Nic, We encountered this situation – see PDB ID 7MYB. We assigned the two stereoisomers to have unique residue names, unique residue numbers, and different alternate location identifiers (the A and B before the residue name below). They can have the same chain ID. The A and B alternative location IDs prevent the molecules from clashing with each other. Here is how we set it up in our case: HETATM18364 C02AUJM B1301 -4.302 21.083 108.824 0.50 33.60 C HETATM18365 C04AUJM B1301 -5.200 19.877 108.429 0.50 32.58 C HETATM18366 C06AUJM B1301 -5.027 17.825 110.133 0.50 31.64 C HETATM18367 C07AUJM B1301 -6.136 18.797 110.502 0.50 32.44 C HETATM18368 C08AUJM B1301 -6.405 19.771 109.357 0.50 34.12 C HETATM18369 O01AUJM B1301 -4.772 22.201 108.497 0.50 30.85 O HETATM18370 O03AUJM B1301 -3.216 20.883 109.410 0.50 35.44 O1- HETATM18371 S05AUJM B1301 -4.377 18.249 108.495 0.50 29.52 S HETATM18372 C02BUJP B1302 -4.324 21.167 108.876 0.31 33.43 C HETATM18373 C04BUJP B1302 -5.334 20.003 108.712 0.31 32.97 C HETATM18374 C06BUJP B1302 -5.399 17.805 110.268 0.31 31.16 C HETATM18375 C07BUJP B1302 -4.356 17.742 109.183 0.31 32.66 C HETATM18376 C08BUJP B1302 -4.618 18.801 108.125 0.31 30.79 C HETATM18377 O01BUJP B1302 -4.720 22.265 108.413 0.31 30.37 O HETATM18378 O03BUJP B1302 -3.227 20.957 109.434 0.31 34.00 O1- HETATM18379 S05BUJP B1302 -6.135 19.451 110.283 0.31 35.84 S ----------------------- John J. Tanner Professor of Biochemistry and Chemistry Associate Chair of Biochemistry Department of Biochemistry University of Missouri 117 Schweitzer Hall 503 S College Avenue Columbia, MO 65211 Phone: 573-884-1280 Email: [email protected]mailto:[email protected] https://cafnrfaculty.missouri.edu/tannerlab/ Lab: Schlundt Annex rooms 3,6,9, 203B, 203C Office: Schlundt Annex 203A From: [email protected] on behalf of Pavel Afonine Date: Thursday, September 14, 2023 at 10:47 PM To: Calvin N Steussy , [email protected] Subject: Re: [phenixbb] racemic ligand refinement WARNING: This message has originated from an External Source. This may be a phishing expedition that can result in unauthorized access to our IT System. Please use proper judgment and caution when opening attachments, clicking links, or responding to this email. On 9/14/23 21:09, Calvin N Steussy wrote: All, I need to refine a ligand that consists of two stereoisomers in my active site. I have decent density and have created models for the r and s forms of the guest with separate cif files. They have been fit independently into the active site density. My questions are; How to show these in the pdb file. Separate chains? Separate amino acids in a given chain? How do I keep them from interacting with one another during refinement? Creating an alt-position seems obvious but I'm not certain how to apply the different stereo restraints in that case. I'm sure someone has solved this before but I can't seem to find that information. Thanks, Nic Steussy Purdue University. _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]mailto:[email protected]