Re: [phenixbb] Real space refine of long side chains
Hi,
We have addressed exactly this problem by writing a script, in which
B-factors are refined first and only then real-space refinement happens.
This allows disordered side-chains to acquire high B-factors and so they
are not pulled into backbone anymore.
This cycle is repeated twice to achieve convergence.
Parameters for B-factor refinement (ADP restrains) were optimized to
account for consistent lack of density for acidic side chains in cryoEM.
It is described in: https://www.ncbi.nlm.nih.gov/pubmed/31492636
If needed, I can send a script.
Best
Leonid
--
Prof. Leonid Sazanov FRS
IST Austria
Am Campus 1
A-3400 Klosterneuburg
Austria
Phone: +43 2243 9000 3026
E-mail: [email protected]
Date: Mon, 25 Nov 2019 19:11:16 +0000
From: Luca Pellegrini
Hi, does anyone has a clear example that demonstrates this issue and that you can share with me? Having such an example would be most helpful as it will allow me to investigate the problem and hopefully address it centrally. I suspect this can potentially happen at low resolution (perhaps 4-4.5A and lower) when main-chain density looks like tubes and there isn't much density for side chains, so the main chain density attracts side chains. However, with default setting this should not happen as there are rotamer restraints. So I'm still not sure what's happening and this is why I'm looking for an example. Thanks, Pavel On 11/26/19 03:55, Leonid Sazanov wrote:
Hi,
We have addressed exactly this problem by writing a script, in which B-factors are refined first and only then real-space refinement happens.
This allows disordered side-chains to acquire high B-factors and so they are not pulled into backbone anymore.
This cycle is repeated twice to achieve convergence.
Parameters for B-factor refinement (ADP restrains) were optimized to account for consistent lack of density for acidic side chains in cryoEM.
It is described in: https://www.ncbi.nlm.nih.gov/pubmed/31492636
If needed, I can send a script.
Best
Leonid
Hi,
This sounds similar to the issues I have been having (but with x-ray data) from version 1.14 onward (Pavel I have previously sent you files regarding this, but can send again if you need). It happens for me even with high resolution (better than 2A) structures, but mostly with flexible side chains that have poor density. The side chains even push other residues (often symmetry related residues) out of their density. To me it seemed it might be connected to over zealous rotamer correction that began for me from version 1.14. As noted in the recent post 'Differences in refinement statistics', version 1.17 no longer gives me over corrected 0% rotamer outliers (versions 1.14-1.16 moved residues out of density to 'correct' rotamer outliers), but still pulls some side chains into the wrong density (although not as bad as versions 1.14-1.16). So currently I still use version 1.13 as later versions give me problems with side chains (unless I turn off real space refinement).
Bye for now,
Gyles.
________________________________
From: [email protected]
Hi,
We have addressed exactly this problem by writing a script, in which B-factors are refined first and only then real-space refinement happens.
This allows disordered side-chains to acquire high B-factors and so they are not pulled into backbone anymore.
This cycle is repeated twice to achieve convergence.
Parameters for B-factor refinement (ADP restrains) were optimized to account for consistent lack of density for acidic side chains in cryoEM.
It is described in: https://www.ncbi.nlm.nih.gov/pubmed/31492636
If needed, I can send a script.
Best
Leonid
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Dear Pavel, As you probably know, due to specific radiation damage cryo-EM maps have a peculiarity that for most carboxylic side-chains density is absent (unless those Glu/Asp are involved in salt bridges). For these reasons the ADP refinement I think may need to be somewhat differently restrained than for X-ray. We found that individual (not group) B-factor refinement with sphere_radius=2.5 and distance_power = 2.3 seems to work well to allow residues with no side chain density and good backbone density to acquire high B-factors for side-chains but still reasonable B-factors for backbone. For that to work we have to convert .ccp4 map to .mtz and use phenix.refine (just for B-factor refinement only). If that is run first, then subsequent run of RSR with .ccp4 map does not try to move those side-chains into backbone anymore. We find that this is useful to do with maps at least in the 3.0 to 4.0 A resolution range, not only at low resolution like 4 A. At 2.0 it may be less useful, not sure. In usual RSR run B-factor refinement is done only at the end, which may be suboptimal and indeed it would be better if something similar to the above was an option in the normal RSR run. I can send you some example off-list. Best Leonid Prof. Leonid Sazanov FRS IST Austria Am Campus 1 A-3400 Klosterneuburg Austria Phone: +43 2243 9000 3026 E-mail: [email protected] On 26.11.19 20:02, Pavel Afonine wrote:
Hi,
does anyone has a clear example that demonstrates this issue and that you can share with me? Having such an example would be most helpful as it will allow me to investigate the problem and hopefully address it centrally.
I suspect this can potentially happen at low resolution (perhaps 4-4.5A and lower) when main-chain density looks like tubes and there isn't much density for side chains, so the main chain density attracts side chains. However, with default setting this should not happen as there are rotamer restraints. So I'm still not sure what's happening and this is why I'm looking for an example.
Thanks, Pavel
On 11/26/19 03:55, Leonid Sazanov wrote:
Hi,
We have addressed exactly this problem by writing a script, in which B-factors are refined first and only then real-space refinement happens.
This allows disordered side-chains to acquire high B-factors and so they are not pulled into backbone anymore.
This cycle is repeated twice to achieve convergence.
Parameters for B-factor refinement (ADP restrains) were optimized to account for consistent lack of density for acidic side chains in cryoEM.
It is described in: https://www.ncbi.nlm.nih.gov/pubmed/31492636
If needed, I can send a script.
Best
Leonid
participants (3)
-
Gyles Cozier -
Leonid Sazanov -
Pavel Afonine