default bondlengths - metal
Hi, all, Recently following the phenixbb, I was made aware of phenix.metal_coordination. So I just gave it a try for a structure of mine with sodium in it. Specifically, I decided to turn the use-default-bondlengths option on. The result was surprising, because the output file thinks that sodum to oxygen distances are supposed to be 1.9 Angstroms. Work done by Marjorie Harding and others have shown that this distance should be about 2.4 (Acta Cryst. D62 (2006), 678-682; for a summary of their numbers, http://tanna.bch.ed.ac.uk/newtargs_06.html). I wonder why phenix.metal_coordination chose 1.9 A as the default Na-O distance, or is the default option a different type of bond distance, I am not sure. Any clarification from the authors would be appreciated. Below is part of the output, showing the distance: refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name NA and chain N and resname NA and resseq 1 atom_selection_2 = name O and chain A and resname PHE and resseq 76 distance_ideal = 1.920420 sigma = 0.01 } } Engin
Engin Thanks for the posting. You have discovered a hole in the coverage of the default bond lengths data. Thanks for the link. I'm sure it will be incorporated in the near future. In the meantime, I'm sure you are aware that you can change the value in the "edits" file. Nigel On 2/28/09 9:44 AM, Engin Ozkan wrote:
Hi, all,
Recently following the phenixbb, I was made aware of phenix.metal_coordination. So I just gave it a try for a structure of mine with sodium in it. Specifically, I decided to turn the use-default-bondlengths option on. The result was surprising, because the output file thinks that sodum to oxygen distances are supposed to be 1.9 Angstroms. Work done by Marjorie Harding and others have shown that this distance should be about 2.4 (Acta Cryst. D62 (2006), 678-682; for a summary of their numbers, http://tanna.bch.ed.ac.uk/newtargs_06.html). I wonder why phenix.metal_coordination chose 1.9 A as the default Na-O distance, or is the default option a different type of bond distance, I am not sure.
Any clarification from the authors would be appreciated.
Below is part of the output, showing the distance:
refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name NA and chain N and resname NA and resseq 1 atom_selection_2 = name O and chain A and resname PHE and resseq 76 distance_ideal = 1.920420 sigma = 0.01 } }
Engin _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Fax : 510-486-5909 Email : [email protected] Web : CCI.LBL.gov
Thanks, Nigel. I had actually created the restraints manually with the literature values (and that did match what I saw in density). I was just testing this new tool, because it sure is bound to come handy. It also gave me chance to point out the literature on this matter; this work even suggests sigma values specifically for structure refinement. Engin Nigel W Moriarty wrote:
Engin
Thanks for the posting. You have discovered a hole in the coverage of the default bond lengths data. Thanks for the link. I'm sure it will be incorporated in the near future.
In the meantime, I'm sure you are aware that you can change the value in the "edits" file.
Nigel
On 2/28/09 9:44 AM, Engin Ozkan wrote:
Hi, all,
Recently following the phenixbb, I was made aware of phenix.metal_coordination. So I just gave it a try for a structure of mine with sodium in it. Specifically, I decided to turn the use-default-bondlengths option on. The result was surprising, because the output file thinks that sodum to oxygen distances are supposed to be 1.9 Angstroms. Work done by Marjorie Harding and others have shown that this distance should be about 2.4 (Acta Cryst. D62 (2006), 678-682; for a summary of their numbers, http://tanna.bch.ed.ac.uk/newtargs_06.html). I wonder why phenix.metal_coordination chose 1.9 A as the default Na-O distance, or is the default option a different type of bond distance, I am not sure.
Any clarification from the authors would be appreciated.
Below is part of the output, showing the distance:
refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name NA and chain N and resname NA and resseq 1 atom_selection_2 = name O and chain A and resname PHE and resseq 76 distance_ideal = 1.920420 sigma = 0.01 } }
Engin _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
While we are on the matter, I needed a clarification in default H-bond distances in for water picking. The default parameters are: h_bond_min_mac = 1.8 h_bond_min_sol = 1.8 h_bond_max = 3.2 These values do work well, actually. Are these numbers the distance between the H-bond acceptor and the hydrogen itself? More commonly, people speak of acceptor to donor distances, but these values are too small for that (which are usually ~2.3-3.5 A)? Engin Engin Ozkan wrote:
Thanks, Nigel. I had actually created the restraints manually with the literature values (and that did match what I saw in density). I was just testing this new tool, because it sure is bound to come handy. It also gave me chance to point out the literature on this matter; this work even suggests sigma values specifically for structure refinement.
Engin
Nigel W Moriarty wrote:
Engin
Thanks for the posting. You have discovered a hole in the coverage of the default bond lengths data. Thanks for the link. I'm sure it will be incorporated in the near future.
In the meantime, I'm sure you are aware that you can change the value in the "edits" file.
Nigel
On 2/28/09 9:44 AM, Engin Ozkan wrote:
Hi, all,
Recently following the phenixbb, I was made aware of phenix.metal_coordination. So I just gave it a try for a structure of mine with sodium in it. Specifically, I decided to turn the use-default-bondlengths option on. The result was surprising, because the output file thinks that sodum to oxygen distances are supposed to be 1.9 Angstroms. Work done by Marjorie Harding and others have shown that this distance should be about 2.4 (Acta Cryst. D62 (2006), 678-682; for a summary of their numbers, http://tanna.bch.ed.ac.uk/newtargs_06.html). I wonder why phenix.metal_coordination chose 1.9 A as the default Na-O distance, or is the default option a different type of bond distance, I am not sure.
Any clarification from the authors would be appreciated.
Below is part of the output, showing the distance:
refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name NA and chain N and resname NA and resseq 1 atom_selection_2 = name O and chain A and resname PHE and resseq 76 distance_ideal = 1.920420 sigma = 0.01 } }
Engin _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Hi Engin, these are the distances between non-hydrogen atoms (even if H atoms are present in the model). The soft low limit cutoff allows to account for map imperfections due to data and model quality. I did not systematically investigate this. If I recall correctly, I put these numbers in based on 1) looking "what others do"; 2) PDB survey; 3) tests with a few models. Pavel. On 2/28/09 6:38 PM, Engin Ozkan wrote:
While we are on the matter, I needed a clarification in default H-bond distances in for water picking. The default parameters are: h_bond_min_mac = 1.8 h_bond_min_sol = 1.8 h_bond_max = 3.2 These values do work well, actually.
Are these numbers the distance between the H-bond acceptor and the hydrogen itself? More commonly, people speak of acceptor to donor distances, but these values are too small for that (which are usually ~2.3-3.5 A)?
Engin
Engin Ozkan wrote:
Thanks, Nigel. I had actually created the restraints manually with the literature values (and that did match what I saw in density). I was just testing this new tool, because it sure is bound to come handy. It also gave me chance to point out the literature on this matter; this work even suggests sigma values specifically for structure refinement.
Engin
Nigel W Moriarty wrote:
Engin
Thanks for the posting. You have discovered a hole in the coverage of the default bond lengths data. Thanks for the link. I'm sure it will be incorporated in the near future.
In the meantime, I'm sure you are aware that you can change the value in the "edits" file.
Nigel
On 2/28/09 9:44 AM, Engin Ozkan wrote:
Hi, all,
Recently following the phenixbb, I was made aware of phenix.metal_coordination. So I just gave it a try for a structure of mine with sodium in it. Specifically, I decided to turn the use-default-bondlengths option on. The result was surprising, because the output file thinks that sodum to oxygen distances are supposed to be 1.9 Angstroms. Work done by Marjorie Harding and others have shown that this distance should be about 2.4 (Acta Cryst. D62 (2006), 678-682; for a summary of their numbers, http://tanna.bch.ed.ac.uk/newtargs_06.html). I wonder why phenix.metal_coordination chose 1.9 A as the default Na-O distance, or is the default option a different type of bond distance, I am not sure.
Any clarification from the authors would be appreciated.
Below is part of the output, showing the distance:
refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name NA and chain N and resname NA and resseq 1 atom_selection_2 = name O and chain A and resname PHE and resseq 76 distance_ideal = 1.920420 sigma = 0.01 } }
Engin _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Thanks Pavel, If my memory from grad school serves me well, short or high-energy hydrogen bonds are between 2.2 to 2.5 A. They are observed in protein structures (and did generate a few nice review papers and controversy at the time, if I remember correctly), but any distance smaller than ~2.1 A (say, a 1.8 A hydrogen bond as phenix.refine is allowed to pick) does not sound likely given my limited understanding of the subject (The distances are between H-acceptor to H-donor). Any recent biophysical chemistry graduates with fresh minds in the audience? I did check my pdb files that were refined with phenix.refine defaults, and asked coot to "Check/Delete Waters". Happily enough, coot found no waters nearer than 2.3 A to protein (which is the coot default: 2.3 to 3.5). That was the reason that made me think the phenix default distances of 1.8 to 3.2 might be something else. At the end of the day, the defaults work, so that's good. Engin Pavel Afonine wrote:
Hi Engin,
these are the distances between non-hydrogen atoms (even if H atoms are present in the model).
The soft low limit cutoff allows to account for map imperfections due to data and model quality.
I did not systematically investigate this. If I recall correctly, I put these numbers in based on 1) looking "what others do"; 2) PDB survey; 3) tests with a few models.
Pavel.
On 2/28/09 6:38 PM, Engin Ozkan wrote:
While we are on the matter, I needed a clarification in default H-bond distances in for water picking. The default parameters are: h_bond_min_mac = 1.8 h_bond_min_sol = 1.8 h_bond_max = 3.2 These values do work well, actually.
Are these numbers the distance between the H-bond acceptor and the hydrogen itself? More commonly, people speak of acceptor to donor distances, but these values are too small for that (which are usually ~2.3-3.5 A)?
Engin
Engin Ozkan wrote:
Thanks, Nigel. I had actually created the restraints manually with the literature values (and that did match what I saw in density). I was just testing this new tool, because it sure is bound to come handy. It also gave me chance to point out the literature on this matter; this work even suggests sigma values specifically for structure refinement.
Engin
Nigel W Moriarty wrote:
Engin
Thanks for the posting. You have discovered a hole in the coverage of the default bond lengths data. Thanks for the link. I'm sure it will be incorporated in the near future.
In the meantime, I'm sure you are aware that you can change the value in the "edits" file.
Nigel
On 2/28/09 9:44 AM, Engin Ozkan wrote:
Hi, all,
Recently following the phenixbb, I was made aware of phenix.metal_coordination. So I just gave it a try for a structure of mine with sodium in it. Specifically, I decided to turn the use-default-bondlengths option on. The result was surprising, because the output file thinks that sodum to oxygen distances are supposed to be 1.9 Angstroms. Work done by Marjorie Harding and others have shown that this distance should be about 2.4 (Acta Cryst. D62 (2006), 678-682; for a summary of their numbers, http://tanna.bch.ed.ac.uk/newtargs_06.html). I wonder why phenix.metal_coordination chose 1.9 A as the default Na-O distance, or is the default option a different type of bond distance, I am not sure.
Any clarification from the authors would be appreciated.
Below is part of the output, showing the distance:
refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name NA and chain N and resname NA and resseq 1 atom_selection_2 = name O and chain A and resname PHE and resseq 76 distance_ideal = 1.920420 sigma = 0.01 } }
Engin _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
------------------------------------------------------------------------
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
Dear all, AutoBuild has successfully built almost my entire model - I copied loops built better in one NCS copy to the other, and now only one 16 residue loop connecting two helices is missing. It initially built a chain through the density for this loop, but could not join it to the rest of the structure or place the sequence there, so I deleted it. When I re-run autobuild on my modified model, rebuild_in_place=True is automatically set and this loop is not completed. The density is there, so it should be possible. How does one instruct AutoBuild to finish an almost complete model (in particular this loop), without much change to the existing model? --James
Hi James, I'm sorry for the slow reply, I missed your email when you sent it and just saw it today. There are several ways you can try and get autobuild to build just a little more. One is just to put in the last model from the previous run in as model=mybestmodel.pdb and specify "rebuild_in_place=false" and run it again. In your case it sounds like you really want to fit a loop. Here is a good way to do that: phenix.autobuild data=mydata.mtz model=model_missing_loop.pdb \ input_map_file=map.mtz seq_file=sequence.dat rebuild_in_place=false \ include_input_model=true number_of_models=0 fit_loops=true \ connect=true build_outside=false insert_helices=False \ helices_strands_start=False n_cycle_rebuild_max=1 \ thorough_loop_fit=true number_of_parallel_models=1 Here the key parameters are fit_loops=true and skipping build_outside_model and insert_helices. The connect=true will help if you do not have sequence assigned at the ends of your loop. The thorough_loop_fit=true tell it to try hard for the loop. The number_of_models=0 says don't bother to rebuild the model from scratch. This should run relatively quickly. It is possible that it will "lose" some good parts of your model, so it may be necessary to do some splicing if that happens. All the best, Tom T Thomas C. Terwilliger Mail Stop M888 Los Alamos National Laboratory Los Alamos, NM 87545 Tel: 505-667-0072 email: [email protected] Fax: 505-665-3024 SOLVE web site: http://solve.lanl.gov PHENIX web site: http:www.phenix-online.org ISFI Integrated Center for Structure and Function Innovation web site: http://techcenter.mbi.ucla.edu TB Structural Genomics Consortium web site: http://www.doe-mbi.ucla.edu/TB CBSS Center for Bio-Security Science web site: http://www.lanl.gov/cbss On Mar 3, 2009, at 6:37 AM, James Whittle wrote:
Dear all,
AutoBuild has successfully built almost my entire model - I copied loops built better in one NCS copy to the other, and now only one 16 residue loop connecting two helices is missing. It initially built a chain through the density for this loop, but could not join it to the rest of the structure or place the sequence there, so I deleted it.
When I re-run autobuild on my modified model, rebuild_in_place=True is automatically set and this loop is not completed. The density is there, so it should be possible.
How does one instruct AutoBuild to finish an almost complete model (in particular this loop), without much change to the existing model?
--James _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
participants (5)
-
Engin Ozkan -
James Whittle -
Nigel W Moriarty -
Pavel Afonine -
Tom Terwilliger