[ccp4bb] PDBe maintenance downtime
Dear Users, The PDBe site is scheduled for hardware maintenance on Thursday 26th November starting at 2pm. This will effect all web resources until 10am on the 27th. Additionally all deposition and annotation services of new entries will not available. We shall update the status on the PDBe main page (http://www.ebi.ac.uk/pdbe/) and the Depositions pages (http://www.ebi.ac.uk/pdbe-xdep/autodep/ , http://www.ebi.ac.uk/pdbe-emdep/emdep/). Our sincere apologies for any inconvenience, and we appreciate your understanding. Best Regards, Gaurav Sahni PDB Depositions
Re: [ccp4bb] Help request: Failed MR using the same molecule as model
I think you have a found a supercell and dont really need to run any MR program to find the solution - just reposition the molecule Your P422 point group cell is 126.514 126.514 76.766 90.00 90.00 90.00 Your I422 point group cellis: 180.096 180.096 152.530 90.00 90.00 90.00 Note c is doubled a = b = a_P422 * sqrt(2) And you have a large off origin peak in the Patterson ( that is the meaning of the "As shown in"Analyse Data for MR", the first peak is 100 and second is 68.92" message You dont give the coordinates but I bet it is related to the supercell ness ( P42 22 is a subgroup of I422) By the way where is that peak? Si I suspect the structures are the same and you have either integrated in too large cell for the I422 version,or missed some data in the P4222; I suggest you take your P42 22 solution. rotate the coordinates by 45 degrees to get to the I422 axes pdbset xyzin P4.pdb xyzout I422A.pdb cell180.096 180.096 152.530 90.00 90.00 90.00 rotate euler 0 0 45 end Then generate the translated molecule pdbset xyzin I422A.pdb xyzout I422B.pdb shift frac x y z (taken for the off origin translation from above) end Combine the two pdbs I422A.pdb and I422B.pdb (Edit them to make sure there is only one header and end card ) Try that as a solution. Eleanor Actually, another thing could be going on as well. You show a large off-origin peak in the Patterson in I422 so you may have pseudotranslation going on and you processed in the supercell. You could probably try to reindex choosing fewer spots and get your P422 cell. I am sure there is some law that would convert your P422 cell to I422 (or vice versa), but I don't know it off the top of my head. That way you could just look at your cell lengths and see if this is possible. Its probably the same crystal form, except this crystal has PTS. Jon Chao Quan wrote: Dear CCP4 community: I am a beginner to crystallography and therefore my apologies if this question is too simple. Basically we obtained several crystal forms of the same molecule, which is a hetero- trimer containing protein A(18kD), protein B(16kD) and a RNA segment(40nt or about 15kD). We have solved the structure of one crystal form(form_1); its information is as follows: space group = P 42 22; unit cell = 126.514 126.514 76.766 90.00 90.00 90.00 resolution = 2.7A; Rwork = 0.25, Rfree = 0.265; solvent content = 60%; Number of molecules per Asymmetric Unit = 1; Data redundancy = 5; Data Completeness = 94%; I am now trying to solve the structure of form_2 crystal using molecular replacement. So far the information I know about form_2 is as follows: space group = I 422 or I 41 22; unit cell = 180.096 180.096 152.530 90.00 90.00 90.00 (unit cell is about 4 times the size of form_1) resolution = 3.3A; (which is low) Number of molecules per Asymmetric Unit = 2 or 3; Data redundancy = 4; Data Completeness = 92%; There is no twinning(as shown by Sfcheck); As shown in"Analyse Data for MR", the first peak is 100 and second is 68.92; I am not sure if this indicates translation in a Asymmetric Unit; The problem is, I can not get a good solution by MR using Phaser (both I422 and I4122 are tried). When I searched for 3 molecules per Asymmetric Unit, Phaser did not give solutions at all. When I used 2/ASU instead, I was able to get some solutions, with typical statistics as follows: RFZ=14, TFZ=35.9, PAK=0, LLG=1036; However, these solutions had high R values(like Rwork=0.59 and Rfree=0.58), which indicated that they are not solutions at all. Still, I tried refinement using refmac5, but R values did not go down even after 50 rounds; sometimes they even increased after refinement. Besides, the RMS values bond length, bond angle and chiral center were all 0 as show by refmac5. I tried limiting resolution range to 15-4A in Phaser, which did not help either. Now I am completely stuck. Could anyone give me some advice? I know this situation is very strange, because I am using the SAME molecule for MR but can not can a solution. Thanks a lot, P.S. 1) Both form_1 and form_2 crystals were grown using Selenomethionine-containing samples. There are 3 Sel_Met in protein A and 1 in protein B. 2) A 10-aa internal segment of protein B is missing in the solved structure, which may indicate high flexibility. Chao
[ccp4bb]
hello this is not a new question i was searching this in archives but i did'nt get . just send me link for this . i want to link AMP covalently with lysine in my structure (phosphoamide bond)how i will do this in coot and refmac . in turbo there is option make bond but in this no option is there . thanx
Re: [ccp4bb] decrease of background with distance?
> The source for the X-ray background are points along the air path
> post-collimator including the sample with loop and cryoprotecdant (or
> capillary and mother liquor). So the 1/r^2 falloff is
> noticable going from
> 100 mm to 200 mm. The same counts in a 2x2 pixel area is now
> seen in a 4x4
> pixel area.
Hi Jim,
I think it may be a bit more complicated than this because the
background contribution from the crystalline scattering consists of
non-Bragg elastic ('diffuse') scattering, plus inelastic ('Compton')
scattering, though the latter is probably small & can be ignored. DS
consists of a number of contributions, notably the 'optic' component due
to short range correlated displacements (e.g. of secondary structure
elements), and the 'acoustic' component due to longer range correlated
displacements of whole molecules in adjacent unit cells (i.e. scattering
by lattice phonons). Now the 'optic' component can be regarded as
attached to the reciprocal lattice, so does scale exactly in the way you
describe. However the acoustic component probably represents the
biggest contributor to the X-ray background under normal conditions and
is responsible for the 'tails' under the Bragg spots; in fact the
acoustic DS peaks right under the Bragg spots & there's no practical way
of separating them, because AFAIK (though I could be wrong) the acoustic
peaks scale with the Bragg spots. I don't think it's possible (though
admittedly I've never tried) to separate the acoustic DS tails from the
spots merely by moving the detector further away as you seem to be
implying! I'm by no means an expert on dynamical scattering theory so I
could be talking nonsense!
> The source for Bragg reflections at a synchtrotron is
> upstream a couple
> dozen meters. The divergence is not large as well, so the
> spread in the
> spots (for a source ~30 meters upstream) goes from 1/(30.1 *
> 30.1)^2 to
> 1/(30.2 * 30.2)^2 which is really not that noticable.
I'm genuinely confused by this because I thought the whole point of
modern focusing optics (or at least the confocal mirror design) is to
focus the beam onto (or close to) the sample, in which case wouldn't the
photons diverge from the 'virtual source' (actually a real image of the
real source) at the crystal, instead of from the real source? So then
Bragg spots (and therefore also the acoustic DS) should diverge from the
position of this virtual source?
Cheers
-- Ian
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Re: [ccp4bb] Bad geometry for alt. conformation refined in Refmac5
Hmm - I dont understand that. I ran structure idealisation on both examples and that tidies up the geometry perfectly.. Are there some clashes with pre-existing water molecules or other indicators in the log file that one conformation is suspect?(Look for warnings..) Eleanor John Pascal wrote: Hello All, We are trying to refine ARG residues with two conformations in Refmac5, and the refined atom positions in the output PDB file are all over the place, as if the geometry restraints are not well defined. We've tried several different formats for the input file, based on previous postings to the bulletin board and the PDB standard (two examples below), but the result is always the same. We are using Refmac5 in CCP4 Suite 6.1.2, GUI 2.0.5 on Mac OSX. We'd appreciate any suggestions. Thanks. -John Examples of ARG format: 1) ATOM 1472 N ARG A 1 -5.737 26.887 38.372 1.00 29.53 CN ATOM 1473 CA ARG A 1 -5.445 25.560 37.882 1.00 30.24 CC ATOM 1474 CB ARG A 1 -5.314 24.548 39.036 1.00 30.63 CC ATOM 1475 CG ARG A 1 -5.426 23.052 38.627 1.00 34.81 CC ATOM 1476 CD AARG A 1 -4.827 22.075 39.644 0.50 37.09 CC ATOM 1477 CD BARG A 1 -4.301 22.419 39.279 0.50 37.09 CC ATOM 1478 NE AARG A 1 -3.430 21.777 39.304 0.50 42.71 CN ATOM 1479 NE BARG A 1 -4.482 21.902 40.627 0.50 42.71 CN ATOM 1480 CZ AARG A 1 -2.998 20.868 38.402 0.50 44.91 CC ATOM 1481 CZ BARG A 1 -3.648 22.142 41.638 0.50 44.91 CC ATOM 1482 NH1AARG A 1 -3.841 20.117 37.678 0.50 45.20 CN ATOM 1483 NH1BARG A 1 -2.584 22.912 41.464 0.50 45.20 CN ATOM 1484 NH2AARG A 1 -1.688 20.715 38.210 0.50 44.99 CN ATOM 1485 NH2BARG A 1 -3.878 21.619 42.831 0.50 44.99 CN ATOM 1486 C ARG A 1 -6.518 25.176 36.830 1.00 29.97 CC ATOM 1487 O ARG A 1 -7.675 25.501 36.971 1.00 31.02 CO 2) ATOM 44 N AARG A 1 26.671 62.112 46.990 0.50 30.13 AN ATOM 45 CA AARG A 1 26.970 63.346 47.667 0.50 30.65 AC ATOM 46 CB AARG A 1 27.172 64.495 46.676 0.50 31.07 AC ATOM 47 CG AARG A 1 27.152 65.897 47.322 0.50 34.20 AC ATOM 48 CD AARG A 1 27.993 66.976 46.599 0.50 37.16 AC ATOM 49 NE AARG A 1 27.726 67.425 45.342 0.50 42.06 AN ATOM 50 CZ AARG A 1 28.315 67.639 44.168 0.50 44.78 AC ATOM 51 NH1AARG A 1 29.525 67.160 43.918 0.50 45.37 AN ATOM 52 NH2AARG A 1 27.690 68.340 43.240 0.50 45.67 AN ATOM 53 C AARG A 1 25.839 63.640 48.622 0.50 30.37 AC ATOM 54 O AARG A 1 24.690 63.377 48.340 0.50 31.24 AO ATOM 55 N BARG A 1 26.667 62.080 47.010 0.50 30.13 AN ATOM 56 CA BARG A 1 26.921 63.329 47.640 0.50 30.65 AC ATOM 57 CB BARG A 1 27.108 64.390 46.581 0.50 31.07 AC ATOM 58 CG BARG A 1 27.138 65.756 47.103 0.50 34.20 AC ATOM 59 CD BARG A 1 28.447 66.452 46.933 0.50 37.16 AC ATOM 60 NE BARG A 1 28.377 67.657 47.707 0.50 42.06 AN ATOM 61 CZ BARG A 1 29.349 68.269 48.373 0.50 44.78 AC ATOM 62 NH1BARG A 1 30.572 67.836 48.373 0.50 45.37 AN ATOM 63 NH2BARG A 1 29.066 69.368 49.034 0.50 45.67 AN ATOM 64 C BARG A 1 25.822 63.636 48.638 0.50 30.37 AC ATOM 65 O BARG A 1 24.698 63.372 48.403 0.50 31.24 AO John Pascal, PhD Thomas Jefferson University Department of Biochemistry & Molecular Biology 233 South 10th Street, BLSB 804 Philadelphia, Pennsylvania 19107 ph 215.503.4596 fx 215.923.2117
Re: [ccp4bb] decrease of background with distance?
Ian
Maybe - maybe not.
Investigations of acoustic and optical components of diffuse scatter
from proteins were carried out in the 80s and 90s including of course
work at Birkbeck (which I am sure you are aware of)
Refs can be found in Glover et. al. Acta Cryst. (1991). B47, 960-968.
This paper includes the statement
"We have exploited the characteristic fine collimation of synchrotron
radiation in the collection of data in which the acoustic scattering
contributions are minimized
to assess the effect on model refinement"
I think if the acoustic mode is due to correlations extending over 6
cells (say) then the width of the acoustic scatter will reflect this.
The diffuse feature will spread out as the spots separate when the
detector is moved back. However, as you say, separating them from the
diffraction peak could still be a problem. Should this intensity be
regarded as part of the Bragg peak or should it be subtracted from it?
With a poorly collimated beam or close detector distance this problem
does not arise as the acoustic scatter is in any case buried in the rest
of the Bragg peak.
Oh no - something else to argue about!
Colin
-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
Ian Tickle
Sent: 26 November 2009 11:20
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] decrease of background with distance?
> The source for the X-ray background are points along the air path
> post-collimator including the sample with loop and cryoprotecdant (or
> capillary and mother liquor). So the 1/r^2 falloff is noticable going
> from 100 mm to 200 mm. The same counts in a 2x2 pixel area is now
> seen in a 4x4 pixel area.
Hi Jim,
I think it may be a bit more complicated than this because the
background contribution from the crystalline scattering consists of
non-Bragg elastic ('diffuse') scattering, plus inelastic ('Compton')
scattering, though the latter is probably small & can be ignored. DS
consists of a number of contributions, notably the 'optic' component due
to short range correlated displacements (e.g. of secondary structure
elements), and the 'acoustic' component due to longer range correlated
displacements of whole molecules in adjacent unit cells (i.e. scattering
by lattice phonons). Now the 'optic' component can be regarded as
attached to the reciprocal lattice, so does scale exactly in the way you
describe. However the acoustic component probably represents the
biggest contributor to the X-ray background under normal conditions and
is responsible for the 'tails' under the Bragg spots; in fact the
acoustic DS peaks right under the Bragg spots & there's no practical way
of separating them, because AFAIK (though I could be wrong) the acoustic
peaks scale with the Bragg spots. I don't think it's possible (though
admittedly I've never tried) to separate the acoustic DS tails from the
spots merely by moving the detector further away as you seem to be
implying! I'm by no means an expert on dynamical scattering theory so I
could be talking nonsense!
> The source for Bragg reflections at a synchtrotron is upstream a
> couple dozen meters. The divergence is not large as well, so the
> spread in the spots (for a source ~30 meters upstream) goes from
> 1/(30.1 *
> 30.1)^2 to
> 1/(30.2 * 30.2)^2 which is really not that noticable.
I'm genuinely confused by this because I thought the whole point of
modern focusing optics (or at least the confocal mirror design) is to
focus the beam onto (or close to) the sample, in which case wouldn't the
photons diverge from the 'virtual source' (actually a real image of the
real source) at the crystal, instead of from the real source? So then
Bragg spots (and therefore also the acoustic DS) should diverge from the
position of this virtual source?
Cheers
-- Ian
Disclaimer
This communication is confidential and may contain privileged
information intended solely for the named addressee(s). It may not be
used or disclosed except for the purpose for which it has been sent. If
you are not the intended recipient you must not review, use, disclose,
copy, distribute or take any action in reliance upon it. If you have
received this communication in error, please notify Astex Therapeutics
Ltd by emailing i.tic...@astex-therapeutics.com and destroy all copies
of the message and any attached documents.
Astex Therapeutics Ltd monitors, controls and protects all its messaging
traffic in compliance with its corporate email policy. The Company
accepts no liability or responsibility for any onward transmission or
use of emails and attachments having left the Astex Therapeutics domain.
Unless expressly stated, opinions in this message are those of the
individual sender and not of Astex Therapeutics Ltd. The recipient
should check this email and any attachments for the presence of computer
viruses. Astex Therapeutics Ltd accepts no liability for damage caused
by any virus transmitted by this email. E-mail is susceptible to da
Re: [ccp4bb] decrease of background with distance?
Hi Colin
Yes I know, I worked with David Moss at Birkbeck for many years to
develop software to process the DS data. I think the point of using
finely collimated SRS X-rays (from the Daresbury SRS of course!) was to
scale down the spot size of both the Bragg & acoustic peaks by the same
factor, so that the peak integration included both contributions in the
'peak' region of the integration box in Mosflm, in order to prevent the
tail of the acoustic peak from straying into the 'background' region of
the adjacent spots.
David had developed an empirical theory to model the air, solvent,
Compton & acoustic contributions and correct the integrated data for
these, without background correction of course since the optic DS
background was ultimately to be our data! It was only the Bragg & optic
DS components that were interesting from a structure/function point of
view. I don't recall any discussion that we could get a handle on
separating the Bragg and acoustic components by changing the divergence
of the beam or the distance.
Cheers
-- Ian
> -Original Message-
> From: owner-ccp...@jiscmail.ac.uk
> [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of
> colin.n...@diamond.ac.uk
> Sent: 26 November 2009 11:54
> To: Ian Tickle; CCP4BB@JISCMAIL.AC.UK
> Subject: RE: [ccp4bb] decrease of background with distance?
>
>
> Ian
> Maybe - maybe not.
> Investigations of acoustic and optical components of diffuse scatter
> from proteins were carried out in the 80s and 90s including of course
> work at Birkbeck (which I am sure you are aware of)
>
> Refs can be found in Glover et. al. Acta Cryst. (1991). B47, 960-968.
> This paper includes the statement
> "We have exploited the characteristic fine collimation of synchrotron
> radiation in the collection of data in which the acoustic scattering
> contributions are minimized
> to assess the effect on model refinement"
>
> I think if the acoustic mode is due to correlations extending over 6
> cells (say) then the width of the acoustic scatter will reflect this.
> The diffuse feature will spread out as the spots separate when the
> detector is moved back. However, as you say, separating them from the
> diffraction peak could still be a problem. Should this intensity be
> regarded as part of the Bragg peak or should it be subtracted from it?
> With a poorly collimated beam or close detector distance this problem
> does not arise as the acoustic scatter is in any case buried
> in the rest
> of the Bragg peak.
>
> Oh no - something else to argue about!
>
> Colin
>
>
>
> -Original Message-
> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
> Ian Tickle
> Sent: 26 November 2009 11:20
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] decrease of background with distance?
>
> > The source for the X-ray background are points along the air path
> > post-collimator including the sample with loop and
> cryoprotecdant (or
> > capillary and mother liquor). So the 1/r^2 falloff is
> noticable going
>
> > from 100 mm to 200 mm. The same counts in a 2x2 pixel area is now
> > seen in a 4x4 pixel area.
>
> Hi Jim,
>
> I think it may be a bit more complicated than this because the
> background contribution from the crystalline scattering consists of
> non-Bragg elastic ('diffuse') scattering, plus inelastic ('Compton')
> scattering, though the latter is probably small & can be ignored. DS
> consists of a number of contributions, notably the 'optic'
> component due
> to short range correlated displacements (e.g. of secondary structure
> elements), and the 'acoustic' component due to longer range correlated
> displacements of whole molecules in adjacent unit cells (i.e.
> scattering
> by lattice phonons). Now the 'optic' component can be regarded as
> attached to the reciprocal lattice, so does scale exactly in
> the way you
> describe. However the acoustic component probably represents the
> biggest contributor to the X-ray background under normal
> conditions and
> is responsible for the 'tails' under the Bragg spots; in fact the
> acoustic DS peaks right under the Bragg spots & there's no
> practical way
> of separating them, because AFAIK (though I could be wrong)
> the acoustic
> peaks scale with the Bragg spots. I don't think it's possible (though
> admittedly I've never tried) to separate the acoustic DS
> tails from the
> spots merely by moving the detector further away as you seem to be
> implying! I'm by no means an expert on dynamical scattering
> theory so I
> could be talking nonsense!
>
> > The source for Bragg reflections at a synchtrotron is upstream a
> > couple dozen meters. The divergence is not large as well, so the
> > spread in the spots (for a source ~30 meters upstream) goes from
> > 1/(30.1 *
> > 30.1)^2 to
> > 1/(30.2 * 30.2)^2 which is really not that noticable.
>
> I'm genuinely confused by this because I thought the whole point of
> modern focusing optics (or at least the confocal mirr
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Re: [ccp4bb] decrease of background with distance?
Ian Surely the Bragg peaks, acoustic and optic components of the diffuse scatter all occupy a finite volume in reciprocal space. In x-ray scattering/diffraction the area they occupy on a detector therefore expands as the detector is moved further away. However, one will not always see this. If the beam divergence is large (or the detector resolution poor) the size of the feature on the detector is instead dominated by these instrument parameters. By improving these instrument parameters one will eventually see the true shape of the Bragg peaks (the sharpest feature) and be able to distinguish them optimally from the various types of diffuse scatter (originally called background!). After this, moving the detector further away will cause the size of the diffraction spots to increase just like the diffuse scatter components and no further benefit would be obtained. However, the acoustic mode will still be centred on the Bragg peak and it is not clear (to me) how one should treat it if one wants to have the best integrated intensities. You imply that it should be included within the peak. I think this is right but it is not clear that the profile fitting programs will always do this. In the majority of cases it probably doesn't matter but there might be some case where it does. As you say, the acoustic scatter has little interest from the structure function point of view. I think I had a discussion about this with James Holton some time ago but can't remember the conclusions! Colin -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ian Tickle Sent: 26 November 2009 14:00 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] decrease of background with distance? Hi Colin Yes I know, I worked with David Moss at Birkbeck for many years to develop software to process the DS data. I think the point of using finely collimated SRS X-rays (from the Daresbury SRS of course!) was to scale down the spot size of both the Bragg & acoustic peaks by the same factor, so that the peak integration included both contributions in the 'peak' region of the integration box in Mosflm, in order to prevent the tail of the acoustic peak from straying into the 'background' region of the adjacent spots. David had developed an empirical theory to model the air, solvent, Compton & acoustic contributions and correct the integrated data for these, without background correction of course since the optic DS background was ultimately to be our data! It was only the Bragg & optic DS components that were interesting from a structure/function point of view. I don't recall any discussion that we could get a handle on separating the Bragg and acoustic components by changing the divergence of the beam or the distance. Cheers -- Ian > -Original Message- > From: owner-ccp...@jiscmail.ac.uk > [mailto:owner-ccp...@jiscmail.ac.uk] On Behalf Of > colin.n...@diamond.ac.uk > Sent: 26 November 2009 11:54 > To: Ian Tickle; CCP4BB@JISCMAIL.AC.UK > Subject: RE: [ccp4bb] decrease of background with distance? > > > Ian > Maybe - maybe not. > Investigations of acoustic and optical components of diffuse scatter > from proteins were carried out in the 80s and 90s including of course > work at Birkbeck (which I am sure you are aware of) > > Refs can be found in Glover et. al. Acta Cryst. (1991). B47, 960-968. > This paper includes the statement > "We have exploited the characteristic fine collimation of synchrotron > radiation in the collection of data in which the acoustic scattering > contributions are minimized to assess the effect on model refinement" > > I think if the acoustic mode is due to correlations extending over 6 > cells (say) then the width of the acoustic scatter will reflect this. > The diffuse feature will spread out as the spots separate when the > detector is moved back. However, as you say, separating them from the > diffraction peak could still be a problem. Should this intensity be > regarded as part of the Bragg peak or should it be subtracted from it? > With a poorly collimated beam or close detector distance this problem > does not arise as the acoustic scatter is in any case buried in the > rest of the Bragg peak. > > Oh no - something else to argue about! > > Colin > > > > -Original Message- > From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of > Ian Tickle > Sent: 26 November 2009 11:20 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] decrease of background with distance? > > > The source for the X-ray background are points along the air path > > post-collimator including the sample with loop and > cryoprotecdant (or > > capillary and mother liquor). So the 1/r^2 falloff is > noticable going > > > from 100 mm to 200 mm. The same counts in a 2x2 pixel area is now > > seen in a 4x4 pixel area. > > Hi Jim, > > I think it may be a bit more complicated than this because the > background contribution from the crystallin
[ccp4bb] Unsubscribe
Please unsubsribe me for all the listings from CCP4b. Thanks Sapna
[ccp4bb] phenix rigid body ref.
Apologies, i know this is not phenix bb but since i am here (and not subscr. there), does anyone know how to control rigid body ref positions in phenix.refine, i am trying to do very low res check (6 Å) with quite many molecules, and they start landing on each other while the MR solution from molrep has perfect packing isnt there a packing constraint somwhere saying atoms cant be on top of each other... there was something about clashes but didnt seem to do anything.. the parameter definitions in .eff are bit cryptic to me in places... (would it be possible to step back a bit (sorry if i am wrong) to the ancient world of x-plor, still like that manual a lot..). thanks Tommi K.
[ccp4bb] ligand fitting, refinement?
Hi, I found this old post in ccp4 and it's very useful. I used the same procedure Scott described to add a ligand into pdb file. What I did, is in coot, search for the ligand in the library and find the ligand and then merge. However, when I tried to refine in refmac, it has some problems, it complains about that "New ligand has been encountered, stop now". I didn't create the cif file myself, it's been pulled from the library directory. Do anyone know what could be wrong? Thanks a lot for your help. Thanks. On Thu, Feb 5, 2009 at 10:55 AM, Scott Pegan wrote: > Andy, > > We do a lot of liganding fitting with CCP4. This is the general order of > steps we take (post initial solution of the protein itself): > > 1) Build the potential ligand in CCP4 Sketcher > >a) Rename all the Hydrogens to H#, CCP4 Refmac has some issues with > Hydrogens marked OH1, NH1, etc. To simplify things I normally just renumber > all the Hydrogens starting from 1. Also makes for less hassle when using > the definition file, as the labels in the definition file has to match the > pdb of the ligand (this will be more important below). > >b) Use the regularize function with Refmac > > 2) Using Coot, load the protein and maps > > 3) Load the ligand and definition file (_mon_lib.cif) > > 4) Use the find ligand function in Coot (find it under other modeling > tools) > >a) select the protein, map you want to search > > 5) If you find results you desire, merge those ligands with the main pdb > > 6) Run Refmac on the merged PDB with the library for the ligand in the > library input space. > > Hope this helps, > > Scott > > On Thu, Feb 5, 2009 at 9:27 AM, ANDY DODDS wrote: > >> Hello, >> >> does anyone know of a tutorial which lays out some sort of pipeline, >> hopefully using CCP4 packages, to fit and refine a small molecule >> ligand please? >> >> cheers >> >> andy >> >> > > > -- > Scott D. Pegan, Ph.D. > Senior Research Specialist > Center for Pharmaceutical > Biotechnology > University of Illinois at Chicago >
Re: [ccp4bb] phenix rigid body ref.
Hi Tommi You will find all the information you need on the following web page: http://www.phenix-online.org/documentation/refinement.htm as per your question, you could try : phenix.refine yourdataset.mtz yourmodel.pdb strategy=rigid_body rigid_body.number_of_zones=1 sites.rigid_body="chain A" sites.rigid_body="chain B" sites.rigid_body="chain C" sites.rigid_body="chain D" etc... (I suggest you take only one zone for the rigid body refinement because at 6A you only have so many reflections) Best Jacques Le Nov 26, 2009 à 8:32 PM, Tommi Kajander a écrit : Apologies, i know this is not phenix bb but since i am here (and not subscr. there), does anyone know how to control rigid body ref positions in phenix.refine, i am trying to do very low res check (6 Å) with quite many molecules, and they start landing on each other while the MR solution from molrep has perfect packing isnt there a packing constraint somwhere saying atoms cant be on top of each other... there was something about clashes but didnt seem to do anything.. the parameter definitions in .eff are bit cryptic to me in places... (would it be possible to step back a bit (sorry if i am wrong) to the ancient world of x-plor, still like that manual a lot..). thanks Tommi K.
[ccp4bb] More job opportunities at PDBe/EBI!
Dear colleagues! I would like to draw your attention to two new job opportunities that have opened up at the Protein Data Bank in Europe (PDBe) at the EBI (Hinxton, UK) and that will hopefully interest some of you: - Software Engineer/Scientific Programmer - to work on database integration and the development of new ways to access and use the structural archive: http://www.embl.de/aboutus/jobs/jobs_embl_ebi_hinxton/2010/w_09_095_ebi/index.html (contact: Sameer Velankar - sam...@ebi.ac.uk) - Software Engineer/Scientific Programmer - to work on developing new tools for the EM field (as part of the EM Data Bank, EMDB): http://www.embl.de/aboutus/jobs/jobs_embl_ebi_hinxton/2010/w_09_109_ebi/index.html (contact: Christoph Best - b...@ebi.ac.uk) Two other positions are also still open (although the odds of finding suitable candidates for them on CCP4BB are perhaps a tad worse): - Database Engineer (closes on Monday!): http://www.embl.de/aboutus/jobs/jobs_embl_ebi_hinxton/2009/w_09_078_ebi/index.html (contact: Tom Oldfield - oldfi...@ebi.ac.uk) - NMR Project Leader - a great opportunity for a talented and ambitious young NMR-ist to help define how NMR structural data is validated, represented and served back to the wider biological community: http://www.embl.de/aboutus/jobs/jobs_embl_ebi_hinxton/2009/w_09_077_ebi/index.html (contact: Wim Vranken - w...@ebi.ac.uk) I'm looking forward to receiving many applications from CCP4BB readers! --Gerard --- Gerard Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk http://www.ebi.ac.uk/pdbe/ Secretary: Celia Copp pdbe_ad...@ebi.ac.uk
Re: [ccp4bb] phenix rigid body ref.
this doesnt exactly go to the detail i was looking for... but thanks, i do know where the pages are. tommi On Nov 26, 2009, at 9:52 PM, Jacques-Philippe Colletier wrote: Hi Tommi You will find all the information you need on the following web page: http://www.phenix-online.org/documentation/refinement.htm as per your question, you could try : phenix.refine yourdataset.mtz yourmodel.pdb strategy=rigid_body rigid_body.number_of_zones=1 sites.rigid_body="chain A" sites.rigid_body="chain B" sites.rigid_body="chain C" sites.rigid_body="chain D" etc... (I suggest you take only one zone for the rigid body refinement because at 6A you only have so many reflections) Best Jacques Le Nov 26, 2009 à 8:32 PM, Tommi Kajander a écrit : Apologies, i know this is not phenix bb but since i am here (and not subscr. there), does anyone know how to control rigid body ref positions in phenix.refine, i am trying to do very low res check (6 Å) with quite many molecules, and they start landing on each other while the MR solution from molrep has perfect packing isnt there a packing constraint somwhere saying atoms cant be on top of each other... there was something about clashes but didnt seem to do anything.. the parameter definitions in .eff are bit cryptic to me in places... (would it be possible to step back a bit (sorry if i am wrong) to the ancient world of x-plor, still like that manual a lot..). thanks Tommi K. Tommi Kajander, Ph.D. Structural Biology and Biophysics Institute of Biotechnology University of Helsinki Viikinkaari 1 (P.O. Box 65) 00014 Helsinki Finland p. +358-9-19158903 tommi.kajan...@helsinki.fi
Re: [ccp4bb] decrease of background with distance?
David had developed an empirical theory to model the air, solvent, Compton & acoustic contributions and correct the integrated data for these, without background correction of course since the optic DS background was ultimately to be our data! ... Hi Ian, did David publish this theory somewhere? I'd love to get a reference. I'm genuinely confused by this because I thought the whole point of modern focusing optics (or at least the confocal mirror design) is to focus the beam onto (or close to) the sample, in which case wouldn't the photons diverge from the 'virtual source' (actually a real image of the real source) at the crystal, instead of from the real source? So then Bragg spots (and therefore also the acoustic DS) should diverge from the position of this virtual source? Cheers -- Ian This does seem confusing now. Here at CHESS, focus is either at the collimator (just upstream of the sample), or, in the case of capillaries, on the sample. In rare cases, on the detector. True, the focal spot would be a virtual source and, if the spot is reflected by an ideal crystal, that wouldn't change anything. But it is a very well collimated source even though it is slightly divergent (by a few mrad at most) ... this is in contrast to background scatter where photons are emitted in the whole q range (assuming it is "that kind" of scatter). So maybe it is more accurate to say Bragg reflections and background scatter are two rather different kinds of sources located at the crystal. Pardon my ignorance, but how can lattice phonons be a significant effect at low temperature? I presume the correlated displacements you refer to must be phonon modes frozen in place to create static disorder or something like that ... or perhaps stuff is moving more than I think at 100 K. Richard
Re: [ccp4bb] ligand fitting, refinement?
Hi Rui, for some reasons, I also always encounter problems when building new ligand by CCP4 Sketcher. You can try PRODRUG ( http://davapc1.bioch.dundee.ac.uk/prodrg/index.html) to build your new ligand and get the cif from the server, it always works for me. HTH, Matt 2009/11/27 rui > Hi, > > I found this old post in ccp4 and it's very useful. I used the same > procedure Scott described to add a ligand into pdb file. What I did, is in > coot, search for the ligand in the library and find the ligand and then > merge. However, when I tried to refine in refmac, it has some problems, it > complains about that "New ligand has been encountered, stop now". I didn't > create the cif file myself, it's been pulled from the library directory. Do > anyone know what could be wrong? Thanks a lot for your help. > > Thanks. > > On Thu, Feb 5, 2009 at 10:55 AM, Scott Pegan wrote: > >> Andy, >> >> We do a lot of liganding fitting with CCP4. This is the general order of >> steps we take (post initial solution of the protein itself): >> >> 1) Build the potential ligand in CCP4 Sketcher >> >>a) Rename all the Hydrogens to H#, CCP4 Refmac has some issues with >> Hydrogens marked OH1, NH1, etc. To simplify things I normally just renumber >> all the Hydrogens starting from 1. Also makes for less hassle when using >> the definition file, as the labels in the definition file has to match the >> pdb of the ligand (this will be more important below). >> >>b) Use the regularize function with Refmac >> >> 2) Using Coot, load the protein and maps >> >> 3) Load the ligand and definition file (_mon_lib.cif) >> >> 4) Use the find ligand function in Coot (find it under other modeling >> tools) >> >>a) select the protein, map you want to search >> >> 5) If you find results you desire, merge those ligands with the main pdb >> >> 6) Run Refmac on the merged PDB with the library for the ligand in the >> library input space. >> >> Hope this helps, >> >> Scott >> >> On Thu, Feb 5, 2009 at 9:27 AM, ANDY DODDS wrote: >> >>> Hello, >>> >>> does anyone know of a tutorial which lays out some sort of pipeline, >>> hopefully using CCP4 packages, to fit and refine a small molecule >>> ligand please? >>> >>> cheers >>> >>> andy >>> >>> >> >> >> -- >> Scott D. Pegan, Ph.D. >> Senior Research Specialist >> Center for Pharmaceutical >> Biotechnology >> University of Illinois at Chicago >> > > -- Matthew L.H. Chu, PhD The University of Manchester, UK Hong Kong Tel: (852) 26729515 [home] / (852) 9169 2427 [mobile] Email: linghonmatt...@gmail.com Facebook: http://www.facebook.com/MatthewLingHonChu MSN: chuling_...@hotmail.com Skype: matthew.lh.chu
