Hi: I’m refining a site where there’s two compounds, each at partial occupancy. I modeled that using alt codes and insertion codes combined, like this ATOM 6500 CA ACYS B 101B ATOM 6490 CA BXXX B 101A How can I constrain the occupancies so that they sum to unity? I tried several option, but the distinct insertions seem to refine independently. Sorry if a similar question has been posted before, but I could not find a solution searching phenixbb. Thanks! Henry
Dear Henry, you can find the answer here https://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=12 example 5. Unfortunately 1EJG does not open in coot, because of a coordinate read error ERROR 42 READ: Duplicate sequence number and insertion code. LINE #875 ATOM 414 CA BSER A 22 6.034 13.399 -2.687 0.21 1.55 However pymol works. The example is crambin Here is pasted and changed a bit one sentence from the newsletter: If residuenumber and chain ids are identical,while altloc are different, as well as residue names are allowed to be different. So you have to remove 27 AChar iCode Code for insertion of residues. this should work ATOM 6500 CA ACYS B 101 ATOM 6490 CA BXXX B 101 Phenix will handle this then automatically. Best regards, Georg. On 10/15/2016 11:15 PM, van den Bedem, Henry wrote:
Hi:
I’m refining a site where there’s two compounds, each at partial occupancy. I modeled that using alt codes and insertion codes combined, like this
ATOM 6500 CA ACYS B 101B
ATOM 6490 CA BXXX B 101A
How can I constrain the occupancies so that they sum to unity? I tried several option, but the distinct insertions seem to refine independently. Sorry if a similar question has been posted before, but I could not find a solution searching phenixbb.
Thanks!
Henry
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Hi Henry, have you created a proper constraint group including both compounds as described in the manual under special cases for occupancy refingement? That should work, I presume. Cheers Christian Am 15.10.2016 um 22:15 schrieb van den Bedem, Henry:
Hi:
I’m refining a site where there’s two compounds, each at partial occupancy. I modeled that using alt codes and insertion codes combined, like this
ATOM 6500 CA ACYS B 101B
ATOM 6490 CA BXXX B 101A
How can I constrain the occupancies so that they sum to unity? I tried several option, but the distinct insertions seem to refine independently. Sorry if a similar question has been posted before, but I could not find a solution searching phenixbb.
Thanks!
Henry
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Hi Henry, first off you don't need to use insertion codes to do what you are trying to do. Second, it looks like this scenario is described in section 5 here (page 42): "13 typical occupancy refinement scenarios and available options in phenix.refine" https://www.phenix-online.org/newsletter/CCN_2015_07.pdf Please let me know if this is not your case, or it is still not clear, or you need help with this anyway.. Good luck, Pavel On 10/17/16 11:05, Christian Roth wrote:
Hi Henry,
have you created a proper constraint group including both compounds as described in the manual under special cases for occupancy refingement? That should work, I presume.
Cheers
Christian
Am 15.10.2016 um 22:15 schrieb van den Bedem, Henry:
Hi:
I’m refining a site where there’s two compounds, each at partial occupancy. I modeled that using alt codes and insertion codes combined, like this
ATOM 6500 CA ACYS B 101B
ATOM 6490 CA BXXX B 101A
How can I constrain the occupancies so that they sum to unity? I tried several option, but the distinct insertions seem to refine independently. Sorry if a similar question has been posted before, but I could not find a solution searching phenixbb.
Thanks!
Henry
Hi Pavel,
Thanks! Yes, several others privately also pointed me to the newsletter. It’s precisely our scenario. Dropping the insertion codes solved my problem.
Henry
From: Pavel Afonine
participants (4)
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Christian Roth -
Georg Mlynek -
Pavel Afonine -
van den Bedem, Henry