User: ac.research

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ac.research10
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Posts by ac.research

<prev • 27 results • page 1 of 3 • next >
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Comment: C: Phi/Psi torsion angles replication
... hmmm, good idea. I added the function to include also the Omega angles which helped "a bit" check out the structure: [new protein][1]. But it is still corrupted, compare it with the original structure. what other variables would I need to include? [1]: https://pasteboard.co/Hc2HUkx.png ...
written 4 months ago by ac.research10
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Phi/Psi torsion angles replication
... So I am trying to fold a primary structure using only the torsion angles from a natural protein's crystal structure. But I found this strange phenomena, which I cannot understand nor explain. My protocol is as follow: 1. I am taking a normal protein (figure 1) 2. Then I take the phi and psi torsio ...
math sequence protein written 4 months ago by ac.research10 • updated 3 months ago by Biostar ♦♦ 20
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Comment: C: Collaboration Request to Accomplish a Task
... And I would prefer it written in python so it can fit into my other python scripts. ...
written 4 months ago by ac.research10
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Comment: C: Collaboration Request to Accomplish a Task
... Wait, i think you miss understood the task. I am not trying to extract GLY from a PDB file. I have a file (test.pdb) that ONLY has GLY's CA atoms (top example). and I am trying to add the remaining C, O, and N atoms to make up a full GLY amino acid, but also all of the GLY amino acids are oriented ...
written 4 months ago by ac.research10
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Comment: A: Sequence extaction using Biopython
... People, this might be an old post, but from Bio import SeqIO does not seem to work. is it depreciated? ...
written 7 months ago by ac.research10
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Comment: C: Module to RMSD two proteins with Python?
... Hi, I know this might be very late to comment to it, but Bio.SVDSuperimposer does not seem to rotate the proteins to get the lowest RMSD: i get RMSD = 0.2 for chains that when aligned in PyMOL give RMSD = 0.06 here is my code: fixed = Bio.PDB.Selection.unfold_entities(Bio.PDB.Polypeptide.PPBu ...
written 7 months ago by ac.research10
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Comment: C: Calculate Radius of Gyration [python 3]
... I fixed the PyMol script to make it a stand alone script capable of running on python3 independent of PyMol. Here is a link to it in case someone wants to use it in the future :-) https://github.com/sarisabban/Rg ...
written 8 months ago by ac.research10
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Comment: C: Calculate Radius of Gyration [python 3]
... Hmmm, the script from pymol does not work out of the box, but I modified it and it works now. Thanks. But the issue is that I cannot call it from within another python script (in other words I cannot run the script with python3 scriptname.py rather pymol -c scriptname.py) which means I cannot inclu ...
written 8 months ago by ac.research10
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Calculate Radius of Gyration [python 3]
... Hello Everyone, I am trying to find a way to calculate the Rg (Radius of Gyration) of a protein. I searched through Biopython but I could not find a way to do it. Is it possible to do this calculation from Biopython? Is there a script someone has written that I can use, even if it uses a library ...
pdb python radius of gyration biopython protein written 8 months ago by ac.research10
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Answer: A: How to upload fasta file to SSH Supercomputer
... There is a very simple command: scp from to Example to supercomputer: scp /path/to/your/file username@132.343.12.3:/path/to/your/destination/on/supercomputer scp /home/acresearch/desktop/uniprot90 acresearch@castor:/home/acresearch/databses Example from supercomputer: scp userna ...
written 10 months ago by ac.research10

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