msmbuilder-legacy

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Section headers don't look like headers in Sphinx theme

2

For example, the `Notes` section on the tICA class page: http://msmbuilder.org/api/generated/msmbuilder.reduce.tICA.tICA.html#msmbuilder.reduce.tICA.tICA I think this is a general problem with the available themes for Sphinx, as it seems that the default...

kyleabeauchamp

I have a problem about ConvertDataToHDF.py command.The following is my fault durning running: ## [root@localhost c1-h21r]# ConvertDataToHDF.py -t 7 -s c1-h21r.pdb -i XTC MSMBuilder version 2.6.0.dev-Unknown See file AUTHORS for...

smileyujun

Feature request: separate alignment and rmsd

4

I got a feature request for adding the ability to specify one set of atom indices for alignment and one for the rmsd calculation. Thought I'd put it out here...

gbowman

``` -------------------------------------------------------------------------------- Copyright 2011 Stanford University. MSMBuilder comes with ABSOLUTELY NO WARRANTY. ```

jimsnyderjr

ContinuousContact.prepare_trajectory bug

1

The continuous contact metric uses mdtraj.compute_contacts to prepare a trajectory, but the problem is that mdtraj function returns both the prepared trajectory and a list of the contacts used. the...

schwancr

Use MDTraj instead of LPRMSD in msmb.metrics.Positions

3

I forget, but is our MDTraj RMSD stuff now sufficiently general to stop using LPRMSD here? I guess the key factor is aligning to a subset of atoms, then calculating...

kyleabeauchamp

Hey guys, I've been trying to develop a way to calculate an accurate metastability for a kinetic intermediate state in my protein system, and I came up with I think...

jadeshi

AttributeError: type object 'RMSD' has no attribute 'TheoData'

1

Using the latest Master build, attempted to cluster some trajectory data using LPRMSD with the following script: ``` alignment=lprmsd # Alignment method stride=50 # Stride cluster=hierarchical # Clustering metric align_atoms=ProteinIndices.dat...

s-gordon

Update tICA docs

26

So there's a file docs/tICA/tICA.pdf that shares a lot in common with http://msmbuilder.s3-website-us-east-1.amazonaws.com/theory/tICA.html However, there are several key differences: 1. HTML version is missing the actual MSMBuilder commands I also...

kyleabeauchamp

Question: Criteria for selecting an 'appropriate' number of microstates

1

Hi all. My understanding is that when making a fine-grained MSM, the intention is make as many states as possible to gain a sufficiently detailed kinetic landscape, yet at the...

s-gordon