[phenixbb] RealSpaceRefine Nucleic acid SS restraints ?

Wed Jan 31 17:36:25 PST 2024

Hi Philippe,

occupancy refinement should not affect coordinate refinement at all in 
any way.

What happens if you run pure geometry regularization using your input 
model and SS restraints? In this case there is no experimental data 
involved whatsoever and the resulting regularized model *must* literally 
obey the geometry specified by the restraints (with some possibly tiny 
deviations in case regularization has not converged):

phenix.geometry_minimization model.pdb restraints.eff

where restraints.eff specify your SS restraints.

If in this case restraints are still not obeyed in the regularized 
model, please send us input files and we will investigate.

Pavel

On 1/30/24 22:49, CUNIASSE Philippe wrote:
>
> Dear Oleg,
>
> sorry for the log.
>
> The strange thing is that the input structure (output from NAMD MDFF 
> where we also apply SS restraints to NA has a correct and better SS 
> than the one at the end of the RealSpace refine.
>
> I also checked the restraints in the .geo file and it seems correct. I 
> only found in previious calculations that the atom identity of some 
> atoms (in the charmm 36 topology) must be changed for the NA 
> restraints to be correctly set by phenix (C3M of THY must be changed 
> for C7).
>
> My only hypothesis at the moment is that the occupancy refinement 
> (currently at a value of 1.00 for all atoms) tends to distort strongly 
> the extremities of the duplex because the electron density is weak in 
> these regions with a bad shape and that this (presumlably) distorts 
> the NA structure to fit the poor density that does not ressemble the 
> one for a B-DNA in these regions. This could be solved if we have a 
> way to increase the harmonic constants for the SS restraints, but i 
> dont see this possibility.
>
> Your advice on this hypothesis is welcome.
>
> Best regards.
>
> Philippe.
>
>
> Philippe Cuniasse, PhD/HDR.
> Institute for Integrative Biology of the Cell (I2BC)
> UMR 9198 CNRS-CEA-Univ Paris Sud
> Bat 144 CE-Saclay
> 91191 Gif-sur-Yvette Cedex, France
>
> Tel: (33) 1 69 08 56 35
> Fax: (33) 1 69 08 47 12
> Email: philippe.cuniasse at cea.fr <mailto:philippe.cuniasse at cea.fr 
> <mailto:philippe.cuniasse at cea.fr>>
> Web: http://biodev.cea.fr/rasmot3d/ <http://biodev.cea.fr/rasmot3d/>
> Web: https://www.i2bc.paris-saclay.fr <https://www.i2bc.paris-saclay.fr>
>
> -----------------------------------------------
>
> ------------------------------------------------------------------------
> *De :* Oleg Sobolev <osobolev at lbl.gov>
> *Envoyé :* mardi 30 janvier 2024 18:21:02
> *À :* CUNIASSE Philippe
> *Cc :* phenixbb at phenix-online.org
> *Objet :* Re: [phenixbb] RealSpaceRefine Nucleic acid SS restraints ?
> Dear Philippe,
>
> Most often the problem is that the geometry of the input model is so 
> distorted that the procedure fails to find base pairs and therefore 
> restrain them.
>
> Couple of ways to check for this are:
> 1. Look in the .log into
>   Finding SS restraints...
>     Secondary structure from input PDB file:
>       0 helices and 0 sheets defined
>       0.0% alpha, 0.0% beta
>       12 base pairs and 21 stacking pairs defined.
>     Time for finding SS restraints: 0.04
>   Creating SS restraints...
>
>     No hydrogen bonds defined for protein.
>     Restraints generated for nucleic acids:
>       32 hydrogen bonds
>       64 hydrogen bond angles
>       0 basepair planarities
>       12 basepair parallelities
>       21 stacking parallelities
>
> This part would give a general idea if anything worked at all.
>
> 2. Inspect .geo file after refinement and look for "Basepair 
> parallelity restraints" and "Bond-like restraints" (secondary 
> structure H-bonds) sections. Here you can see exactly what restraints 
> were applied and if the basepairs in question were in fact restrained.
>
> If you supply the restraints in the .parameter file, check 
> the nucleic_acid.hbond_distance_cutoff parameter. The default is 3.4, 
> you may need to increase it so your annotations are not filtered out.
>
> I'm happy to look at your files (model and parameter, if any) to 
> figure out what is happening. Please send them off-list indicating 
> problematic residues. Files will be treated confidentially.
>
> Best regards,
> Oleg Sobolev.
>
> On Tue, Jan 30, 2024 at 7:20 AM CUNIASSE Philippe 
> <Philippe.CUNIASSE at cea.fr> wrote:
>
>     Dear all,
>
>     I am currently refining a protein-nucleic acid structure obtained
>     by MDFF (NAMD) with a 2.9 Å cryo-EM map.
>
>     Dues to the poor density of the map at the end of the DNA duplex
>     (likely due to breathing at the ends of the duplex), the structure
>     of the DNA tends to be distorted.
>
>     I tried to set up a set of nucleic acid restraints (Base pairing
>     and base stacking for the full sequence), however, despite the
>     fact that the syntax was checked and no error message is present
>     in the log file, it seems that the restraints are not taken into
>     account as if the constant restraints were two weak. And indeed
>     when examining the refined structure, the pairing and stacking
>     restraints for the base pairs at the extremities of the DNA
>     duplex are not fulfilled.
>
>     Have you a suggestion to solve this problem ?
>
>     Thanks in advance for your help.
>
>     Best regards.
>
>     Philippe.
>
>
>     -----------------------------------------------
>
>     Philippe Cuniasse, PhD/HDR.
>
>     Institute for Integrative Biology of the Cell (I2BC)
>
>     UMR 9198 CNRS-CEA-Univ Paris Sud
>
>     Bat 144 CE-Saclay
>
>     91191 Gif-sur-Yvette Cedex, France
>
>     Tel:      (33) 1 69 08 56 35
>
>     Fax:      (33) 1 69 08 47 12
>
>     Email: philippe.cuniasse at cea.fr <mailto:philippe.cuniasse at cea.fr>
>
>     Web:http://biodev.cea.fr/rasmot3d/ <http://biodev.cea.fr/rasmot3d/>
>
>     Web:https://www.i2bc.paris-saclay.fr
>     <https://www.i2bc.paris-saclay.fr>
>
>     signature_2602492259
>
>
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