Does anyone know the method to change the phi/psi/omega angles using the mouse in pymol?
I know the command:
Set_dihdral but want to play with the dihedral angles using the mouse.
Thank you,
Steve
You can. I would recommend you to, first, change the visualization to "ball and stick" (Action > Preset > ball and stick) and then hiding the side chain (Hide > Side Chain).
Then you click in the area with the informations about the mode buttons (as below). It will change the Mouse Mode to 3-Button Editing.
Finally, you press CTRL + Right Click on the angle you want to change and it's done.
HTH
Pymol Tips:
Ctrlright click on a bond to know the dihedral/torsion angle.
Ctrlleft click and drag to change the dihedral/torsion angle.
Command to set the dihedral/torsion angle:
set_dihedral atom1_name, atom2_name, atom3_name, atom4_name, angle
Example:
set_dihedral 23/CA, 23/C, 24/N, 24/CH3, 60
I've not seen this in PyMOL but Gaussian has a feature like this. You can set bond lengths, angles, and dihedral angles with slide bars and watch them update in real time.
I've used this before to edit PDB files but I've only needed to do so once in a while.
EDIT: Chimera can do this too and it's better suited for macromolecules than Gaussian. Ctrl double click on a bond and then Tools > Structure Editing > Adjust Torsions
UPDATE: I just figured out how to do this in PyMOL. Wizard > Sculpting, click on the residue containing the torsion angle of interest, then in the sculpting menu in the lower right change "Residue Shells" to "One Residue", now ctrl-right click on a bond then ctrl-left click and drag to change the torsion angle. You may want to change the settings in Build > Sculpting > Restraints.
Related
I want to make the ground in this place of the terrain a bit deeper a bit lower but left shift key or right shift key and the left mouse button does not change anything on the terrain.
I've been looking for an answer for hours, and I finally found it.
If you are trying to lower a piece of land that is already at 0 height, you will not be able.
You can only lower areas that are above to height 0. In short, height 0 is the minimum: you cannot go to snow values due to the way the terrain is created.
To be able to make valleys then you have to select the tool "Set Height", enter a height and raise all the ground to that height with "Flatten All", or small pieces of land by dragging the mouse on the ground.
If you click "Flatten All", all the terrain will be brought to that height, losing all the changes made previously for the mountains.
However, if you have already made land and you don't want to lose it and redo it from scratch, you can use the following solution:
Export the current heightmap;
Open the image in an editor; (I'm not an expert in Photoshop or other
graphics programs, but I'm sure Photoshop has a way. If there isn't
an entry in the program, find out how to use scripts in photoshop)
Find a way to set the pixels according to a formula: maximum depth of
valleys + current value of the grayscale pixel * original height /
(original height + maximum depth of valleys);
Export the image in Raw format;
Go back to Unity and import it on the ground as you read in the link
above;
In the terrain settings set the height equal to the value you used
in the formula called "original height" + the “maximum depth of
valleys” value;
You should now have the ground as before, but higher. Set the value
in the transform of the Y position equal to "-maximum depth of
valleys" so that it is at the same height as before.
You should now be able to create valleys!
I haven't tried the process, but I've thought about it so much I'm pretty sure it will work.
Good work!
I want to be able to split the editor when I drag them but not have to point as much at the corners of the editor when I drag them
The red line is the minimum distance for the horizontal division option to come out, which is approximately 10% of the width of the editor
Is there any configuration in vs-code that allows to increase that?
How can I increase the point size in Meshlab for point clouds? I found how I can show / hide specific PCs, but I do not see where to change their display properties : size, color, symbol ...
If you are using Meshlab 1.3, you have to do 3 steps:
View->Show Layers Dialog to enable the panel at the right.
Render->Show Vertex Dots, to show the vertices as small circles.
There is a Dot size field in the Layer Dialog that let you change the size of the circles.
If you are using Meshlab-2016 or later, it is even easier...
Click on the tab of vertex and choose the option Dot Decorator (1)
Change the size of dots with the Point Size Bar (2)
In MeshLab, you can just use Alt + mouse wheel to control point size.
Or you can find the point size setting in:
Tools->Options->MeshLab::Appearance::pointSize.
I am drawing a visio diagram and would like to change (i.e. reduce) the radius of the corners of some of my rounded boxes.
I searched the program's help and googled for >1/2 hour but can't find any hint on how to achieve this - at least none that works.
The context dialog shows a Rounded corner section (Right-click => Format => Line), but any change done there has no effect whatsoever. Does one maybe have to "unprotect" these settings? If so: how?
Any expert who knows how to change the corners' radius?
Later Edit: I just realized: I had used a flow chart symbol "Rounded Process" instead of a plain vanilla rounded box to draw this diagram. That's why I can't change these corners!
Is there an elegant way to globally change a shape into another type, i.e. these flowchart shapes into plain vanilla boxes? Ideally while keeping the associated text?
M.
not without coding.
However, I'm pretty sure that Sandrilla has a ready to use tool.
It's available for reasonable money. http://www.sandrila.co.uk/
You can create your own shape in such situation, you can can create your own Stencil and then add the your predefined shapes into it. To add the predefined shapes into the stencil just follow the procedure
Select the shape from an existing Stencil and Right click on it
From the Menu select 'Add to My Shapes'
Create New stencil or add it to an existing Stencil.
Now you can edit the master shape but before that you have to put the Stencil in the Edit mode.
Right click on the newly added shape in the Stencil and click 'Edit Master' -> 'Edit Master Shape'
You can now modify the Shape as per your need , for ex. If you want to edit the Corner of the Shape then you right click on the Shape in the Master and then Select 'Format' - > 'Line' and then select type of corner from the 'Round corner' section.
I inherited a figure (as a .fig-file) and want to change the layout of the legend. I would like to stretch the legend, from taking up half of the right side of the plot to taking up all of the right side of the plot.
I was initially hoping that the "Align distribution" tool could help with this, but as it turns out, the "patches" (i.e., the color samples) refuse to move! I cannot move them with "Align distribution", or drag and drop them by hand. However, there is no problem moving the text corresponding to the patches.
Is there a way to move the color patches?
Is there a way to automate the spreading out of the legend?