Defining planarity for Phenix.refine

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PHENIX refine: detached sidechain...

Peter Grey

19 Apr 2010 19 Apr '10

10:23 a.m.

Dear all, I have an RNA/Protein big complex at low resolution (roughly 4A). I would like to have the base pairs in the RNA as close as possible to ideal base pairs. I added restraints for distances between base pair hydrogen-bonding atoms but this is not enough to ensure that the bases will be in the same plane. Could you suggest how to define for Phenix.refine this planarity ? I am grateful for your advice, Peter

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Francis E Reyes

19 Apr 19 Apr

12:21 p.m.

Peter Restraining RNA base pairs is a debated topic. Some say that you shouldn't do this and let the X-ray data speak for itself. Some say defining these base pairs should allow the refinement to converge and not distort the rna bases too much. @ 4A, you're asking for a lot if you're refining with individual_sites. You may want to stay with rigid body refinement with group adp /tls until you've nearly completed the model and then use individual_sites. While I don't think phenix.refine takes base pairing restraints specifically, one option is to heavily restricting wxc_scale to a small value. Another option is to select your atoms such that A-form helices are not refined with individual_sites and place them precisely with COOT. Another option is to use refinement.geometry_restraints.edits option of phenix.refine. Another option is to switch to CNS in which you can restrain the base pairing in the way you suggest. Just my $0.02, F On Apr 19, 2010, at 4:23 AM, Peter Grey wrote:

...

Dear all,

I have an RNA/Protein big complex at low resolution (roughly 4A). I would like to have the base pairs in the RNA as close as possible to ideal base pairs. I added restraints for distances between base pair hydrogen-bonding atoms but this is not enough to ensure that the bases will be in the same plane. Could you suggest how to define for Phenix.refine this planarity ?

I am grateful for your advice,

Peter

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

Peter Grey

1:30 p.m.

Francis On Mon, Apr 19, 2010 at 2:21 PM, Francis E Reyes

...

wrote:

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Peter

Restraining RNA base pairs is a debated topic. Some say that you shouldn't do this and let the X-ray data speak for itself. Some say defining these base pairs should allow the refinement to converge and not distort the rna bases too much.

@ 4A, you're asking for a lot if you're refining with individual_sites. You may want to stay with rigid body refinement with group adp /tls until you've nearly completed the model and then use individual_sites.

With enough of secondary structure and NCS restraints 4A is fine for RNA

...

While I don't think phenix.refine takes base pairing restraints specifically, one option is to heavily restricting wxc_scale to a small value. Another option is to select your atoms such that A-form helices are not refined with individual_sites and place them precisely with COOT. Another option is to use refinement.geometry_restraints.edits option of phenix.refine. Another option is to switch to CNS in which you can restrain the base pairing in the way you suggest.

refinement.geometry.restraints.edits does not support, as far as I see, "improper" torsion angles or other way of defining planes. Is CNS really my only option ????

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Just my $0.02,

F

On Apr 19, 2010, at 4:23 AM, Peter Grey wrote:

...
Dear all,

I have an RNA/Protein big complex at low resolution (roughly 4A). I would like to have the base pairs in the RNA as close as possible to ideal base pairs. I added restraints for distances between base pair hydrogen-bonding atoms but this is not enough to ensure that the bases will be in the same plane. Could you suggest how to define for Phenix.refine this planarity ?

I am grateful for your advice,

Peter

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--------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Engin Özkan

3:50 p.m.

I am thoroughly puzzled. I am seeing so many messages in the bulletin boards with suggestions of rigid body refinement at lower than 3 Angstrom resolution datasets, especially with strict arguments of data:parameter ratio (which cannot be easily determined due to the presence of restraints). Last week, rigid body was suggested for a case of 3.3 A structure. Are there papers out there that advocate residue-by-residue rigid body refinement for >3 Angstrom structures? To me, it sounds like a recipe for clashes and bond/angle outliers (when individual coordinate refinement can be worked out with proper restraining). Any research to back this strategy up, and make it regularly applicable in the 3 to 4 Angstrom range, or an easy option in phenix.refine? (I have seen grouped B-factors tame unruly B-factor refinement, that actually works) I should say that I have never worked with DNA in crystal structures, and due to its structure, it might be better suited to parameterization that allows accurate rigid bodies. I just don't know. I would also like to point out recent work by Axel Brunger's group on low-resolution refinement (Schröder et al, Nature, 2010 and references therein). Low-resolution refinement, while not straightforward, is becoming mainstream. Engin On 4/19/10 5:21 AM, Francis E Reyes wrote:

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Peter

Restraining RNA base pairs is a debated topic. Some say that you shouldn't do this and let the X-ray data speak for itself. Some say defining these base pairs should allow the refinement to converge and not distort the rna bases too much.

@ 4A, you're asking for a lot if you're refining with individual_sites. You may want to stay with rigid body refinement with group adp /tls until you've nearly completed the model and then use individual_sites.

While I don't think phenix.refine takes base pairing restraints specifically, one option is to heavily restricting wxc_scale to a small value. Another option is to select your atoms such that A-form helices are not refined with individual_sites and place them precisely with COOT. Another option is to use refinement.geometry_restraints.edits option of phenix.refine. Another option is to switch to CNS in which you can restrain the base pairing in the way you suggest.

Just my $0.02,

F

On Apr 19, 2010, at 4:23 AM, Peter Grey wrote:

...
Dear all,

I have an RNA/Protein big complex at low resolution (roughly 4A). I would like to have the base pairs in the RNA as close as possible to ideal base pairs. I added restraints for distances between base pair hydrogen-bonding atoms but this is not enough to ensure that the bases will be in the same plane. Could you suggest how to define for Phenix.refine this planarity ?

I am grateful for your advice,

Peter

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

_______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

-- Engin Özkan Post-doctoral Scholar Laboratory of K. Christopher Garcia Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111

Nathaniel Echols

5:50 p.m.

On Mon, Apr 19, 2010 at 8:50 AM, Engin Özkan wrote:

...

I should say that I have never worked with DNA in crystal structures, and due to its structure, it might be better suited to parameterization that allows accurate rigid bodies. I just don't know.

I'm not a nucleic acid crystallographer either, but aren't the helices (especially A-form) significantly more flexible than, say, a protein alpha-helix (or entire globular domain)? I would also like to point out recent work by Axel Brunger's group on

...

low-resolution refinement (Schröder et al, Nature, 2010 and references therein). Low-resolution refinement, while not straightforward, is becoming mainstream.

What is still needed is general-purpose minimization in torsion-angle space, which should be especially powerful for nucleic acids (since each base will be a single rigid group). This still requires more work on the minimizer to make it practical for phenix.refine.

Francis E Reyes

6:56 p.m.

On Apr 19, 2010, at 11:50 AM, Nathaniel Echols wrote:

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On Mon, Apr 19, 2010 at 8:50 AM, Engin Özkan wrote: I should say that I have never worked with DNA in crystal structures, and due to its structure, it might be better suited to parameterization that allows accurate rigid bodies. I just don't know.

I'm not a nucleic acid crystallographer either, but aren't the helices (especially A-form) significantly more flexible than, say, a protein alpha-helix (or entire globular domain)?

Let's be clear on what is meant by 'flexible'. In solution, A-form RNA helicies are generally not flexible. They're fairly rigid in solution and that can be observed by many of inline probing experiments. Now let's talk about flexibility during refinement. Without restraining the bases with some kind of strict geometry weight, or in the case of the OP, specifically restraining coplanar base pairing for canonical watson crick pairing, depending on the quality of the phases, I've seen phenix.refine and refmac pull bases that we know to be base paired in an A-form helix out of the 'coplanar base pair' orientation. If I were solving an RNA from scratch, I'd know apriori that this is a true base pair, and it's almost offensive that a refinement program would say otherwise. It's not drastic, but any RNA/ DNA structural biologist will look at your structure and clearly see that there's something wrong with the geometry. While it maybe a minor nuisance to correct this manually, I can only wonder how it affects the refinement. F --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

Nathaniel Echols

8:56 p.m.

On Mon, Apr 19, 2010 at 11:56 AM, Francis E Reyes < [email protected]> wrote:

...

Now let's talk about flexibility during refinement. Without restraining the bases with some kind of strict geometry weight, or in the case of the OP, specifically restraining *coplanar* *base pairing for canonical watson crick pairing*, depending on the quality of the phases, I've seen phenix.refine and refmac pull bases that we know to be base paired in an A-form helix out of the 'coplanar base pair' orientation. If I were solving an RNA from scratch, I'd know apriori that this is a true base pair, and it's almost offensive that a refinement program would say otherwise. It's not drastic, but any RNA/DNA structural biologist will look at your structure and clearly see that there's something wrong with the geometry. While it maybe a minor nuisance to correct this manually, I can only wonder how it affects the refinement.

Okay; it probably isn't very difficult to add base pair restraints to Phenix, we're just not quite sure how to make a general solution (which would support planarity restraints in addition to H-bonds). The main bottlenecks right now are a) figuring out a convenient reduced representation for base pairs, and b) identifying base pairs in a model. Aren't non-WC base pairs going to be very important in large RNA structures? Are there (free, open-source) tools that will generate a listing of *all* base pairs found in a model, not just the canonical ones? (Actually, a simple and more-or-less machine-readable listing of the bonds formed by each base pair type would be close enough.) -Nat

Francis E Reyes

20 Apr 20 Apr

2:06 a.m.

On Apr 19, 2010, at 2:56 PM, Nathaniel Echols wrote:

...

On Mon, Apr 19, 2010 at 11:56 AM, Francis E Reyes wrote: Now let's talk about flexibility during refinement. Without restraining the bases with some kind of strict geometry weight, or in the case of the OP, specifically restraining coplanar base pairing for canonical watson crick pairing, depending on the quality of the phases, I've seen phenix.refine and refmac pull bases that we know to be base paired in an A-form helix out of the 'coplanar base pair' orientation. If I were solving an RNA from scratch, I'd know apriori that this is a true base pair, and it's almost offensive that a refinement program would say otherwise. It's not drastic, but any RNA/DNA structural biologist will look at your structure and clearly see that there's something wrong with the geometry. While it maybe a minor nuisance to correct this manually, I can only wonder how it affects the refinement.

Okay; it probably isn't very difficult to add base pair restraints to Phenix, we're just not quite sure how to make a general solution (which would support planarity restraints in addition to H-bonds). The main bottlenecks right now are a) figuring out a convenient reduced representation for base pairs, and b) identifying base pairs in a model. Aren't non-WC base pairs going to be very important in large RNA structures? Are there (free, open-source) tools that will generate a listing of *all* base pairs found in a model, not just the canonical ones? (Actually, a simple and more-or-less machine-readable listing of the bonds formed by each base pair type would be close enough.)

http://nar.oxfordjournals.org/cgi/content/full/31/13/3450 or http://rna.bgsu.edu/FR3D/basepairs/ Leontis-Westhof nomenclature for RNA base pairs would be the one I'd look to. They have a program called RNAVIEW that'll create an RNAML file specifying the base pair geometries if you give it a PDB. However, completely specifying base pair restraints for every kind of non-canonical WC base pair is a lot of work (could be worked on eventually though). A starting point for phenix.refine it would be nice to restrain the sugar puckers, the planarity of the bases (themselves), and the planarity of WC base pairs and the distances between them (the implementation in CNS). A useful machine readable format that the user can use for this is the dot-bracket notation (http://rna.tbi.univie.ac.at/help.html#A6) and the inclusion of the brackets ( [ ] ) for pseudoknots. The user specifies the dot bracket notation and the sequence and its easy to write the secondary structure (essentially establishing all the base pairs). Eventually it would be nice to input the type of interaction among bases (according to http://rna.bgsu.edu/FR3D/basepairs/). Offtopic: Including base pair information into phenix.refine would definitely help with refinements when the phases/resolution are poor. However including this kind of information into autosol would greatly help with RNA/DNA building. I cross-ref autosol in this conversation because the language for specifying this information is established (mostly, see RNA Ontology Consotrium for efforts on more complete descriptions of RNA motifs). Extremely off topic: Francois Major (http://www.major.iric.ca/MajorLabEn/Home.html) has developed a pipeline for a user inputting a sequence and folding in 3D (which I believe is based on pattern matching your sequence with what's seen in the PDB). You and I talked about experimental phaseless structure solving (say via molecular replacement) at RapiData. MC-Sym/MC-Fold I think is a step in the right direction. I can only dream of a stage where in AutoSol, you have an RNA brute-force molecular replacement module that takes the models from MC-SYM/MC-Fold pipeline and perform a distributed molecular replacement across cores or clusters. F --------------------------------------------- Francis Reyes M.Sc. 215 UCB University of Colorado at Boulder gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D 8AE2 F2F4 90F7 9640 28BC 686F 78FD 6669 67BA 8D5D

Jeff Headd

2:23 a.m.

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A starting point for phenix.refine it would be nice to restrain the sugar puckers, the planarity of the bases (themselves), and the planarity of WC base pairs and the distances between them (the implementation in CNS). A useful machine readable format that the user can use for this is the dot-bracket notation (http://rna.tbi.univie.ac.at/help.html#A6) and the inclusion of the brackets ( [ ] ) for pseudoknots. The user specifies the dot bracket notation and the sequence and its easy to write the secondary structure (essentially establishing all the base pairs).

Thanks for the suggestions, that's very helpful moving forward. Phenix.refine currently does have restraints for both 3' and 2' sugar pucker, as well as pucker-specific backbone restraints. Each sugar pucker is determined automatically, and the proper restraints applied. Nat and I are currently working on how to restraint WC base pairs as a start, so hopefully that will be included very soon. Thanks for the suggestions on how to allow user input, I'll take a closer look at these links as we move along. Take care, Jeff

Scott Classen

22 Jun 22 Jun

9:21 p.m.

New subject: hydrogen-bond restraints for Watson-Crick base pairs

Hello friendly Phenix developers, According to the CHANGES for phenix.refine 1.6.2-432 there is a new feature: "hydrogen-bond restraints for Watson-Crick base pairs" How do I use this? I couldn't find any documentation... or is it automagic? Thanks, Scott ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Scott Classen, Ph.D. SIBYLS Beamline 12.3.1 sibyls.als.lbl.gov Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Rd MS6R2100 Berkeley, CA 94720 C) 510.206.4418 O) 510.495.2697 Beamline) 510.495.2134 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Nathaniel Echols

9:37 p.m.

New subject: hydrogen-bond restraints for Watson-Crick base pairs

On Tue, Jun 22, 2010 at 2:21 PM, Scott Classen wrote:

...

Hello friendly Phenix developers,

According to the CHANGES for phenix.refine 1.6.2-432 there is a new feature:

"hydrogen-bond restraints for Watson-Crick base pairs"

How do I use this? I couldn't find any documentation... or is it automagic?

Automagic, I hope. Start with "main.secondary_structure_restraints=True", and it will attempt to find existing base pairs by analyzing hydrogen bonds. If your geometry is still a little screwy, the parameter syntax is like this: refinement.secondary_structure.nucleic_acids { base_pair { base1 = chain "A" and resseq 1 base2 = chain "B" and resseq 10 } } One piece of advice: make sure your structure has either all hydrogen atoms where they should be, or none at all - if you're missing any, the secondary structure restraints will probably break. The automatic mechanism will also restrain protein helices and sheets, but you can easily turn this off (restrain_helices=False restrain_sheets=False). It will probably be necessary to fiddle with the sigma and slack parameters for hydrogen bonds; it isn't clear yet how much these need to be tuned for individual structures, but the defaults don't always work best for all structures. I am working on a brief sort-of-article on the secondary structure restraints, which has more information about the general mechanism (currently more focused on proteins, which is perhaps a defect). I'll send you a copy of the current draft. (A modified version of this will eventually become the official documentation.) -Nat

Scott Classen

9:56 p.m.

New subject: hydrogen-bond restraints for Watson-Crick base pairs

Hi all, I set main.secondary_struc and it appears that From the log file: ============================= No existing secondary Interpreting HELIX Running PROBE to identify base pairs 34 helices and 4 sheets defined 52.1% alpha, 9.0% beta The eff file shows My DNA looks like this: HETATM 1 O5* Ad D 1 ANISOU 1 O5* Ad D 1 HETATM 2 C5* Ad D 1 ANISOU 2 C5* Ad D 1 HETATM 3 C4* Ad D 1 ANISOU 3 C4* Ad D 1 HETATM 4 O4* Ad D 1 ANISOU 4 O4* Ad D 1 HETATM 5 C3* Ad D 1 ANISOU 5 C3* Ad D 1 HETATM 6 O3* Ad D 1 ANISOU 6 O3* Ad D 1 HETATM 7 C2* Ad D 1 ANISOU 7 C2* Ad D 1 HETATM 8 C1* Ad D 1 ANISOU 8 C1* Ad D 1 HETATM 9 N9 Ad D 1 ANISOU 9 N9 Ad D 1 HETATM 10 C8 Ad D 1 ANISOU 10 C8 Ad D 1 HETATM 11 N7 Ad D 1 ANISOU 11 N7 Ad D 1 HETATM 12 C5 Ad D 1 ANISOU 12 C5 Ad D 1 HETATM 13 C4 Ad D 1 ANISOU 13 C4 Ad D 1 HETATM 14 N1 Ad D 1 ANISOU 14 N1 Ad D 1 HETATM 15 C2 Ad D 1 ANISOU 15 C2 Ad D 1 HETATM 16 N3 Ad D 1 ANISOU 16 N3 Ad D 1 HETATM 17 C6 Ad D 1 ANISOU 17 C6 Ad D 1 HETATM 18 N6 Ad D 1 ANISOU 18 N6 Ad D 1 Is there any reason Thanks, Scott On Jun 22, 2010, ture_restraints = True protein ss elements are found and added to the geo file, but watson crick pairs are not. Secondary structure ============================= structure definitions found. and SHEET records from PDB file only helix and sheet records and no nucleic_acid records -47.740 -49.121 -17.972 1.00 91.44 O 13002 6701 15042 3404 -258 -1747 O -47.012 -48.219 -17.145 1.00 89.95 C 12785 6488 14904 3328 -133 -1848 C -45.570 -48.166 -17.612 1.00 87.82 C 12704 6315 14346 3354 213 -1700 C -45.517 -47.624 -18.952 1.00 85.51 O 12694 6248 13549 3345 56 -1589 O -44.642 -47.267 -16.812 1.00 88.97 C 12860 6436 14508 3299 389 -1783 C -43.312 -47.719 -17.004 1.00 87.64 O 12793 6290 14216 3376 787 -1645 O -44.883 -45.902 -17.456 1.00 88.06 C 12951 6509 13998 3224 84 -1819 C -45.055 -46.290 -18.922 1.00 86.43 C 12944 6475 13420 3268 -4 -1650 C -46.030 -45.477 -19.640 1.00 88.99 N 13415 6923 13476 3202 -408 -1684 N -47.262 -45.061 -19.205 1.00 91.41 C 13632 7157 13943 3159 -766 -1828 C -47.919 -44.338 -20.086 1.00 91.51 N 13857 7306 13606 3115 -1076 -1814 N -47.057 -44.279 -21.180 1.00 89.60 C 13841 7242 12960 3112 -900 -1656 C -45.889 -44.979 -20.917 1.00 87.68 C 13517 6968 12828 3174 -500 -1580 C -46.108 -43.812 -23.301 1.00 83.38 N 13478 6809 11393 3063 -789 -1439 N -45.046 -44.522 -22.903 1.00 82.39 C 13235 6642 11427 3141 -430 -1387 C -44.840 -45.143 -21.741 1.00 83.98 N 13201 6650 12057 3203 -253 -1442 N -47.151 -43.666 -22.454 1.00 87.19 C 13821 7135 12171 3057 -1043 -1571 C -48.209 -42.954 -22.862 1.00 88.07 N 14074 7286 12102 2999 -1409 -1621 N it wouldn't be recognized by PROBE? at 2:21 PM, Scott Classen wrote:

...

Hello friendly Phenix developers,

According to the CHANGES for phenix.refine 1.6.2-432 there is a new feature:

"hydrogen-bond restraints for Watson-Crick base pairs"

How do I use this? I couldn't find any documentation... or is it automagic?

Thanks, Scott

Nathaniel Echols

10:03 p.m.

New subject: hydrogen-bond restraints for Watson-Crick base pairs

On Tue, Jun 22, 2010 at 2:56 PM, Scott Classen wrote:

...

I set main.secondary_structure_restraints = True and it appears that protein ss elements are found and added to the geo file, but watson crick pairs are not.

My DNA looks like this:

HETATM 1 O5* Ad D 1 -47.740 -49.121 -17.972 1.00 91.44 O ANISOU 1 O5* Ad D 1 13002 6701 15042 3404 -258 -1747 O

Is there any reason it wouldn't be recognized by PROBE?

Jeff says that PROBE probably won't recognize "Ad" (it expects "dA" instead), and the default behavior probably requires O5', not O5*. The atom naming we can probably work around, the residue names are more difficult. What program generated these residues? If you can send us the model (or just enough of it to have base pairs, actually), we'll take a look. -Nat

Scott Classen

10:17 p.m.

New subject: hydrogen-bond restraints for Watson-Crick base pairs

Hi Nat, The Ad and * stuff comes from coot OK I renamed all my DNA residues and atom to the PDB version 3 "standard" Ad becomes DA and * becomes ' etc etc. HETATM 1 O5' DA D 1 -47.740 -49.121 -17.972 1.00 91.44 O ANISOU 1 O5' DA D 1 13002 6701 15042 3404 -258 -1747 O HETATM 2 C5' DA D 1 -47.012 -48.219 -17.145 1.00 89.95 C ANISOU 2 C5' DA D 1 12785 6488 14904 3328 -133 -1848 C HETATM 3 C4' DA D 1 -45.570 -48.166 -17.612 1.00 87.82 C ANISOU 3 C4' DA D 1 12704 6315 14346 3354 213 -1700 C HETATM 4 O4' DA D 1 -45.517 -47.624 -18.952 1.00 85.51 O ANISOU 4 O4' DA D 1 12694 6248 13549 3345 56 -1589 O HETATM 5 C3' DA D 1 -44.642 -47.267 -16.812 1.00 88.97 C ANISOU 5 C3' DA D 1 12860 6436 14508 3299 389 -1783 C HETATM 6 O3' DA D 1 -43.312 -47.719 -17.004 1.00 87.64 O ANISOU 6 O3' DA D 1 12793 6290 14216 3376 787 -1645 O HETATM 7 C2' DA D 1 -44.883 -45.902 -17.456 1.00 88.06 C ANISOU 7 C2' DA D 1 12951 6509 13998 3224 84 -1819 C HETATM 8 C1' DA D 1 -45.055 -46.290 -18.922 1.00 86.43 C ANISOU 8 C1' DA D 1 12944 6475 13420 3268 -4 -1650 C HETATM 9 N9 DA D 1 -46.030 -45.477 -19.640 1.00 88.99 N ANISOU 9 N9 DA D 1 13415 6923 13476 3202 -408 -1684 N HETATM 10 C8 DA D 1 -47.262 -45.061 -19.205 1.00 91.41 C ANISOU 10 C8 DA D 1 13632 7157 13943 3159 -766 -1828 C HETATM 11 N7 DA D 1 -47.919 -44.338 -20.086 1.00 91.51 N ANISOU 11 N7 DA D 1 13857 7306 13606 3115 -1076 -1814 N HETATM 12 C5 DA D 1 -47.057 -44.279 -21.180 1.00 89.60 C ANISOU 12 C5 DA D 1 13841 7242 12960 3112 -900 -1656 C HETATM 13 C4 DA D 1 -45.889 -44.979 -20.917 1.00 87.68 C ANISOU 13 C4 DA D 1 13517 6968 12828 3174 -500 -1580 C HETATM 14 N1 DA D 1 -46.108 -43.812 -23.301 1.00 83.38 N ANISOU 14 N1 DA D 1 13478 6809 11393 3063 -789 -1439 N HETATM 15 C2 DA D 1 -45.046 -44.522 -22.903 1.00 82.39 C ANISOU 15 C2 DA D 1 13235 6642 11427 3141 -430 -1387 C HETATM 16 N3 DA D 1 -44.840 -45.143 -21.741 1.00 83.98 N ANISOU 16 N3 DA D 1 13201 6650 12057 3203 -253 -1442 N HETATM 17 C6 DA D 1 -47.151 -43.666 -22.454 1.00 87.19 C ANISOU 17 C6 DA D 1 13821 7135 12171 3057 -1043 -1571 C HETATM 18 N6 DA D 1 -48.209 -42.954 -22.862 1.00 88.07 N Still no luck On Jun 22, 2010, at 3:03 PM, Nathaniel Echols wrote:

...

On Tue, Jun 22, 2010 at 2:56 PM, Scott Classen wrote: I set main.secondary_structure_restraints = True and it appears that protein ss elements are found and added to the geo file, but watson crick pairs are not.

My DNA looks like this:

HETATM 1 O5* Ad D 1 -47.740 -49.121 -17.972 1.00 91.44 O ANISOU 1 O5* Ad D 1 13002 6701 15042 3404 -258 -1747 O

Is there any reason it wouldn't be recognized by PROBE?

Jeff says that PROBE probably won't recognize "Ad" (it expects "dA" instead), and the default behavior probably requires O5', not O5*. The atom naming we can probably work around, the residue names are more difficult. What program generated these residues?

If you can send us the model (or just enough of it to have base pairs, actually), we'll take a look.

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Jeff Headd

10:41 p.m.

New subject: hydrogen-bond restraints for Watson-Crick base pairs

Hi Scott, I'm not sure why that's not working, it looks to me to be formatted correctly. Could you send me (directly to my email, not the board) a larger section of DNA that should have WC base pairs? That will help to trouble shoot what is going on. Thanks, Jeff On Tue, Jun 22, 2010 at 3:17 PM, Scott Classen wrote:

...

Hi Nat,

The Ad and * stuff comes from coot

OK I renamed all my DNA residues and atom to the PDB version 3 "standard" Ad becomes DA and * becomes ' etc etc.

HETATM 1 O5' DA D 1 -47.740 -49.121 -17.972 1.00 91.44 O ANISOU 1 O5' DA D 1 13002 6701 15042 3404 -258 -1747 O HETATM 2 C5' DA D 1 -47.012 -48.219 -17.145 1.00 89.95 C ANISOU 2 C5' DA D 1 12785 6488 14904 3328 -133 -1848 C HETATM 3 C4' DA D 1 -45.570 -48.166 -17.612 1.00 87.82 C ANISOU 3 C4' DA D 1 12704 6315 14346 3354 213 -1700 C HETATM 4 O4' DA D 1 -45.517 -47.624 -18.952 1.00 85.51 O ANISOU 4 O4' DA D 1 12694 6248 13549 3345 56 -1589 O HETATM 5 C3' DA D 1 -44.642 -47.267 -16.812 1.00 88.97 C ANISOU 5 C3' DA D 1 12860 6436 14508 3299 389 -1783 C HETATM 6 O3' DA D 1 -43.312 -47.719 -17.004 1.00 87.64 O ANISOU 6 O3' DA D 1 12793 6290 14216 3376 787 -1645 O HETATM 7 C2' DA D 1 -44.883 -45.902 -17.456 1.00 88.06 C ANISOU 7 C2' DA D 1 12951 6509 13998 3224 84 -1819 C HETATM 8 C1' DA D 1 -45.055 -46.290 -18.922 1.00 86.43 C ANISOU 8 C1' DA D 1 12944 6475 13420 3268 -4 -1650 C HETATM 9 N9 DA D 1 -46.030 -45.477 -19.640 1.00 88.99 N ANISOU 9 N9 DA D 1 13415 6923 13476 3202 -408 -1684 N HETATM 10 C8 DA D 1 -47.262 -45.061 -19.205 1.00 91.41 C ANISOU 10 C8 DA D 1 13632 7157 13943 3159 -766 -1828 C HETATM 11 N7 DA D 1 -47.919 -44.338 -20.086 1.00 91.51 N ANISOU 11 N7 DA D 1 13857 7306 13606 3115 -1076 -1814 N HETATM 12 C5 DA D 1 -47.057 -44.279 -21.180 1.00 89.60 C ANISOU 12 C5 DA D 1 13841 7242 12960 3112 -900 -1656 C HETATM 13 C4 DA D 1 -45.889 -44.979 -20.917 1.00 87.68 C ANISOU 13 C4 DA D 1 13517 6968 12828 3174 -500 -1580 C HETATM 14 N1 DA D 1 -46.108 -43.812 -23.301 1.00 83.38 N ANISOU 14 N1 DA D 1 13478 6809 11393 3063 -789 -1439 N HETATM 15 C2 DA D 1 -45.046 -44.522 -22.903 1.00 82.39 C ANISOU 15 C2 DA D 1 13235 6642 11427 3141 -430 -1387 C HETATM 16 N3 DA D 1 -44.840 -45.143 -21.741 1.00 83.98 N ANISOU 16 N3 DA D 1 13201 6650 12057 3203 -253 -1442 N HETATM 17 C6 DA D 1 -47.151 -43.666 -22.454 1.00 87.19 C ANISOU 17 C6 DA D 1 13821 7135 12171 3057 -1043 -1571 C HETATM 18 N6 DA D 1 -48.209 -42.954 -22.862 1.00 88.07 N

Still no luck

On Jun 22, 2010, at 3:03 PM, Nathaniel Echols wrote:

...
On Tue, Jun 22, 2010 at 2:56 PM, Scott Classen wrote: I set main.secondary_structure_restraints = True and it appears that protein ss elements are found and added to the geo file, but watson crick pairs are not.

My DNA looks like this:

HETATM 1 O5* Ad D 1 -47.740 -49.121 -17.972 1.00 91.44 O ANISOU 1 O5* Ad D 1 13002 6701 15042 3404 -258 -1747 O

Is there any reason it wouldn't be recognized by PROBE?

Jeff says that PROBE probably won't recognize "Ad" (it expects "dA" instead), and the default behavior probably requires O5', not O5*. The atom naming we can probably work around, the residue names are more difficult. What program generated these residues?

If you can send us the model (or just enough of it to have base pairs, actually), we'll take a look.

-Nat _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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Nathaniel Echols

11:42 p.m.

New subject: hydrogen-bond restraints for Watson-Crick base pairs

On Tue, Jun 22, 2010 at 2:21 PM, Scott Classen wrote:

...

Hello friendly Phenix developers,

According to the CHANGES for phenix.refine 1.6.2-432 there is a new feature:

"hydrogen-bond restraints for Watson-Crick base pairs"

Okay, small correction: "hydrogen-bond restraints for Watson-Crick base pairs in RNA" Sorry about the confusion - I don't know why I ever thought the DNA would work. It's a pretty simple fix, so we'll probably have something available in a few days. -Nat

Alan Cheung

19 Apr 19 Apr

1:50 p.m.

Hi Peter - i've managed to do this for some nucleic acids by using a custom cif file that contained planar restraint links for each type of base pair, and then specifying a phenix .params file that applies these cif links to specific base pairs in my model. e.g. for a G-C base pair (DNA-RNA hybrid), the cif file would have... data_link_list loop_ _chem_link.id _chem_link.comp_id_1 _chem_link.mod_id_1 _chem_link.group_comp_1 _chem_link.comp_id_2 _chem_link.mod_id_2 _chem_link.group_comp_2 _chem_link.name GdCr Gd . . Cr . . GdCr data_link_GdCr loop_ _chem_link_plane.link_id _chem_link_plane.plane_id _chem_link_plane.atom_comp_id _chem_link_plane.atom_id _chem_link_plane.dist_esd GdCr p 1 N1 0.02 GdCr p 1 C2 0.02 GdCr p 1 N2 0.02 GdCr p 2 O2 0.02 GdCr p 2 C2 0.02 GdCr p 2 N3 0.02 GdCr p 1 N1 0.02 GdCr p 1 C6 0.02 GdCr p 1 O6 0.02 GdCr p 2 N4 0.02 GdCr p 2 C4 0.02 GdCr p 2 N3 0.02 ...and in the .params file... refinement.pdb_interpretation.apply_cif_link { data_link = GdCr residue_selection_1 = chain T and resname Gd and resid 23 residue_selection_2 = chain P and resname Cr and resid 7 } I also had to combine it with h-bond base pair restraints with the usual refinement.geometry.restraints.edits settings. Alan On 19/04/2010 12:23, Peter Grey wrote:

...

Dear all,

I have an RNA/Protein big complex at low resolution (roughly 4A). I would like to have the base pairs in the RNA as close as possible to ideal base pairs. I added restraints for distances between base pair hydrogen-bonding atoms but this is not enough to ensure that the bases will be in the same plane. Could you suggest how to define for Phenix.refine this planarity ?

I am grateful for your advice,

Peter

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-- Alan Cheung Gene Center Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax: +49-89-2180-76999 E-mail: [email protected]

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Alan Cheung
Engin Özkan
Francis E Reyes
Jeff Headd
Nathaniel Echols
Peter Grey
Scott Classen