May 2023 - phenixbb - phenix-online.org

map deposition strategy after density modification
by Daniel Larsson 20 Sep '23

20 Sep '23

Hi Phenix community, I’ve been using density modification with some success for my data and am considering the most appropriate way to do model building/refinement and then deposition of my results. Here are some questions/observations: 1) Which map should I refine against (most importantly, do the final minimization using phenix.real_space_refine)? The DM map is the most clear one, so I’m favoring to do it against this one (as long as the geometry/validation is also best for this one). 2) Which map should I deposit as my main map? Is it the autosharpened one or the DM one? Since the DM map looks the best, I want the user who only downloads one map to see this one, so again I favoring this map. 3) Which nominal resolution should I quote for my reconstruction? Since the procedure seems to introduce correlation between the two maps (see point 4 below), it does not seem to be possible to obtain a gold-standard FSC value between two truly independent half-maps. As the DM procedure supposedly actually improves the map (by leveraging knowledge about what solvent and macromolecular maps usually looks like and thereby improves the Fourier coefficients), it feels like it would be misrepresenting the data by quoting the FSC_0.143 from the original reconstruction. Should I use the FSC_0.5 estimated value that phenix.resolve_cryo_em outputs? 4) Which FSC curve should I deposit? When I calculate the FSC between the two density modified half-maps, I get a funny (or rather not so funny) looking curve with a bump at around 3Å and it does not go to zero at Nyquist (which does not agree with the map quality). This must again be due to the induced correlation between the maps, presumably during the masking of solvent and macromolecule density. Phenix.resolve_cryo_em calculates a FSC curve to calculate the FSC_0.5 value, which according to the manual page corrects for the correlation induced between the two maps: "Density modification introduces some correlations between half-maps due to solvent flattening. This can have a small effect on the resolution estimates obtained with half-map FSC. The resolution estimates provided by the program are corrected for this effect." But is this curve good enough? I think OneDeposit wants to have the gold-standard FSC curve, right? 5) Which (nowadays mandatory) half-maps should one deposit? Here I would say that the original half-maps before DM makes more sense, since these are less processed. But if one specify these as the half-maps, there will be inconsistencies during validation, since the DM map will look quite different from the average between the two original half-maps. Also the automatic FSC curve will be very different from the deposited one. So in conclusion, despite what I say above, the most conservative thing would be to deposit the conventionally sharpened map as my main map and use the original half-maps for calculating the FSC-curve and use the 0.143 threshold from this curve to estimate the resolution. The DM map can be used during rebuilding/refinement, but I think final minimization should be against the main map during deposition (with restraints if the geometry gets worse). The DM map can be deposited as an auxiliary map. Do the community and the developers agree? Regards, Daniel När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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AlphaFold button
by James Holton 31 May '23

31 May '23

Maybe I'm doing it wrong, but I was trying to show a class last week how to use the AlphaFold features of phenix, only to find that the Colab seems to no longer exist? I know the dedicated server is up now, but the current stable release does not have that feature in the GUI. Will a new stable release be released soon? Just asking, -James

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NCS operators
by Dmitry A. Semchonok 23 May '23

23 May '23

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real space R value calculation
by heinea＠mailer.uni-marburg.de 22 May '23

22 May '23

Dear mailing list, how can I calculate real space R-values fur individual residues or regions in a protein using Phenix? Any advice would be greatly appreciated. Thank you very much in advance, Andreas

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NCS operators
by Dmitry A. Semchonok 19 May '23

19 May '23

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generating half maps for combined map using phenix.combine_focused_maps
by Manoj saxena 16 May '23

16 May '23

Hi all, I have a question for generating half half maps for the combined map in Phenix, I am combining 6 regions of a complex (using local refined maps) and supplying the reference map and a reference model for the complex. Additionally, I am supplying the 2 half maps for the whole complex as input fines. I was wondering if I need to supply 2 half maps for each of the local refined regions as input files in addition to the half maps for the reference map. Thank you regards Manoj

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Pb executing phenix.model_idealization
by CUNIASSE Philippe 16 May '23

16 May '23

Dear all, I tried to use the phenix.model_idealization code of phenix (in command line) following the syntax suggested inhttps://phenix-online.org/documentation/reference/model_idealization.html phenix.model_idealization xxxx.pdb But the code stops on the error : Traceback (most recent call last): File "/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py", line 1118, in <module> run(sys.argv[1:]) File "/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py", line 1106, in run mi_object.run() File "/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py", line 548, in run self._setup_model_h() File "/Applications/phenix-1.20.1-4487/build/../modules/cctbx_project/mmtbx/command_line/model_idealization.py", line 478, in _setup_model_h params_h.pdb_interpretation = self.model._pdb_interpretation_params.pdb_interpretation AttributeError: 'NoneType' object has no attribute 'pdb_interpretation' Thanks in advance for any suggestion to solve this. Best regards. Philippe. ----------------------------------------------- Philippe Cuniasse, PhD/HDR. Institut de Biologie Integrative de la cellule. 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(a)cea.fr<mailto:[email protected]> Web: http://biodev.cea.fr/rasmot3d/ [signature_3031510868][signature_394100311][signature_2972121752] -----------------------------------------------

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How to exclude one part of a model to be taken into account during Real_Space_refinement ?
by CUNIASSE Philippe 16 May '23

16 May '23

Dear all, I am trying to do a phenix.real_space_refine in a CryoEM map at 4.2 Å with a model obtained by MDFF (NAMD, a protein DNA complex) because the resulting structure, despite a good CC and a good molecular geometry has a poor Ramachandran Map. When doing the phenix.real_space_refine, the CC is slightly increased with respect to the starting structure, the Ramachandran is dramatically increased but some part of the model ( in the case, the first three bases pairs a DNA duplex) are strongly distorted because of a lack of density in the corresponding region of the map. For some reason, this does not append with the MDFF method. I was wondering if there is a mean, in phenix.real_space_refine, to exclude a part of the model from being fitted in the map. Indeed, the distortion I observe in the DNA duplex is likely due to the fact that the real_space_refine tries to put the atoms at the extremity of the duplex in the closest density at the price of a strong distortion of the structure. Thank in advance for your suggestions. Best regards. Philippe. ----------------------------------------------- Philippe Cuniasse, PhD/HDR. Institut de Biologie Integrative de la cellule. 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(a)cea.fr<mailto:[email protected]> Web: http://biodev.cea.fr/rasmot3d/ [signature_3454313285][signature_3433042689][signature_3416814468] -----------------------------------------------

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phenix.combine_focused_maps
by Manoj saxena 10 May '23

10 May '23

Hi , I am trying the following command using PHENIX VERSION: 1.20.1-4487. to generate a composite map from locally refined maps (cryo-EM) of my complex. I have selected multiple regions each one correspond to one of the six locally refined maps that I wish to combine using this command. I would be grateful if you can suggest if this is the correct way to do it. In this test1.pdb contains the complete model. One of my doubts is that if instead of selection, I supply individual model files for each map region can they have multiple chain Ids. Asking because I was told that I would need to combine all chains and rename them as one chain (per map region) to have the correct weighted map. Many thanks Manoj phenix.combine_focused_maps map_file=Relion_deepEmhancer_reference_.mrc map_file=Base_map4.mrc map_file=Base_map1.mrc map_file=Base_map2.mrc map_file=Base_map3.mrc map_file=Base_map5.mrc map_file=Base_map6.mrc model_file=test1.pdb region_selection="(chain P and resid 366-401) or (chain P and resid 179-297) or \ (chain O and resid 401-555) or (chain N and resid 458-530) or (chain N and resid 311-457) or (chain R and resid 13-79) or \ (chain N and resid 726-577) or (chain N and resid 823-880) or (chain I and resid 350-409) or (chain N and resid 577-726) or (chain O and resid 667-722) or \ (chain Q and resid 264-276) or (chain N and resid 928-981) or (chain O and resid 926-971) or \ (chain O and resid 875-899) or (chain Q and resid 208-244) or (chain O and resid 717-739) or (chain N and resid 877-898) or \ (chain M and resid 7-101) or (chain L and resid 2047-2141) or (chain L and resid 1718-1746) or (chain L and resid 2001-2025) or (chain N and resid 880-900) or (chain P and resid 430-440) or (chain L and resid 1954-1965) or (chain P and resid 131-154)" composite_map_file=composite_map.mrc composite_half_map_1_file=composite_half_A_map.mrc composite_half_map_2_file=composite_half_B_map.mrc local_weighting=True rigid_body_refinement_single_unit=False nproc=8 resolution=4.0

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Issue resorting water chain
by Victor Rangel 05 May '23

05 May '23

Dear bb, I'm using phenix.sort_hetatms to sort my water molecule chain based on their bfactor. My macromolecule and water chains are separated, and I'd very much like them to remain so. When adding *preserve_chain_id=True*, the program outputs: *"Warning: no corresponding macromolecule chain match for C 1"*. The program still writes the output pdb, but it changes the water chain name from "C" to "X", and it does not sort them by bfactor. I'm using Phenix 1.20.1-4487 My command is: *phenix.sort_hetatms file_name="refine.pdb" output_file="resorted_refine.pdb" preserve_chain_id=True sort_waters_by=*b_iso* Not sure where my mistake is. Any suggestions? Best, Victor

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