[Chimera-users] [External] Re: in *.gro file, chimera takes CL atom as C (in compound) and gives it wrong color

Lei Qian tuk04130 at temple.edu
Sun Mar 21 19:54:34 PDT 2021

Hi Eric,
Sorry for my late reply.
Yes you are right.
I tried it again: I made a new gro file containing only CL and K as ions,
and opened it using chimera.
I found chimera colored K as violet, which is good; but it colored CL as
the same color as Carbon: yellow.
Thank you again for your help!

On Tue, Feb 23, 2021 at 5:04 AM Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> Hi Lei,
> There is no explicit indication of the chemical element type in a .gro
> file, so it's all guesswork.  Chimera assumes that atom names that begin
> with any of the letters C, O, P, S, H, or N are the corresponding single
> letter element type.  This prevents atom names like CA and HG from being
> interpreted as calcium and mercury, rather than carbon and hydrogen.
> There aren't any great solutions.  One option is to read in the .gro file,
> write it out as a .mol2 file, then edit that file to change the atom type
> of the CL atoms to Cl, then read that back in.  Another is to select your
> CL atoms and use the "Modify Structure" tab of the Build Structure tool to
> change their element to Cl.
> --Eric
> Eric Pettersen
> UCSF Computer Graphics Lab
> On Feb 18, 2021, at 8:30 PM, Lei Qian <tuk04130 at temple.edu> wrote:
> Dear users,
> Could I ask a question on chimera? Thanks!
> I tried to open a gro file (small compound) using chimera. Like below:
> ... ...
>     1  LIG   CL   18   x.xxx    x.xxx      x.xxx
>     1  LIG  CL1   19   x.xxx    x.xxx      x.xxx
> ... ...
> Although chimera shows the CL name "CL" when the cursor is above the atom,
> but the CL atom color is incorrect: the same as Carbon.
> I tried to change the "CL" to "BR", and the chimera shows the correct
> color: dark red. It seems weird to me. Could you please give me any
> suggestions?
> Thanks!
> Best,
> Lei
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