#215 JSMOL Color by chain or residue number

v10
open
nobody
5
2014-05-22
2014-04-18
Eleanor
No

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

Feature Requests: #215

Discussion

  • Bob Hanson

    Bob Hanson - 2014-04-18

    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:


    Status: open
    Group: v10
    Labels: Color residue number chain JSMOL
    Created: Fri Apr 18, 2014 07:55 PM UTC by Eleanor
    Last Updated: Fri Apr 18, 2014 07:55 PM UTC
    Owner: nobody

    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!

    Sent from sourceforge.net because you indicated interest in
    https://sourceforge.net/p/jmol/feature-requests/215/

    To unsubscribe from further messages, please visit
    https://sourceforge.net/auth/subscriptions/

    --
    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

  • Eleanor

    Eleanor - 2014-04-19

    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?

     
    • Bob Hanson

      Bob Hanson - 2014-04-19

      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:

      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?

      Status: open
      Group: v10
      Labels: Color residue number chain JSMOL
      Created: Fri Apr 18, 2014 07:55 PM UTC by Eleanor
      Last Updated: Fri Apr 18, 2014 07:55 PM UTC
      Owner: nobody

      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!

      Sent from sourceforge.net because you indicated interest in
      https://sourceforge.net/p/jmol/feature-requests/215/

      To unsubscribe from further messages, please visit
      https://sourceforge.net/auth/subscriptions/

      --
      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

  • Eleanor

    Eleanor - 2014-04-23

    I sent an email a couple nights ago. Have you received it?

     
    • Bob Hanson

      Bob Hanson - 2014-04-23

      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:

      I sent an email a couple nights ago. Have you received it?

      Status: open
      Group: v10
      Labels: Color residue number chain JSMOL
      Created: Fri Apr 18, 2014 07:55 PM UTC by Eleanor
      Last Updated: Sat Apr 19, 2014 06:43 PM UTC
      Owner: nobody

      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!

      Sent from sourceforge.net because you indicated interest in
      https://sourceforge.net/p/jmol/feature-requests/215/

      To unsubscribe from further messages, please visit
      https://sourceforge.net/auth/subscriptions/

      --
      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

  • Eleanor

    Eleanor - 2014-04-23

    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.

     
  • Eleanor

    Eleanor - 2014-04-26

    Here are the files. I would really like to know the best solution for this.

     
  • Bob Hanson

    Bob Hanson - 2014-04-26

    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

     
  • Eleanor

    Eleanor - 2014-04-26

    Great! That's it! Thank you! Sorry for the confusion!

     
  • Eleanor

    Eleanor - 2014-05-17

    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!

     
    • Bob Hanson

      Bob Hanson - 2014-05-17

      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:

      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!

      [feature-requests:#215] JSMOL Color by chain or residue number

      Status: open
      Group: v10
      Labels: Color residue number chain JSMOL
      Created: Fri Apr 18, 2014 07:55 PM UTC by Eleanor
      Last Updated: Sat Apr 26, 2014 02:16 PM UTC
      Owner: nobody

      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!

      Sent from sourceforge.net because you indicated interest in https://sourceforge.net/p/jmol/feature-requests/215/

      To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/

       

      Related

      Feature Requests: #215

  • Eleanor

    Eleanor - 2014-05-22

    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.

     

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