[Chimera-users] Save pdb problem

[Eric Pettersen]

Hi Rui,
	The first thing you have to do is combine the two models into one.  Do this by going to the Model Panel and choosing “copy/combine…” on the right.  In the resulting dialog, make sure to check the “Close source models” box.
	You then have two options to change the chain IDs.  The most straightforward one is to simply save a PDB file and hand edit the chain ID column from blank to the proper chain ID for those residues that are missing IDs.  Tedious but simple.
	The other option is to select the parts missing chain IDs and using a Python script that I have attached to set the chain IDs.  First you would select the parts you want to get chain ID ‘A’ and then run the script (simply by opening it).  Then you would select the parts you want to get chain ID B and edit the first line of the Python file to change ‘A’ to ‘B’ and then run the script.  The simplest way to do the select is to again use the Model Panel and pick “select chains…” on the right.  Use the right side of the resulting dialog to select by connectivity.  You will be able to select the entirety of chain A (and later chain B), including its glycans.  The you can use the script to set the selection to the proper ID.
	This will leave the ligand with no ID because it isn’t connected to anything.  Nonetheless, you can then select it with the command (Favorites→Command Line) “sel ~:.A-B” (i.e. select everything that doesn’t have chain ID A or B).  Then you can again use the script to set its ID to whatever you want.

—Eric

	Eric Pettersen
	UCSF Computer Graphics Lab



> On Nov 25, 2019, at 4:22 PM, Rui Chen <rchen6 at ualberta.ca> wrote:
> 
> Please find attached the PDB files. The first one is the monomer/ligand PDB file, the second is the homodimer PDB file, the last one is the PDB file saved by chimera. Thank you. Have a good night.
> 
> On Mon, Nov 25, 2019 at 5:18 PM Rui Chen <rchen6 at ualberta.ca <mailto:rchen6 at ualberta.ca>> wrote:
> Hello, 
> 
> I docked a ligand into a monomer, now I want to save a new pdb file. In the new pdb file, chian A will be docked monomer, chain B will be the chain B of homodimer. I already superimposed the two PDB files and deleted chain A of homodimer. I also used change chain ID to add chain IDs to the combined PDB file. However I got the following problems:
> 1. In my system, there are glycans (residue name: 0YB), I cannot add chain ID to the glycans (residue 209-216 belongs to chain A, residue 425-432 belongs to chain B)
> 2. In my system, I also have a small molecule docked in chain A, I realized only the last line of the ligand was given a chain ID "h", is this a problem?
> 3. I want to save these two PDB files as two chains, not two models (actually it's a homodimer except for the ligand)
> 4. Can I manually delete all the connections?
> 
> Looking forward to your reply.
> 
> Best regards,
> Rui
> 
> <rep0_chianA_6058_pose1.pdb><rep0_dimer_prepared.pdb><rep0_6058_pose1_dimer.pdb>_______________________________________________
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