Re: [phenixbb] CCN Jan 2012 article : find_alt_origin_sym_mate
Dear Bryan, The factor 0.9 is a purely empirical term. It serves two functions. One is to soften the minimas when atoms coalesce and to also prevent taking the logarithm of a negative number. The closer it gets to zero the more accurately it pinpoints the global minimum when the MLAD score is used for identifying the best superposition betweent two molecules. But if it becomes two small chances are that the landscape of MLAD values will be dotted with many very deep local minima which might lead to wrong results. The square boxes under the min, max symbols are typos to be ignored, sorry. There are currently no plans to publish further details about find_alt_origin_sym_mate. Regards, Robert Oeffner On Wed, Feb 15, 2012 at 4:33 PM, Bryan Lepore <bryanlepore at gmail.com> wrote:
will the find_alt_origin_sym_mate article in CCN Jan. 2012 be described in any other publications?
... e.g. Acta Cryst., because I am interested in particular : 1. what is the significance of the factor of 0.9 2. is the MLAD a novel formula also, the 'min' and 'max' on p. 6 have small boxes under them [*] as if missing a character - are these integrals? -Bryan [*] tried evince and Adobe Reader on Linux, Adobe Acrobat on OSX 10.5.8 -- Robert Oeffner, Ph.D. Research Associate Department of Haematology, University of Cambridge Cambridge Institute of Medical Research Wellcome Trust / MRC Building, Hills Road, Cambridge, CB2 0XY www-structmed.cimr.cam.ac.uk, tel:01223763234, mobile:07712 887162
Nigel and Robert, thanks, that makes sense. -Bryan
I also have a question regarding MLAD score. Why do you take the sum of absolute dr_i components? This is not orientation invariant. The attached screenshot is like figure 3 from the article, but rotates the system from 0 to 90 degrees. I think this: |dr_i,x| + |dr_i,y| + |dr_i,z| needs to be replaced by this: |dr_i| right? Regards, Thomas On 02/21/2012 01:31 AM, R.D. Oeffner wrote:
Dear Bryan,
The factor 0.9 is a purely empirical term. It serves two functions. One is to soften the minimas when atoms coalesce and to also prevent taking the logarithm of a negative number. The closer it gets to zero the more accurately it pinpoints the global minimum when the MLAD score is used for identifying the best superposition betweent two molecules. But if it becomes two small chances are that the landscape of MLAD values will be dotted with many very deep local minima which might lead to wrong results.
The square boxes under the min, max symbols are typos to be ignored, sorry.
There are currently no plans to publish further details about find_alt_origin_sym_mate.
Regards,
Robert Oeffner
-- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen
Dear Thomas, Thank you for pointing this out. I'm pleased to say that there is no significant change to the scatter plots of MLAD versus correlation coeeficients when using your change. So you should still be fine using the current version of find_alt_origin_sym_mate. The next release of PHENIX will use the changed version of the MLAD formula. This will eventually be documented online. Many thanks, Robert On Feb 21 2012, Thomas Holder wrote:
I also have a question regarding MLAD score.
Why do you take the sum of absolute dr_i components? This is not orientation invariant. The attached screenshot is like figure 3 from the article, but rotates the system from 0 to 90 degrees.
I think this:
|dr_i,x| + |dr_i,y| + |dr_i,z|
needs to be replaced by this:
|dr_i|
right?
Regards, Thomas
On 02/21/2012 01:31 AM, R.D. Oeffner wrote:
Dear Bryan,
The factor 0.9 is a purely empirical term. It serves two functions. One is to soften the minimas when atoms coalesce and to also prevent taking the logarithm of a negative number. The closer it gets to zero the more accurately it pinpoints the global minimum when the MLAD score is used for identifying the best superposition betweent two molecules. But if it becomes two small chances are that the landscape of MLAD values will be dotted with many very deep local minima which might lead to wrong results.
The square boxes under the min, max symbols are typos to be ignored, sorry.
There are currently no plans to publish further details about find_alt_origin_sym_mate.
Regards,
Robert Oeffner
-- Robert Oeffner, Ph.D. Research Associate Department of Haematology, University of Cambridge Cambridge Institute of Medical Research Wellcome Trust / MRC Building, Hills Road, Cambridge, CB2 0XY www-structmed.cimr.cam.ac.uk, tel:01223763234, mobile:07712 887162
Hi all, In my structure, the ASN and the linked NAG has two conformations. The pdb: ATOM 3685 C1 ANAG A2061 4.069 2.862 24.649 0.47 31.33 C ANISOU 3685 C1 ANAG A2061 3426 4664 3813 -664 421 625 C ATOM 3686 C1 BNAG A2061 9.105 0.384 22.719 0.53 40.81 C ANISOU 3686 C1 BNAG A2061 5087 5333 5084 24 -72 -116 C ATOM 3690 C2 ANAG A2061 4.508 1.905 25.749 0.47 34.38 C ANISOU 3690 C2 ANAG A2061 3953 4727 4383 -441 142 473 C ATOM 3691 C2 BNAG A2061 8.311 -0.893 22.808 0.53 40.91 C ANISOU 3691 C2 BNAG A2061 5087 5438 5018 13 -55 -37 C ATOM 3694 N2 ANAG A2061 5.010 0.727 25.059 0.47 35.56 N ANISOU 3694 N2 ANAG A2061 4185 4888 4437 -466 149 254 N ATOM 3695 N2 BNAG A2061 7.220 -0.767 23.761 0.53 40.82 N ANISOU 3695 N2 BNAG A2061 5159 5512 4836 246 -144 -112 N ATOM 3698 C7 ANAG A2061 6.312 0.507 24.874 0.47 34.61 C ANISOU 3698 C7 ANAG A2061 4357 4653 4141 -406 202 282 C ATOM 3699 C7 BNAG A2061 5.974 -1.172 23.460 0.53 41.98 C ANISOU 3699 C7 BNAG A2061 5327 5677 4943 117 8 -149 C ATOM 3700 O7 ANAG A2061 7.194 1.236 25.322 0.47 35.05 O ANISOU 3700 O7 ANAG A2061 4292 4626 4396 -724 290 343 O ATOM 3701 O7 BNAG A2061 5.625 -1.665 22.371 0.53 44.02 O ANISOU 3701 O7 BNAG A2061 5616 5774 5335 6 -122 -208 O ATOM 3702 C8 ANAG A2061 6.699 -0.698 24.067 0.47 33.30 C ANISOU 3702 C8 ANAG A2061 4119 4700 3832 -193 57 303 C ATOM 3703 C8 BNAG A2061 4.933 -0.984 24.514 0.53 42.31 C ANISOU 3703 C8 BNAG A2061 5260 5612 5203 157 -4 -125 C ATOM 3710 C3 ANAG A2061 3.357 1.608 26.717 0.47 34.94 C ANISOU 3710 C3 ANAG A2061 3903 4950 4420 -528 289 456 C ATOM 3711 C3 BNAG A2061 9.296 -2.001 23.171 0.53 40.83 C ANISOU 3711 C3 BNAG A2061 5144 5347 5021 31 -211 -83 C ATOM 3714 O3 ANAG A2061 3.801 0.844 27.813 0.47 37.07 O ANISOU 3714 O3 ANAG A2061 4043 5387 4655 -327 106 508 O ATOM 3715 O3 BNAG A2061 8.608 -3.231 23.147 0.53 41.68 O ANISOU 3715 O3 BNAG A2061 5286 5504 5046 -142 -263 97 O ATOM 3718 C4 ANAG A2061 2.696 2.880 27.229 0.47 33.38 C ANISOU 3718 C4 ANAG A2061 3490 4870 4323 -715 378 575 C ATOM 3719 C4 BNAG A2061 10.480 -2.021 22.187 0.53 39.61 C ANISOU 3719 C4 BNAG A2061 4854 5338 4854 85 -226 -13 C ATOM 3722 O4 ANAG A2061 1.507 2.534 27.956 0.47 35.04 O ANISOU 3722 O4 ANAG A2061 3669 4878 4766 -843 393 668 O ATOM 3723 O4 BNAG A2061 11.583 -2.708 22.745 0.53 37.22 O ANISOU 3723 O4 BNAG A2061 4397 5524 4220 146 -644 59 O ATOM 3726 C5 ANAG A2061 2.336 3.744 26.026 0.47 34.15 C ANISOU 3726 C5 ANAG A2061 3749 4890 4334 -733 503 550 C ATOM 3727 C5 BNAG A2061 11.003 -0.643 21.780 0.53 39.23 C ANISOU 3727 C5 BNAG A2061 4886 5258 4760 33 -165 -30 C ATOM 3730 C6 ANAG A2061 1.625 5.025 26.471 0.47 35.40 C ANISOU 3730 C6 ANAG A2061 4140 4847 4461 -657 269 378 C ATOM 3731 C6 BNAG A2061 11.764 -0.744 20.462 0.53 39.76 C ANISOU 3731 C6 BNAG A2061 5000 5228 4877 79 -185 -106 C ATOM 3736 O6 ANAG A2061 2.432 5.674 27.428 0.47 37.10 O ANISOU 3736 O6 ANAG A2061 4302 5083 4710 -773 428 205 O ATOM 3737 O6 BNAG A2061 10.918 -1.227 19.435 0.53 40.11 O ANISOU 3737 O6 BNAG A2061 4599 5472 5169 313 -83 -277 O ATOM 3740 O5 ANAG A2061 3.507 4.032 25.210 0.47 33.36 O ANISOU 3740 O5 ANAG A2061 3905 4796 3974 -742 445 909 O ATOM 3741 O5 BNAG A2061 9.974 0.304 21.624 0.53 39.18 O ANISOU 3741 O5 BNAG A2061 5023 5184 4676 -220 -99 -108 O ATOM 1157 N ASN A 61 8.496 4.626 20.319 1.00 26.85 N ANISOU 1157 N ASN A 61 3029 4695 2476 -1809 -655 1273 N ATOM 1158 CA AASN A 61 7.080 4.398 20.655 0.50 24.65 C ANISOU 1158 CA AASN A 61 2996 4000 2368 -1776 -634 980 C ATOM 1159 CA BASN A 61 7.083 4.446 20.752 0.50 25.61 C ANISOU 1159 CA BASN A 61 3174 4178 2376 -1622 -618 912 C ATOM 1162 CB AASN A 61 6.952 3.807 22.077 0.50 23.96 C ANISOU 1162 CB AASN A 61 2901 3704 2497 -1862 -440 1083 C ATOM 1163 CB BASN A 61 7.016 4.118 22.260 0.50 26.04 C ANISOU 1163 CB BASN A 61 3226 4291 2376 -1605 -554 824 C ATOM 1168 CG AASN A 61 5.499 3.653 22.494 0.50 27.33 C ANISOU 1168 CG AASN A 61 3048 4420 2914 -1388 -585 598 C ATOM 1169 CG BASN A 61 7.882 2.975 22.608 0.50 27.64 C ANISOU 1169 CG BASN A 61 3195 4695 2612 -1576 -444 650 C ATOM 1170 OD1AASN A 61 4.659 3.204 21.697 0.50 27.73 O ANISOU 1170 OD1AASN A 61 3349 4200 2986 -1314 -644 873 O ATOM 1171 OD1BASN A 61 8.908 3.141 23.291 0.50 30.84 O ANISOU 1171 OD1BASN A 61 3734 4991 2990 -1345 -880 129 O ATOM 1172 ND2AASN A 61 5.182 4.096 23.716 0.50 34.27 N ANISOU 1172 ND2AASN A 61 3736 5474 3811 -832 -539 234 N ATOM 1173 ND2BASN A 61 7.512 1.797 22.152 0.50 34.10 N ANISOU 1173 ND2BASN A 61 5062 4644 3251 -1031 -186 246 N I put link in .def file like this: apply_cif_link { data_link = "NAG-ASN" residue_selection_1 = chain A and resname ANAG and resid 2061 residue_selection_2 = chain A and resname AASN and resid 61 } apply_cif_link { data_link = "NAG-ASN" residue_selection_1 = chain A and resname BNAG and resid 2061 residue_selection_2 = chain A and resname BASN and resid 61 } but when I run the .def file, I got an error message: couldn't find :residue_selection_1 = chain A and resname ANAG and resid 2061 Is there any wrong in my file? Thank you very much! yamei The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Could you try this?
apply_cif_link {
data_link = "NAG-ASN"
residue_selection_1 = chain A and resname NAG and resid 2061
residue_selection_2 = chain A and resname ASN and resid 61
}
I hope this works for both conformers.
Off the top of my head I'm not sure anymore how exactly we handle the
conformers. If the above doesn't work insert "and altloc A", with a copy
for "and altloc B", similar to what you tried.
Ralf
On Tue, Feb 21, 2012 at 5:15 PM, Qiang Chen
Hi all,
In my structure, the ASN and the linked NAG has two conformations. The pdb: ATOM 3685 C1 ANAG A2061 4.069 2.862 24.649 0.47 31.33 C ANISOU 3685 C1 ANAG A2061 3426 4664 3813 -664 421 625 C ATOM 3686 C1 BNAG A2061 9.105 0.384 22.719 0.53 40.81 C ANISOU 3686 C1 BNAG A2061 5087 5333 5084 24 -72 -116 C ATOM 3690 C2 ANAG A2061 4.508 1.905 25.749 0.47 34.38 C ANISOU 3690 C2 ANAG A2061 3953 4727 4383 -441 142 473 C ATOM 3691 C2 BNAG A2061 8.311 -0.893 22.808 0.53 40.91 C ANISOU 3691 C2 BNAG A2061 5087 5438 5018 13 -55 -37 C ATOM 3694 N2 ANAG A2061 5.010 0.727 25.059 0.47 35.56 N ANISOU 3694 N2 ANAG A2061 4185 4888 4437 -466 149 254 N ATOM 3695 N2 BNAG A2061 7.220 -0.767 23.761 0.53 40.82 N ANISOU 3695 N2 BNAG A2061 5159 5512 4836 246 -144 -112 N ATOM 3698 C7 ANAG A2061 6.312 0.507 24.874 0.47 34.61 C ANISOU 3698 C7 ANAG A2061 4357 4653 4141 -406 202 282 C ATOM 3699 C7 BNAG A2061 5.974 -1.172 23.460 0.53 41.98 C ANISOU 3699 C7 BNAG A2061 5327 5677 4943 117 8 -149 C ATOM 3700 O7 ANAG A2061 7.194 1.236 25.322 0.47 35.05 O ANISOU 3700 O7 ANAG A2061 4292 4626 4396 -724 290 343 O ATOM 3701 O7 BNAG A2061 5.625 -1.665 22.371 0.53 44.02 O ANISOU 3701 O7 BNAG A2061 5616 5774 5335 6 -122 -208 O ATOM 3702 C8 ANAG A2061 6.699 -0.698 24.067 0.47 33.30 C ANISOU 3702 C8 ANAG A2061 4119 4700 3832 -193 57 303 C ATOM 3703 C8 BNAG A2061 4.933 -0.984 24.514 0.53 42.31 C ANISOU 3703 C8 BNAG A2061 5260 5612 5203 157 -4 -125 C ATOM 3710 C3 ANAG A2061 3.357 1.608 26.717 0.47 34.94 C ANISOU 3710 C3 ANAG A2061 3903 4950 4420 -528 289 456 C ATOM 3711 C3 BNAG A2061 9.296 -2.001 23.171 0.53 40.83 C ANISOU 3711 C3 BNAG A2061 5144 5347 5021 31 -211 -83 C ATOM 3714 O3 ANAG A2061 3.801 0.844 27.813 0.47 37.07 O ANISOU 3714 O3 ANAG A2061 4043 5387 4655 -327 106 508 O ATOM 3715 O3 BNAG A2061 8.608 -3.231 23.147 0.53 41.68 O ANISOU 3715 O3 BNAG A2061 5286 5504 5046 -142 -263 97 O ATOM 3718 C4 ANAG A2061 2.696 2.880 27.229 0.47 33.38 C ANISOU 3718 C4 ANAG A2061 3490 4870 4323 -715 378 575 C ATOM 3719 C4 BNAG A2061 10.480 -2.021 22.187 0.53 39.61 C ANISOU 3719 C4 BNAG A2061 4854 5338 4854 85 -226 -13 C ATOM 3722 O4 ANAG A2061 1.507 2.534 27.956 0.47 35.04 O ANISOU 3722 O4 ANAG A2061 3669 4878 4766 -843 393 668 O ATOM 3723 O4 BNAG A2061 11.583 -2.708 22.745 0.53 37.22 O ANISOU 3723 O4 BNAG A2061 4397 5524 4220 146 -644 59 O ATOM 3726 C5 ANAG A2061 2.336 3.744 26.026 0.47 34.15 C ANISOU 3726 C5 ANAG A2061 3749 4890 4334 -733 503 550 C ATOM 3727 C5 BNAG A2061 11.003 -0.643 21.780 0.53 39.23 C ANISOU 3727 C5 BNAG A2061 4886 5258 4760 33 -165 -30 C ATOM 3730 C6 ANAG A2061 1.625 5.025 26.471 0.47 35.40 C ANISOU 3730 C6 ANAG A2061 4140 4847 4461 -657 269 378 C ATOM 3731 C6 BNAG A2061 11.764 -0.744 20.462 0.53 39.76 C ANISOU 3731 C6 BNAG A2061 5000 5228 4877 79 -185 -106 C ATOM 3736 O6 ANAG A2061 2.432 5.674 27.428 0.47 37.10 O ANISOU 3736 O6 ANAG A2061 4302 5083 4710 -773 428 205 O ATOM 3737 O6 BNAG A2061 10.918 -1.227 19.435 0.53 40.11 O ANISOU 3737 O6 BNAG A2061 4599 5472 5169 313 -83 -277 O ATOM 3740 O5 ANAG A2061 3.507 4.032 25.210 0.47 33.36 O ANISOU 3740 O5 ANAG A2061 3905 4796 3974 -742 445 909 O ATOM 3741 O5 BNAG A2061 9.974 0.304 21.624 0.53 39.18 O ANISOU 3741 O5 BNAG A2061 5023 5184 4676 -220 -99 -108 O ATOM 1157 N ASN A 61 8.496 4.626 20.319 1.00 26.85 N ANISOU 1157 N ASN A 61 3029 4695 2476 -1809 -655 1273 N ATOM 1158 CA AASN A 61 7.080 4.398 20.655 0.50 24.65 C ANISOU 1158 CA AASN A 61 2996 4000 2368 -1776 -634 980 C ATOM 1159 CA BASN A 61 7.083 4.446 20.752 0.50 25.61 C ANISOU 1159 CA BASN A 61 3174 4178 2376 -1622 -618 912 C ATOM 1162 CB AASN A 61 6.952 3.807 22.077 0.50 23.96 C ANISOU 1162 CB AASN A 61 2901 3704 2497 -1862 -440 1083 C ATOM 1163 CB BASN A 61 7.016 4.118 22.260 0.50 26.04 C ANISOU 1163 CB BASN A 61 3226 4291 2376 -1605 -554 824 C ATOM 1168 CG AASN A 61 5.499 3.653 22.494 0.50 27.33 C ANISOU 1168 CG AASN A 61 3048 4420 2914 -1388 -585 598 C ATOM 1169 CG BASN A 61 7.882 2.975 22.608 0.50 27.64 C ANISOU 1169 CG BASN A 61 3195 4695 2612 -1576 -444 650 C ATOM 1170 OD1AASN A 61 4.659 3.204 21.697 0.50 27.73 O ANISOU 1170 OD1AASN A 61 3349 4200 2986 -1314 -644 873 O ATOM 1171 OD1BASN A 61 8.908 3.141 23.291 0.50 30.84 O ANISOU 1171 OD1BASN A 61 3734 4991 2990 -1345 -880 129 O ATOM 1172 ND2AASN A 61 5.182 4.096 23.716 0.50 34.27 N ANISOU 1172 ND2AASN A 61 3736 5474 3811 -832 -539 234 N ATOM 1173 ND2BASN A 61 7.512 1.797 22.152 0.50 34.10 N ANISOU 1173 ND2BASN A 61 5062 4644 3251 -1031 -186 246 N
I put link in .def file like this: apply_cif_link { data_link = "NAG-ASN" residue_selection_1 = chain A and resname ANAG and resid 2061 residue_selection_2 = chain A and resname AASN and resid 61 } apply_cif_link { data_link = "NAG-ASN" residue_selection_1 = chain A and resname BNAG and resid 2061 residue_selection_2 = chain A and resname BASN and resid 61 } but when I run the .def file, I got an error message: couldn't find :residue_selection_1 = chain A and resname ANAG and resid 2061
Is there any wrong in my file?
Thank you very much!
yamei
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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participants (5)
-
Bryan Lepore -
Qiang Chen -
R.D. Oeffner -
Ralf Grosse-Kunstleve -
Thomas Holder