hI, very useful tutorial, one question: how can I delete one particular region of my protein so Ican only display the rest? For example, if I want only display the first 100th residues of the protein, or the 200th residues between the 200-400? it`d be a great help for my project thank you
You can specify that by going to "Graphics -> Representations" and typing in the Specify Atoms section. www.ks.uiuc.edu/Research/vmd/vmd-1.3/ug/node132.html
The video was very informative but could you please say where you are moving you mouse- since the video is pixelated and I have to stop the video every time to follow your movements. Thanks!
Arushi Prakash, thanks for the comment. The tutorial has a video quality as high as HD 720p. Your problem should be solved if you set the quality accordingly and wait for the whole video to load in case of poor internet connection.
Hi, great tutorial, thanks for that. Please let us know if it's possible to colour only the the carbon atoms differently in vmd when two drug molecules are present in the structure..the non carbon atoms can have similar colour patters, eg red for oxygen and blue for nitrogen etc. as done conventionally. Similarly, is it possible custom colour different parts (by parts i mean according to residue sequence eg. aa233 to 244 in red and 255 to 266 in white) of the same alpha-helix differently? Sorry for the lengthy questions, hope you don't mind. Thanks for your patience.
Nice video! I've tried this ... but actually I also had to resize the display to a higher resolution to get a high resolution image. Maybe you could add this =)
childof thesun , thanks for the comment and glad that you liked the tutorial! To change the display, you can enter "display resize 1920 1080" in the TkConsole to make it 1080p resolution. For an ultra-large poster/banner, one could make it arbitrarily large, just that it might also take an proportionally long time to complete.
Thanks for the video it was quite helpful. Could you make a brief video about isosurface drawing method ? I need to use two isosurfaces and they have to have same isovalue with opposite sign, but i couldn't figured it to do so. Thanks again.
Ozan Dernek It is pretty simple. You just need to create two separate isosurface representations. You can follow the following steps which i lifted from sites.google.com/a/poissonboltzmann.org/software/apbs/examples/visualization/apbs-electrostatics-in-vmd 1. First, choose Graphics → Representations... from the VMD Main window. 2. Hit the Create Rep button and change Drawing Method to "Isosurface".3. Change Draw from "Points" to "Solid Surface" and Material to "Transparent".Note that the current isovalue is 0; change this to 1 (or 5 or 10 or whatever) depending on your personal preferences.4. To use the tradition of electrostatic potential coloring, choose "ColorID 0" for the Coloring Method.5. For the negative isocontour, hit "Create Rep" and select the newly created representation. Change the isosurface value to -1 (or 5 or 10...) and the ColorID to 1.
I really appreciate your effort. However, I have a problem here: I cannot obtain any isosurface visual from the rep that I assign the negative isovalue. Am I missing something or the molecule I am working on is problematic ? Only working isovalue is around 0.6; nothing happens when I assign the value as -0.6.
Ozan Dernek I believe the density map you are working on might not have value -0.6. If you have any further problem on the VMD end, you can e-mail vmd@ks.uiuc.edu. Thanks.
Hi, I would like to label some sections of my molecule by highlighting them and then giving them a name. Is there a way to do this in VMD? I haven't figured out yet how to do this and would appreciate any help you could give me :)
phạm hải dương There isn't a TH-cam tutorial on how to render videos using VMD yet, but we have an online tutorial "VMD Images and Movies Tutorial" at www.ks.uiuc.edu/Training/Tutorials/ Feel free to check it out!
+Zach Mitchell I think it can be easily converted in Mac and Linux machines using the command 'convert'. If you are on Windows, you should be able to find softwares or online webserver that do the conversion.
Can you please explain
How do I convert .TGA TO .JPEG without compromising resolution ?
hI, very useful tutorial, one question: how can I delete one particular region of my protein so Ican only display the rest? For example, if I want only display the first 100th residues of the protein, or the 200th residues between the 200-400?
it`d be a great help for my project thank you
You can specify that by going to "Graphics -> Representations" and typing in the Specify Atoms section.
www.ks.uiuc.edu/Research/vmd/vmd-1.3/ug/node132.html
Could you please tell me how to do molecular simulation for protein-ligand? Can we use the docked final structure result?
The video was very informative but could you please say where you are moving you mouse- since the video is pixelated and I have to stop the video every time to follow your movements. Thanks!
Arushi Prakash, thanks for the comment. The tutorial has a video quality as high as HD 720p. Your problem should be solved if you set the quality accordingly and wait for the whole video to load in case of poor internet connection.
Hi, great tutorial, thanks for that.
Please let us know if it's possible to colour only the the carbon atoms differently in vmd when two drug molecules are present in the structure..the non carbon atoms can have similar colour patters, eg red for oxygen and blue for nitrogen etc. as done conventionally.
Similarly, is it possible custom colour different parts (by parts i mean according to residue sequence eg. aa233 to 244 in red and 255 to 266 in white) of the same alpha-helix differently?
Sorry for the lengthy questions, hope you don't mind. Thanks for your patience.
Thank you , you are the best of all!
Nice video! I've tried this ... but actually I also had to resize the display to a higher resolution to get a high resolution image. Maybe you could add this =)
childof thesun , thanks for the comment and glad that you liked the tutorial! To change the display, you can enter "display resize 1920 1080" in the TkConsole to make it 1080p resolution. For an ultra-large poster/banner, one could make it arbitrarily large, just that it might also take an proportionally long time to complete.
Hello ,
Where to find ramachandran plot?
Thanks for the video it was quite helpful. Could you make a brief video about isosurface drawing method ? I need to use two isosurfaces and they have to have same isovalue with opposite sign, but i couldn't figured it to do so. Thanks again.
Ozan Dernek It is pretty simple. You just need to create two separate isosurface representations. You can follow the following steps which i lifted from sites.google.com/a/poissonboltzmann.org/software/apbs/examples/visualization/apbs-electrostatics-in-vmd
1. First, choose Graphics → Representations... from the VMD Main window.
2. Hit the Create Rep button and change Drawing Method to "Isosurface".3. Change Draw from "Points" to "Solid Surface" and Material to "Transparent".Note that the current isovalue is 0; change this to 1 (or 5 or 10 or whatever) depending on your personal preferences.4. To use the tradition of electrostatic potential coloring, choose "ColorID 0" for the Coloring Method.5. For the negative isocontour, hit "Create Rep" and select the newly created representation. Change the isosurface value to -1 (or 5 or 10...) and the ColorID to 1.
I really appreciate your effort. However, I have a problem here: I cannot obtain any isosurface visual from the rep that I assign the negative isovalue. Am I missing something or the molecule I am working on is problematic ?
Only working isovalue is around 0.6; nothing happens when I assign the value as -0.6.
Ozan Dernek I believe the density map you are working on might not have value -0.6. If you have any further problem on the VMD end, you can e-mail vmd@ks.uiuc.edu. Thanks.
grande loco!!
Hi, I would like to label some sections of my molecule by highlighting them and then giving them a name. Is there a way to do this in VMD? I haven't figured out yet how to do this and would appreciate any help you could give me :)
Very nice! Now I need to do that to a 43k atoms system, with lipids, water and ligands and make it look nice. HAHAHA
Thanks for uploading this! Very helpful! But I wonder how can you render some videos by VMD? Please help me!
phạm hải dương There isn't a TH-cam tutorial on how to render videos using VMD yet, but we have an online tutorial "VMD Images and Movies Tutorial" at www.ks.uiuc.edu/Training/Tutorials/
Feel free to check it out!
TCBG UIUC This is exactly what I expect! Thank you for your help!
How to automatically import all these settings?
How do I get the *.tga file into a normal image format?
+Zach Mitchell I think it can be easily converted in Mac and Linux machines using the command 'convert'. If you are on Windows, you should be able to find softwares or online webserver that do the conversion.
Great for beginners!
nice!
Não entendo está lingua
that didnt help at all