Re: [ccp4bb] manipulation of water molecules in pdb files
The old fashioned water tidy will try to assign matching (non-standard) names to matching H2Os which is useful for analysis of structural waters, but cannot be deposited. I think coot has a tool to move waters to be near the protein but maybe that isn't all you want. Why not start deposition and use PDBe renaming then download the pdb file again to continue refinement? Eleanor On 30 Jul 2012, at 09:27, Zhiyi Wei wrote: Dear all, I have a refine structure with 8 ncs copies and several hundreds of water molecules (which was put in one chain). Now I try to separate these molecules by renaming to the chain id of each adjacent protein molecule. I know RCSB can do this during deposition process. Do anyone know a program can do a similar task? Many thanks! Best, Zhiyi
Re: [ccp4bb] refinement of ligands
What do you mean - running REFMAC directly on the output file? Are you sure you have the same space group given in the mtz file and the PDB file? If the MR has placed your structure in P32 say, nd the input mtz has SG P31, you need to change the mtz header to include the now-known SG. There are various ways given on the Reflection Utility task in the GUI. Eleanor On 30 Jul 2012, at 11:04, Damian Niegowski wrote: Dear all, I am currently trying to refine co-crystallized ligand structures at 2.8-3.4 Å resolution. After initial molecular replacement the density in the maps, both 2Fo-Fc and Fo-Fc looks good and the ligand seams to have bound. However after running Refmac directly on the output files the maps get much worse. I am using a clean pdb, without ligand or water for the Phaser and subsequent Refmac runs. Also when refining with the ligand in the B factors are a lot higher for the ligand then the surrounding residues, only when lowering the occupancy to 0.7-0.8 for the ligand the B factors look better. Is that acceptable to do at this resolution? R-free is in the 0.24-0.27 range. There is only a marginal change in R-free with the addition of ligand. TLS refinement seams to help alot for overall R values but does not improve the maps. I have also tried Phenix with simulated annealing, rigid body and reference structures. So the question is how best to proceed with refinement at the rather low resolution?? Regards, Damian Damian Niegowski Ph.D. Institute of Medical Biochemistry and Biophysics Karolinska Institutet Scheeles väg 2 171 77 STOCKHOLM e-mail: damian.niegow...@ki.se phone: 0046 8 524 876 33 fax: 0046 8 736 04 39
[ccp4bb] refmac5.7 refine pesudo-translational symmetry
Dear all, Can I use the twin refinement to refine the pesudo-translational symmetry dataset? Thanks a lot for your help. Best wishes, Qixu Cai
Re: [ccp4bb] refmac5.7 refine pesudo-translational symmetry
My understanding is that ML functions in the presence of pseudo-translational symmetry are suboptimal (see a very short discussion in Acta Cryst. (2011). D67, 355–367. Acta Cryst. (2008). D64, 99–107 is also a good reading). Having said that if your crystal/dataset exhibits twinning on top of pseduo-translation you should activate the twin refinement option in Refmac. Roberto On 31 Jul 2012, at 10:47, Qixu Cai wrote: Dear all, Can I use the twin refinement to refine the pesudo-translational symmetry dataset? Thanks a lot for your help. Best wishes, Qixu Cai Roberto Steiner Randall Division of Cell and Molecular Biophysics King's College London Room 3.10A New Hunt's House Guy's Campus SE1 1UL, London, UK Tel 0044-20-78488216 Fax 0044-20-78486435 roberto.stei...@kcl.ac.ukmailto:roberto.stei...@kcl.ac.uk
Re: [ccp4bb] refmac5.7 refine pesudo-translational symmetry
It's a P212121 dataset. I have used phaser to find four solution in ASU. This is the phaser log file: PEUDO-TRANSLATIONAL NCS VECTOR -- Space Group : P 21 21 21 Patterson Symmetry: P m m m Resolution of All Data (Number):2.45 49.00 (22968) Resolution of Patterson (Number): 5.00 9.99 (2364) There were 2 non-origin distinct peaks (i.e. more than 15 angstroms from the origin) !--SUMMARY_BEGIN-- 84.1% origin: FRAC 0.500 0.000 0.250 (ORTH 32.00.0 32.2) 72.2% origin: FRAC 0.000 0.000 0.500 (ORTH0.00.0 64.4) !--SUMMARY_END-- More than one pseudo-translational ncs vector found Correction factors will not be applied PS: I have used phenix.xtrige and found the p-value of pseudo-translational ncs is very little, which indicates the exist of the pseudo-translational ncs. And no twin found in this dataset. Now the problem is two in the four molecules of an ASU have worse electron density than the other two molecules. And after rigidbody and restraint refinement by refmac without twin refinement, the R/Rfree is a little high (0.33/0.36). And if I turn on the twin refinement in refmac, the R/Rfree is 0.30/0.33. So, my question is, there is not twin in my data but pseudo-translational ncs, is it suitable to use twin refinement in refmac, which has a good R/Rfree result. Thanks a lot for your help. Best wishes, Qixu Cai 2012/7/31, Eleanor Dodson eleanor.dod...@york.ac.uk: More details - what do you mean by pesudo-translational symmetry ? Are there two molecules related by a translation vector? or its it something more complicated? Eleanor On 31 July 2012 10:47, Qixu Cai caiq...@gmail.com wrote: Dear all, Can I use the twin refinement to refine the pesudo-translational symmetry dataset? Thanks a lot for your help. Best wishes, Qixu Cai -- Qixu Cai Email: caiq...@gmail.com School of Life Sciences, Xiamen University, Fujian, China
Re: [ccp4bb] refmac5.7 refine pesudo-translational symmetry
Hi, The second Patterson peak is twice the first (considering lattice translations, where 1 is equivalent to 0 modulo 1), and then if you triple the first vector you'll get minus the first vector (again considering lattice translations, i.e. 3/4 is equal to 1 - 1/4 which is equivalent to -1/4), which is equivalent by symmetry to the first vector so wouldn't appear in the peak list. So the Patterson indicates 4 copies separated by 0, 1, 2 and 3 times the top Patterson vector, in approximately the same orientation. We've haven't fully dealt with the complications of multiple tNCS-related copies in Phaser yet, but for this type of case there is a reasonable treatment. You should add two commands to the Phaser job: TNCS NMOL 4 TNCS PATT PERCENT 80 The first says that the Patterson translation is repeated 4 times, and the second will cause the second Patterson peak to be ignored. I'd suggest repeating the Phaser run with these commands and making sure that you end up with the same solution as you got when the tNCS was ignored. When tNCS is ignored, it's possible to end up with a solution that is only partially correct, which would be one explanation for having some molecules that look better in density than others. Best wishes, Randy Read On 31 Jul 2012, at 13:11, Qixu Cai wrote: It's a P212121 dataset. I have used phaser to find four solution in ASU. This is the phaser log file: PEUDO-TRANSLATIONAL NCS VECTOR -- Space Group : P 21 21 21 Patterson Symmetry: P m m m Resolution of All Data (Number):2.45 49.00 (22968) Resolution of Patterson (Number): 5.00 9.99 (2364) There were 2 non-origin distinct peaks (i.e. more than 15 angstroms from the origin) !--SUMMARY_BEGIN-- 84.1% origin: FRAC 0.500 0.000 0.250 (ORTH 32.00.0 32.2) 72.2% origin: FRAC 0.000 0.000 0.500 (ORTH0.00.0 64.4) !--SUMMARY_END-- More than one pseudo-translational ncs vector found Correction factors will not be applied PS: I have used phenix.xtrige and found the p-value of pseudo-translational ncs is very little, which indicates the exist of the pseudo-translational ncs. And no twin found in this dataset. Now the problem is two in the four molecules of an ASU have worse electron density than the other two molecules. And after rigidbody and restraint refinement by refmac without twin refinement, the R/Rfree is a little high (0.33/0.36). And if I turn on the twin refinement in refmac, the R/Rfree is 0.30/0.33. So, my question is, there is not twin in my data but pseudo-translational ncs, is it suitable to use twin refinement in refmac, which has a good R/Rfree result. Thanks a lot for your help. Best wishes, Qixu Cai 2012/7/31, Eleanor Dodson eleanor.dod...@york.ac.uk: More details - what do you mean by pesudo-translational symmetry ? Are there two molecules related by a translation vector? or its it something more complicated? Eleanor On 31 July 2012 10:47, Qixu Cai caiq...@gmail.com wrote: Dear all, Can I use the twin refinement to refine the pesudo-translational symmetry dataset? Thanks a lot for your help. Best wishes, Qixu Cai -- Qixu Cai Email: caiq...@gmail.com School of Life Sciences, Xiamen University, Fujian, China -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
[ccp4bb] value of observed criterion sigma
Dear all i have two basic queries 1) i have processed my data in HKL 2000 and during pdb submission i need to know the value of observed criterion sigma (F) and observed criterion sigma (I). 2) during entering data in category resolution shell whether one needs to mention the statistics of each and every resolution shell or only two entries i.e. the maximum resolution and minimum resolution entry is enough in the whole columns. -- Regards Faisal School of Life Sciences JNU
Re: [ccp4bb] Space group R32 and H32
Dear Ian,
Yes, the expression lattice mode I used is synonymous with centring
type. The choice of a rhombohedral vs. a hexagonal cell would be a choice
of centring type, whereas the choice of obverse vs. reverse would be a
choice of setting. A clear operational difference between the two is that a
change of centring type affects reflection conditions (i.e. introduces new
ones or removes existing ones) whereas a change of setting doesn't affect
them. Like you I would be sorry to see a word as bland as description be
given a precise and structured meaning of the kind we are talking about: we
need both centring type and setting, not some amalgamation of them.
As for the question of conventions regarding cells and unique axes, we
have corresponded on this topic before. It should be remembered that the 230
distinct entities listed in the standard classification are space-group
TYPES, i.e. what one gets when taking into account every possible way in
which sets of lattice-preserving orthogonal transformations can be viewed as
equivalent. This includes reduction through changes of setting (in group-
theoretic parlance: under the action of the normaliser), and it so happened
that instead of giving a space-group type a separate name, one chose a
particular space group of that type (unavoidably, with some arbitrariness
that the word convention tries to make more palatable) as its
representative - hence the tautologically conventional nature of the
conventions, as you point out. Much discontent has been directed at poor
P21212, as if it had been granted an unjustified privilege over P22121 and
P21221; while in fact P21212 was singled out only as the canonical
representative of its space-group type, to which the others also belong,
being equivalent to it by a change of setting. Here, it is the confusion of
terminology, particularly in software where we used to ask for the name of a
space-group *type* (i.e. something to be chosen among 230 possibilities)
while at the same time expecting to be given a set of integer matrices and
fractional translations defining a specific space group within that type,
that has been (at least partly) responsible for the problem.
With best wishes,
Gerard.
--
On Tue, Jul 31, 2012 at 12:28:43PM +0100, Ian Tickle wrote:
Dear Gerard
Your point concerning my admittedly somewhat cavalier usage of the
term 'setting' in the R23:r vs R23:h context is well taken, however I
would point out that a) I'm not the first to use this terminology
(e.g. the CCN article I referred to talks about triple-cell
settings), and b) ITC doesn't use the specific term 'lattice mode'
either, though it does use 'centring type' which I guess means the
same thing? It would clearly be nice to have a single term that
encapsulates both concepts, otherwise what are we to call, for
example, the symbol R32:r - does it define a setting or a centring
type?
In ITC the rhombohedral/hexagonal dichotomy is dealt with by assigning
a property called alternatively 'centring type' and 'description'; the
first is too specific for what we want, the second it seems to me
rather too bland and general. Either way it would appear that R32:r
is both a symbol for the setting in the context of obverse vs reverse
rhombohedral settings (conventionally the obverse is chosen so
presumably the symbol R32:r applies only to that setting, otherwise
it's ambiguous), and a symbol for the centring type in the context of
rhombohedral vs hexagonal cells! However 'description' does seem to
be the common denominator term: it is used in ITC to indicate both
settings and centring types - but as I said it does seem rather bland
('space group description' could mean almost anything!). As you
indicate, for practical purposes getting a consistent vocabulary would
seem to be of lesser importance than getting a consistent
nomenclature.
On the question of primitive vs centred monoclinic lattice types, I
would point out that in ITC unique axis 'a' settings are also not
considered to be candidates for the conventional cell, though 'b' and
'c' settings are. So self-evidently not all possible 'descriptions'
are considered to be conventional and the subset listed in ITC is
merely a matter of convention (a tautology if ever there was!).
Cheers
-- Ian
On 30 July 2012 17:55, Gerard Bricogne g...@globalphasing.com wrote:
Dear Ian,
I made a modest contribution to this discussion a long time ago, and I
will only limit myself to one point.
I think you may be confusing setting and lattice mode. A change of
setting is performed by an integer matrix with determinant 1 (a unimodular
matrix) whereas a change of lattice mode involves two mutually inverse
integer matrices with determinants (mutually inverse, of course) different
from 1.
The case of R32 and H32 seems to stick out like a sore thumb because we
never use the primitive-lattice versions of the
[ccp4bb] Master in Crystallography and Crystallisation?
Hi folks First off, apologies to all who are not members of the BCA, since this is a question for the BCA members amongst you - I asked BCA to send out an advert for this course, and their admin people say they have done so - but I haven't received it, so I was wondering if anyone had got it? If you are a member and either have or have not received it, could you let me know asap? PLEASE don't reply to the BB, reply to me directly! BTW, the URL for the course is http://lafactoria.lec.csic.es/mcc/ Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] Summary for scale out data
Hi Uma, The scale.log file contains all of those values. They're all near the bottom of the file. Also, once you refine your structure, refmac will print out most of those numbers in the .pdb file. --- Greg Costakes PhD Candidate Department of Structural Biology Purdue University Hockmeyer Hall, Room 320 240 S. Martin Jischke Drive, West Lafayette, IN 47907 ** Hard work often pays of in time, but Procrastination always pays off now ** - Original Message - From: Uma Ratu rosiso2...@gmail.com To: CCP4BB@JISCMAIL.AC.UK Sent: Tuesday, July 31, 2012 9:27:37 AM Subject: [ccp4bb] Summary for scale out data Dear All: I process my data using HKL2000. After scale, the program generates several files, including .out, .log and .sca. Is there a way that I can generate a summary report file from the .out file, such as Rmerge, total number of observation, and completeness so on. XDS give a nice report with such information. With HKL, one has to dig into the tables to find out. Does CCP4 have a program to run such task? Thank you for advice Uma
Re: [ccp4bb] Summary for scale out data
Hi Uma, In HKL2000, if you go to Report menu (near to Help menu) you will see the option for generation of tables. Hope this helps. With regards S. Karthikeyan On 7/31/2012 6:57 PM, Uma Ratu wrote: Dear All: I process my data using HKL2000. After scale, the program generates several files, including .out, .log and .sca. Is there a way that I can generate a summary report file from the .out file, such as Rmerge, total number of observation, and completeness so on. XDS give a nice report with such information. With HKL, one has to dig into the tables to find out. Does CCP4 have a program to run such task? Thank you for advice Uma __ सà¥à¤à¥à¤·à¥à¤®à¤à¥à¤µ पà¥à¤°à¥à¤¦à¥à¤¯à¥à¤à¤¿à¤à¥ सà¤à¤¸à¥à¤¥à¤¾à¤¨ (वà¥à¤à¥à¤à¤¾à¤¨à¤¿à¤ à¤à¤¦à¥à¤¯à¥à¤à¤¿à¤ ठनà¥à¤¸à¤à¤§à¤¾à¤¨ परिषद) Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR) सà¥à¤à¥à¤à¤° 39 à¤, à¤à¤£à¥à¤¡à¥à¤à¤¢à¤¼ / Sector 39-A, Chandigarh पिन à¤à¥à¤¡/PIN CODE :160036 दà¥à¤°à¤à¤¾à¤·/EPABX :0172 6665 201-202
Re: [ccp4bb] value of observed criterion sigma
HKL2000 does not have an observed criterion sigma (F) since Scalepack deals with intensities. Leave that entry blank. Scalepack uses observed criterion sigma (I) = -3 On question #2 you always want to quote the statistics (completeness, Rsym, I/sigI etc) for the highest resolution shell but I'm not sure it makes any sense to report it for the lowest resolution shell unless your data is unusually incomplete there. The default for PDB REMARK 200 is just the high resolution shell and the overall values for the entire dataset. Also be aware that last time I checked the I/sigI reported by Scalepack in the log file is I/sigma(I) and not I/sigma(I) for the shell. The PDB format in REMARK 200 wants the latter. One of these days one hopes RCSB might include Rmeas in REMARK 200. Phil Jeffrey Princeton On 7/31/12 8:54 AM, Faisal Tarique wrote: Dear all i have two basic queries 1) i have processed my data in HKL 2000 and during pdb submission i need to know the value of observed criterion sigma (F) and observed criterion sigma (I). 2) during entering data in category resolution shell whether one needs to mention the statistics of each and every resolution shell or only two entries i.e. the maximum resolution and minimum resolution entry is enough in the whole columns. -- Regards Faisal School of Life Sciences JNU
[ccp4bb] rigidbody group in refmac5
Dear all, When we are running the rigidbody refinement of refmac5, if we do not assign the rigidbody group in CCP4i GUI, what's the default rigidbody group in refmac5? Is it a rigidbody for each chain? Thanks a lot.
[ccp4bb] FW: Principal Scientist, Crystallography at Takeda California (San Diego)
Resending for posting. From: Marshman, David (TSD) Sent: Tuesday, July 31, 2012 9:00 AM To: ccp4bb@jiscmail.ac.uk Subject: Principal Scientist, Crystallography at Takeda California (San Diego) Principal Scientist, Crystallography at Takeda California (San Diego) Summary Plays a leading role in the design, optimization, and integration of all crystallography work to advance drug discovery projects in order to advance those programs into preclinical development Responsibilities * Provides motivation/inspiration to colleagues and consistently communicates with molecular biologists, protein chemists, crystallographers and key stakeholders within the chemistry department to optimize work flow and proactively achieve positive solutions in complex and challenging projects. * Formulates innovative crystallography ideas that make major impacts on the advancement of preclinical drug discovery projects. * Solves X-ray structures of proteins and protein/ligand complexes to advance project goals. * Develops and contributes to company's intellectual property domain by way of patents and/or publications, often as principal author. * Influences the course of projects, scientific methods and/or technical company direction; develops and executes innovative methodologies to influence research approaches and efforts; devises complex approaches to apply scientific knowledge to solve problems. * Manages other PhDs and/or Research Associates; typically a combination of direct and indirect reports; provides mentoring to all scientific staff. Requirements * Ph.D. in life science with thesis, publication(s) and minimum 8+ years of relevant industry experience * High level of professional expertise in modern laboratory and analytical methods * Demonstrated track record of scientific contributions in the field of crystallography * Significant expertise performing X-ray structure determination of proteins and protein/ligand complexes * Demonstrated inter-disciplinary knowledge of drug discovery and ability to use this knowledge to influence project strategy * Demonstrated ability to successfully direct multiple scientific endeavors simultaneously * High degree of scientific discretion/intuition To Apply, follow this link: https://home.eease.com/recruit2/?id=1567911t=1goback=.gna_1773514.gde_ 1773514_member_139634354
[ccp4bb] July 2012 Computational Crystallography Newsletter
Folks The latest issue of the Computational Crystallography Newsletter is available on-line at http://www.phenix-online.org/newsletter for download. The articles are of general interest to protein crystallographers and are listed below. Enjoy Nigel Moriarty Articles --- cctbx tools for transparent job execution on clusters On the analysis of residual density distributions on an absolute scale Short communications DETAC: tools to detect alternative conformations by unrestrained refinement ERRASER, a powerful new system for correcting RNA models Fitting tips - Rotamer correction with backrub -- Nigel W. Moriarty, PhD Building 64R0246B, Physical Biosciences Division Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : nwmoria...@lbl.gov Fax : 510-486-5909 Web : CCI.LBL.gov
Re: [ccp4bb] manipulation of water molecules in pdb files
Thank you all for quick replies. The issue has been solved by using sortwater and a little manual editing. Using PDBe could be a easier way. Next time I may try it. Best, Zhiyi On 7/31/12, Eleanor Dodson eleanor.dod...@york.ac.uk wrote: The old fashioned water tidy will try to assign matching (non-standard) names to matching H2Os which is useful for analysis of structural waters, but cannot be deposited. I think coot has a tool to move waters to be near the protein but maybe that isn't all you want. Why not start deposition and use PDBe renaming then download the pdb file again to continue refinement? Eleanor On 30 Jul 2012, at 09:27, Zhiyi Wei wrote: Dear all, I have a refine structure with 8 ncs copies and several hundreds of water molecules (which was put in one chain). Now I try to separate these molecules by renaming to the chain id of each adjacent protein molecule. I know RCSB can do this during deposition process. Do anyone know a program can do a similar task? Many thanks! Best, Zhiyi
Re: [ccp4bb] rigidbody group in refmac5
Dear Lakshmanan Govindasamy, I cannot find the related information in refmac5 document. Could you please help me? Thanks. Qixu Cai Email: caiq...@gmail.com School of Life Sciences, Xiamen University, Fujian, China **from thunderbird** On 08/01/2012 04:43 AM, Lakshmanan Govindasamy wrote: refer CCP4 Refmac5 manual for rigid body refinement instruction and clarification. Govinda On Tue, Jul 31, 2012 at 11:35 AM, Qixu Cai caiq...@gmail.com mailto:caiq...@gmail.com wrote: Dear all, When we are running the rigidbody refinement of refmac5, if we do not assign the rigidbody group in CCP4i GUI, what's the default rigidbody group in refmac5? Is it a rigidbody for each chain? Thanks a lot.
