[Chimera-users] Problem with Rainbow and "abnormal" PDB data

Christian Schudoma schudoma at mpimp-golm.mpg.de
Fri Sep 17 02:13:25 PDT 2010

Dear Eric and Elaine,

thanks very much, the bfactor + rangecolor - option works for me and 
Elaine's points might come in handy at a later point in time.


On 09/16/2010 08:38 PM, Elaine Meng wrote:
> Hi Christian,
> I would only add a couple of points to Eric's suggestion to use the 
> "bfactor" attribute.  These may or may not be relevant to your situation:
> (1) Coloring by attribute is particularly nice for continuous-valued 
> things, because they can be mapped to continuous gradations of color. 
>  I can't tell whether you want continuous coloring (e.g. red gradually 
> shading to blue from one value to another) or discrete (e.g. exactly 
> red for one group, exactly blue for another group).  In the Render by 
> Attribute tool, your value distribution will be shown in a histogram. 
>  One way to achieve discrete coloring would be to bracket each value 
> with two thresholds (the vertical colored sliders that define the 
> color mapping on the histogram) of the same color.  Or, you could use 
> commands something like
> color hot pink @/bfactor=1
> color orange @/bfactor=2
> (2) Attributes could also be assigned with a separate input file, 
> instead of the PDB file.  It is a simple tab-separated column format, 
> description and examples here:
> <http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/defineattrib/defineattrib.html#attrfile>
> That allows assigning multiple different attributes without having to 
> make more PDB files. These attributes can be of different value types 
> (float, integer, boolean, color, character string), they can be named 
> anything you want instead of just bfactor, and if they are 
> floating-point numbers of high precision you can use more digits than 
> are available in the bfactor field in standard PDB format.
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Sep 16, 2010, at 11:08 AM, Eric Pettersen wrote:
>> Hi Christian,
>> I'm happy you like Chimera enough to mis-use in in this way! :-) 
>>  However, I don't think "rainbow" is the way to go here.  Rainbow 
>> only affects connected strings of residues.  For example, if you 
>> rainbow a protein system, waters and ligands will retain their 
>> original colors (and for your system, Chimera really has no way of 
>> knowing that your "residues" aren't peptide ligands).
>> SInce you are creating your own PDB files anyway, what I suggest is 
>> that your put your "grouping info" into the bfactor field.  Then you 
>> can use the Render by Attribute tool (or the rangecolor command) to 
>> color your points based on their bfactor.
>> --Eric
>>                         Eric Pettersen
>>                         UCSF Computer Graphics Lab
>> http://www.cgl.ucsf.edu <http://www.cgl.ucsf.edu/>

Christian Schudoma, M.Sc.
Ph.D. Student

Bioinformatics Group
Max Planck Institute of Molecular Plant Physiology
Am Muehlenberg 1
14476 Potsdam-Golm

phone: +49 (331) 567-8624
email: schudoma at mpimp-golm.mpg.de

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