Re: [PyMOL] [EXTERNAL] How to compute the interface surface between ligand and protein?

So, Thomas, you don't see anything wrong in the way I compute the surfaces? The numbers should be like that, right? The reason I need both the molecular surface and the SASA in not directly related to a physical quantity. I do SQM scoring of compounds bound to proteins, but the bulkier molecules,

Re: [PyMOL] tertiary structure/protein folding

Hi Grace, You may want to use a protein homology modeling software for more advanced structure building, such as Modeller. https://salilab.org/modeller/ Nese From: Grace Ciabattoni Sent: Thursday, May 21, 2020 12:49 PM To: pymol-users@lists.sourceforge.net

Re: [PyMOL] tertiary structure/protein folding

Hi, Predicting tertiary structure with high accuracy is the holy grail... I can suggest to perform homology modeling. See Modeller. If your target is small, you can use molecular dynamics (w replica exchange). Tamas On 2020. 05. 21. 18:49, Grace Ciabattoni wrote: Hello, I am trying to model

Re: [PyMOL] [EXTERNAL] How to compute the interface surface between ligand and protein?

Hi Thomas and Blaine, SASA is probably the correct feature to evaluate here, not molecular surface. Of course it may depend the actual goal of this exercise, but typically when talking about interface surface, you're putting that into context with binding energy or solvation effects, and only

Re: [PyMOL] Consistent coloring between sticks of sidechains and cartoon backbones in spectrum coloring

I tried that. that is actually how I found this is a way to color them according the CA color assigned in the spectrum. Charles From: Olson, Linda Sent: Thursday, May 21, 2020 12:24 PM To: Chen, Qiang Subject: Re: Consistent coloring between sticks of

[PyMOL] tertiary structure/protein folding

Hello, I am trying to model my protein of interest using the builder function in version 2.3. Is there a way to induce protein folding to properly mimic tertiary structure, or is secondary structure the highest manipulatable level of protein order in PyMol? Thank you, Grace

Re: [PyMOL] Consistent coloring between sticks of sidechains and cartoon backbones in spectrum coloring

Thanks, Prof. Mooers. I tried your script. It did not report any error. but the selected residues are colored as the default, green for carbon. Then I figured out I made things complicated. I created a new object (cnsp) for the cartoon representation colored with spectrum. Then I selected

Re: [PyMOL] Consistent coloring between sticks of sidechains and cartoon backbones in spectrum coloring

Hi Charles, This pml script does want you want, # Color the carvons atoms of the sidechain the same as the color of the CA atom col=[] # edit resi here iterate resi 10+20+30 and name ca, col.append((chain,resi,name,cmd.get_color_tuple(color))) # Define the colors ca10, ca20, and ca40