Thanks George The residues of the loops are already assigned with ARESNAME and BRESNAME and it is ok to refine both loops What I would like to do is then to add the ligand. But in the apo state it clashes with one residue of the loop. So I thought fixing the occupancy to 0 (zero), for one ALT of the ligand (with apo loop) and having a second ALT with an occupancy <1 (bound loop) to try to prevent atom clashing. Is it the right strategy ? And how to do it ? Moreover, it seems to get more complicated as the bound ligand can also exist with at least 2 different alternatives (different orientation of a central indole ring).

Le 24 juil. 2018 à 09:49, G_Kontopidis a écrit :

Hi Havier,

You got the formula right alternate loop A" occupancy = X and "alternate loop B" occupancy = ligand occupancy = 1-X You may have also some water include in the model correspond to alternate loop A" occupancy = X I have done it many times using RefMac and SHELX I am sure it is working in Phenix as well . you do not need something specific in a parameter file for the protein atom. The PDB file look like the following. ATOM 258 CA AGLN A 35 2.979 -4.265 69.678 0.40 46.35 C ANISOU 258 CA AGLN A 35 4942 7133 5533 0 946 -219 C ATOM 259 CA BGLN A 35 3.127 -4.246 69.643 0.60 47.74 C ANISOU 259 CA BGLN A 35 5152 7285 5702 0 930 -219 C The alternative atom specified with letter A and B before the amino acid three letters. Regards,

George From: [email protected] [mailto:[email protected]] On Behalf Of Xavier Brazzolotto Sent: Tuesday, July 24, 2018 9:50 AM To: [email protected] Subject: [phenixbb] Ligand occupancy and conformational change

I am struggling with a ligand bound structure. The ligand seems to induce a small conformational change of one loop. However, despite my efforts I did not get any data with a full occupancy for this ligand yet.

As a result, I have to deal with a loop in apo state (where ligand occupancy = 0) and a loop with a bound ligand (where ligand occupancy <1) and where the ligand is clashing with the modelled loop in the apo state. Hope I did myself clear.

How to deal with this situation ? I am sure that phenix.refine can do it but how ? What I would like to try is something like that "alternate loop A" occupancy = X and "alternate loop B" occupancy = ligand occupancy = 1-X Maybe something specific in a parameter file ?

Thank you for your help Xavier

Xavier Brazzolotto, PhD [email protected] Département de Toxicologie et Risques Chimiques Unité Neurotoxiques Institut de Recherche Biomédicale des Armées 1 Place du Général Valérie André, BP 73 91223 Brétigny sur Orge France Phone +33 (0) 1 78 65 14 00 Alt Phone +33 (0) 4 57 42 87 19 Cell +33 (0) 6 58 36 39 09 The information in this e-mail may be privileged and confidential, intended only for the use of the addressee(s) above. Any unauthorized use or disclosure of this information is prohibited. If you have received this e-mail by mistake, please delete it and immediately contact the sender. This is not an official email address of the French Ministry of the Armed Forces. It does not allow diffusion of protected informations and does not necessarily complies to the ministry cyber security policy.

Hi Xavier, In addition to Edward's suggestion, you can have a look at "13 typical occupancy refinement scenarios and available options in phenix.refine" article here: http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=12 Scenario #7 looks like your case, but you will have your ligand only in one conformation. Best regards, Oleg Sobolev. On Tue, Jul 24, 2018 at 8:25 AM, Edward A. Berry wrote:

You can make very general alternate conformations with the "constrained_group" construction. Say the loop is N12:14 and ligand is R221 present only in A conformation. You can also add waters to either conformation. The following is for running from .eff script, but I expect it is available from the Gui. There is a detailed description of handling alt conf in one of the newsletters.

refine { occupancies { constrained_group { selection = ((chain N and resseq 12:14) or (chain R and resid 221)) \ and altloc A selection = (chain N and resseq 12:14) and altloc B

}

}} On 07/24/2018 02:49 AM, Xavier Brazzolotto wrote:

...

I am struggling with a ligand bound structure. The ligand seems to induce a small conformational change of one loop. However, despite my efforts I did not get any data with a full occupancy for this ligand yet.

As a result, I have to deal with a loop in apo state (where ligand occupancy = 0) and a loop with a bound ligand (where ligand occupancy <1) and where the ligand is clashing with the modelled loop in the apo state. Hope I did myself clear.

How to deal with this situation ? I am sure that phenix.refine can do it but how ? What I would like to try is something like that "alternate loop A" occupancy = X and "alternate loop B" occupancy = ligand occupancy = 1-X Maybe something specific in a parameter file ?

Thank you for your help Xavier

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