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#236 How to color residues based on RSRZ values in jsmol?
Hello,
I'm just wondering if it's possible to color residues based on RSRZ values in jsmol? I'm trying to add a new feature to color RNA 3D motifs by RSRZ values in our web applications. Here is an example of page: http://rna.bgsu.edu/rna3dhub/pdb/6TNA/interactions/fr3d/basepairs. But I'm not sure what is the best way of doing this. Has anyone tried doing something similar before?
Hi, Sri Devan
We will need some more details:
You might load any data using the "load data" or "data" command; of course Jmol need to know which atom each datum belongs to.
Hi Angel Herraez,
We are interested in mapping various structure quality measurements that cover over a range of numerical values to the residues in the PDB structures. One of such quality measurements is the RSRZ which stands for Real Space R value Z score: (http://www.wwpdb.org/validation/legacy/XrayValidationReportHelp)
and ranges from -3 to 3. At the moment these values are stored in our database. So I basically would like to create a custom coloring scheme (Green < 1, Yellow < 2, Orange < 3, Red >= 3) to color the residues by RSRZ. At the moment, I'm not sure how I can map these values to the residues in a structure? I basically have a javascript object that stores key-pair values of the residue and the RSRZ. What would be the best way to map these values to the residues in the coordinate files? Can you give me some pointers how I can achieve this? Thanks
This should be no problem.
load *1d66.pdb/val
color property_rsrz
You can adjust the color scheme -- see documentation at
https://chemapps.stolaf.edu/jmol/docs
However, there are two issues:
1) color property_xxxx is broken. (Will fix today or tomorrow.)
2) it looks like the call to EBI for the validation information is not
working the way it used to. I'm looking into that.
Bob Hanson