[buster-discuss] FAD dictionary issues
Clemens Vonrhein
vonrhein at globalphasing.com
Wed Jun 16 20:39:54 CEST 2010
Dear Alejandro,
we have a FAD dictionary in
$BDG_home/tnt/data/cofactor_geo.dat
whihc usually BUSTER should pick up automatically. This dictionary
should be fairly good for refining FAD.
However, there is the possibility of a mix-up between PDB v3 and v2
atom naming. What happens if you run
% pdbvconv -p your.pdb -o tmp.pdb
This should detect the PDB version in your PDB file (and convert from
that version into the other, so it can go v2->v3 as well as v3->v2).
The important thing is that you don't have a mixture of the two
formats. And since at the moment BUSTER still uses (internally) v2
atom naming, I would recommend getting your FAD atom names into v2
format.
I attach the two version of FAD you would get for residue A1001 from
Jose's 3h8i entry.
FAD_3h8i_A1001_v3.pdb (as in PDB entry/file)
FAD_3h8i_A1001_v2.pdb (after running pdbvconv on it)
Cheers
Clemens
On Wed, Jun 16, 2010 at 12:37:23PM -0300, alebus at pasteur.edu.uy wrote:
> Dear Jose,
>
> thank you for your practical suggestion (although knowing how to input
> modified dictionaries in a proper way, still seems important to
> me...see below)
>
> ...unfortunately, after carefully modifying my pdb to match the one
> you point me to, refinement is even worse....! (I know it's very easy
> to mess up these pdb editing efforts by hand; I did go with extreme
> care though...)
>
> bottom line : still needing help!
>
> thanks a lot
> alejandro
>
>
> Quoting Jose Artur Brito <jbrito at itqb.unl.pt>:
>
> > Dear Alejandro,
> > please take a look at entry 3H8I of the PDB. It has a covalently bound
> > FAD and it was refined with BUSTER so the atom names should be correct
> > and recognized by BUSTER and CCP4 libraries.
> > Cheers,
> > Jose
> >
> >
> > On 06/16/2010 11:00 AM, buster-discuss-request at globalphasing.com wrote:
> >> ----------------------------------------------------------------------
> >>
> >> Message: 1
> >> Date: Wed, 16 Jun 2010 06:33:16 -0300
> >> From: alebus at pasteur.edu.uy
> >> Subject: [buster-discuss] how to handle user defined stereochemical
> >> dictionaries
> >> To: buster-discuss at globalphasing.com
> >> Message-ID:<20100616063316.xhyu4mlwk84cc4go at www.pasteur.edu.uy>
> >> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes";
> >> format="flowed"
> >>
> >> Dear BUSTER community,
> >>
> >> I am having some problems refining a protein that contains FAD.
> >> Some of the 'available' dictionaries (such as ccp4) seem to have some
> >> errors (adenine N6 is not included in the corresponding planarity
> >> restraint, etc)
> >> in the end, I'm obtaining some distorted geometries (res 2.8?, SG 18)
> >>
> >> So, two questions:
> >>
> >> 1. What is the proper way to use a user-defined dictionary?
> >>
> >> I tried including the -l option for the autobuster refine command,
> >> immediately followed by the name of the dictionary (both a .cif,
> >> refmac style; or one .dic derived from that one using MakeTNT).
> >> Autobuster refine will tell me in the beginning "Dictionary versions
> >> picked up from NOTE BUSTER_RESTRAINT_DICT cards as: ... ------
> >> restraints FAD by MakeTNT_2.4.0 from REFMAC dictionary...". (although
> >> I actually do not find the name of my dictionary anywhere...probably
> >> not reading it I guess)
> >> But then, a few lines lower it will invariably say "Have no dictionary
> >> entry giving ccp4 atom types for residue types: FAD SO4
> >> will use default ccp4 atom types CUNK NUNK OUNK PUNK SUNK
> >> .... where possible."
> >> (by the way, SO4 is actually in the 'regular' dictionaries: why can't
> >> it find it? I saw this question from Miguel Ortiz, but then no follow
> >> up on that...)
> >>
> >> 2. What is the procedure to look at this "fast"?
> >> I mean, without actually running a full refinement protocol, just look
> >> at if buster actually read and kept the desired dictionary, and to
> >> which idealized model those restraints would actually be pointing to
> >> in further buster refinement cycles.
> >>
> >> Thanks a lot for any advice!
> >>
> >> Alejandro
> >>
> >
> > --
> > ____________________________________________
> > José Artur Brito, B.Sc. (Eng.), PhD Student
> >
> > Membrane Protein Crystallography Lab
> > Instituto de Tecnologia Química e Biológica
> > Oeiras - Portugal
> >
> > Tel.: +351.21.446.97.61
> > Fax: +351.21.443.36.44
> >
> > E-mail: jbrito at itqb.unl.pt
> > URL: http://xtal.itqb.unl.pt
> >
> > _______________________________________________
> > buster-discuss mailing list
> > buster-discuss at globalphasing.com
> > https://www.globalphasing.com/mailman/listinfo/buster-discuss
>
>
>
> --
> Alejandro Buschiazzo, PhD
> Research Scientist
> Unit of Protein Crystallography
> Pasteur Institute of Montevideo
> Mataojo 2020
> Montevideo 11400
> URUGUAY
>
> Phone: +5982 5220910 int. 120
> Fax: +5982 5224185
> _______________________________________________
> buster-discuss mailing list
> buster-discuss at globalphasing.com
> https://www.globalphasing.com/mailman/listinfo/buster-discuss
--
***************************************************************
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
* Global Phasing Ltd.
* Sheraton House, Castle Park
* Cambridge CB3 0AX, UK
*--------------------------------------------------------------
* BUSTER Development Group (http://www.globalphasing.com)
***************************************************************
-------------- next part --------------
LINK SG CYS A 129 C8M FAD A1001 1555 1555 1.53
SITE 3 AC5 9 FAD A1001
HETATM 5591 PA FAD A1001 -105.746 -6.747 -23.245 1.00 46.92 P
HETATM 5592 O1A FAD A1001 -106.781 -6.354 -22.251 1.00 47.29 O
HETATM 5593 O2A FAD A1001 -105.251 -5.754 -24.204 1.00 47.73 O
HETATM 5594 O5B FAD A1001 -106.481 -7.815 -24.114 1.00 47.18 O
HETATM 5595 C5B FAD A1001 -107.488 -8.570 -23.466 1.00 47.46 C
HETATM 5596 C4B FAD A1001 -108.061 -9.490 -24.526 1.00 47.60 C
HETATM 5597 O4B FAD A1001 -108.696 -10.547 -23.828 1.00 47.59 O
HETATM 5598 C3B FAD A1001 -109.140 -8.766 -25.291 1.00 47.55 C
HETATM 5599 O3B FAD A1001 -109.193 -9.259 -26.599 1.00 48.76 O
HETATM 5600 C2B FAD A1001 -110.399 -9.099 -24.580 1.00 47.45 C
HETATM 5601 O2B FAD A1001 -111.538 -8.914 -25.389 1.00 48.30 O
HETATM 5602 C1B FAD A1001 -110.086 -10.523 -24.193 1.00 47.34 C
HETATM 5603 N9A FAD A1001 -110.870 -11.000 -23.072 1.00 47.17 N
HETATM 5604 C8A FAD A1001 -111.009 -10.425 -21.842 1.00 47.51 C
HETATM 5605 N7A FAD A1001 -111.798 -11.100 -21.040 1.00 47.84 N
HETATM 5606 C5A FAD A1001 -112.200 -12.184 -21.781 1.00 47.37 C
HETATM 5607 C6A FAD A1001 -113.043 -13.294 -21.501 1.00 48.09 C
HETATM 5608 N6A FAD A1001 -113.664 -13.489 -20.321 1.00 48.84 N
HETATM 5609 N1A FAD A1001 -113.214 -14.215 -22.477 1.00 48.15 N
HETATM 5610 C2A FAD A1001 -112.602 -14.048 -23.674 1.00 48.48 C
HETATM 5611 N3A FAD A1001 -111.786 -13.050 -24.055 1.00 48.11 N
HETATM 5612 C4A FAD A1001 -111.620 -12.141 -23.060 1.00 47.14 C
HETATM 5613 N1 FAD A1001 -98.540 -0.288 -23.267 1.00 51.66 N
HETATM 5614 C2 FAD A1001 -97.325 -0.068 -23.855 1.00 51.82 C
HETATM 5615 O2 FAD A1001 -96.533 -1.022 -24.148 1.00 52.50 O
HETATM 5616 N3 FAD A1001 -96.929 1.246 -24.034 1.00 52.03 N
HETATM 5617 C4 FAD A1001 -97.709 2.390 -23.774 1.00 52.33 C
HETATM 5618 O4 FAD A1001 -97.385 3.589 -23.905 1.00 53.75 O
HETATM 5619 C4X FAD A1001 -99.073 2.104 -23.249 1.00 51.50 C
HETATM 5620 N5 FAD A1001 -99.867 3.118 -23.001 1.00 52.06 N
HETATM 5621 C5X FAD A1001 -101.119 2.811 -22.471 1.00 51.17 C
HETATM 5622 C6 FAD A1001 -101.974 3.902 -22.234 1.00 51.92 C
HETATM 5623 C7 FAD A1001 -103.286 3.712 -21.759 1.00 52.23 C
HETATM 5624 C7M FAD A1001 -104.222 4.886 -21.546 1.00 54.30 C
HETATM 5625 C8 FAD A1001 -103.698 2.362 -21.483 1.00 51.92 C
HETATM 5626 C8M FAD A1001 -105.076 2.009 -20.925 1.00 52.86 C
HETATM 5627 C9 FAD A1001 -102.796 1.270 -21.706 1.00 51.20 C
HETATM 5628 C9A FAD A1001 -101.498 1.464 -22.168 1.00 50.80 C
HETATM 5629 N10 FAD A1001 -100.608 0.388 -22.412 1.00 50.66 N
HETATM 5630 C10 FAD A1001 -99.385 0.654 -22.979 1.00 51.04 C
HETATM 5631 C1' FAD A1001 -100.933 -1.001 -22.087 1.00 50.49 C
HETATM 5632 C2' FAD A1001 -101.689 -1.895 -23.018 1.00 50.01 C
HETATM 5633 O2' FAD A1001 -103.034 -1.428 -23.004 1.00 50.82 O
HETATM 5634 C3' FAD A1001 -101.744 -3.223 -22.255 1.00 49.82 C
HETATM 5635 O3' FAD A1001 -100.494 -3.413 -21.530 1.00 50.40 O
HETATM 5636 C4' FAD A1001 -102.091 -4.318 -23.248 1.00 49.74 C
HETATM 5637 O4' FAD A1001 -103.376 -4.058 -23.824 1.00 50.19 O
HETATM 5638 C5' FAD A1001 -102.089 -5.667 -22.585 1.00 49.55 C
HETATM 5639 O5' FAD A1001 -102.456 -6.608 -23.606 1.00 49.16 O
HETATM 5640 P FAD A1001 -103.173 -8.006 -23.299 1.00 48.62 P
HETATM 5641 O1P FAD A1001 -103.307 -8.643 -24.643 1.00 49.33 O
HETATM 5642 O2P FAD A1001 -102.337 -8.656 -22.247 1.00 48.86 O
HETATM 5643 O3P FAD A1001 -104.524 -7.531 -22.709 1.00 48.18 O
-------------- next part --------------
LINK SG CYS A 129 C8M FAD A1001 1555 1555 1.53
SITE 3 AC5 9 FAD A1001
HETATM 5591 AP FAD A1001 -105.746 -6.747 -23.245 1.00 46.92 P
HETATM 5592 AO1 FAD A1001 -106.781 -6.354 -22.251 1.00 47.29 O
HETATM 5593 AO2 FAD A1001 -105.251 -5.754 -24.204 1.00 47.73 O
HETATM 5594 AO5* FAD A1001 -106.481 -7.815 -24.114 1.00 47.18 O
HETATM 5595 AC5* FAD A1001 -107.488 -8.570 -23.466 1.00 47.46 C
HETATM 5596 AC4* FAD A1001 -108.061 -9.490 -24.526 1.00 47.60 C
HETATM 5597 AO4* FAD A1001 -108.696 -10.547 -23.828 1.00 47.59 O
HETATM 5598 AC3* FAD A1001 -109.140 -8.766 -25.291 1.00 47.55 C
HETATM 5599 AO3* FAD A1001 -109.193 -9.259 -26.599 1.00 48.76 O
HETATM 5600 AC2* FAD A1001 -110.399 -9.099 -24.580 1.00 47.45 C
HETATM 5601 AO2* FAD A1001 -111.538 -8.914 -25.389 1.00 48.30 O
HETATM 5602 AC1* FAD A1001 -110.086 -10.523 -24.193 1.00 47.34 C
HETATM 5603 AN9 FAD A1001 -110.870 -11.000 -23.072 1.00 47.17 N
HETATM 5604 AC8 FAD A1001 -111.009 -10.425 -21.842 1.00 47.51 C
HETATM 5605 AN7 FAD A1001 -111.798 -11.100 -21.040 1.00 47.84 N
HETATM 5606 AC5 FAD A1001 -112.200 -12.184 -21.781 1.00 47.37 C
HETATM 5607 AC6 FAD A1001 -113.043 -13.294 -21.501 1.00 48.09 C
HETATM 5608 AN6 FAD A1001 -113.664 -13.489 -20.321 1.00 48.84 N
HETATM 5609 AN1 FAD A1001 -113.214 -14.215 -22.477 1.00 48.15 N
HETATM 5610 AC2 FAD A1001 -112.602 -14.048 -23.674 1.00 48.48 C
HETATM 5611 AN3 FAD A1001 -111.786 -13.050 -24.055 1.00 48.11 N
HETATM 5612 AC4 FAD A1001 -111.620 -12.141 -23.060 1.00 47.14 C
HETATM 5613 N1 FAD A1001 -98.540 -0.288 -23.267 1.00 51.66 N
HETATM 5614 C2 FAD A1001 -97.325 -0.068 -23.855 1.00 51.82 C
HETATM 5615 O2 FAD A1001 -96.533 -1.022 -24.148 1.00 52.50 O
HETATM 5616 N3 FAD A1001 -96.929 1.246 -24.034 1.00 52.03 N
HETATM 5617 C4 FAD A1001 -97.709 2.390 -23.774 1.00 52.33 C
HETATM 5618 O4 FAD A1001 -97.385 3.589 -23.905 1.00 53.75 O
HETATM 5619 C4A FAD A1001 -99.073 2.104 -23.249 1.00 51.50 C
HETATM 5620 N5 FAD A1001 -99.867 3.118 -23.001 1.00 52.06 N
HETATM 5621 C5A FAD A1001 -101.119 2.811 -22.471 1.00 51.17 C
HETATM 5622 C6 FAD A1001 -101.974 3.902 -22.234 1.00 51.92 C
HETATM 5623 C7 FAD A1001 -103.286 3.712 -21.759 1.00 52.23 C
HETATM 5624 C7M FAD A1001 -104.222 4.886 -21.546 1.00 54.30 C
HETATM 5625 C8 FAD A1001 -103.698 2.362 -21.483 1.00 51.92 C
HETATM 5626 C8M FAD A1001 -105.076 2.009 -20.925 1.00 52.86 C
HETATM 5627 C9 FAD A1001 -102.796 1.270 -21.706 1.00 51.20 C
HETATM 5628 C9A FAD A1001 -101.498 1.464 -22.168 1.00 50.80 C
HETATM 5629 N10 FAD A1001 -100.608 0.388 -22.412 1.00 50.66 N
HETATM 5630 C10 FAD A1001 -99.385 0.654 -22.979 1.00 51.04 C
HETATM 5631 C1* FAD A1001 -100.933 -1.001 -22.087 1.00 50.49 C
HETATM 5632 C2* FAD A1001 -101.689 -1.895 -23.018 1.00 50.01 C
HETATM 5633 O2* FAD A1001 -103.034 -1.428 -23.004 1.00 50.82 O
HETATM 5634 C3* FAD A1001 -101.744 -3.223 -22.255 1.00 49.82 C
HETATM 5635 O3* FAD A1001 -100.494 -3.413 -21.530 1.00 50.40 O
HETATM 5636 C4* FAD A1001 -102.091 -4.318 -23.248 1.00 49.74 C
HETATM 5637 O4* FAD A1001 -103.376 -4.058 -23.824 1.00 50.19 O
HETATM 5638 C5* FAD A1001 -102.089 -5.667 -22.585 1.00 49.55 C
HETATM 5639 O5* FAD A1001 -102.456 -6.608 -23.606 1.00 49.16 O
HETATM 5640 P FAD A1001 -103.173 -8.006 -23.299 1.00 48.62 P
HETATM 5641 O1P FAD A1001 -103.307 -8.643 -24.643 1.00 49.33 O
HETATM 5642 O2P FAD A1001 -102.337 -8.656 -22.247 1.00 48.86 O
HETATM 5643 O3P FAD A1001 -104.524 -7.531 -22.709 1.00 48.18 O
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