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

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! Best, Lei On Tue, Feb 23, 2021 at 5:04 AM Eric Pettersen 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 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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