Tag: pymol

[PyMOL] PyMol & PDBe

Hi Filip, This is already done. The update was in PyMOL 1.8.4.2 and in Open-Source PyMOL rev 4165. The object names are still the same, so it’s backwards compatible. The only difference is the file format, previously we downloaded omap format, now it’s ccp4 map format (larger files but higher…

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Summer Intern – Bioinformatics Jobs – VacancyPaper.com

Job Summary Illumina, is currently hiring on a vacant job post of Summer Intern – Bioinformatics based in Cambridge England United Kingdom. Please read the job detail carefully before applying. Job Title: Summer Intern – Bioinformatics Company Name: Illumina Job Type: Full Time Job Location: Cambridge England United Kingdom Salary:…

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Bioinformatics Research Scientist (Blue Sky Initiative), Memphis, Tennessee

M. Madan Babus Group and the Center for Data-Driven Discovery in the Department of Structural Biology is seeking a highly driven, Full time Machine Learning Research Scientist support the Kalodimos and Babu Groups on the Blue Sky Initiative “Seeing the Invisible in Protein Kinases.” This project is supported by $35…

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Maestro (schrodinger) data in PyMOL : comp_chem

Hello everyone, I recently ran some docking experiments in Maestro at a university computer. The problem is that I cannot be at that computer all the time. Is it possible to open the data in, for example, PyMOL so I can work on my personal computer? And if so, would…

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Modeling an Enzyme Active Site using Molecular Visualization Freeware

Visualizing biological macromolecules is a critical skill for students and professionals in the biological sciences. In this protocol, we demonstrate how to model the active site of the enzyme glucokinase using four freely available programs for molecular modeling. This tutorial highlights several steps of the protocol for each program, which…

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How do I view data in pymol via Ipymol for visualisation in a Jupyter notebook?

Question: How do I view data in pymol via Ipymol for visualisation in a Jupyter notebook? 1 I am analysing protein data using Python programming language and Jupyter notebook. In the Terminal I have put an alias in a hidden file on the home directory entitled .bash_profile, in order to…

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AlphaFold2 | DGX GPU Cluster

AlphaFold2 from DeepMind has been released as an open source application.  At UNC Research Computing Center, we are able to run AlphaFold2 in our machines to provide protein 3D structure from a chain of amino acids.  Following the steps below, we will be able to invoke AlphaFold2 in Longleaf cluster….

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How to open 2 separate pymol windows from a script, and run commands after pymol window closes

How to open 2 separate pymol windows from a script, and run commands after pymol window closes 0 Hello, In short, I’m playing around with pymol and have come across 2 problems. How can I open 2 separate windows of pymol from the same script Closing pymol closes the entire…

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Characterization and Structural Prediction of ORF10, ORF7b, ORF7a, ORF6, Membrane Glycoprotein, and Envelope Protein in SARS-CoV-2 Bangladeshi Variant through Bioinformatics Approach

Abstract The acute respiratory disease induced by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global epidemic in just less than a year by the first half of 2020. The subsequent efficient human-to-human transmission of this virus eventually affected millions of people worldwide. The most devastating thing…

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Capri Criteria For Evaluating Docked Protein Complexes

In our lab we use Profit (www.bioinf.org.uk/software/profit/) for the ligand and interface RMSD calculations. Depending on the complexity of your system this might be easy or not at all. The steps we take are: 1 – Define an interface region between both chains in the native structure. Basically, check for…

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Gromacs Contact Map | Contact Information Finder

Listing Results Gromacs Contact Map Contact maps using Gromacs ResearchGate Just Now Researchgate.net View All Contact maps using Gromacs ? I used gmx mdmat in gromacs to create contact maps, but it seems that the mdmat gives the minimum average distance rather than the average centre-of-mass distance. Estimated Reading Time:…

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alphafold colab github

for the third time worked! Found inside – Page iiThe eight-volume set comprising LNCS volumes 9905-9912 constitutes the refereed proceedings of the 14th European Conference on Computer Vision, ECCV 2016, held in Amsterdam, The Netherlands, in October 2016. Please make sure you have a large enough hard drive space, bandwidth…

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rosetta fold vs alphafold 2

S. Both AlphaFold and Xu use simple folding engines L-BFGS (L- Broyden–Fletcher–Goldfarb– Shanno (BFGS)) and CNS (Crystallography and NMR System), respectively, i.e., improvements come from a better energy potential using distributional information. The phase problem is a problem, to the point that in the past decade, several structures, such as M-PMV…

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Pymolrc settings help in pymol

Pymolrc settings help in pymol 0 Hello, I wanted to set up pymol, so I get the highest resolution every time it starts. this can be done in the Pymolrc file. this file can be accessed via file->edit pymolrc my code for pymolrc is bg white util.performance(0) rebuild and I…

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How I can merge 2 pdb files correctly on pyMol

How I can merge 2 pdb files correctly on pyMol 1 Hi there, Please, I’m not experienced in this field and I need help. I want to check the ligand-interaction of 2 molecules, but I’m not able to merge the 2 PDB files correctly, because it’s like the ligand is…

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How to show intermolecular forces between two chains within the same protein in Pymol

How to show intermolecular forces between two chains within the same protein in Pymol 0 Hello! Would anyone know how to show intermolecular forces such as Vanderwaal forces, hydrogen bonds etc in Pymol using a python script? I would like to analyze the forces between two chains in the same…

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AutoDock Flexible Molecular Docking Tutorial

AutoDock Flexible Molecular Docking Tutorial Autodock is a molecular docking software package, open source and free, the official website is autodock.scripps.edu/, the latest version is AutoDock 4.2.6, including AutoDock and AutoGrid two modules, AutoDock software package download address It is autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/, including Linux, Mac OS and Windows versions…

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What to do with a bunch of AlphaFold2 structures?

What to do with a bunch of AlphaFold2 structures? 1 I’ve ended up with the structures of a dozen or so proteins predicted by AlphaFold2 by happenstance. The proteins are all orthologs. The provenance of the sequences is transcriptomic (de novo assemblies, to be specific). I’d like to try and…

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Alternative way to generate .PDBQT file for AutoDock Vina? : bioinformatics

For context: I’m using macOS Big Sur and have successfully run AutoDock Vina through my terminal, after which I’ll view the output in ChimeraX. Also, I’m an undergrad attempting to teach myself how to use docking software for a personal project and future use, so I may very well have…

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how to calculate positive and negative for a given protein sequence

how to calculate positive and negative for a given protein sequence 0 Hello, I would like to know how once could calculate positive and negative for a given sequence? The PDB of the protein is 1ak4. It has two chain A and B. I am looking to find a way…

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Output Polar Contacts Between Chains to Text File

  PYMOL: Output Polar Contacts Between Chains to Text File 0   I am new to PyMOL but have a very specific task that I need to do. I have a PDB structure file of protein homo-oligomer, and I want to use PyMol to determine polar contacts between chain A…

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PyMol – molecule export problem

PyMol – molecule export problem 0 Dear all, I have a molecule in PyMol which I want to open in ChimeraX. But after exporting the molecule as .pdb, some structural information seems to be lost – regions that in the PyMol session file are embedded into helices are now loops…

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