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Hi,
After using 'BuildMSM.py', a macro-state network is obtained. Let's say 100-node network.I am wondering how to extract the centroid structures. Or is there a built-in function which calculates th…
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Using the latest Master build, attempted to cluster some trajectory data using LPRMSD with the following script:
```
alignment=lprmsd # Alignment method
stride=50 # Stride
cluste…
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File like
mode | affinity | dist from best mode
| (kcal/mol) | rmsd l.b.| rmsd u.b.
-----+------------+----------+----------
because it appears in my terminal only i want this as extra file…
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I think it would be great to implement the calculation of diffusion coefficients using the Green-Kubo and/or Einstein formulas.
This feature is among [gromacs](http://www.gromacs.org/Documentation/…
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The first file contain hydrogen but when i use --no-hydrogen and --reorder ,it's still reported that structure not same size .They are both 169 residues.
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I am working with a system composed of one protein and a ligand. When I open the docking results generated by GaudiMM with gaudiview and I try to cluster them this error appears:
```
Traceback (in…
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**Is your feature request related to a problem? Please describe.**
I need to align by the maximum common substructure.
**Describe the solution you'd like**
*Corrected code:*
```python
def mc…
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### Issue summary
Docking simulation was performed using vina and gnina, respectively.
Next, we calculated the RMSD of the template and simulation results using the TOOL provided by “The Yang Zhan…
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Here's a "fun" one: when using Coot my map contour will only adjust if I scroll very, very slowly. Here is a relevant section of the log:
```
pushing statusbar text: Map 0 contour_level 0.463 n-…
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So my one beef with the current scripts is how the meaning of various flags _changes_ as you move from left to right. I know we're short on characters, but I bet a lot of people are troubled by the f…