[ccp4bb] Observed criterion sigma(I|F)

[Graeme Winter]

Hi Folks,

A xia2 user wrote in asking where to find

'observed criterion sigma(F)' and 'observed criterion sigma(I)'

in the xia2 logs (i.e. from Scala or Aimless or XSCALE)... I have no idea
what they are so will struggle to give a helpful answer ;o) and
surprisingly google was not a lot of use coming up with

*Data processing information* : high and low resolution limits, observed
criterion sigma (F) cut-off or observed criterion sigma (I) cut-off, number
of unique measured reflections (all and observed), percent of possible
reflections observed, R-merge I (observed) or R-sym I (observed), details
about the highest resolution shell

Can anyone point me in the right direction?

Thanks in advance & best wishes, Graeme

Re: [ccp4bb] Observed criterion sigma(I|F)

[Andrew Leslie]

Hi Graeme,

There was a CCP4BB thread about this quite recently (14th Nov 2013). I've coped 
below responses from Edward Berry and Matthew Franklin.

SCALA & AIMLESS have no sigma cutoffs, but TRUNCATE does. According to the 
documentation, reflections with intensities  less than minus 4 standard 
deviations are rejected. However, in the code this seems to be less than minus 
3.7 standard deviations (rather than 4). So for data that has been processed by 
TRUNCATE, I think that the observed criterion sigma(I) is -3.7. This is 
hard-wired in the code.

It is interesting (perhaps) that this number only seems to be requested for PDB 
depositions processed by RCSB, PDBe do not seem to ask for this (at least, not 
the last time I deposited).

Andrew



Edward Berry:
As I understand it this refers to the decision whether an observation is valid 
or not, and the default value in HKL suite is -3 sigma (note the negative 
sign). The
denzo/scalepack manual explains that while it is important not to exclude 
observations
that are slightly negative due to random errors of measurement, anything that 
comes
in below -3 sigma is likely to be a fluke and should be discarded.
I'm not sure whether this refers to measurements before adding partials, or to 
the
summed full reflection observation.  anyway, I always put -3s for that value
and haven't had any negative feedback from the annotators.

Matthew Franklin:

HKL2000 (Denzo/Scalepack) use I greater than -3 sigma (that's NEGATIVE 3) as 
the observed criterion, so that's what you would put down for this entry.  
There is another place where you're asked to provide an observed criterion for 
F's used during refinement.  I always put down 0 (i.e. use all F's) for this 
one.

I have no idea what Scala does.




On 25 Nov 2013, at 09:21, Graeme Winter  wrote:

> Hi Folks,
> 
> A xia2 user wrote in asking where to find
> 
> 'observed criterion sigma(F)' and 'observed criterion sigma(I)'
> 
> in the xia2 logs (i.e. from Scala or Aimless or XSCALE)... I have no idea 
> what they are so will struggle to give a helpful answer ;o) and surprisingly 
> google was not a lot of use coming up with
> 
> Data processing information : high and low resolution limits, observed 
> criterion sigma (F) cut-off or observed criterion sigma (I) cut-off, number 
> of unique measured reflections (all and observed), percent of possible 
> reflections observed, R-merge I (observed) or R-sym I (observed), details 
> about the highest resolution shell 
> 
> Can anyone point me in the right direction?
> 
> Thanks in advance & best wishes, Graeme

Re: [ccp4bb] Observed criterion sigma(I|F)

[Graeme Winter]

Thanks Andrew, slight feeling of embarrassment now that this was a thread
two weeks ago (though this was off the bottom of the ccp4bb folder and did
not 'google' in my defense... I guess I was also looking in the wrong
place...)

Best wishes, Graeme




On 25 November 2013 11:15, Andrew Leslie  wrote:

> Hi Graeme,
>
> There was a CCP4BB thread about this quite recently (14th Nov 2013). I've
> coped below responses from Edward Berry and Matthew Franklin.
>
> SCALA & AIMLESS have no sigma cutoffs, but TRUNCATE does. According to the
> documentation, reflections with intensities  less than minus 4 standard
> deviations are rejected. However, in the code this seems to be less than
> minus 3.7 standard deviations (rather than 4). So for data that has been
> processed by TRUNCATE, I think that the observed criterion sigma(I) is
> -3.7. This is hard-wired in the code.
>
> It is interesting (perhaps) that this number only seems to be requested
> for PDB depositions processed by RCSB, PDBe do not seem to ask for this (at
> least, not the last time I deposited).
>
> Andrew
>
>
>
> Edward Berry:
> As I understand it this refers to the decision whether an observation is
> valid or not, and the default value in HKL suite is -3 sigma (note the
> negative sign). The
> denzo/scalepack manual explains that while it is important not to exclude
> observations
> that are slightly negative due to random errors of measurement, anything
> that comes
> in below -3 sigma is likely to be a fluke and should be discarded.
> I'm not sure whether this refers to measurements before adding partials,
> or to the
> summed full reflection observation.  anyway, I always put -3s for that
> value
> and haven't had any negative feedback from the annotators.
>
> Matthew Franklin:
>
> HKL2000 (Denzo/Scalepack) use I greater than -3 sigma (that's NEGATIVE 3)
> as the observed criterion, so that's what you would put down for this
> entry.  There is another place where you're asked to provide an observed
> criterion for F's used during refinement.  I always put down 0 (i.e. use
> all F's) for this one.
>
> I have no idea what Scala does.
>
>
>
>
>
> On 25 Nov 2013, at 09:21, Graeme Winter  wrote:
>
> Hi Folks,
>
> A xia2 user wrote in asking where to find
>
> 'observed criterion sigma(F)' and 'observed criterion sigma(I)'
>
> in the xia2 logs (i.e. from Scala or Aimless or XSCALE)... I have no idea
> what they are so will struggle to give a helpful answer ;o) and
> surprisingly google was not a lot of use coming up with
>
> *Data processing information* : high and low resolution limits, observed
> criterion sigma (F) cut-off or observed criterion sigma (I) cut-off, number
> of unique measured reflections (all and observed), percent of possible
> reflections observed, R-merge I (observed) or R-sym I (observed), details
> about the highest resolution shell
>
> Can anyone point me in the right direction?
>
> Thanks in advance & best wishes, Graeme
>
>
>

[ccp4bb] CCP4 Study Weekend - Diamond MX User Meeting programme

[ralf . flaig]

Dear colleagues,

the CCP4 Study Weekend - Diamond MX User Meeting programme is now available
at the following web site:

http://www.cse.scitech.ac.uk/events/CCP4_2014/UserMeeting.html


We hope that you will find the programme interesting and that we will
see you at the meeting which takes place Friday 3rd January 2014, starting at 
15:00h,
East Midlands Conference Centre, Nottingham.

Best regards,

Pierre Aller and Ralf Flaig






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Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

[ccp4bb] Web site for the list of european macromolecular crystallographers

[Michal Harel]

Hi,  We have been maintaing a list of european (and a few outlying countries) 
macromolecular crystallographers on the Web for ca. 10 years.  This list is 
updated annually and contains relevant addresses and emails ordered by 
countries and labs.  Since the list keeps growing and entails more work in 
updating, the question arises as to how useful is it.I'd appreciate it if 
those who used it send me feedback as to whether you have  found it useful or 
not.

The list can be accessed at http://www.weizmann.ac.il/esf_xtal

Regards - Michal.


Dr. Michal Harel
Dept. of Structural Biology  
michal.ha...@weizmann.ac.il
Weizmann Inst. of Science  tel:  972-8-9342647
Rehovot 76100, ISRAEL  fax:  972-8-9344159
   mobile: 
972-54-7679684
---

[ccp4bb] CPRODRG segfault on Mac OS X 10.9,

[Oliver Clarke]

Hi all,

I have recently been trying to use the LIDIA ligand-viewer of Coot, which calls 
cprodrg.

I am running CCP4 6.4.0 with all the latest updates on a Macbook Air (mid-2012 
model) with OS X 10.9 installed and the latest nightly build of coot (r4833).

Unfortunately, when I run cprodrg either via coot or from the command line, it 
crashes with what appears to be a segmentation violation (stderr reproduced 
below). Does anyone have any thoughts as to what may be causing this or how to 
fix it?

Many thanks,
Oliver


 





 ###
 ###
 ###
 ### CCP4 6.4: PRODRGversion 2.5-AA0717 : ##
 ###
 User: olibclarke  Run date: 25/11/2013 Run time: 08:34:44


 Please reference: Collaborative Computational Project, Number 4. 1994.
 "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 
760-763.
 as well as any specific reference in the program write-up.


forrtl: severe (180): SIGBUS, bus error occurred
Image  PCRoutineLineSource
cprodrg000113FC  Unknown   Unknown  Unknown
cprodrg000111AC  Unknown   Unknown  Unknown
cprodrg00011164  Unknown   Unknown  Unknown

Re: [ccp4bb] Water or ion

[Uma Ratu]

Dear All:

Many thanks for your comments and inputs!

Uma

On Sat, Nov 23, 2013 at 7:14 PM, Uma Ratu  wrote:

>  Dear All:
>
>
> I use Coot to check water molecules in my model.
> Most of them are in good coordinates for water.
>
> Some of these waters have unusual coordinates.
>
> For example, one is in the H-bond distance with 2 nitrogen and 2 oxygen of
> protein residues, plus one oxygen from ligand (W_230.jpg), and the other is
> in the H-bond distance with 3 nitrogen, 1 oxygen of protein residue,
> plus one water(W_300.jpg).
>
> Would you advice if these molecules are water, or something else, ions?
>
> I tried Coot - "highly coordinated water", and "check/delete water".
> The program does not pick up anything unusual.
>
> Thank you
>
> Uma
>
>

Re: [ccp4bb] CPRODRG segfault on Mac OS X 10.9,

[Eugene Krissinel]

Dear All,

CCP4 Core Group is aware of the issue and is looking into it. Once fixed, new 
cprodrg will be put into update.

Thank you,

Eugene Krissinel

On 25 Nov 2013, at 13:46, Oliver Clarke wrote:

> Hi all,
> 
> I have recently been trying to use the LIDIA ligand-viewer of Coot, which 
> calls cprodrg.
> 
> I am running CCP4 6.4.0 with all the latest updates on a Macbook Air 
> (mid-2012 model) with OS X 10.9 installed and the latest nightly build of 
> coot (r4833).
> 
> Unfortunately, when I run cprodrg either via coot or from the command line, 
> it crashes with what appears to be a segmentation violation (stderr 
> reproduced below). Does anyone have any thoughts as to what may be causing 
> this or how to fix it?
> 
> Many thanks,
> Oliver
> 
> 
>  
> 
> 
> 
> 
> 
> ###
> ###
> ###
> ### CCP4 6.4: PRODRGversion 2.5-AA0717 : ##
> ###
> User: olibclarke  Run date: 25/11/2013 Run time: 08:34:44
> 
> 
> Please reference: Collaborative Computational Project, Number 4. 1994.
> "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 
> 760-763.
> as well as any specific reference in the program write-up.
> 
> 
> forrtl: severe (180): SIGBUS, bus error occurred
> Image  PCRoutineLineSource
> cprodrg000113FC  Unknown   Unknown  Unknown
> cprodrg000111AC  Unknown   Unknown  Unknown
> cprodrg00011164  Unknown   Unknown  Unknown


-- 
Scanned by iCritical.

[ccp4bb] Ligandfit - problem with ligand_start

[Danilo Belviso]

 Dear all,

 I am working on a membrane protein covalently bound to a molecular 
antanna: it is known that this molecule binds to lysine residue but I do 
not know how many and which lysine residues it binds. 20 diffraction 
datasets of this protein-ligand complex have been obtained and now, I 
would quickly localize the ligand using the Fo-Fc map of each data set 
and using the information on the covalent bound protein-ligand.


 Ligandfit tool (PHENIX) seems to be indicated to do this; to use the 
information on the covalent bound, I am using the ligand_start keyword 
with a pdb containing a ghost atom (however present in ligand model) 
perfectly superposed to the lysine atom that should bind the ligand.


 The command used is:

 phenix.ligandfit data=prot.mtz model=prot.pdb ligand=lig.pdb 
ligand_start=lig_start.pdb  input_labels="FOFCWT PHFOFCWT" \ 
refine_ligand=True  \ nproc=32 \ cif_def_file_list=lig.cif


 description:
 - prot.mtz   (data)
 - prot.pdb   (protein without ligand)
 - lig.pdb(ligand containing ghost atom)
 - lig_start.pdb  (ghost atom superpose to NZ of a lysine)
 - lig.cif(restrain of lig.pdb)

 Strangely, no ligand is found at the end of the process even reducing 
ligand_cc_min to 0.01. I have run the same command by using an other 
protein where an other ligand has been correctly fitted but, also in 
this case, no ligand has been detected. Conversely, without the use of 
ligand_start, ligandfit properly localizes the ligand.


 I'm doing some mistake in the use of ligand_start? Do you know an 
other tool to perform a ligand fitting in these conditions?


 Thanks for your answers.

 Danilo

Re: [ccp4bb] Ligandfit - problem with ligand_start

[Terwilliger, Thomas C]

Hi Danilo,
I'll answer you on the Phenix mailing list!
All the best,
Tom T

On Nov 25, 2013, at 8:14 AM, Danilo Belviso wrote:

> Dear all,
> 
> I am working on a membrane protein covalently bound to a molecular antanna: 
> it is known that this molecule binds to lysine residue but I do not know how 
> many and which lysine residues it binds. 20 diffraction datasets of this 
> protein-ligand complex have been obtained and now, I would quickly localize 
> the ligand using the Fo-Fc map of each data set and using the information on 
> the covalent bound protein-ligand.
> 
> Ligandfit tool (PHENIX) seems to be indicated to do this; to use the 
> information on the covalent bound, I am using the ligand_start keyword with a 
> pdb containing a ghost atom (however present in ligand model) perfectly 
> superposed to the lysine atom that should bind the ligand.
> 
> The command used is:
> 
> phenix.ligandfit data=prot.mtz model=prot.pdb ligand=lig.pdb 
> ligand_start=lig_start.pdb  input_labels="FOFCWT PHFOFCWT" \ 
> refine_ligand=True  \ nproc=32 \ cif_def_file_list=lig.cif
> 
> description:
> - prot.mtz   (data)
> - prot.pdb   (protein without ligand)
> - lig.pdb(ligand containing ghost atom)
> - lig_start.pdb  (ghost atom superpose to NZ of a lysine)
> - lig.cif   (restrain of lig.pdb)
> 
> Strangely, no ligand is found at the end of the process even reducing 
> ligand_cc_min to 0.01. I have run the same command by using an other protein 
> where an other ligand has been correctly fitted but, also in this case, no 
> ligand has been detected. Conversely, without the use of ligand_start, 
> ligandfit properly localizes the ligand.
> 
> I'm doing some mistake in the use of ligand_start? Do you know an other tool 
> to perform a ligand fitting in these conditions?
> 
> Thanks for your answers.
> 
> Danilo

[ccp4bb] ESRF Users' Meeting & Associated Structural Biology Workshop Deadline for registration: Tuesday 21 January 2014

[Beatrice Vallone]

Please check the announcement for 2014 ESRF Users' Meeting & Associated 
Structural Biology Workshop.

Invitation to the 2014 ESRF Users' Meeting & Associated Workshops to meet and 
discuss with fellow users, get inspired, establish new scientific 
collaborations and learn about future opportunities offered by the ESRF for 
your research.

Workshop on "Structural Biology at ESRF: Past, Present & Future"
3 - 5 February

The Plenary Meeting  will feature:
   5 plenary lectures by world leading scientists covering a large spectrum of 
ESRF activities;
a presentation on the status of the facility and on the progress of the Upgrade 
Programme;
a talk by the winner of the prestigious "ESRF Young Scientist Award";
a poster session;
a banquet, with awards to the ESRF Young Scientist Award and for the best poster
Programs for the Meeting and Workshops are available at:

http://www.esrf.eu/home/events/conferences/um2014.html

   Regards to all,

   Beatrice Vallone
ESRF User Organization Committee

Re: [ccp4bb] CPRODRG segfault on Mac OS X 10.9,

[Charles Ballard]

Dear All

as Eugene says this will go into an update, but until then there is a probable 
fixed binary at

ftp://ftp.ccp4.ac.uk/ccp4/6.4.0/updates/osx/cprodrg

Charles Ballard

On 25 Nov 2013, at 14:03, Eugene Krissinel wrote:

> Dear All,
> 
> CCP4 Core Group is aware of the issue and is looking into it. Once fixed, new 
> cprodrg will be put into update.
> 
> Thank you,
> 
> Eugene Krissinel
> 
> On 25 Nov 2013, at 13:46, Oliver Clarke wrote:
> 
>> Hi all,
>> 
>> I have recently been trying to use the LIDIA ligand-viewer of Coot, which 
>> calls cprodrg.
>> 
>> I am running CCP4 6.4.0 with all the latest updates on a Macbook Air 
>> (mid-2012 model) with OS X 10.9 installed and the latest nightly build of 
>> coot (r4833).
>> 
>> Unfortunately, when I run cprodrg either via coot or from the command line, 
>> it crashes with what appears to be a segmentation violation (stderr 
>> reproduced below). Does anyone have any thoughts as to what may be causing 
>> this or how to fix it?
>> 
>> Many thanks,
>> Oliver
>> 
>> 
>>  
>> 
>> 
>> 
>> 
>> 
>> ###
>> ###
>> ###
>> ### CCP4 6.4: PRODRGversion 2.5-AA0717 : ##
>> ###
>> User: olibclarke  Run date: 25/11/2013 Run time: 08:34:44
>> 
>> 
>> Please reference: Collaborative Computational Project, Number 4. 1994.
>> "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50, 
>> 760-763.
>> as well as any specific reference in the program write-up.
>> 
>> 
>> forrtl: severe (180): SIGBUS, bus error occurred
>> Image  PCRoutineLineSource
>> cprodrg000113FC  Unknown   Unknown  Unknown
>> cprodrg000111AC  Unknown   Unknown  Unknown
>> cprodrg00011164  Unknown   Unknown  Unknown
> 
> 
> -- 
> Scanned by iCritical.
> 

--
Scanned by iCritical.

[ccp4bb] Refinement of data with pseudo translation symmetry

[Niu Tou]

Dear All,

Does any body know if the existence of pseudo translation symmetry will
affect refinement ? If it does, is there any keyword or method to avoid it?
Thanks!

Best,
Niu

Re: [ccp4bb] Observed criterion sigma(I|F)

[Edward A. Berry]

I would note that the cutoff in HKL must be a somewhat different statistic than 
that
in truncate, since the former is applied to individual measurements 
(observations?)
before averaging, while truncate normally never sees the individual measurements
but only the averages.
Ed

Andrew Leslie wrote:

Hi Graeme,

There was a CCP4BB thread about this quite recently (14th Nov 2013). I've coped 
below
responses from Edward Berry and Matthew Franklin.

SCALA & AIMLESS have no sigma cutoffs, but TRUNCATE does. According to the 
documentation,
reflections with intensities  less than minus 4 standard deviations are 
rejected. However,
in the code this seems to be less than minus 3.7 standard deviations (rather 
than 4). So
for data that has been processed by TRUNCATE, I think that the observed 
criterion sigma(I)
is -3.7. This is hard-wired in the code.

It is interesting (perhaps) that this number only seems to be requested for PDB
depositions processed by RCSB, PDBe do not seem to ask for this (at least, not 
the last
time I deposited).

Andrew



Edward Berry:
As I understand it this refers to the decision whether an observation is valid 
or not, and
the default value in HKL suite is -3 sigma (note the negative sign). The
denzo/scalepack manual explains that while it is important not to exclude 
observations
that are slightly negative due to random errors of measurement, anything that 
comes
in below -3 sigma is likely to be a fluke and should be discarded.
I'm not sure whether this refers to measurements before adding partials, or to 
the
summed full reflection observation.  anyway, I always put -3s for that value
and haven't had any negative feedback from the annotators.

Matthew Franklin:

HKL2000 (Denzo/Scalepack) use I greater than -3 sigma (that's NEGATIVE 3) as 
the observed
criterion, so that's what you would put down for this entry.  There is another 
place where
you're asked to provide an observed criterion for F's used during refinement.  
I always
put down 0 (i.e. use all F's) for this one.

I have no idea what Scala does.




On 25 Nov 2013, at 09:21, Graeme Winter mailto:graeme.win...@gmail.com>> wrote:


Hi Folks,

A xia2 user wrote in asking where to find

'observed criterion sigma(F)' and 'observed criterion sigma(I)'

in the xia2 logs (i.e. from Scala or Aimless or XSCALE)... I have no idea what 
they are
so will struggle to give a helpful answer ;o) and surprisingly google was not a 
lot of
use coming up with

/Data processing information/: high and low resolution limits, observed 
criterion sigma
(F) cut-off or observed criterion sigma (I) cut-off, number of unique measured
reflections (all and observed), percent of possible reflections observed, 
R-merge I
(observed) or R-sym I (observed), details about the highest resolution shell

Can anyone point me in the right direction?

Thanks in advance & best wishes, Graeme

[ccp4bb] postdoctoral position - structural biology of microtubule regulators

[Antonina Roll-Mecak]

*Postdoctoral Fellow – structural biology *

*Cell Biology and Biophysics Unit, National Institutes of Health*


 A postdoctoral fellow position is available in the Cell Biology and
Biophysics Unit headed by Dr. Antonina Roll-Mecak to work on structural
studies of microtubule regulators. Research in the Roll-Mecak lab focuses
on understanding the interplay between microtubules and their regulators
and how tubulin post-translational modifications tune the behavior of
motors and microtubule associated proteins (see for instance Garnham and
Roll-Mecak, 2012; Szyk et al., 2011). We use a combination of biochemistry,
structural biology, cell biology and single-molecule fluorescence
techniques and a member of this lab will have an opportunity to be exposed
to all these areas. The research facilities in the lab are outstanding and
the lab has state-of-the-art equipment such as crystallization robots, TIRF
microscopes and regular access to the synchrotron. For more information
about the lab and living in the Washington D.C. area, please visit:
http://intra.ninds.nih.gov/rm_lab/



The successful candidate must have a Ph.D. in a relevant discipline with a
strong publication record and expertise in molecular biology, biochemistry
and crystallography. The position offers a generous salary and benefits
package. Please send a CV, a one-page research experience summary and
contact information of three references to anton...@mail.nih.gov  Please
write “Fellow- structural biology” in the subject header.