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18 January 2021 10,005 3 View

If we use an oil-immersion objective in dry conditions (air), will the maximum collection angle of the objective change?

What if we use an immersion oil objective in the air (medium between the objective and the sample)? Will the effective NA change? What about the maximum collection angle?

22 January 2020 7,842 1 View

How do I resolve the following error I get during the execution of WRF gen_be for creating background error covariance file?

I am trying to generate the be.dat file using the gen_be facility of WRF. I have 12 hour and 24 hour outputs from WRF at 00 UTC and 12 UTC for a month. When I try to run gen_be_wrapper.ksh on my...

15 January 2020 244 2 View

Protein extraction from a non-cellular structure?

I am trying to look at protein in a non-cellular structure using SDS-PAGE. I will be collecting plenty of those structures from the model organism on different days. Is it wise if I collect...

12 January 2020 2,918 6 View

What happens to palladium [pd (0)] at the electrode surface during electro chemical sensing. Has it change its oxidation state?

What happens to palladium [pd (0)] at the electrode surface during electro chemical sensing. Has it change its oxidation state?

25 July 2019 2,600 1 View

From a mechanical engineering point of view, What are the functional requirements that are required in the design of the mid-sole of a shoe?

I am working on a project on designing and testing new materials and different structure(3D-infill) configurations as prototypes for the mid-sole of a running shoe. I was wondering about the...

02 April 2019 1,040 2 View

Is 6-311G APFD-DFT++ a right choice for carrying out an opt+freq calculation of cyclopentyl methyl ether and cyclopentanol?

I want to optimize Cyclopentanol and cyclopentylmethyl ether using Gaussian.

12 January 2019 8,515 4 View

How to find structurally similar protein?

I have a protein obtained through ab initio modeling. I would like to know whether this protein is exhibiting any kind of structural similarities with other proteins available in the PDB. How I...

01 October 2017 7,058 4 View

Mice footpad histology protocol?

13 July 2017 5,533 5 View

Can any one suggest me how to compare the active sites of two different proteins?

I am trying to design multi-target directed ligands. I have found some similar common ligands for both proteins. When I docked these ligands I have seen the score is almost similar. But these...

08 March 2017 1,898 2 View

How to repeat an operation on an atom selection for multiple times in PyMol?

Hi, I am trying to construct a multi-layer fibril structure from a single layer in PyMol by translating the layer along the fibril axis. For now, I am able to use the Translate command in PyMol...

02 March 2021 4,569 4 View

What program can I use to caclulate dipole moment efficiently and without the need of excessive computation?

Hi, I am a third year chemistry undergrad doing my group project in which I need to predict the HPLC retention time of 20 aromatic molecules. to do this we require the chemical properties of these...

24 February 2021 1,384 3 View

How can I make a center of mass vs time graph?

I have a trajectory file of about 1000 frames which I have calculated a center of mass for each frame. I would like to use the first frame as a reference and see how much the center of mass...

04 February 2021 5,774 1 View

How do I refine a specific region of my protein model so that it perfectly superposes with a template peptide PDB with the same sequence?

I have a protein model and want to replace a 12-amino acids-long region within the center of the model with those of a PDB file containing a 12-amino acids long peptide of the same sequence. This...

02 February 2021 779 2 View

Can we incorporate unnatural amino acids into protein using software for graphical image purpose?

I am looking to incorporate a unnatural amino acids which is not available in the swisssidechain database into a protein crystal structure of pdb? I am using chimera 1.14 vis. tool?

26 January 2021 4,064 3 View

What is the best way for mobility estimation in GROMACS?

I need to estimate the mobility of some atoms in the molecule within a molecular dynamics simulation and compare the values for different simulations. I use trjconv -fit rot+trans to fit C-alpha...

19 January 2021 531 3 View

Does GROMACS gmx trjconv sometimes leave a split in a protein?

I have been processing some trajectory files from my molecular dynamics simulation using GROMACS by removing pbc, which often requires a sequence of gmx trjconv steps. This time, my protein...

30 December 2020 849 4 View

Is there any online webserver for DNA-ligand docking?

I have used Autodock 4.2 for docking studies and trying haddock for DNA-Ligand docking. It shows an error and not supported DNA PDB file. Suggest a template for DNA and ligand PDB file and also...

29 December 2020 1,322 8 View

How to generate topology file for ligand for Gromacs?

Dear all, I converted a PDB file into Mol2 file using Openbabel (H added) and then fixed the bond order number using this command: perl sort_mol2_bonds.pl jz4.mol2 jz4_fix.mol2 When I try to...

22 December 2020 303 4 View

How shall I prepare a protein PDB file in a particular pH for docking and simulation?

I wanted to prepare a protein at an alkaline pH for molecular docking as that is the pH I want to perform my in vitro assays in? I prepared my protein at the required pH through H++ server;...

13 December 2020 2,272 3 View