Gyration for a specific part of a protein?

Hey Guys, I have a ubiquitin, I am planning to claculate radius of gyration for residue 1 to 24 and 25 to 76. How can I make this? What command shall I use? Thank you. Maryam

11 December 2017 3,373 3 View

Warning message in gromacs for radius of gyration?

Hey Guys, I am calculationg radius of gyration for 1ubq. My reference file is a pdb file. and I cannot change it. So I have to deal with it!! The problem is that I receive 2 warnings: WARNING:...

11 December 2017 5,153 6 View

Unfolding in negative ion mode in gromacs?

Hi friends! I am running my simulations in negative ion mode, gromacs. The problem is that, my proteins completely unfold, and rotate badly. At the very begininng they start unfolding and...

10 November 2017 5,988 1 View

Unwanted rotation in gromacs?

09 October 2017 1,566 7 View

How to calculate radius of gyration using .gro files?

Hello! How can I calculate radius of gyration for the proteins using .gro files. We use .tpr and .xtc files to calculate R of G but right now I need to use my .gro files. Thank you.

07 August 2017 3,062 4 View

Combining100 .gro files to just one .gro file?

Hello friends! I have 100 .gro files. How can I combine them and create just one .gro file? Thank you! Maryam

07 August 2017 8,750 1 View

Buffer or additive for Mass spec in negative ion mode?

Hello friends, I am really really desparate right now! I am working in negative mode in Mass spec. I added formic acid+acetonitrile+water to my protein and I didn't receive any signal. I added...

02 March 2017 3,735 10 View

How to determine nterm only on central protein?

Hello everyone! I have 1 central protein in pymol with 6 surrounding proteins. I want to find a command to say: please select nterm only on central protein. How can I do this? Thank you.

01 February 2017 996 0 View

How to select only 1 atom in pymol?

Hi! How can I select only 1 atom in pymol? only 1 atom, instead of selecting residues. Thanks

01 February 2017 5,677 1 View

How to determine side chains which I have measured the distances between?

01 February 2017 9,159 9 View

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 View

Gel electrophoresis result for total RNA samples, 1.5 Agarose gel was used, How to improve the integrity of RNA?

Gel electrophoresis, RNA degradation, RNA extraction from fresh tissue

02 March 2021 5,433 5 View

Does anyone know HRM channel in a 2 plex QIAGEN Rotor- Gene Q qPCR can be used as a separate channel?

I am going to have 3 different probes in my qPCR work that I am going to do. But I realized that the machine we have in the lab is a Rotor-Gene Q 2plex HRM Platform, saying it has green, yellow,...

01 March 2021 8,544 1 View

Which cell line should we use to perform biological dosimetry experiments?

We are preparing some experiments based on irradiating cells under different conditions in order to evaluate the effects in terms of DNA damage, genetic expression, etc. As our project is...

01 March 2021 3,355 3 View

Problem with shRNA transfection. Why are only two plates getting contaminated instead of all?

I transfected my LNCaP-WT cells with 3 shRNA plus their NTC two weeks ago and split two puromycin selected cell plates on Friday last week(Feb 26). I checked for GFP in the cells, and they all...

28 February 2021 4,949 3 View

Any specific pipeline or parameter to analyse total transcriptomics study of brain tissue samples?

I have two groups of brain samples, control and treated for example. It was total RNA nova seq sequencing. I tried all the available pipeline like: star+rsem+deseq2, Hista+stringtie+cuffdiff,...

27 February 2021 356 6 View

Why is the efficiency of viral mRNA electroporation in PBMC low?

Hello, I have been struggling with the electroporation of PBMC with HIV-I mRNA. Although the quality of the RNA generated is good, and the handling of the cells in meticulous, the frequency of...

27 February 2021 9,233 3 View

Calculating volume of DNA required from DNA concentration?

Hi I am a bit confused. They are asking me to find out the volume of DNA required in ul (a total of 30-100 ng for genomic DNA) from the DNA concentration in the nanodrop reading which was 404.8...

26 February 2021 5,029 2 View

Has anyone used the Illumina ITS1 primer sets?

Hi everyone, Illumina provides a list of primers to amplify with high taxonomic coverage the ITS1 region for further fungal sequencing, but I cannot find the exact amount necessary of each...

25 February 2021 6,969 3 View

What's the concentration recommend for recombinant protein use in western blotting?

I'm currently working having problem with the concentration for recombinant protein use in western blot, the one been used is Recombinant Human CD19 Fc Chimera Protein-rndsystem which does not...

24 February 2021 8,514 3 View