What do XDA and DAY angles show in Discovery Studio?

05 April 2021 0 7K Report

I am looking at the interactions between a ligand and a protein. I have set parameters in order to rule out 'irrelevant' interactions and these parameters have set values for distances and angles. However, the angles set in the parameters are the HDA and HAY angles that are used in the literature, but Discovery Studio is only showing me XDA and DAY angles.

Are these the same as the HDA and HAY angles respectively or do they show something different? Is there a way to get discovery studio to show me the HDA and HAY angles instead?

Badges
Science topic

More Gregory Dunphy's questions See All

Bayesian decision trees and bayesian regression trees in Python and/or R?

I am looking for implementation of bayesian decision trees and bayesian regression trees in Python and/or R.. Do you know if the existing libraries support this

23 February 2021 6,689 3 View

How do you integrate undergads into research?

I'm passionate about mentoring undergrads into the research process--not just collecting data, lit review, but also analysis. How do others go about working with undergrads in research? How do you...

30 November 2020 3,138 6 View

In Ansys HFSS, how do I replace all instances of a Local Variable within a Design with another variable?

I have created a fairly complex antenna that has a parameterized wire radius (wire_r), however I would like to change the name of the variable to better reflect its purpose (e.g. wire_r_cu). Since...

04 November 2020 7,168 1 View

In Ansys HFSS, is there a method of creating an oscillating (AC) magnetic bias, without resonant peaks, within a non-magnetic substrate, e.g. Air?

A loop sniffer probe antenna for HF/UHF is being developed and we'd like to apply a known, constant across frequency AC B-Field source to the region within the substrate where the probe exists (in...

01 November 2020 5,717 3 View

Is it advisable to dichotomize an independent variable measured using a Likert scale?

I am working on a research project to identify the relationship between sexual esteem and sadistic behavior. Both of my independent and dependent variable have been measured using standard...

16 April 2020 7,062 4 View

Survey Data Anlysis/Testing Support - any help?

Hi - hoping someone might be able to help me please? I've had to totally change my MSc project as a result of COVID and as I can no longer do face to face testing, I have created a survey and...

14 April 2020 6,292 9 View

How to preserve endogenous GFP/RFP during IHC?

I have a dual reporter mouse that expresses RFP and GFP under two promoters. I would like to also do IHC on this tissue but the antigen retrieval step (heat) denatures the GFP. Moreover, if I skip...

11 December 2019 403 3 View

Good example of building communication theory using research data?

A colleague and I are working on developing a communication theory. This of course synthesizes prior literature, but we also have survey data we gathered to help us "make the case" for how the...

06 October 2019 1,048 1 View

Can an euryhaline seahorse, such as H. kuda, be selectively bred to tolerate freshwater? Can Aquarium Salt vs. Marine Salt satisfy their saline needs?

I've been researching strategies for the humane genetic engineering of a freshwater seahorse for some time now. I've found some research into developing an artificially convergently evolved...

01 June 2019 2,518 3 View

How do I culture more CD11c+ BMDC from mice?

Hello, I am new to harvesting BMDC and my most recent experiment had 45% CD11c+ cells that were viable (also many dead cells, only 20-30% viable). I followed the method from Madaan A, et al....

18 July 2018 5,653 3 View

I am interested in medicinal chemistry field, which books are highly recommended to learn from?

I am at the beginner level in drug design and drug discovery, and I am interested to learn more about this field. Which books are highly recommended to start from and gives me all essential...

02 March 2021 8,437 2 View

Compact antenna for the frequency range 1 MHz-5 MHz?

Hello everybody! I have a problem with developing a compact antenna for the 1MHz-5MHz frequency range. Tell me what type of antenna can be used and what books and articles to read to perform this...

27 February 2021 7,710 4 View

Can impedance of antenna be less than 50 ohms?

I am simulating helix antenna in hfss, right now, giving excitation with 50 ohms port. When I see the results of Z parameter (real). It shows lower than 50 ohms. Do not understand, if it can be...

27 February 2021 4,218 7 View

How to calculate Ligand-active site distance in a ligand-protein complex from MD simulation?

I have run a MD simulation of a ligand-protein complex in GROMACS using CHARMM forcefield. Reviewer has asked me to calculate Ligand-activesite distance and binding free energy of ligand with...

27 February 2021 4,703 1 View

How to generate AA6061 alloy or any aluminium alloy crystal in material studio?

I need to carry out molecular dynamics simulation on Aluminium alloy. For this i need the crystal structure that which could be further replicated to form a structure.

22 February 2021 1,410 1 View

How to construct different filler shape in MD simulations?

Is there any way to construct different initial filler shapes like triangle, square, rectangle, pillar, and tube in any simulation software.

20 February 2021 1,750 1 View

Access to supercomputer resources in India?

Hello everyone, I want to perform some gaussian calculations and want to use Materials studio for my research work. Can anyone guide me how to get access to supercomputer resources in India for...

15 February 2021 8,264 3 View

How long does it take to design and validate transition state analogue inhibitors?

Hi, I'm asking from the point of view of designing a research plan: How long (approximately) can it take to determine the transition state structure of an enzyme substrate using kinetic isotope...

14 February 2021 2,610 1 View

How to check if the PMF profile obtained from ABF simulation is correct?

I am doing ABF simulations to calculate ligand binding enegy. The PMF profile that I get using single long ABF simulation is attached as pmf_total.png. When I do this ABF calculation with 10...

10 February 2021 4,170 2 View

Is there a way to use waveguide ports for circular antenna design in CST?

Hi, whenever i use circular array i get this error "Waveguide ports must be aligned with Cartesian coordinate planes for the transient solver" Does anyone use circular array with waveguide ports?...

09 February 2021 3,609 8 View