I am bit confused,
As when I have input pdb file it had CL1 denotation for Chlorine atoms and in library file it has given me output as Cl1.
Is it obvious?
The I was playing around with my ligand containing chlorine and found that changing CL1 to CL or Cl removes the green, it is green as long it is Cl1 or Cl1.
I my complex file I am getting Cl1, so it should be green only.
________________________________
From: David Case <david.case.rutgers.edu>
Sent: Thursday, February 2, 2017 6:37:35 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Tleap is making C instaed of Cl
On Thu, Feb 02, 2017, Thakur, Abhishek wrote:
>
> But after solvating the system when I am generating the complex pdb and
> viewing in chimera I cannot see green color for Chlorine, it looks like
> carbon. But when I see the atom nae it says Cl1.
Look at the PDB file you are actually loading in Chimera: does the chlorine
atom have the correct element (columns 77-78 in the ATOM line)? If not, we
would need details about how you made the PDB file. If it looks OK, it might
be a Chimera issue (although that sounds kind of unlikely).
Just take a small pdb file (say the ligand itself), and play around with
what you need to do to get Chimera to color the atom the way you want.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.ambermd.org_mailman_listinfo_amber&d=DwICAg&c=y2w-uYmhgFWijp_IQN0DhA&r=0Hah93XWYYBgmROOVcaccg&m=vzUdvQy_lfAZVb1UgtKFhf0481UXpfK6W1yZxFhd3sM&s=qR5eFSbsyhMiaipVSk173umPQlj2-IwVIGYySvAbA1E&e=
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 02 2017 - 10:00:03 PST
