I currently have a protein which is the focus of my study (.pse file) and several ligands (.pdb files) that I wish to bind to this protein to view where and how they bind. However, there are no biological sequences for the given molecules, so I am wondering what command I need to bind the ligand molecules to the main protein 1 at a time.
When I open the ligand files from the main protein file, I can see the ligand molecules but does this show an accurate representation of where they are actually binding?
Thank you!
For those of you who are wondering, you simply need to open your protein file (from MOE) within PyMOL and it will bind correctly, as binding information is stored in the file from MOE.
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I trained my model in Nvidia Digits 5 and I would now like to extract the accuracy and loss plots that were generated during training for a report. Is this data saved somewhere so that it would possible to extract the data for these plots so that I could plot it in Python and perhaps ultimately modify the plots to compare different models etc?
The best solution I have found is to either look at the HTML file or to scan the text file caffe_output.log that is produced by Caffe. The text file is usually stored in /var/digits/jobs/insert_your_job_id/ but you can also just run on linux systems:
locate caffe_output.log
Go to your DIGITS job folder and locate your job's subfolder. Inside you'll find a file status.pickle, which is a pickled object containing all your job's information.
You can load it in python like so:
import digits
import pickle
data = pickle.load(open('status.pickle','rb'))
This object is somewhat generic and may contain multiple tasks. For a typical classification task it will likely be just one, but you will still need to access it via data.tasks[0]. From there you can grab the plots:
data.tasks[0].combined_graph_data()
which returns a somewhat convoluted dict (unfortunately - since your network can produce many accuracy/loss outputs, as well as even custom ones). It contains everything you need though - I managed to plot accuracy with:
plt.plot( data.tasks[0].combined_graph_data()['columns'][2][1:] )
but it's likely that you'll have to write a bit of custom code. As always, dir() is your friend.
How could I read Garmin's .fit file on Linux. I'd like to use it for some data analysis but the file is a binary file.
I have visited http://garmin.kiesewetter.nl/ but the website does not seem to work.
Thanks
You can use GPSbabel to do this. It's a command-line tool, so you end up with something like:
gpsbabel -i garmin_fit -f {filename}.fit -o csv -F {output filename}.csv
and you'll get a text file with all the lat/long coordinates.
What's trickier is getting out other data, ie: if you want speed, time, or other information from the .fit file. You can easily get those into a .gpx, where they're in xml and human-readable, but I haven't yet found a single line solution for getting that data into a csv.
The company that created ANT made an SDK package available here:
https://www.thisisant.com/resources/fit
When unzipping this, there is a java/FitCSVTool.jar file. Then:
java -jar java/FitCSVTool.jar -b input.fit output.csv
I tested with a couple of files and it seems to work really well. Then of course the format of the csv can be a little bit complex.
For example, latitude and longitude are stored in semicircles, so it should be multiplied by 180/(2^31) to give GPS coordinates.
You need to convert the file to a .csv, the Garmin repair tool at http://garmin.kiesewetter.nl/ will do this for you. I've just loaded the site fine, try again it may have been temporarily down.
To add a little more detail:
"FIT or Flexible and Interoperable Data Transfer is a file format used for GPS tracks and routes. It is used by newer Garmin fitness GPS devices, including the Edge and Forerunner." From the OpenStreetMap Wiki http://wiki.openstreetmap.org/wiki/FIT
There are many tools to convert these files to other formats for different uses, which one you choose depends on the use. GPSBabel is another converer tool that may help. gpsbabel.org (I can't post two links yet :)
This page parses the file and lets you download it as tables. https://www.fitfileviewer.com/ The fun bit is converting the timestamps from numbers to readable timestamps Garmin .fit file timestamp
I am putting together a project where I need to be able to source outside data as a means of inputting skeleton joint positions into Maya. Basically I have a spreadsheet of sequential joint positions for the skeleton which I would like to load into Maya and then link to the skin. Does anyone know a way to upload or reference these positions (as FK into Maya)?
Probably the easiest thing to do is to convert your spreadsheet data to atom format
Atom is a json based format for exchanging animation data and, since its JSON based you should be able to concoct a CSV to ATOM translator using Python's built in csv and json modules.
So I'm using a PyMOL script to find the surface residues on a protein (found at http://www.pymolwiki.org/index.php/FindSurfaceResidues). And I need it to write a text file containing the name of the protein that is currently selected in the PyMOL session. As far as I've searched, I can't find a PyMOL command to get the name of the selected protein. Does anyone with more experience with PyMOL have an idea on how to accomplish this?
Thanks
I think you are looking for the get_names function.
I m trying to find gene_info file with genenames and chromosomal location. However, I can't seem to locate it on NCBI FTP site. Can anyone give me a pointer?
See: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/README for details of what is in what files at the NCBI ftp site.
If you want to get the data from NCBI itself you will need to combine multiple files, probably a gene2accession (which also includes position information) and a gene_info file which maps ids to symbols and names etc.
It is probably more convenient to go to the UCSC site for this information, they also provide a public mysql database if you want to explore what is available:
http://workshops.arl.arizona.edu/sql1/sql_workshop/mysql/mysqlclient.html
If you just want human, mouse or rat data then the Rat Genome Database has already compiled the data you want (fresh from the NCBI and Ensembl sources):
ftp://rgd.mcw.edu/pub/data_release
e.g. for human data look at: ftp://rgd.mcw.edu/pub/data_release/GENES_HUMAN.txt