User: Reyhaneh

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Reyhaneh480
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United Kingdom
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4 years, 9 months ago
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Posts by Reyhaneh

<prev • 92 results • page 1 of 10 • next >
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Getting the interacting protein chains in a PDB file
... Hi I am trying to write a script which automatically picks the subunits for a protein complex. Instead of the PDB I am using the IMGT format which is just different numbering system. For example for 1KJ3, we have: http://www.imgt.org/3Dstructure-DB/cgi/details.cgi?pdbcode=1KJ3&Part=File By l ...
pdb python interaction protein biopython written 4.8 years ago by Reyhaneh480
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Pymol fails to run on Mac
... Hi,   I have installed pymol on my Mac using: brew install homebrew/science/pymol when I try to run pymol I get the following error: MP02s-iMac:$ pymol Traceback (most recent call last): File "/usr/local/Cellar/pymol/1.7.6.0/libexec/lib/python2.7/site-packages/pymol/__init__.py", line 71, ...
mac python pymol written 4.8 years ago by Reyhaneh480 • updated 4.7 years ago by Biostar ♦♦ 20
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RMSD between two Ligands
... I have several docked conformations of one ligand docked to a receptor and I would like to calculate the RMSD between each docked ligand and the native ligand after superposing the docked receptor on the native receptor. Currently my code does all the steps above but when calculating the RMSD betwee ...
rmsd ligand rmsd ligand written 5.8 years ago by Reyhaneh480
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Building Rotamer Library for Side Chain Prediction
... I have a dataset of proteins (PDBs) and I would like to build a Rotamer Library from the Side Chains of these proteins. I know that there are plenty of methods out there which does it and their libraries are available. But I have failed to find the tools which you can actually use to generate the li ...
rotamer library rotamer side chains written 5.8 years ago by Reyhaneh480
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Detecting Terminals In Protein Structures
... Hi I want to detect C-terminals and N-terminals in a set of protein PDB files. The loop structure (with no helical/sheet secondary structure) at start of the structure can be counted as N-terminal and similarly the loop region at end for C-terminal. But the problem is that these loops are not alw ...
pdb protein written 6.8 years ago by Reyhaneh480 • updated 6.8 years ago by andreas.prlic290
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Plop (Protein Local Optimization Program) Protein Loop Prediction
... Hi Has anybody used PLOP (Protein Local Optimization Program) to perform loop prediction. I want to predict the loop which is located between resi 42-46 on chain A of input 2IGD.pdb. My control command looks like this: datadirectory /PLOPDirectory/data file logfile modeled_plop_job.log load pdb ...
protein-structure protein written 7.0 years ago by Reyhaneh480
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Psiblast Fasta Formatted Output
... Hi, I have a FASTA formatted protein sequence (stored in DsbA.fa) and I would like to use PSI-BLAST (not the web server. The command line in the BLAST+ package) to generate hits. I am using the following command line: ./psiblast -query DsbA.fa -db Proteobacteria -num_iterations=6 -evalue=0.005 -ou ...
fasta blast+ written 7.0 years ago by Reyhaneh480 • updated 2.1 years ago by Biostar ♦♦ 20
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Comment: C: Weighted Graph Matching In Bioinformatics
... have you checked this? http://string-db.org/ ...
written 7.5 years ago by Reyhaneh480
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Compare Quality Of 3D Structural Alignement
... Hi; I am looking for a measure to compare the quality of several pairwise protein interface alignments. assume that I have 4 protein interfaces (A,B,C and D) and I align (A with C) (A-C) and (B with D)(B-D). Mainly RMSD is used for showing how well the interfaces are aligned but the problem is i ...
alignment protein written 7.5 years ago by Reyhaneh480
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Reduce Pymol Session (.Pse) File Size
... Hi; I am using pymol to display a protein complex with 3 chains: Two chains in cartoon mode (one with 800 residues and the other one with 300 residues). The third chain in surface representation (300 residues). I have also highlighted some specific residues in the display. The problem is tha ...
pymol protein written 7.6 years ago by Reyhaneh480 • updated 5.3 years ago by Biostar ♦♦ 20

Latest awards to Reyhaneh

Great Question 5.1 years ago, created a question with more than 5,000 views. For What Is A Heavy Atom?
Popular Question 5.1 years ago, created a question with more than 1,000 views. For Where To Access Protein Quaternary Structure (Pqs) Data
Popular Question 5.1 years ago, created a question with more than 1,000 views. For Csharp For Programming In Bioinformatics
Popular Question 5.1 years ago, created a question with more than 1,000 views. For Aligning One Protein Sequence With A Multiple Sequence Alignment
Popular Question 5.1 years ago, created a question with more than 1,000 views. For Pymol-Generate Pymol Movie To Mpeg
Popular Question 5.1 years ago, created a question with more than 1,000 views. For Generating All Interacting Partners Of A Protein
Popular Question 5.1 years ago, created a question with more than 1,000 views. For What Is A Heavy Atom?
Popular Question 5.1 years ago, created a question with more than 1,000 views. For Protein Sequence Alignment Based On 3D Structure Alignment- For Windows
Great Question 5.5 years ago, created a question with more than 5,000 views. For Calculate Percentage Of Identity Between Protein Sequences Using Clustalw
Popular Question 5.8 years ago, created a question with more than 1,000 views. For Aligning One Protein Sequence With A Multiple Sequence Alignment
Popular Question 5.8 years ago, created a question with more than 1,000 views. For Csharp For Programming In Bioinformatics
Popular Question 5.8 years ago, created a question with more than 1,000 views. For What Is A Heavy Atom?
Appreciated 6.7 years ago, created a post with more than 5 votes. For Functional Classification Of Protein Complexes
Good Question 6.7 years ago, asked a question that was upvoted at least 5 times. For Functional Classification Of Protein Complexes
Popular Question 6.7 years ago, created a question with more than 1,000 views. For What Is A Heavy Atom?
Popular Question 6.7 years ago, created a question with more than 1,000 views. For Csharp For Programming In Bioinformatics
Popular Question 6.7 years ago, created a question with more than 1,000 views. For Pymol-Generate Pymol Movie To Mpeg
Popular Question 6.7 years ago, created a question with more than 1,000 views. For Blast Against Pdb Standalone Version
Popular Question 6.7 years ago, created a question with more than 1,000 views. For Capri Criteria For Evaluating Docked Protein Complexes
Popular Question 6.7 years ago, created a question with more than 1,000 views. For Calculate Percentage Of Identity Between Protein Sequences Using Clustalw
Popular Question 6.7 years ago, created a question with more than 1,000 views. For Blast+ Stand Alone Version For Sequence Alignment
Supporter 6.7 years ago, voted at least 25 times.
Teacher 6.7 years ago, created an answer with at least 3 up-votes. For A: Same Protein Across Different Species In Pdb (Suitability For Docking?)
Student 6.7 years ago, asked a question with at least 3 up-votes. For Aligning One Protein Sequence With A Multiple Sequence Alignment
Student 6.7 years ago, asked a question with at least 3 up-votes. For Where To Access Protein Quaternary Structure (Pqs) Data

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