[ccp4bb] sigma value in structure file
Dear all During PDB deposition the annotator me to verify and review the sigma value in the structure file which in my case was -0.03. I have some basic queries and request you all to please answer them. My first question is, what actually is a sigma value of a structure file. 2nd) where the value is mentioned?. 3rd) and What is the optimum sigma value range ? -- Regards Faisal School of Life Sciences JNU
[ccp4bb] VMX submicron Beamline Scientist position at Diamond
Dear All, I'd like to draw your attention to the following exciting opportunity at Diamond Light Source for a Beamline Scientist to assist in designing and building the new VMX submicron MX beam line that is currently in the early stages of design. The beam line raises many challenges and as such provides significant opportunities for new developments in instrumentation, software and data collection methodology. Details of the post and how to apply can be found here. http://www.diamond.ac.uk/Home/Jobs/Current/DIA0842_NH.html Please forward this information to anyone else who you believe would be suitable for this position. All the best, Gwyndaf -- Dr Gwyndaf Evans I24 and VMX Principal Beamline Scientist Diamond Light Source Didcot OX11 0DE, UK. Tel: +44-1235-778164 -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
[ccp4bb] PhD position in Paris
A three-years PhD fellowship is available at the Laboratoire de Chimie des Processus Biologiques, Collège de France, CNRS, Paris, France starting October 2013. We are seeking an independent and highly motivated PhD student for protein expression and structural studies on RNase Y, an essential membranous enzyme involved in messenger RNA degradation and control of genetic expression. The position is financed by the LABEX (Laboratories of Excellence) DYNAMO. A solid background in protein purification, biochemistry and biophysics is essential and experience with advanced techniques in molecular biology and protein crystallography is desirable. Applicants must hold a master’s degree in molecular biology, biochemistry, biophysics or equivalent. Interested candidates are requested to send their CV, summary of previous research experience and 2 references to Dr Béatrice Golinelli-Pimpaneau Laboratoire de Chimie des Processus Biologiques Collège de France 11 place Marcelin Berthelot 75005 Paris France tel: 01 44 27 12 52 beatrice.goline...@college-de-france.fr http://www.college-de-france.fr/site/laboratoires/membres-de-lunite.htm
Re: [ccp4bb] sigma value in structure file
The only thing that seems to make sense is bonds rmsd - but you should ask the annotator for specifics directly. If it is bonds rmsd, this has been discussed many times - just google rmsd bonds ccp4bb and look for most recent entries. On Mon, 2013-06-17 at 12:11 +0530, Faisal Tarique wrote: Dear all During PDB deposition the annotator me to verify and review the sigma value in the structure file which in my case was -0.03. I have some basic queries and request you all to please answer them. My first question is, what actually is a sigma value of a structure file. 2nd) where the value is mentioned?. 3rd) and What is the optimum sigma value range ? -- Regards Faisal School of Life Sciences JNU -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore -- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. -- / Lao Tse /
[ccp4bb] AW: [ccp4bb] sigma value in structure file
Dear Faisal, I might be missing something, but why not ask the annotator instead of the bulletin board? He should know which value is meant. For me, a sigma belongs to a set of observations or parameters and without any further information one can only guess (as Ed just did) which set. My guess would be, that instead of structure file, structure factor file was meant and that somehow a negative sigma slipped in for one of the structure factors, but again that is just guessing. My two cents, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Faisal Tarique Gesendet: Montag, 17. Juni 2013 08:41 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] sigma value in structure file Dear all During PDB deposition the annotator me to verify and review the sigma value in the structure file which in my case was -0.03. I have some basic queries and request you all to please answer them. My first question is, what actually is a sigma value of a structure file. 2nd) where the value is mentioned?. 3rd) and What is the optimum sigma value range ? -- Regards Faisal School of Life Sciences JNU
[ccp4bb] OT: (a bit) shelx(pro)
At the risk of (more) people pointing at me and laughing... I used to use SHELXPRO to get my .ins files sorted for SHELX, but that seems to have gone. How is it done now? I want to do a full-matrix refinement to get ESUs on some (specific) atoms and as far as I can remember SHELXL is the best way to go. Any advice gratefully received, if its RTFM, then a refernce/link to th right page would be nice. best wishes, Peter
[ccp4bb] str solving problem
Dear group I have a crystal data diffracted around 2.9 A*, during the data reduction HKL2000 not convincingly showed the space group (indexed in lower symmetry p1), while the mosflm given C-centered Orthorhombic, and again with little play around HKL2000 given CO, now the model for molecular replacement with closest identity of 31 given a contrast of 2, score 0.30 and wrfac 0.60. but balbes uses different models with lesser identity, no matter which way I am going the rFree keep on increasing during refinement in refmac, when I build the model in coot with deletion and addition of residue it starts with relatively low but gradually rises through almost all cycles although model fits to the density well and residue are building, coot validation parameters are also reasonable OK for geometry, rotamer, density fit,.. now my question * where should i first check for possible correction? * In molecular replacement what should be the red line for identity and related criteria? * if initial rFree starts around 50, how likely that its not the right way? * my rms bond angle is close to 1 while the bond length is 0.01 and chiral 0.1 concludes what is serious? *sincere apology for amateur query* if any... thanks in advance pramod -- Pramod Kumar. Graduate Student. Crystallography lab. Department Of Biotechnology. Indian Institute Of Technology Roorkee Uttranchal.247667 India +919359189657.
Re: [ccp4bb] str solving problem
Hi Pramod, 1. You should try to identify the correct space group first. Did you integrate in p1 and run pointless? 2. A template with 31% identity is not a great model. The number of molecules in ASU will affect your chances of success. Hopefully it's not large. wrfac of 0.6 and Rfree of 0.5 suggest the solution may be incorrect. Did you try phaser? 3. Did you check for twinning? Thanks, Abhinav JCSG@SSRL, SLAC (650) 926-2992 On 06/17/2013 09:35 AM, Pramod Kumar wrote: Dear group I have a crystal data diffracted around 2.9 A*, during the data reduction HKL2000 not convincingly showed the space group (indexed in lower symmetry p1), while the mosflm given C-centered Orthorhombic, and again with little play around HKL2000 given CO, now the model for molecular replacement with closest identity of 31 given a contrast of 2, score 0.30 and wrfac 0.60. but balbes uses different models with lesser identity, no matter which way I am going the rFree keep on increasing during refinement in refmac, when I build the model in coot with deletion and addition of residue it starts with relatively low but gradually rises through almost all cycles although model fits to the density well and residue are building, coot validation parameters are also reasonable OK for geometry, rotamer, density fit,.. now my question * where should i first check for possible correction? * In molecular replacement what should be the red line for identity and related criteria? * if initial rFree starts around 50, how likely that its not the right way? * my rms bond angle is close to 1 while the bond length is 0.01 and chiral 0.1 concludes what is serious? *sincere apology for amateur query* if any... thanks in advance pramod -- Pramod Kumar. Graduate Student. Crystallography lab. Department Of Biotechnology. Indian Institute Of Technology Roorkee Uttranchal.247667 India +919359189657.
Re: [ccp4bb] OT: (a bit) shelx(pro)
Dear Peter, i am planning to produce a new pdb2ins containing several improvements, but until this is ready please continue to use the old shelxpro. Best wishes, George On 17.06.2013 16:57, Peter Moody wrote: At the risk of (more) people pointing at me and laughing... I used to use SHELXPRO to get my .ins files sorted for SHELX, but that seems to have gone. How is it done now? I want to do a full-matrix refinement to get ESUs on some (specific) atoms and as far as I can remember SHELXL is the best way to go. Any advice gratefully received, if its RTFM, then a refernce/link to th right page would be nice. best wishes, Peter -- Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-33021 or -33068 Fax. +49-551-39-22582
Re: [ccp4bb] str solving problem
*Dear Abhinav Kumar * *thanks for kind suggestions * * I have tried as follow. 1. You should try to identify the correct space group first. *integration in p21 given the following statics in pointless * * Alternative reindexing Lklhd CC R(E^2) Number Cell_deviation* * [h,k,l] 0.5660.9570.094 25580 0.00* * [l,-k,h] 0.4340.8530.195 25580 0.20 * * *integration in c2221 given the following statics in pointless * * Spacegroup TotProb SysAbsProb Reindex Conditions* * * * ( 20)0.997 0.997 00l: l=2n (zone 1) * * moreover Zanuda and molrep's chekall space group option also suggests c2221, 2. A template with 31% identity is not a great model. The number of molecules in ASU will affect your chances of success.Hopefully it's not large. wrfac of 0.6 and Rfree of 0.5 suggest the solution may be incorrect. Did you try phaser? * * * this is the limitation of my data that came from three month old crystal, there are two molecules in ASU (what is the extant to say reasonably good please ?), initially phaser was failed, with the balbes output as ensemble it worked with following profile .. * *** Phaser Module: AUTOMATED MOLECULAR REPLACEMENT 2.5.2 *** * * * Current is Best Solution (first)* * New Best LLG : 101.7 (8.70)* * Best Search Component so far: ensemble1 * * * *** Phaser Module: MOLECULAR REPLACEMENT REFINEMENT AND PHASING 2.5.2 *** * * * Resolution of All Data (Number):2.91 47.64 (15877)* * Resolution of Selected Data (Number): 2.91 47.64 (15877)* * * * * * Refinement Table (Unsorted)* * ---* * #+ = input number#* = results number* * #+ #* (Initial LLG Rval) (Refined LLG Rval) Unique =# Tmplt SpaceGroup * * 11 908.3 48.8 1804.3 46.4YES C 2 2 21 * * * * * * Refinement Table (Sorted)* * -* * #+ = input number#* = results number* * #+ #* (Initial LLG Rval) (Refined LLG Rval) Unique =# Tmplt SpaceGroup * * 11 908.3 48.8 1804.3 46.4YES C 2 2 21 **but again the refmac is showing * * *R factor 0.4404 0.4203 R free 0.4955 0.5027 Rms BondLength 0.0254 0.0093 Rms BondAngle 3.1234 1.4581 Rms ChirVolume 0.1741 0.0706 * * * * * * *3. Did you check for twinning? * *TWINNING SUMMARY* * * *Twinning fraction from H-test: 0.00* *L-statistic from L-Test: 0.48* * * * Relation between L statistics and twinning fraction:* * Twinning fraction = 0.000 L statistics = 0.500:* * Twinning fraction = 0.100 L statistics = 0.440:* * Twinning fraction = 0.500 L statistics = 0.375:* *NO Twinning detected* * * * * *thanks and regards * * pramod... * * * * * * * * * *On Mon, Jun 17, 2013 at 10:15 PM, Abhinav Kumar abhin...@slac.stanford.edu wrote: * *Hi Pramod, 1. You should try to identify the correct space group first. Did you integrate in p1 and run pointless? ** 2. A template with 31% identity is not a great model. The number of molecules in ASU will affect your chances of success. Hopefully it's not large. wrfac of 0.6 and Rfree of 0.5 suggest the solution may be incorrect. Did you try phaser? 3. Did you check for twinning? * * Thanks, Abhinav * * JCSG@SSRL, SLAC (650) 926-2992 * * On 06/17/2013 09:35 AM, Pramod Kumar wrote: * *Dear group * * I have a crystal data diffracted around 2.9 A*, during the data reduction HKL2000 not convincingly showed the space group (indexed in lower symmetry p1), while the mosflm given C-centered Orthorhombic, and again with little play around HKL2000 given CO, now the model for molecular replacement with closest identity of 31 given a contrast of 2, score 0.30 and wrfac 0.60. but balbes uses different models with lesser identity, no matter which way I am going the rFree keep on increasing during refinement in refmac, when I build the model in coot with deletion and addition of residue it starts with relatively low but gradually rises through almost all cycles although model fits to the density well and residue are building, coot validation parameters are also reasonable OK for geometry, rotamer, density fit,.. ** * *now my question * ** where should i first check for possible correction? * ** In molecular replacement what should be the red line for identity and related criteria? * ** if initial rFree starts around 50, how likely that its not the right way? * ** my rms bond angle is close to 1 while the bond length is 0.01 and chiral 0.1 concludes what is serious? * * *
[ccp4bb] ctruncate bug?
I noticed something strange when processing a dataset with imosflm. The final output ctruncate_etc.mtz, contains IMEAN and F columns, which should be the conversion according to FrenchWilson. Problem is that IMEAN has no missing values (100% complete) while F has about 1500 missing (~97% complete)! About half of the reflections that go missing are negative, but half are positive. About 5x more negative intensities are successfully converted. Most impacted are high resolution shells with weak signal, so I am sure impact on normal refinement would be minimal. However, I am just puzzled why would ctruncate reject positive intensities (or negative for that matter - I don't see any cutoff described in the manual and the lowest I/sigI for successfully converted reflection is -18). Is this a bug or feature? Cheers, Ed. -- I don't know why the sacrifice thing didn't work. Science behind it seemed so solid. Julian, King of Lemurs
Re: [ccp4bb] ctruncate bug?
Hi Ed, I'm not directly familiar with the ctruncate implementation of French and Wilson, but from the implementation that I put into Phenix (based on the original FW paper) I can tell you that any reflection where (I/sigI) - (sigI/mean_intensity) is less than a defined cutoff (in our case -4.0), then it is rejected. Depending on sigI and the mean intensity for a given shell, this can result in positive intensities that are also rejected. Typically this will effect very small positive intensities as you've observed. I don't recall the mathematical justification for this and don't have a copy of FW here at home, but I can have a look in the morning when I get into the lab and let you know. Jeff On Mon, Jun 17, 2013 at 5:04 PM, Ed Pozharski epozh...@umaryland.eduwrote: I noticed something strange when processing a dataset with imosflm. The final output ctruncate_etc.mtz, contains IMEAN and F columns, which should be the conversion according to FrenchWilson. Problem is that IMEAN has no missing values (100% complete) while F has about 1500 missing (~97% complete)! About half of the reflections that go missing are negative, but half are positive. About 5x more negative intensities are successfully converted. Most impacted are high resolution shells with weak signal, so I am sure impact on normal refinement would be minimal. However, I am just puzzled why would ctruncate reject positive intensities (or negative for that matter - I don't see any cutoff described in the manual and the lowest I/sigI for successfully converted reflection is -18). Is this a bug or feature? Cheers, Ed. -- I don't know why the sacrifice thing didn't work. Science behind it seemed so solid. Julian, King of Lemurs
Re: [ccp4bb] ctruncate bug?
Jeff,
thanks - I can see the same equation and cutoff applied in ctruncate
source.Here is the relevant part of the code
// Bayesian statistics tells us to modify I/sigma by
subtracting off sigma/S
// where S is the mean intensity in the resolution shell
h = I/sigma - sigma/S;
// reject as unphysical reflections for which I -3.7 sigma,
or h -4.0
if (I/sigma -3.7 || h -4.0 ) {
nrej++;
if (debug) printf(unphys: %f %f %f %f\n,I,sigma,S,h);
return(0);
}
This seems to be arbitrary cutoff choice, given that they are
hard-coded. At the very least, cutoffs should depend on the total
number of reflections to represent famyliwise error rates.
It is however the h-based rejection that seems most problematic to me.
In the dataset in question, up to 20% reflections are rejected in the
highest resolution shell (granted, I/sigI there is 0.33). I would
expect that reflections are rejected when they are deemed to be outliers
due to reasons other than statistical errors (e.g. streaks, secondary
lattice spots in the background, etc). I must say that this was done
with extremely good quality data, so I doubt that 1 out of 5 reflections
returns some physically impossible measurement.
What is happening is that sigma=3S in the highest resolution shell,
and for many reflection h-4.0. This does not mean that reflections are
unphysical though, just that shell as a whole has mostly weak data (in
this case 89% with I/sigI2 and 73% with I/sigI1).
What is counterintuitive is why do I have to discard reflections that
are just plain weak, and not really outliers?
Cheers,
Ed.
On 06/17/2013 10:29 PM, Jeff Headd wrote:
Hi Ed,
I'm not directly familiar with the ctruncate implementation of French
and Wilson, but from the implementation that I put into Phenix (based
on the original FW paper) I can tell you that any reflection where
(I/sigI) - (sigI/mean_intensity) is less than a defined cutoff (in our
case -4.0), then it is rejected. Depending on sigI and the mean
intensity for a given shell, this can result in positive intensities
that are also rejected. Typically this will effect very small positive
intensities as you've observed.
I don't recall the mathematical justification for this and don't have
a copy of FW here at home, but I can have a look in the morning when
I get into the lab and let you know.
Jeff
On Mon, Jun 17, 2013 at 5:04 PM, Ed Pozharski epozh...@umaryland.edu
mailto:epozh...@umaryland.edu wrote:
I noticed something strange when processing a dataset with
imosflm. The
final output ctruncate_etc.mtz, contains IMEAN and F columns, which
should be the conversion according to FrenchWilson. Problem is that
IMEAN has no missing values (100% complete) while F has about 1500
missing (~97% complete)!
About half of the reflections that go missing are negative, but
half are
positive. About 5x more negative intensities are successfully
converted. Most impacted are high resolution shells with weak signal,
so I am sure impact on normal refinement would be minimal.
However, I am just puzzled why would ctruncate reject positive
intensities (or negative for that matter - I don't see any cutoff
described in the manual and the lowest I/sigI for successfully
converted
reflection is -18).
Is this a bug or feature?
Cheers,
Ed.
--
I don't know why the sacrifice thing didn't work.
Science behind it seemed so solid.
Julian, King of Lemurs
--
Oh, suddenly throwing a giraffe into a volcano to make water is crazy?
Julian, King of Lemurs
