Dear list, I'm trying to undestand the NCS symmetry in a unit cell with 8 molecules (2 A resolution). The unit cell is almost orthorhombic (68.900 79.240 90.040 89.97 90.04 89.97), but only P1 + twinning worked for MR and for refining the structure (Rfree=0.22; Rcryst=0.18). The crystal simulated a P222 space group (the best seemed to be P21212), so I'd expect NCS axis parallel to . Now I've used phenix.simple_ncs_from_pdb to get the symmtery operators (see ouput below). I've read the manual, but I'm nevertheless finding it difficult to " see" the NCS axis. Any suggestions, please, on how to interpret the output, please, and "draw" the axis or on any alternatives on how to proceed? Many many thanks and a huge apology for the naive question (this is only my third strutcure...). Claudia --------------------------------------------------------------------------- # simple_ncs_from_pdb # # Find ncs among chains in a PDB file # type simple_ncs_from_pdb --help for help Parameters used for simple_ncs_from_pdb: find_ncs { temp_dir = "" min_length = 10 njump = 1 njump_recursion = 10 min_length_recursion = 50 min_percent = 95 max_rmsd = 2 quick = True max_rmsd_user = 3 domain_finding_parameters { find_invariant_domains = True initial_rms = 0.5 match_radius = 2 similarity_threshold = 0.75 smooth_length = 0 min_contig_length = 3 min_fraction_domain = 0.2 max_rmsd_domain = 2 } verbose = False } Chains in this PDB file: ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H'] GROUPS BASED ON QUICK COMPARISON: [['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H']] Looking for invariant domains for ...: ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H'] [[[19, 130], [148, 253]], [[21, 130], [148, 253]], [[21, 130], [148, 253]], [[19, 128], [149, 253]], [[19, 130], [148, 253]], [[21, 128], [148, 253]], [[19, 130], [149, 253]], [[21, 129], [149, 253]]] GROUP 1 Summary of NCS group with 8 operators: ID of chain/residue where these apply: [['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H'], [[[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130], [149, 253]]]] RMSD (A) from chain A: 0.0 0.46 0.47 0.53 0.54 0.48 0.48 0.59 Number of residues matching chain A:[213, 212, 212, 211, 212, 210, 213, 211] Source of NCS info: sortwaterxyzout.pdb OPERATOR 1 CENTER: 19.3475 -10.7352 7.9738 ROTA 1: 1.0000 0.0000 0.0000 ROTA 2: 0.0000 1.0000 0.0000 ROTA 3: 0.0000 0.0000 1.0000 TRANS: 0.0000 0.0000 0.0000 OPERATOR 2 CENTER: 53.8092 24.2127 11.0612 ROTA 1: 0.9998 0.0043 -0.0190 ROTA 2: 0.0045 -0.9999 0.0114 ROTA 3: -0.0190 -0.0115 -0.9998 TRANS: -34.3014 13.1765 20.2795 OPERATOR 3 CENTER: 55.6227 -15.2644 6.2461 ROTA 1: -0.9928 -0.0019 -0.1198 ROTA 2: -0.0045 -0.9986 0.0530 ROTA 3: -0.1197 0.0532 0.9914 TRANS: 75.3327 -25.9880 9.2016 OPERATOR 4 CENTER: 21.4489 28.7297 12.8232 ROTA 1: -0.9923 0.0066 0.1235 ROTA 2: -0.0001 0.9985 -0.0545 ROTA 3: -0.1236 -0.0541 -0.9909 TRANS: 38.7377 -38.6213 24.9897 OPERATOR 5 CENTER: 33.2332 16.3336 52.0552 ROTA 1: 0.9959 0.0207 -0.0884 ROTA 2: -0.0168 0.9988 0.0450 ROTA 3: 0.0892 -0.0433 0.9951 TRANS: -9.4176 -28.8046 -46.0499 OPERATOR 6 CENTER: 35.8216 -23.2140 56.1297 ROTA 1: -0.9985 -0.0249 -0.0490 ROTA 2: -0.0273 0.9985 0.0479 ROTA 3: 0.0477 0.0492 -0.9976 TRANS: 57.2101 10.9031 63.4545 OPERATOR 7 CENTER: 70.2188 11.8599 54.2973 ROTA 1: -0.9987 0.0207 0.0473 ROTA 2: -0.0234 -0.9981 -0.0569 ROTA 3: 0.0460 -0.0580 0.9973 TRANS: 86.6599 5.8364 -48.7180 OPERATOR 8 CENTER: 67.5293 -27.9008 58.5120 ROTA 1: 0.9959 -0.0146 0.0888 ROTA 2: -0.0120 -0.9995 -0.0303 ROTA 3: 0.0892 0.0291 -0.9956 TRANS: -53.5269 -35.9247 61.0251 NCS operators written in format for resolve to: simple_ncs_from_pdb.resolve NCS operators written in format for phenix.refine to: simple_ncs_from_pdb.ncs NCS written as ncs object information to: simple_ncs_from_pdb.ncs_spec Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 _________________________________________________________________ Explore the seven wonders of the world http://search.msn.com/results.aspx?q=7+wonders+world&mkt=en-US&form=QBRE
Hi again Claudia, Looking at the little PDB file that I sent you, I think that I am wrong...there may not be 222 symmetry there. The rotations are right, but the translations do not seem to make it actually 222. I will look into it more... You can tell all this by aligning the PDB I sent along the x,y, and z axes in coot. They do not seem to form perpendicular 2-folds as expected for 222, though it is quite possible I have missed it... -Tom T
Dear list,
I'm trying to undestand the NCS symmetry in a unit cell with 8 molecules (2 A resolution). The unit cell is almost orthorhombic (68.900 79.240 90.040 89.97 90.04 89.97), but only P1 + twinning worked for MR and for refining the structure (Rfree=0.22; Rcryst=0.18). The crystal simulated a P222 space group (the best seemed to be P21212), so I'd expect NCS axis parallel to .
Now I've used phenix.simple_ncs_from_pdb to get the symmtery operators (see ouput below). I've read the manual, but I'm nevertheless finding it difficult to " see" the NCS axis. Any suggestions, please, on how to interpret the output, please, and "draw" the axis or on any alternatives on how to proceed?
Many many thanks and a huge apology for the naive question (this is only my third strutcure...).
Claudia
---------------------------------------------------------------------------
# simple_ncs_from_pdb # # Find ncs among chains in a PDB file # type simple_ncs_from_pdb --help for help Parameters used for simple_ncs_from_pdb: find_ncs { temp_dir = "" min_length = 10 njump = 1 njump_recursion = 10 min_length_recursion = 50 min_percent = 95 max_rmsd = 2 quick = True max_rmsd_user = 3 domain_finding_parameters { find_invariant_domains = True initial_rms = 0.5 match_radius = 2 similarity_threshold = 0.75 smooth_length = 0 min_contig_length = 3 min_fraction_domain = 0.2 max_rmsd_domain = 2 } verbose = False }
Chains in this PDB file: ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H'] GROUPS BASED ON QUICK COMPARISON: [['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H']] Looking for invariant domains for ...: ['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H'] [[[19, 130], [148, 253]], [[21, 130], [148, 253]], [[21, 130], [148, 253]], [[19, 128], [149, 253]], [[19, 130], [148, 253]], [[21, 128], [148, 253]], [[19, 130], [149, 253]], [[21, 129], [149, 253]]]
GROUP 1 Summary of NCS group with 8 operators: ID of chain/residue where these apply: [['A', 'B', 'C', 'D', 'E', 'F', 'G', 'H'], [[[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130], [149, 253]], [[20, 117], [121, 130], [149, 253]]]] RMSD (A) from chain A: 0.0 0.46 0.47 0.53 0.54 0.48 0.48 0.59 Number of residues matching chain A:[213, 212, 212, 211, 212, 210, 213, 211] Source of NCS info: sortwaterxyzout.pdb
OPERATOR 1 CENTER: 19.3475 -10.7352 7.9738
ROTA 1: 1.0000 0.0000 0.0000 ROTA 2: 0.0000 1.0000 0.0000 ROTA 3: 0.0000 0.0000 1.0000 TRANS: 0.0000 0.0000 0.0000
OPERATOR 2 CENTER: 53.8092 24.2127 11.0612
ROTA 1: 0.9998 0.0043 -0.0190 ROTA 2: 0.0045 -0.9999 0.0114 ROTA 3: -0.0190 -0.0115 -0.9998 TRANS: -34.3014 13.1765 20.2795
OPERATOR 3 CENTER: 55.6227 -15.2644 6.2461
ROTA 1: -0.9928 -0.0019 -0.1198 ROTA 2: -0.0045 -0.9986 0.0530 ROTA 3: -0.1197 0.0532 0.9914 TRANS: 75.3327 -25.9880 9.2016
OPERATOR 4 CENTER: 21.4489 28.7297 12.8232
ROTA 1: -0.9923 0.0066 0.1235 ROTA 2: -0.0001 0.9985 -0.0545 ROTA 3: -0.1236 -0.0541 -0.9909 TRANS: 38.7377 -38.6213 24.9897
OPERATOR 5 CENTER: 33.2332 16.3336 52.0552
ROTA 1: 0.9959 0.0207 -0.0884 ROTA 2: -0.0168 0.9988 0.0450 ROTA 3: 0.0892 -0.0433 0.9951 TRANS: -9.4176 -28.8046 -46.0499
OPERATOR 6 CENTER: 35.8216 -23.2140 56.1297
ROTA 1: -0.9985 -0.0249 -0.0490 ROTA 2: -0.0273 0.9985 0.0479 ROTA 3: 0.0477 0.0492 -0.9976 TRANS: 57.2101 10.9031 63.4545
OPERATOR 7 CENTER: 70.2188 11.8599 54.2973
ROTA 1: -0.9987 0.0207 0.0473 ROTA 2: -0.0234 -0.9981 -0.0569 ROTA 3: 0.0460 -0.0580 0.9973 TRANS: 86.6599 5.8364 -48.7180
OPERATOR 8 CENTER: 67.5293 -27.9008 58.5120
ROTA 1: 0.9959 -0.0146 0.0888 ROTA 2: -0.0120 -0.9995 -0.0303 ROTA 3: 0.0892 0.0291 -0.9956 TRANS: -53.5269 -35.9247 61.0251
NCS operators written in format for resolve to: simple_ncs_from_pdb.resolve NCS operators written in format for phenix.refine to: simple_ncs_from_pdb.ncs NCS written as ncs object information to: simple_ncs_from_pdb.ncs_spec
Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673
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Hi Claudia, You seem to have these operators: (x ,y,z) ( x-34/68, -y+13/79, -z +20/90) [ a 2 fold screw axis along a] ( -x +75/68, -y-26/79, z+9/90) [stumped] (-x+38/69, y-38/79, -z+24/90) [ two fold screw along b ] (x+9/69, y-28/79, z-46/90) [pseudo translational symmetry] (-x+57/69, y+10/79, -z+63/90) [stumped] (-x + 86/69 , -y + 6/79 , z - 48/90) [ two fold screw along c ] (x-53/69, -y-36/79, -z + 61/90 ) [stumped] Are you sure that it is not P212121 with a pseudo tranlstaional symmetry or two fold NCS parallel to one of the screws? In any case, P1 is bad news, because phenix.refine cannot handle more then two twin domains. I suggest going to all flavours of P2 ( P112x, P12x1, P2x11) if you are absolutely sure about the sg not being p222 or so. Did you run xtriage? Cheers Peter
Dear Peter, Thanks a lot for rebuilding the operators for me! In case you have still time for this: Please, how was it possible to deduce that (x+9/69, y-28/79, z-46/90) was a pseudo-translational symmetry operator? It infact correspond to the small peak in the Native Patterson (not considered signficant in any of the softwares I tried) I mentioned in my previous message. And, please, what's the meaning of "stumped"? You can make a sound laugh at these questions! :-) Thanks agaian, Claudia Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 ----------------------------------------> Date: Wed, 24 Oct 2007 21:17:59 -0700> From: [email protected]> To: [email protected]> Subject: Re: [phenixbb] NCS interpretation>> Hi Claudia,>> You seem to have these operators:>> (x ,y,z)>> ( x-34/68, -y+13/79, -z +20/90) [ a 2 fold screw axis along a]>> ( -x +75/68, -y-26/79, z+9/90) [stumped]>> (-x+38/69, y-38/79, -z+24/90) [ two fold screw along b ]>> (x+9/69, y-28/79, z-46/90) [pseudo translational symmetry]>> (-x+57/69, y+10/79, -z+63/90) [stumped]>> (-x + 86/69 , -y + 6/79 , z - 48/90) [ two fold screw along c ]>> (x-53/69, -y-36/79, -z + 61/90 ) [stumped]>>> Are you sure that it is not P212121 with a pseudo tranlstaional> symmetry or two fold NCS parallel to one of the screws?>> In any case, P1 is bad news, because phenix.refine cannot handle more> then two twin domains. I suggest going to all flavours of P2 ( P112x,> P12x1, P2x11) if you are absolutely sure about the sg not being p222> or so.>> Did you run xtriage?>> Cheers>> Peter> _______________________________________________> phenixbb mailing list> [email protected]> http://www.phenix-online.org/mailman/listinfo/phenixbb _________________________________________________________________ Connect to the next generation of MSN Messenger http://imagine-msn.com/messenger/launch80/default.aspx?locale=en-us&source=wlmailtagline
(x+9/69, y-28/79, z-46/90) is a pseudo translation because the rotational part of the operator is the unity matrix. The only thing this guy does is move a subunit by (9/69,-28/79,-46/90) stumped means that I do not see what kind of operator it is... P Claudia Scotti wrote:
Dear Peter,
Thanks a lot for rebuilding the operators for me! In case you have still time for this:
Please, how was it possible to deduce that (x+9/69, y-28/79, z-46/90) was a pseudo-translational symmetry operator? It infact correspond to the small peak in the Native Patterson (not considered signficant in any of the softwares I tried) I mentioned in my previous message.
And, please, what's the meaning of "stumped"?
You can make a sound laugh at these questions! :-)
Thanks agaian,
Claudia
Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 ----------------------------------------> Date: Wed, 24 Oct 2007 21:17:59 -0700> From: [email protected]> To: [email protected]> Subject: Re: [phenixbb] NCS interpretation>> Hi Claudia,>> You seem to have these operators:>> (x ,y,z)>> ( x-34/68, -y+13/79, -z +20/90) [ a 2 fold screw axis along a]>> ( -x +75/68, -y-26/79, z+9/90) [stumped]>> (-x+38/69, y-38/79, -z+24/90) [ two fold screw along b ]>> (x+9/69, y-28/79, z-46/90) [pseudo translational symmetry]>> (-x+57/69, y+10/79, -z+63/90) [stumped]>> (-x + 86/69 , -y + 6/79 , z - 48/90) [ two fold screw along c ]>> (x-53/69, -y-36/79, -z + 61/90 ) [stumped]>>> Are you sure that it is not P212121 with a pseudo tranlstaional> symmetry or two fold NCS parallel to one of the screws?>> In any case, P1 is bad news, because phenix.refine cannot handle more> then two twin domains. I suggest going to all flavours of P2 ( P112x,> P12x1, P2x11) if you are absolutely sure about the sg not being p222> or so.>> Did you run xtriage?>> Cheers>> Peter> _______________________________________________> phenixbb mailing list> [email protected]> http://www.phenix-online.org/mailman/listinfo/phenixbb
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participants (3)
-
Claudia Scotti -
Peter Zwart -
Thomas C. Terwilliger