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anyuzx / HIPPS-DIMES

Maximum Entropy Based HI-C/Distance Map - Polymer Physics - Structures Method
MIT License
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Visualizing structures #1

Closed jessakay closed 2 years ago

jessakay commented 3 years ago

Thanks for make your method so accessible! It was a breeze to run and your paper was really clear and helpful for me to compute metrics such as F(k) or Q(k). But I'm having some trouble plotting the output structures described in the xyz file, as I'm not so familiar with molecular visualization. Would you mind sharing the script (PyMOL? VMD?) used to generate the 3D structures in your paper? Figure 4 (a) for example.

anyuzx commented 3 years ago

hello, the generated .xyz file should be directly compatible with VMD. Could you send the xyz file so that I can have a look at. Also, in the end of this jupyter notebook https://github.com/anyuzx/HIPPS-DIMES/blob/main/walkthrough.ipynb, there is a screen record for showing how to load the .xyz into VMD. Thanks.

jessakay commented 3 years ago

Sorry that I missed your reply. Please find attached an example xyz file. ESC.chr1.1.xyz.zip

I'm hoping to in the end produce something similar to the your example below image

Apologies in advance for asking such a basic question, I'm not so familiar with VMD and would really appreciate your help

anyuzx commented 3 years ago

hello, the plot you referred to is actually rendered using OVITO. In VMD, it is possible to generate similar plot. However, I don't use script for VMD, the visualization are done by manually select various options. You can check the gif at the end of this notebook https://github.com/anyuzx/HIPPS-DIMES/blob/main/walkthrough.ipynb. I also recommend you to read this tutorial https://www.ks.uiuc.edu/Research/vmd/current/ug/node15.html.