How do I fit the density of one monomer to the other in coot?
After COVID-19 it has seen that EFL learners technological affiliation has raised. In addition, in the post-COVID period learners started to engage AI technologies like ChatGPT while learning...
08 August 2024 8,964 4 View
This larva was captured using a plankton net in the Persian Gulf during the summer. I believe it may be a Facetotecta nauplius.
08 August 2024 3,746 4 View
How we can cite the papers from ResearchGate. I am trying to create citations for this article, Quantum Machine Learning Algorithms for Optimization Problems: Theory, Implementation, and...
08 August 2024 6,690 3 View
I am currently working on LncRNA; to know the lncRNA-protein interactions I want to do RNA pull down assay, so I need to design primers with T7 promoter. I need assistance in this regard.
07 August 2024 6,622 1 View
I want to refine one XRD peak of my in-situ xrd but the background is never working good which ultimately fails the refinement. How to refine and adjust the background using GSAS-II
05 August 2024 5,291 2 View
Hi, i would like to simulate an absorption process in Aspen Plus. I want to use the NRTL model und would like to add some individual Henry coefficients. Is that possible and how?
05 August 2024 2,333 2 View
Hello everyone, I'm encountering an issue with my electrochemical impedance spectroscopy (EIS) measurements and would appreciate some insights. Experimental Setup: Electrodes: Gold interdigitated...
05 August 2024 3,783 2 View
AI tools like ChatGPT can enhance research work significantly when used responsibly and in conjunction with thorough human oversight.
05 August 2024 1,842 3 View
Have you ever seen a LC-MS/MS method uses both internal standards and external standards (in matrix matching purpose) but the concentrations of internal standards are outside the calibration curve...
05 August 2024 3,084 6 View
Hi everyone, I am working on brain slices for visualizing a protein in the soma and dendrites, using a fluorescence tag. However, I need a tool (not paid) for reconstruction of the whole neuron,...
04 August 2024 4,725 2 View
Why is the Coot real space refine zone indicator green even in regions where the model has no density support? Doesn't this indicator combine both stereochemistry and density parameters?
14 April 2024 2,812 1 View
Hi all, I am working on a cryo em map of a multi domain protein. I am using alpha-fold structure model to fit in the cryo em map. However, due to conformational flexibility the whole multi-domain...
08 December 2023 5,886 1 View
Hi, We are setting up a new lab and we are having a hard time trying to determine what MAC desktop specs we need for structural protein research, using Coot, python and Phenix mainly. Any...
04 September 2023 8,947 0 View
Hi! I am unable to do the following two things on Chimera. 1) I need to join two RNA molecules (separate pdbs) through a bond. That is, the end of one molecule and the beginning of the other...
03 September 2023 8,115 0 View
I use HKL-2000 to process my XRD data. One of them has a resolution of 2.3 Å, but I also have other XRD datasets with resolutions worse than 2.5 Å. Can I use these different datasets to improve...
23 August 2023 9,708 1 View
When I used Coot to refine a dimer protein structure, I got a problem. The chain A of dimer protein possesses whole density for cofactor NADP+. But the NADP+ in chain B misses the density in...
22 January 2023 3,764 2 View
Dear community. I'm just studying for a master’s degree in the department of biochemical science & technology, at National Taiwan University. When I try to refine the structure at Coot or...
17 November 2022 531 3 View
I installed CCP4 on my PC (Windows 10), but I can't see graphs in Aimless, phaser and also, Refmac5 is not able to open Coot directly itself. Does anyone experience the same issue? Any...
24 October 2022 7,996 0 View
In working with a protein that possesses a sulfenic acid cysteine in the active site (Cys-SOH/CSO) I`m trying to perform a molecular docking using Auto dock vina. But, in the pdbqt file, the CSO...
14 September 2022 4,432 1 View
To refine the structure, I use the Phenix and Coot programs. I have already removed the loop, rebuilt it using Coot algorithms and try to fit residues manually, the side chains of loop still do...
16 August 2022 8,699 3 View
