Hey thanks for the video. When I copy-pasted your command: show sticks, byres all within 5 of ACH I got invalid syntax error pointing at the s in sticks. Tried without s and it worked.
"ACH" represents the "selection" that you would have named as shown at the beginning of the video. Note also that PyMOL is CasE SenSiTIve and that in the video the "h" was not capitalized, hence written as "ACh" - That in itself would create an error.
@@sabrango i think the code doesn't work for windows. EDIT: it also works for windows. Just check your code. Mine didn't work because of writing "showsticks" instead of "show sticks" go to the url she posted and just copy paste the code then put in the name if your selection.
Thanks for this video! I'm a physicist "gone rogue", starting research on molecular dynamics and docking. This has been so useful! Not only I learned more PyMol stuff, but I also learned some new (for me) biochem.
Wonderful tutorial. I am a graduate student studying structural biology. This was so well paced and clearly explained; helped me really get to grips with how to use Pymol to work smarter, not harder. Thank you so much!
Thank you for this wonderful tutorial. However, I'm not sure if you can help me as you're using a Mac and I'm on a Windows 10 PC, thus there may be different settings. Whenever I click on an residue individually like you do at 9:20, they just disappear instead of getting highlighted, so I've to redo the whole thing again. Am I doing something wrong?
Hi Dr. KP, very informative playlist. I am looking to extract coordinates of active site residues with the Inhibitor. I am able to follow you until 9:05. And whatever I can see at 9:05 on the screen, I want to extract the coordinates of it in PDB format. To do it I guess I need to modify "show sticks, byres all within 5 of N3". So that the resulting structure will be saved as a selection. And then I can use the PyMol commands to extract the coordinates of that selection. Any hint, how I can do it. I am trying to study 6LU7.
Hey, at 18:04 , you mentioned that the range if suitable for vdw forces. May I know what range is okay for vdw forces? It would be helpful if you can help me finding the literature about a good range for vdw forces in protein-ligand interaction.
please can you do a tutorial on predict putative ligand binding sites based on physicochemical properties, conservation analysis, and structural constraints and also protein refinement and looping of modelled protein
I appreciate this video! But I am still unable to visualize the receptor-ligand (protein-protein) polar contacts after ClusPro and HDock docking by following the instructions. Is there any way to resolve this issue?
Thanks for the video. Until now I couldn't manage to drag the molecule as I am using a laptop with a touch pad and couldn't find a solution if you could help. My laptop is Lenovo yoga 900
Hi Ma'am How to pinpoint an active site in the protein (target) when ligand is not attached to it. I mean not all structures in pdf have ligands given with it. How to go about in this case?
Super helpful video, thank you so much! I downloaded a pdb file of a certain receptor-ligand complex from Protein Data Bank website, but when it came to finding polar contacts for the ligand to any atoms of the receptor residues which are 5 A away, it found no contact at all. Any idea why? Also, can I see pi-stacking in PyMOL?
Thank you for your video but i have some problem with the motif and domain of protein, can you show me the way to see the motif or domain in reply here with one or to step by using the mouse. Thank you again
Thank you so much for this amazing video! It really helped me a lot for my manuscript. When I was watching the video, a question concerning hydrogen bonds came into my mind. In this introduction, you mention that hydrogen bond lengths are often in the range between 2.8 - 3.4 A. You also talk about the lengths of van-der-waal forces and ionic interactions. Do you have any citable reference for those values? I was looking for such a source, but I haven't found any suitable so far. Therefore, telling me the names of citable paper would be a great help and I would appreciate it very much! Thanks.
Awesome! At the beginning of the next PyMOL video (working with scenes) I figured out how to make the active site a selection with one typed command. Check it out! :)
I want to compare the binding site for estrogen of human estrogen receptor beta to potential binding site on the surface glycoprotein of CoV2. I have a theory estrogen might be binding to that protein because i found a small pocket of 19 aminoacids with 70 percent positives comparing the two proteins with BLAST as well as the near structure of 50 aminoacids next to this pocket has the same alpha helix structure predicted by HHpred. I am an amateur in using PyMOL however so I would appreciate if anyone else could compare this as well and use the results.
Great video! I would be grateful if somebody could help mi with a basic issue. I obtained a full-length coding sequence of certain alpha-amylase. I determined the signal peptide for the CDS. In the next step, I would like to perform protein structure prediction with RaptorX. My question is: should I use a protein sequence without signal peptide, or should I use a full sequence (with a signal peptide) as an input? I fully understand that signal peptide is usually cleaved from the mature protein. However, I am not sure if the presence of the signal peptide sequence affects the prediction. I assumed yes, but I would like to consult this with more experienced users.
