Walkthrough for lattices on vesicles - Revision history

Daniel Castaño: /* Getting the data */

2025-01-24T12:35:44Z

Getting the data

Raffaele Coray: /* Getting the data */

2024-12-03T12:36:21Z

Getting the data

Raffaele Coray at 12:43, 2 December 2024

2024-12-02T12:43:53Z

Stefano Scaramuzza at 12:19, 18 August 2021

2021-08-18T12:19:26Z

Raffaele Coray: /* Creating a text file */

2021-07-30T09:16:31Z

Creating a text file

Stefano Scaramuzza at 16:32, 29 August 2018

2018-08-29T16:32:21Z

Daniel Castaño: /* Creating a text file */

2017-11-29T12:42:17Z

Creating a text file

Daniel Castaño: /* Cropping the particles */

2017-11-29T12:42:01Z

Cropping the particles

Daniel Castaño: /* In the standalone */

2017-11-29T12:33:43Z

In the standalone

Daniel Castaño: /* Executing the text file */

2017-11-29T12:33:05Z

Executing the text file

@@ Line 13: / Line 13: @@
   <tt>dpkhelp.wiki.downloadExample('hiv');</tt>
-In case this command fails, please try the direct link in linux:
+In case this command fails, please try the direct link:
-<!--<tt> wget  https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/hiv/v17.rec</tt>-->
+  <tt>  {{Template:DownloadLinkBasicHIVTomo}}</tt>
 === Viewing the data ===

@@ Line 15: / Line 15: @@
 In case this command fails, please try the direct link in linux:
- <tt> wget  https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/hiv/v17.rec</tt>
+<!--<tt> wget  https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/hiv/v17.rec</tt>-->
 or the corresponding one in MacOS
- <tt> curl -O https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/hiv/v17.rec</tt>
+<!--<tt> curl -O https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/hiv/v17.rec</tt>-->
 === Viewing the data ===

← Older revision		Revision as of 12:43, 2 December 2024
Line 1:		Line 1:
		+	[[Category:Walkthroughs]]
		+
	This walkthrough shows the approach to process proteins that cover spheroidal vesicles following (approximately) a structured lattice. For demonstration, we use a highly binned tomogram with several viral capsides.		This walkthrough shows the approach to process proteins that cover spheroidal vesicles following (approximately) a structured lattice. For demonstration, we use a highly binned tomogram with several viral capsides.

@@ Line 322: / Line 322: @@
 [[ File:HivDDbrowseCentered.png |thumb|center|600px| <tt> dslices </tt> of a selection of aligned particles]]
-The averages can be consulted with <tt>mapview</tt>. Here,we order the <tt>ddb</tt> command to extract the averages (<tt>a</tt> item) corresponding to iterations  0 and 4 and send the result to the browser <tt>mapview</tt> (flag <tt>-m</tt>)
+The averages can be consulted with <tt>mapview</tt>. We open the averages (<tt>a</tt> item) corresponding to iterations 0 and 4:
-  <tt>ddb pcnt:a:ite=[0,4] -m </tt>
+  <tt>dpkdev.legacy.dynamo_mapview('pcnt:a:ite=[0,4]')</tt>
-This browser is more or less complicated... you can tweak on it to see a depiction of how the average evolved from the first template to iteration number 4.
+You can tweak the visualization to see a depiction of how the average evolved from the first template to iteration number 4.
-[[ File:HivMapviewEvolution.png |thumb|center|600px|  Interactive slice comparison through<tt>mapview</tt> ]]
+[[ File:HivMapviewEvolution.png |thumb|center|600px|  Interactive slice comparison through <tt>mapview</tt> ]]
 As a tip, when you know exactly which features you want to test visually, you can use the command line order <tt>dslices</tt> to directly produce the scene of interest:

@@ Line 152: / Line 152: @@
     tv{i} = v.grepTable();
     tv{i}(:,22) = i;
-    disp(sprintf('Dipole %d will provide %d crop points',i,size(v.crop_points,2)));
+    disp(sprintf('Dipole %d will provide %d crop points',i,size(v.crop_points,1)));
 end
 dwrite(tv,'cellOfTables.mat');

@@ Line 286: / Line 286: @@
 dvput(pr,'is_r1',40);
 dvput(pr,'rf_r1',4);
-dvput(pr,'rf_r1',2);</nowiki>
+dvput(pr,'rff_r1',2);</nowiki>
 We let the particles shift, but not the the edges of the box:

@@ Line 140: / Line 140: @@
 Now paste the text of the commands excluding  comments (# simbols).
-  <nowiki> ds = dread(<YOUR FILE>);;
+  <nowiki>ds = dread(<YOUR FILE>);;
 NDipoles = length(ds.dipoles);

@@ Line 79: / Line 79: @@
 We will describe a protocol to be carried from the command line, explaining each step. In short, we will visit each dipole in the model we just created, define a spherical vesicle centered on the dipole, use it to define a regular distribution of points on each vesicle, define positions pointing outwards and format everything as a [[table]] that can be used directly by ''Dynamo'' to operate an extraction and a subsequent alignment.
-=== Extracting information from the catalogue ===
+=== Table extraction ===
   <nowiki>dcmodels hiv -tc dipoleSet -ws o -gm 1
@@ Line 86: / Line 90: @@
 ds = o.models{1};</nowiki>
-=== Create a table for each vesicle ===
+===== Create a table for each vesicle =====
-Now we can loop on each dipole contained in the dipole set <tt>ds</tt>.
+Now we can loop on each dipole contained in the dipole set <tt>ds</tt>.  The next lines should be copied into a text file (using matlab command <tt>edit</tt>), and executed.
   <nowiki>NDipoles = length(ds.dipoles);
@@ Line 124: / Line 128: @@
-=== In the standalone ===
+==== In the standalone ====
 The standalone can execute matlab scripts, with some restrictions: the scripts need to be self contained: any traffic of variables needs to be carried through writing and reading files. There is no other possibility of transferring workspace variables between your session and the script.
-==== Creating a text file ====
+===== Creating a text file =====
 Create a text file named <tt>commands.m</tt> (arbitrary name) with any text editor available in your system. In Linux <tt>gedit</tt> is probably available.
@@ Line 156: / Line 160: @@
 * Notice that we changed the variable input/output, by hardcoding the names of the files that need to be read and created.
-==== Executing the text file ====
+===== Executing the text file =====
 In a system shell or in ''Dynamo''console, type:
@@ Line 162: / Line 166: @@
   <tt>dynamo commands.m</tt>
-==== Getting the information back into the ''Dynamo''console ====
+===== Getting the information back into the ''Dynamo''console =====
 In the ''Dynamo'' console, type.
   <tt>tv = dread('cellOfTables.mat'); </tt>