How to make publication quality figures | Part 2 | Discovery Studio Visualizer | ChimeraX | Origin
ฝัง
- เผยแพร่เมื่อ 19 ส.ค. 2024
- Use ChimeraX for a surface view of your receptor-ligand interaction
DS Visualizer for 2D interaction
Origin v2021 for 2D plots from Vina binding affinity scores
Very crucial and informative, really appreciate it
Thank you 🙏
thank you for the knowledgeable
Session
My pleasure
Most useful video. Please make a video on representation of MD simulation results
Absolutely
Hello. can you guide how to set up window on Mac?Thanks in advance
Use Docker. th-cam.com/video/xhGYobuG508/w-d-xo.html
Thank you for sharing your knowledge, I wondering about the reason that differences between the chimera and discovery studio in hydorgen interactions, and additionally is there any other options to detect other interactions like hydrophobic in chimera? Thanks in advance :)
Thank you. The main difference is the cutoff or threshold value’s between the two software. I would recommend you to use discovery studio visualizer for calculating H bonds and other types of interactions. And use chimera for publication quality figures.
Seems like a great video. But there is no sound.
Sorry about that. I will try to find the audio. Somehow its messed up.
Fixed. Check it out. Thanks
Ihave a problem when the enzyme separates from the molecule
please help
Do not quite get it whats the actual problem you are facing.
could you share the link of your research article which you have shown in part1 of video
www.science.org/doi/full/10.1126/sciadv.abb8097?rfr_dat=cr_pub++0pubmed&url_ver=Z39.88-2003&rfr_id=ori%3Arid%3Acrossref.org
Your videos are wonderful, I tried to write email which I got from your paper but failed I do not know why? Can you provide alternative email
Thank you very much. Yes its pritampanda.bioinfo@gmail.com
Thank you for the video. I have question, Is necesary to have the license to publish the results of docking visualized with discovery studio?
Yes you can.
hello friend, I want to know if I can publish figures made with the free discovery studio visualizer, although I haven't paid the license
Yes absolutely. You can publish figures with the free version of DS visualizer.
how did you download discovery studio visualizer on mac OS?
Its not for macos. DS only works for windows and linux. In Macos you have to install virtual machine.
which do you use program for figure preparation.
I use a combination of tools to make the figures as I have shown in my video.
Can you please send me the link of your publication of docking
www.science.org/doi/full/10.1126/sciadv.abb8097?rfr_dat=cr_pub++0pubmed&url_ver=Z39.88-2003&rfr_id=ori%3Arid%3Acrossref.org
respected sir, please update next video
Which video do you want? Anything related to visualisation or docking!
@@BioinfoCopilot respected sir, please make video on molecular dynmic simulation
I tried to follow your video, however, in using ChimeraX, Whenever I select the Macromolecule and click on show surface, my ligand get hidden inside the protein as it is placed inside the protein at the active site, is there any way I can make the protein's region around the ligand transparent so that the ligand can be visible?
Thank you. Your videos are quite informative btw.
Yes you can do it by using view/focus option in select. I have also shown in the video how to make it transparent.
Moreover you can select only amino acid residues and then select surface. In that way your ligand will be visible. If its inside the pocket you can use the view/focus option.
@@BioinfoCopilot Thank-you for replying, can you please also suggest some alternative to OriginPro to make graphs as it is a paid software, I also have results in .dlg files from Autodock 4.2 by performing 100 Runs of docking, and I not sure whether to report the all results of 100 runs in research paper or just the cluster histogram information.
@@italhaislam Instead of Origin you can use Qtiplot www.qtiplot.com
@@italhaislam Report all the results using box plot and also use 95% CI for better statistics