User: Harpalss

gravatar for Harpalss
Harpalss310
Reputation:
310
Status:
Trusted
Location:
Last seen:
6 years, 4 months ago
Joined:
9 years, 2 months ago
Email:
h*************@gmail.com

I dont like the new layout :(

Posts by Harpalss

<prev • 26 results • page 1 of 3 • next >
2
votes
1
answer
2.6k
views
1
answer
Getting 'Bus Error: 10' When Running The Prody Package On A Multiple Sequence Alignment
... I am using the prody package to do some co-evolution analysis on my multiple sequence alignment (MSA). When I parse the MSA file using prody I get a Bus error: 10 Code: from prody import * msa = parseMSA('test_aln.fasta') This outputs the following in my terminal: >>> from prody impo ...
python written 7.5 years ago by Harpalss310 • updated 5.0 years ago by Biostar ♦♦ 20
5
votes
1
answer
2.4k
views
5 follow
1
answer
Energy Minimization To Determine Backbone Clashes
... I am currently modelling a protein, I have so far generated 160 models of this protein. I then remve models that have backbone clashes via energy minimisation. Models with a -ve energy after minimisation were considered to have no clashes where as proteins that have +ve energy after minimisation we ...
written 8.0 years ago by Harpalss310 • updated 8.0 years ago by João Rodrigues2.5k
3
votes
1
answer
2.6k
views
1
answer
Why Cluster Pdbs By Rmsd?
... I've been looking into RMSD clustering of PDBs, alot of my google searches just returns RMSD clustering servers, so that lead me to posting this question. Say for example I have 100 PDBs, and to an all against all superposition and calculate the average RMSD, I then cluster the averaged values, Wha ...
clustering written 8.0 years ago by Harpalss310 • updated 8.0 years ago by miquelduranfrigola760
2
votes
1
answer
2.0k
views
1
answer
Calculate Distance Between Two Superposed Equivalent Atoms
... So I can superpose two structures with modeller using the following code: def get_rmsd(self, template, model_strucutre): from modeller import * # Create the environment and append alignment for template env = environ() aln = alignment(env) mdl = model(env, file='./modeller ...
modeling written 8.3 years ago by Harpalss310 • updated 8.3 years ago by João Rodrigues2.5k
3
votes
3
answers
3.9k
views
3
answers
Angstroms And Rmsd
... I've noticed on a few protein Modelling sites they state the following example by their models "12.1±4.4Å (RMSD)" What is the connection between the RMSD and Angstroms? ...
written 8.7 years ago by Harpalss310 • updated 8.7 years ago by Woa2.8k
1
vote
3
answers
1.9k
views
5 follow
3
answers
Parallel Processing In Ucsf Chimera
... Im conducting a number of superpositions (match maker in Chimera) on large protein structures. I was wondering if these superpositions can be parallel processed? So I have a number of superpositions running at once? ...
protein structure written 8.7 years ago by Harpalss310 • updated 8.7 years ago by dimkal730
0
votes
4
answers
3.4k
views
4
answers
Comment: C: Making Scientific Movies
... Collision animations and protein docking animations for example ...
written 8.7 years ago by Harpalss310
9
votes
4
answers
3.4k
views
7 follow
4
answers
Making Scientific Movies
... I am considering making scientific movies for a presentation to scientists who are not familiar with my field, to help them understand the concepts in my introduction and to aid in the explanation of my results. Are there any software packages dedicated to making scientific movies? ...
software written 8.7 years ago by Harpalss310 • updated 8.7 years ago by Alastair Kerr5.2k
4
votes
1
answer
2.5k
views
1
answer
Building A Dimer From No Template
... I have built a homology model for a monomer of a DNA protein. This protein is also known to dimerise. The dimerisation site had been identified. What would be the easiest way to building a Dimer from the monomer I built taking the dimerisation site into account? ...
modeling written 8.7 years ago by Harpalss310 • updated 8.7 years ago by Neilfws48k
0
votes
1
answer
5.3k
views
1
answers
Comment: C: Error: Parsing Pdb File With Biopython
... Just checked the code myself, Works perfectly fine, I also get the discontinuous chain error ...
written 8.7 years ago by Harpalss310

Latest awards to Harpalss

Student 8.7 years ago, asked a question with at least 3 up-votes. For Making Scientific Movies
Student 8.8 years ago, asked a question with at least 3 up-votes. For Beginners Guide To Homology Modeling

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 736 users visited in the last hour