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#215 JSMOL Color by chain or residue number
Is it possible to color by chain using the residue number?
For example, in my pdb file the lines are set up like this:
HETATM 39 C AAA 5 33.92 -59.98 -8.73 1.0 1.0
How would I color the chains by the column where the first “5” is? I have the atoms categorized by that number so that all of the atoms in a specific chain are given one number.
Any help would be greatly appreciated! Thanks!
Related
color chains
will do that. But you can also be more specific and use
color {*:5} red
and you can say
select *:5
":" is the chain indicator.
On Fri, Apr 18, 2014 at 2:55 PM, Eleanor eleffler@users.sf.net wrote:
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
Related
Feature Requests: #215
Okay, I tried that and it did not work. Nothing changed.
I tried this first:
script: "load ./pchd-hydrated-15-cg-10.pdb; color chains; wireframe on; wireframe: 0.1; spacefill on; spacefill 20%; color chains;". I also changed the position within the line.
Am I doing something incorrectly?
Please send the file to hansonr@stolaf.edu so I can see what the issue is.
Maybe you have the wrong column.
On Sat, Apr 19, 2014 at 1:43 PM, Eleanor eleffler@users.sf.net wrote:
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
Related
Feature Requests: #215
I sent an email a couple nights ago. Have you received it?
I was expecting you to send a file to hansonr@stolaf.edu -- have not seen
that. I'm pretty sure you have a column problem; coloring by chain is no
problem.
On Tue, Apr 22, 2014 at 7:49 PM, Eleanor eleffler@users.sf.net wrote:
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
Related
Feature Requests: #215
Yes, I sent it to that address.
If it is a column problem, is there still a way to color by chain using a different ID/column? I'm converting CHIME pages to JSMol and it would be best to not edit the original pdb files, especially since there are so many.
Here are the files. I would really like to know the best solution for this.
Sorry for my confusion, Eleanor. I didn't catch what you said so clearly, that you were using residue number as a placeholder for chain. It is very simple:
color property resno
Great! That's it! Thank you! Sorry for the confusion!
Is there a resource or link that gives the names of each column?
I need the name of the 5th column (to color, again).
Thanks!
Yes. Google RCSB FILE PDB FORMAT
Sent from my stupid iPhone
On May 17, 2014, at 10:27 PM, "Eleanor" eleffler@users.sf.net wrote:
Related
Feature Requests: #215
I want to color by the charge column; however, when I do "color property charge", it only colors numbers the first few and then the rest are one color (blue in my case). A "rangeSelected" command is mentioned in the manual... However, the column goes up to 200, is there a simpler way to color each number differently?
I have attached one xyz file.