VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 05 2002 - 10:35:48 CST

Hi Fei,
  I believe your problem is that you're using the "residue 1" part of
your selection incorrectly. The "residue" numbers are numbered internally
by VMD. If the residue you want is marked as "1" in the PDB file, then
you'll want to use "resid 1" instead. Let me know if that makes sense.
  http://www.ks.uiuc.edu/Research/vmd/vmd-1.7.1/ug/node79.html

2) Your question in part 2) is unclear to me, can you explain this
   in more detail? How did you do the selection? Did you create
   two selections that overlap? If so, then don't :-)
   If you didn't create overlapping selections intentionally, you can
   change the radius of VDW/CPK/Bonds reps etc so that a small selection
   will be visible on the outside of a long/large selection...

3) VMD has more than 1,000 colors if you're using the current version,
   so this should not be an issue for you. Let me know if you have some
   specific needs there.

If you have questions for us that you don't want to go to the entire VMD-L
mailing list, please feel free to mail them to vmd_at_ks.uiuc.edu instead
of vmd-l_at_ks.uiuc.edu. There's nothing wrong in using vmd-l however,
as long as people are courteous and don't flood everyone's inbox.
Let me know if you need more help with this.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Mar 04, 2002 at 11:06:35AM -0500, Fei Xu wrote:
> Hi! Everyone in this group:
> I am sorry to send so many emails about the same topic, but I actually
> meet difficulties in selection and coloring.
> 1 I use the expression like 'chain I ' and 'residue 1' to select the first
> base pair in chain I ( a string of DNA). Unfortunately I got the wrong
> result. I found out that the selected residue was an amino acid residue.
> By the way, I loaded the pdb file named pd0001.pdb, which has chain A to
> H(protein) and chain I and J(DNA). I tried to give individual base pairs
> any color I would like.
>
> 2 After I selected and colored the first base pair , I selected and
> colored the second one. But when the second was colored , the first one
> disappeared. That is to say, the two selection and coloring results can't
> be shown at the same time.
>
>
> 3 Can I create many other colors with RGB values? I used rasmol before,
> and it only shows 20 colors or so. I saw an introduction saying that vmd
> can show about 256 colors. Is that right?
>
> Have a nice day!
>
> Fei Xu 

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NIH Resource for Macromolecular Modeling and Bioinformatics
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