Paths), Cavities, Charges, and Start Points. * PDB for Channel ..."

2013-11-06T19:08:47Z

Created page with "== Output Types == Mole 2.5 Command Line generates these types of output: * XML for Channels (Tunnels, Pores, Paths), Cavities, Charges, and Start Points. * PDB for Channel ..."

New page

== Output Types ==

Mole 2.5 Command Line generates these types of output:

* XML for Channels (Tunnels, Pores, Paths), Cavities, Charges, and Start Points.
* PDB for Channel profiles and lining residues.
* CSV for Channel profiles and "centerline charges".
* PyMol for Channels, Cavities, and Charges.
* Mesh for Channel surfaces and Cavities (can be loaded by JMol).

== Output Specs ==

=== XML ===

XML output is located in <code>WORKING_FOLDER/xml</code> for channels and cavities, and in <code>WORKING_FOLDER/CHARGE_NAME/xml</code> for charges projected on channels.

==== Residue Format ====

Residues are exported in the format <code>NAME NUMBER [CHAIN] [i:INSERTIONCODE] [Backbone]</code> (arguments in [] are optional).
: In some cases, chain is not specified (= empty record in PDB file).
: <code>Backbone</code> indicates that the residue is orientated towards the channel with its main-chain.
: Examples: <code>HEM 508 A</code>, <code>ALA 103 i:A</code>, <code>HIS 203 B Backbone</code>.

==== Channels ====

General shape of the XML:
<pre>
<Tunnels Version="2.5.13.11.6" FoundOrigin="1" Timing="1440">
<Tunnel Id="1" Cavity="1" Auto="0">
<Properties Charge="1" NumPositives="2" NumNegatives="1" Hydrophobicity="-0.67" Hydropathy="-1.99" Polarity="25.03" Mutability="81" />
<Profile>
<Node Radius="1.556" FreeRadius="1.556" T="0.00000" Distance="0.000" X="-25.007" Y="-25.093" Z="-14.627" />
<Node Radius="1.603" FreeRadius="1.603" T="0.01429" Distance="0.078" X="-24.999" Y="-25.066" Z="-14.700" />
...
<Node Radius="2.541" FreeRadius="3.543" T="1.00000" Distance="8.815" X="-29.583" Y="-29.076" Z="-16.942" />

</Profile>
<Layers>
<ResidueFlow>ARG 212 A,GLU 308 A,SER 312 A,LEU 482 A,GLN 484 A,LYS 173 A</ResidueFlow>
<HetResidues>HEM 508 A</HetResidues>
<LayerWeightedProperties Hydrophobicity="-0.87" Hydropathy="-2.37" Polarity="23.56" Mutability="88" />
<Layer MinRadius="1.55623" MinFreeRadius="1.55623" StartDistance="0.00000" EndDistance="0.63649" LocalMinimum="0">
<Residues>ARG 212 A,GLU 308 A</Residues>
<FlowIndices>0,1</FlowIndices>
<Properties Charge="0" NumPositives="1" NumNegatives="1" Hydrophobicity="-0.78" Hydropathy="-4.00" Polarity="50.95" Mutability="80" />
</Layer>
<Layer MinRadius="1.93902" MinFreeRadius="2.00252" StartDistance="0.63649" EndDistance="2.09516" LocalMinimum="0">
<Residues>ARG 212 A,GLU 308 A,SER 312 A</Residues>
<FlowIndices>0,1,2</FlowIndices>
<Properties Charge="0" NumPositives="1" NumNegatives="1" Hydrophobicity="-0.84" Hydropathy="-2.93" Polarity="34.52" Mutability="92" />
</Layer>
...
</Layers>
</Tunnel>
</Tunnels>
</pre>

In the case of pores and paths, the root element is <code>Pores</code> with <code>Pore</code> children, and <code>Paths</code> with <code>Path</code> respectively.

=== Cavities ===

General shape of the XML:
<pre>
<Cavities Version="2.5.13.11.6">
<Cavity Type="Cavity" Volume="3589.534" Depth="20" Id="1">
<Boundary>
<Residues>LEU 47 A,ILE 50 A,LEU 51 A,TYR 53 A,HIS 54 A,GLN 78 A,GLN 79 A,PRO 107 A,GLY 109 A,VAL 111 A,LYS 115 A,ILE 120 A,GLU 122 A,LYS 173 A,ASP 174 A,LYS 208 A,LEU 211 A,ARG 212 A,LEU 216 A,LEU 221 A,PRO 227 A,ILE 230 A,GLU 234 A,TYR 307 A,GLU 308 A,LEU 482 A,GLN 484 A,PRO 485 A,PRO 488 A</Residues>
<Properties Charge="0" NumPositives="4" NumNegatives="4" Hydrophobicity="-0.31" Hydropathy="-0.42" Polarity="9.84" Mutability="71" />
</Boundary>
<Inner>
<Residues>PHE 57 A,ASP 76 A,VAL 81 A,ASN 104 A,ARG 105 A,ARG 106 A,PHE 108 A,SER 119 A,ALA 121 A,GLY 177 A,MET 181 A,ILE 184 A,THR 207 A,PHE 213 A,ASP 214 A,PHE 215 A,PHE 220 A,ILE 223 A,THR 224 A,PHE 241 A,ILE 301 A,PHE 302 A,ILE 303 A,PHE 304 A,ALA 305 A,THR 309 A,SER 311 A,SER 312 A,SER 315 A,PHE 316 A,TYR 319 A,ILE 369 A,ALA 370 A,MET 371 A,ARG 372 A,LEU 373 A,GLU 374 A,ARG 375 A,VAL 376 A,VAL 393 A,MET 395 A,ARG 440 A,ILE 443 A,LEU 475 A,GLY 481 A,LEU 483 A,VAL 489 A,HEM 508 A</Residues>
<Properties Charge="2" NumPositives="5" NumNegatives="3" Hydrophobicity="-0.18" Hydropathy="0.30" Polarity="6.29" Mutability="83" />
</Inner>
<Properties Charge="2" NumPositives="9" NumNegatives="7" Hydrophobicity="-0.23" Hydropathy="0.03" Polarity="7.64" Mutability="78" />
</Cavity>
...
</Cavities>
</pre>

=== Channels with Charges ===

XML output for XML channels is the same as without charges, except that the <code><Node></code> contain an additional attribute <code>Charge</code>:
<pre>
<Node Radius="1.556" FreeRadius="1.556" T="0.00000" Distance="0.000" X="-25.007" Y="-25.093" Z="-14.627" Charge="0.033" />
</pre>

In addition to this, the XML representation of the tunnel surface is available in the form:
<pre>
<Surface TotalValue="-1.268">
<Vertices>
<Vertex Id="0" X="-32.048" Y="-29.039" Z="-17.561" Value="0.349" />
<Vertex Id="1" X="-32.019" Y="-28.874" Z="-17.561" Value="0.341" />
<Vertex Id="2" X="-32.113" Y="-29.039" Z="-16.705" Value="0.177" />
...
</Vertices>
<Triangles>
<Triangle A="2" B="3" C="0" />
<Triangle A="0" B="3" C="1" />
<Triangle A="4" B="3" C="2" />
...
</Triangles>
</Surface>
</pre>