date:20140307

Re: [ccp4bb] density near Histidine

2014-03-07 Thread Avinash Punekar

Dear SDY,

It looks like ethylene glycol to me. Try EDO 
(http://ligand-expo.rcsb.org/pyapps/ldHandler.py?formid=cc-index-search&operation=ccid&target=EDO)

Avinash

--
Avinash S. Punekar
Uppsala University

[ccp4bb] New Deadline for Athens Workshop on "Strategic pipeline planning: from sample preparation to 3D structure determination with bio SAXS and other biophysical techniques"

2014-03-07 Thread Evangelia D. Chrysina

Dear colleagues,

I am writing to inform you that the deadline for our workshop on *"Strategic
pipeline planning: from sample preparation to 3D structure determination
with bio SAXS and other biophysical techniques" *to be held at the National
Hellenic Research Foundation (NHRF) in Athens from April 5th to April 10th,
2014 has been extended to *March 15th 2014.*

For details please either read below or visit

*http://www.eie.gr/nhrf/institutes/ibmcb/News/2014/05_04_2014_Workshop.html

*


*The workshop *will provide training on creating a roadmap towards
determining the 3D structure of a macromolecular target including
troubleshooting and rational decision-making with emphasis on Bio SAXS.

The sessions will include:

   - *Structural Biology in Europe 2014 onwards *(ESFRI actions Instruct -
   a success story, Large scale facilities in Europe & Opportunities for
   transnational access)
   - *Perspectives in structural biology *(An overview of additional main
   stream methods for structural biology: X-ray crystallography, NMR, X-ray
   imaging, ΕΜ)
   - *Sample preparation *(Key objectives and how to benchmark the success
   of a strategy, bottlenecks and troubleshooting, decision making on method
   selection for 3D structure determination)
   - *Bio SAXS at the forefront of structural biology *(Basic principles of
   SAXS, Supporting biophysical techniques e.g. Dynamic Light Scattering, ITC,
   SAXS data analysis software, in vitro and in silico SAXS challenges)
   - *Career development* (Lessons learnt and prospects for young
   scientists in the frame of Horizon 2020)

Confirmed speakers in alphabetical:

*P. Agianian,  T. Bergfors,  J-M. Carazo,  S. Ciofi-Baffoni,  M. Graewert,
 M. Klapa,  M. Kokkinidis,  P. Konarev,  L-M. Korou,  R. Meijers,  U.
Mueller,  G. Nounesis,  R. Owens,  E. Pereiro,  M. Petoukhov,  S. Pispas,
 A. Politou,  E. Saridakis,  S. Savvides, Th. Schneider, P. Shaw-Stewart,
 G. Spyroulias,  Ef. Stratikos,  D. Stuart,  D. Svergun,  CE. Vorgias, M.
Wilmanns.*

*Target Group: *PhD students and post-doctoral scientists, currently
working in the structural biology field and have already some experience in
working with macromolecules. Experienced researchers will also be
considered but priority will be given to younger scientists. A total of 25
participants will be accepted in the course.

*Selection process*: The Biostruct-X and local organizers will be
responsible for the selection process to ensure that equivalent criteria
will be applied. The applicants will be expected to send

   - a CV (max. 2 pages),
   - a motivation letter (max. 1 page) explaining why they wish to
   participate and what they expect from the course and
   - a reference letter.

* Deadline: Saturday, March 15th, 2014  **

*Benefits: *Participants that have been accepted to the course are offered :

   - to *send their protein samples (>90% pure) to the Sample Preparation
   and Characterization (SPC) facility at the EMBL in Hamburg*.
   - *a limited number of fellowships* to be awarded to participants coming
   from INSTRUCT member countries (Belgium, Czech Republic, France, Germany,
   Israel, Italy, Netherlands, Portugal, Spain, Sweden, United Kingdom)
   awarded by INSTRUCT (http://www.structuralbiology.eu).

*Host:* The event will be hosted by NHRF, coordinator of Instruct-EL, the
national distributed research infrastructure that functions as a hub for
structural biology in South East European area and Cyprus.


*The workshop is organized in conjunction with the International Conference
on Research Infrastructures (ICRI-2014) that will also be held in Athens
2-4 April, http://www.icri2014.eu   *
*Registration fee*: EURO 50 for academic participants and EURO 1000 for
participants coming from industry.


*Organizing committee:*
*Local organizers : **National Hellenic Research Foundation (NHRF, host) *(E.D.
Chrysina, V. Papadimitriou, G. Sotiroudis, A. Xenakis, M. Zervou, P.
Zoumpoulakis)
*Hellenic Crystallographic Association *(I.M. Mavridis, S.E. Zographos)
*ICRI-2014 organizers*:
*European Commission*, Directorate General for Research & Innovation
(Octavi Quintana Trias, Director of ERA policy)
*"Athena"- Research and Innovation Center (on behalf of the Greek
presidency/GSRT) *(Yannis Ioannidis, President and General Director)

*Lead contact:* Dr Evangelia Chrysina, echrys...@eie.gr
*For m**ore information *:
http://www.eie.gr/nhrf/institutes/ibmcb/News/2014/05_04_2014_Workshop.html

The workshop is supported by:

   - *European Commission, Seventh Framework Programme (FP7)*
   - *Biostruct-X *(http://www.biostruct-x.eu)
   - *INSTRUCT *(http://www.structuralbiology.eu)
   - *BRITISH COUNCIL *(http://www.britishcouncil.gr)

   - *DECTRIS *(http://www.dectris.com)
   - *Douglas Instruments *(http://www.douglas.co.uk)
   - *Rigaku *(http://www.rigaku.com)
   - *Anelis Analytical Environmenta

Re: [ccp4bb] Validity of Ion Sites in PDB

2014-03-07 Thread Jrh

Dear Jacob,
Ah yes, I see.
Your wording is perfectly clear.
Sorry for my misunderstanding.
Best wishes,
John


Prof John R Helliwell DSc 
 
 

On 7 Mar 2014, at 15:18, "Keller, Jacob"  wrote:

>> You indicate that oxygen anomalous scattering could be used; whilst this is 
>> applicable to chirality  determination in small molecule organic 
>> crystallography the oxygen anomalous signal is very small and to my 
>> knowledge not used thus far in protein crystallography. 
> 
> Perhaps I should have been clearer--I meant that anomalous scattering could 
> be used to distinguish between Cl- and H20, since Cl- does have a small but 
> measurable anomalous signal at the usual wavelengths, whereas water does not, 
> as you point out. Parenthetically, I have found that, in line with Randy 
> Read's suggestion to me, the LLG maps in Phaser are dramatically better than 
> regular adf's for finding such small signals.
> 
> JPK
> 
> ==
> 
> I was curious whether there has been a rigorous evaluation of ion binding 
> sites in the structures in the pdb, by PDB-REDO or otherwise. I imagine that 
> there is a considerably broad spectrum of habits and rigor in assigning 
> solute blobs to ion X or water, and in fact it would be difficult in many 
> cases to determine which ion a given blob really is, but there should be at 
> least some fraction of ions/waters which can be shown from the x-ray data and 
> known geometry to be X and not Y. This could be by small anomalous signals 
> (Cl and H2O for example), geometric considerations, or something else. Maybe 
> this does not even matter in most cases, but it might be important in 
> others...

[ccp4bb] POSTDOCTORAL POSITION AVAILABLE IN STRUCTURAL BIOLOGY

2014-03-07 Thread Carine VAN HEIJENOORT

A postdoctoral position is available at the Laboratory of Structural Biology 
and Chemistry (www.icsn.cnrs-gif.fr/guittet) of the Institute of Chemistry of 
Natural Compounds (ICSN) in Gif-sur-Yvette, France, 20km southwest of Paris.
The project aims at understanding the mechanisms of action of the 275aa, 
intrinsically disordered, C-terminal cytosolic tail of the tyrosine kinase 
receptor ErbB2, whose implication in signaling pathways is established but 
still poorly understood. Over expression of ErbB2 in breast cancer cells 
results in constitutive ligand-independent activation of tyrosine kinase 
signaling which contributes to uncontrolled proliferation, resistance to 
apoptosis and increased motility. Liquid-state NMR is our main research tool, 
complemented with various biophysical techniques available either in-house or 
in the direct vicinity of the laboratory (especially SAXS and X-Ray diffraction 
at the nearby synchrotron SOLEIL). Cellular biologists are also involved in 
this project, who will perform cellular analyses including cell proliferation 
and cell migration, thus allowing integrating the structural data in a cellular 
context.
The candidate should have a strong interest in structural biology, with good 
skills in protein biochemistry and molecular biology.  A background in 
liquid-state NMR spectroscopy is not necessary but the candidate should have a 
strong motivation to use NMR. Interested candidates should have a PhD in 
biochemistry, biophysics, chemistry or structural biology. The successful 
applicant will be exposed to a wide variety of techniques in the area of 
structural biology and possibly cellular biology. Good communication skills in 
English are required.

Our group is located at the Institute of Chemistry of Natural Compounds (ICSN) 
in Gif-sur-Yvette (45mn by train from the center of Paris) in a research campus 
mainly devoted to chemistry and biology 
(http://www.dr4.cnrs.fr/delegation/laboratoires/liste_gif.htm). The campus is 
part of the “Campus Paris Saclay” 
(http://www.campus-paris-saclay.fr/en/The-FCS), that gathers more than 1 
researchers from all research area, among which a strong research community in 
Structural Biology centered in the CNRS (french National Scientific Research 
Center) campus in Gif-sur-Yvette, Paris 11 university in Orsay, the CEA centre 
of Saclay in Gif and the French national synchrotron facility SOLEIL in Gif.  
Our laboratory is particularly well equipped with 4 NMR high field 
spectrometers ranging from 600 to 950MHz equipped with state-of-the-art 
cryoprobes for solution state protein NMR, all the equipment for protein 
production, purification and characterization and complementary biophysical 
techniques. 
Gif-sur-Yvette is an agreeable town, easily accessible from Paris, at the 
border of the «vallée de Chevreuse» regional nature reserve. 

The project is funded by the French National Research Agency, the position is 
offered for a duration of 2 years, possibly with extension, based on additional 
funding.

Motivated candidates should send their application by e-mail to 
carine.van-heijeno...@cnrs.fr. 

Applications must include a CV, a covering letter, and the names and contact 
details of at least two references.

Carine van Heijenoort, phD
ICSN-CNRS
Laboratoire de Chimie et Biologie Structurale
1 avenue de la terrasse
91190 Gif-sur-Yvette

Re: [ccp4bb] CCP4-6.4.0 Update 010

2014-03-07 Thread Charles Ballard

Dear CCP4 Users

as ever with life, a couple of errors have made it into the update

a. ipmosflm.exe 7.1.0 is missing from the windows update

b. a small change in ccp4i/src/imosflm means that MOSFLM_EXEC is not being set 
for csh users.

The suggested remedy is for windows users to hold off this update until we get 
the next update out.  csh shell users should temporarily add MOSFLM_EXEC 
ipmosflm to their environments.

Charles


On 7 Mar 2014, at 11:10, Charles Ballard wrote:

> Dear CCP4 Users,
> 
> An update for the CCP4-6.4.0 series has just been released, consisting of the 
> following changes
> 
> ◆ ARP/wARP (Mac, Linux)
> 1. Fix in the use of free R flag in the ARP/wARP CCP4i interface for solvent 
> building
> 2. Fix in the identification of non-crystallographic symmetry that in some 
> cases led to zero target number of residues
> 3. Fix in recognition of secondary structural elements that in rare cases led 
> to a 'bus error'
> * Many thanks to Marcin Cymborowski, Carmelo Giacovazzo, Ulrich Gohlke and 
> Vito Calderone for reporting these problem cases.
> 
> ◆ imosflm (update to 7.1.0 for all platforms)
> - Multi-lattice implementation
> - Parallel processing of wedges
> 
> ◆ feckless (0.0.2, all)
> - Fixes several major bugs
> 
> ◆ pointless (1.9.2, all)
> - General update for multi-lattice
> 
> ◆ ctruncate (1.13.13, all)
> - Fixes negative eigenvalue exit during anisotropy analysis
> 
> ◆ cnautilus (0.4, all)
> - Some basic output markup and numbering of output sequences
> 
> ◆ refmac5 (5.8.006, all)
> - Fixes for ARP/wARP and forthcoming release of Crank2
> 
> 
> 
> 
> Note that auto-updates work only with CCP4 6.4.0 series, therefore please 
> upgrade if necessary.
> The Update Manager is now included in the package so you do not need to 
> install it separately.
> In addition, all available updates will be installed automatically if you are 
> using Setup Manager for CCP4 installation.
> 
> Please report any bugs to c...@stfc.ac.uk.
> 
> Many thanks for using CCP4.
> 
> the CCP4 core team.
> 
> -- 
> Scanned by iCritical.
> 
> 


-- 
Scanned by iCritical.

Re: [ccp4bb] Validity of Ion Sites in PDB

2014-03-07 Thread Keller, Jacob

>You indicate that oxygen anomalous scattering could be used; whilst this is 
>applicable to chirality  determination in small molecule organic 
>crystallography the oxygen anomalous signal is very small and to my knowledge 
>not used thus far in protein crystallography. 

Perhaps I should have been clearer--I meant that anomalous scattering could be 
used to distinguish between Cl- and H20, since Cl- does have a small but 
measurable anomalous signal at the usual wavelengths, whereas water does not, 
as you point out. Parenthetically, I have found that, in line with Randy Read's 
suggestion to me, the LLG maps in Phaser are dramatically better than regular 
adf's for finding such small signals.

JPK

==

I was curious whether there has been a rigorous evaluation of ion binding sites 
in the structures in the pdb, by PDB-REDO or otherwise. I imagine that there is 
a considerably broad spectrum of habits and rigor in assigning solute blobs to 
ion X or water, and in fact it would be difficult in many cases to determine 
which ion a given blob really is, but there should be at least some fraction of 
ions/waters which can be shown from the x-ray data and known geometry to be X 
and not Y. This could be by small anomalous signals (Cl and H2O for example), 
geometric considerations, or something else. Maybe this does not even matter in 
most cases, but it might be important in others...

[ccp4bb] ARP/wARP 7.4 Patch 2 available

2014-03-07 Thread Ioan Vancea

Dear colleagues,

ARP/wARP 7.4 Patch 2 is available for download on our FTP server, as well. 

If you were installing ARP/wARP as a joint bundle with CCP4-6.4.0, you can 
update ARP/wARP via automatic CCP4 update or download the patches from 
http://www.ccp4.ac.uk/updates/

If you were installing ARP/wARP from a standalone tarball or DMG, please visit 
www.arp-warp.org with further link to download. After receiving an email with 
access details to the download area, you can either download full standalone 
ARP/wARP tarball or DMG, or download only the patch. The README file in the 
download area (or the FAQ pages on www.arp-warp.org) explain how to apply the 
patch with a single command. In either case, the installed ARP/wARP will be 
fully compatible with CCP4-6.4.0.

Many thanks for using ARP/wARP,
The ARP/wARP team

--
Dr. Ioan Vancea
European Molecular Biology Laboratory c/o DESY
Notkestrasse 85, 22607 Hamburg, Germany
Tel: +49 (0)40 89902-340
Email: ivan...@embl-hamburg.de

Re: [ccp4bb] CCP4-6.4.0 Update 010

2014-03-07 Thread Boaz Shaanan

Hi Andrey,

Thanks a lot. I just wanted to make sure that I'm not downgrading refmac5 
before implementing the update. It's fine now and I get 5.8.0069 just like you 
do.

As was said so many times before on the BB, the update mechanism is wonderful.  
Chapeau to you all.

   Boaz

Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710






From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Andrey Lebedev 
[andrey.lebe...@stfc.ac.uk]
Sent: Friday, March 07, 2014 3:42 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] CCP4-6.4.0 Update 010

Hi Boaz

It is 5.8.0069

And it prints the correct version for me on all platforms

Andrey

On 7 Mar 2014, at 13:13, Boaz Shaanan wrote:

Hi,

Is the refmac5  indeed 5.8.006? The current ccp4 version 5.8.0049.

 Boaz



Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710





From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Charles Ballard 
[charles.ball...@stfc.ac.uk]
Sent: Friday, March 07, 2014 1:10 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] CCP4-6.4.0 Update 010

Dear CCP4 Users,

An update for the CCP4-6.4.0 series has just been released, consisting of the 
following changes

◆ ARP/wARP (Mac, Linux)
1. Fix in the use of free R flag in the ARP/wARP CCP4i interface for solvent 
building
2. Fix in the identification of non-crystallographic symmetry that in some 
cases led to zero target number of residues
3. Fix in recognition of secondary structural elements that in rare cases led 
to a 'bus error'
* Many thanks to Marcin Cymborowski, Carmelo Giacovazzo, Ulrich Gohlke and Vito 
Calderone for reporting these problem cases.

◆ imosflm (update to 7.1.0 for all platforms)
- Multi-lattice implementation
- Parallel processing of wedges

◆ feckless (0.0.2, all)
- Fixes several major bugs

◆ pointless (1.9.2, all)
- General update for multi-lattice

◆ ctruncate (1.13.13, all)
- Fixes negative eigenvalue exit during anisotropy analysis

◆ cnautilus (0.4, all)
- Some basic output markup and numbering of output sequences

◆ refmac5 (5.8.006, all)
- Fixes for ARP/wARP and forthcoming release of Crank2

Note that auto-updates work only with CCP4 6.4.0 series, therefore please 
upgrade if necessary.
The Update Manager is now included in the package so you do not need to install 
it separately.
In addition, all available updates will be installed automatically if you are 
using Setup Manager for CCP4 installation.

Please report any bugs to c...@stfc.ac.uk.

Many thanks for using CCP4.

the CCP4 core team.


--
Scanned by iCritical.

Re: [ccp4bb] CCP4-6.4.0 Update 010

2014-03-07 Thread Andrey Lebedev


Hi Boaz

It is 5.8.0069

And it prints the correct version for me on all platforms

Andrey

On 7 Mar 2014, at 13:13, Boaz Shaanan wrote:

Hi,

Is the refmac5  indeed 5.8.006? The current ccp4 version 5.8.0049.

 Boaz



Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710





From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Charles Ballard 
[charles.ball...@stfc.ac.uk]
Sent: Friday, March 07, 2014 1:10 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] CCP4-6.4.0 Update 010

Dear CCP4 Users,

An update for the CCP4-6.4.0 series has just been released, consisting of the 
following changes

◆ ARP/wARP (Mac, Linux)
1. Fix in the use of free R flag in the ARP/wARP CCP4i interface for solvent 
building
2. Fix in the identification of non-crystallographic symmetry that in some 
cases led to zero target number of residues
3. Fix in recognition of secondary structural elements that in rare cases led 
to a 'bus error'
* Many thanks to Marcin Cymborowski, Carmelo Giacovazzo, Ulrich Gohlke and Vito 
Calderone for reporting these problem cases.

◆ imosflm (update to 7.1.0 for all platforms)
- Multi-lattice implementation
- Parallel processing of wedges

◆ feckless (0.0.2, all)
- Fixes several major bugs

◆ pointless (1.9.2, all)
- General update for multi-lattice

◆ ctruncate (1.13.13, all)
- Fixes negative eigenvalue exit during anisotropy analysis

◆ cnautilus (0.4, all)
- Some basic output markup and numbering of output sequences

◆ refmac5 (5.8.006, all)
- Fixes for ARP/wARP and forthcoming release of Crank2

Note that auto-updates work only with CCP4 6.4.0 series, therefore please 
upgrade if necessary.
The Update Manager is now included in the package so you do not need to install 
it separately.
In addition, all available updates will be installed automatically if you are 
using Setup Manager for CCP4 installation.

Please report any bugs to c...@stfc.ac.uk.

Many thanks for using CCP4.

the CCP4 core team.


--
Scanned by iCritical.

Re: [ccp4bb] Validity of Ion Sites in PDB

2014-03-07 Thread Philippe BENAS

Dear all and dear Jacob

Please have also a look at another paper from Manfred where they show that 
"both difference electron-density maps and anomalous difference 
electron-density maps suggest that in crystals grown from a sodium sulfate 
solution PPE binds Na+ in its metal-binding site." [Porcine  pancreatic  
elastase] :
Weiss,
M. S., Panjikar, S., Nowak, E. & Tucker, P. A. (2002). Acta crystallographica. 
Section D, Biological crystallography 58,
1407-1412


All the best,
Philippe
 


Philippe BENAS, Ph.D.
X-ray diffraction and computing facilities manager

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS

E-mails: philippe.be...@parisdescartes.fr, philippe_be...@yahoo.fr
URLs: http://lcrbw.pharmacie.univ-paris5.fr/ , 
http://lcrbw.pharmacie.univ-paris5.fr/spip.php?article18








 De : Manfred S. Weiss 
À : CCP4BB@JISCMAIL.AC.UK 
Envoyé le : Vendredi 7 mars 2014 13h02
Objet : Re: [ccp4bb] Validity of Ion Sites in PDB
 

There is another paper out there, which describes the use of long
wavelengths
to define anomalously scattering substructures. This method certainly
helps to
distinguish water molecules from something else, such as chloride for
instance.

http://journals.iucr.org/d/issues/2007/03/00/dz5094/index.html

Cheers, Manfred


On 07.03.2014 11:12, Murray, James W wrote:
> Dear all,
>
> It is well known that  you can look at anomalous difference maps to see 
> heavier atoms - although I think not enough people do it. One technique that 
> I think is powerful, but under-used is to calculate element-specific maps by 
> taking the difference of anomalous difference data from just above and below 
> the absorption edge. This paper introduces the technique and explains it well 
> http://journals.iucr.org/d/issues/2005/05/00/he5321/index.html. I suspect if 
> this method were more used, many mis-labeled metals in proteins would come to 
> light.
>
> James
>
> --
> Dr. James W. Murray
> Lecturer in Biotechnology
> Dept. Life Sciences
> Imperial College, London
> Tel: +44 (0)20 759 48895
> 
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Tim Gruene 
> [t...@shelx.uni-ac.gwdg.de]
> Sent: Friday, March 07, 2014 9:44 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Validity of Ion Sites in PDB
>
> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
>
> Dear Jacob,
>
> the 'check-my-metal' server at http://csgid.org/csgid/metal_sites/
> lists a couple of references which might be of interest.
>
> As usual in crytallography one must understand the science in order to
> understand the reliability of the models from the PDB. They are not
> the truth but only models to explain the data from a diffraction
> experiment.
>
> Best,
> Tim
>
>
>
> On 03/06/2014 08:45 PM, Keller, Jacob wrote:
>> Dear Crystallographers,
>>
>> I was curious whether there has been a rigorous evaluation of ion
>> binding sites in the structures in the pdb, by PDB-REDO or
>> otherwise. I imagine that there is a considerably broad spectrum of
>> habits and rigor in assigning solute blobs to ion X or water, and
>> in fact it would be difficult in many cases to determine which ion
>> a given blob really is, but there should be at least some fraction
>> of ions/waters which can be shown from the x-ray data and known
>> geometry to be X and not Y. This could be by small anomalous
>> signals (Cl and H2O for example), geometric considerations, or
>> something else. Maybe this does not even matter in most cases, but
>> it might be important in others...
>>
>> All the best,
>>
>> Jacob Keller
>>
>>
>> *** Jacob Pearson Keller,
>> PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr,
>> Ashburn, VA 20147 email: kell...@janelia.hhmi.org
>> ***
>>
> - --
> - --
> Dr Tim Gruene
> Institut fuer anorganische Chemie
> Tammannstr. 4
> D-37077 Goettingen
>
> GPG Key ID = A46BEE1A
>
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1.4.12 (GNU/Linux)
> Comment: Using GnuPG with Icedove - http://www.enigmail.net/
>
> iD8DBQFTGZUEUxlJ7aRr7hoRAtC+AKDr6cJzgWgUAWPO6AYmDHMlFs6gbwCg8+E/
> Yj2NVdKiYBq9O28v9eCQWDA=
> =YkXc
> -END PGP SIGNATURE-

--
Dr. Manfred. S. Weiss
Helmholtz-Zentrum Berlin für Materialien und Energie
Macromolecular Crystallography (HZB-MX)
Albert-Einstein-Str. 15
D-12489 Berlin
GERMANY
Fon:   +49-30-806213149
Fax:   +49-30-806214975
Web:  http://www.helmholtz-berlin.de/bessy-mx
Email: mswe...@helmholtz-berlin.de




Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. 
Vorsitzende Dr. Beatrix Vierkorn-Rudolph
Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking

Si

Re: [ccp4bb] Validity of Ion Sites in PDB

2014-03-07 Thread Jrh

Dear Jacob,
An example where special efforts were made to investigate biocatalysis and the 
role of ions, harnessing both softer X-rays and ion substitutions and a WASP 
analysis to be sure as possible of their identity, can be found here:-
http://www.ncbi.nlm.nih.gov/pubmed/20099851

The review article on metal atoms in proteins by M M Harding Crystallography 
Reviews 2010 http://www.tandfonline.com/doi/full/10.1080/0889311X.2010.485616
which I see just now has been downloaded 722 times thus far, should also prove 
instructive.

I commend to you also the wiki:-
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Properties_of_proteins

You indicate that oxygen anomalous scattering could be used; whilst this is 
applicable to chirality  determination in small molecule organic 
crystallography the oxygen anomalous signal is very small and to my knowledge 
not used thus far in protein crystallography. 

Best wishes,
John

Prof John R Helliwell DSc 
 
 

On 6 Mar 2014, at 19:45, "Keller, Jacob"  wrote:

> Dear Crystallographers,
> 
> I was curious whether there has been a rigorous evaluation of ion binding 
> sites in the structures in the pdb, by PDB-REDO or otherwise. I imagine that 
> there is a considerably broad spectrum of habits and rigor in assigning 
> solute blobs to ion X or water, and in fact it would be difficult in many 
> cases to determine which ion a given blob really is, but there should be at 
> least some fraction of ions/waters which can be shown from the x-ray data and 
> known geometry to be X and not Y. This could be by small anomalous signals 
> (Cl and H2O for example), geometric considerations, or something else. Maybe 
> this does not even matter in most cases, but it might be important in 
> others...
> 
> All the best,
> 
> Jacob Keller
> 
> 
> ***
> Jacob Pearson Keller, PhD
> Looger Lab/HHMI Janelia Farms Research Campus
> 19700 Helix Dr, Ashburn, VA 20147
> email: kell...@janelia.hhmi.org
> ***

Re: [ccp4bb] CCP4-6.4.0 Update 010

2014-03-07 Thread Boaz Shaanan




Hi, 


Is the refmac5  indeed 5.8.006? The current ccp4 version 5.8.0049.


     Boaz


 
 
Boaz Shaanan, Ph.D.

Dept. of Life Sciences  
Ben-Gurion University of the Negev  
Beer-Sheva 84105    
Israel  
    
E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan  
Fax:   972-8-647-2992 or 972-8-646-1710
 
 








From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Charles Ballard [charles.ball...@stfc.ac.uk]
Sent: Friday, March 07, 2014 1:10 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] CCP4-6.4.0 Update 010




Dear CCP4 Users,


An update for the CCP4-6.4.0 series has just been released, consisting of the following changes



◆ ARP/wARP (Mac, Linux)
1. Fix in the use of free R flag in the ARP/wARP CCP4i interface for solvent building

2. Fix in the identification of non-crystallographic symmetry that in some cases led to zero target number of residues

3. Fix in recognition of secondary structural elements that in rare cases led to a 'bus error'

* Many thanks to Marcin Cymborowski, Carmelo Giacovazzo, Ulrich Gohlke and Vito Calderone for reporting these problem cases.




◆ imosflm (update to 7.1.0 for all platforms)
- Multi-lattice implementation

- Parallel processing of wedges




◆ feckless (0.0.2, all)
- Fixes several major bugs



◆ pointless (1.9.2, all)
- General update for multi-lattice




◆ ctruncate (1.13.13, all)
- Fixes negative eigenvalue exit during anisotropy analysis



◆ cnautilus (0.4, all)
- Some basic output markup and numbering of output sequences




◆ refmac5 (5.8.006, all)
- Fixes for ARP/wARP and forthcoming release of Crank2




Note that auto-updates work only with CCP4 6.4.0 series, therefore please upgrade if necessary.
The Update Manager is now included in the package so you do not need to install it separately.
In addition, all available updates will be installed automatically if you are using Setup Manager for CCP4 installation.


Please report any bugs to c...@stfc.ac.uk.


Many thanks for using CCP4.


the CCP4 core team.

-- 
Scanned by iCritical.

[ccp4bb] docking program

2014-03-07 Thread Careina Edgooms

Can anyone recommend a good docking program to look at protein-DNA interactions?

Re: [ccp4bb] CCP4 lib file

2014-03-07 Thread Paul Emsley


On 07/03/14 11:51, Remie wrote:


I ended up using a glucose ligand lib file from a different protein 
that my friend used and refinement Refmac5 worked out.


The mind boggles :)...  well, OK.

However I need to add the LINK Command in PDB so CCP4 recognizes that 
glucoses connected.




In Coot, at least: Extensions -> Modelling -> Make a Link
[click, click]

Paul.

Re: [ccp4bb] Validity of Ion Sites in PDB

2014-03-07 Thread Manfred S. Weiss


There is another paper out there, which describes the use of long
wavelengths
to define anomalously scattering substructures. This method certainly
helps to
distinguish water molecules from something else, such as chloride for
instance.

http://journals.iucr.org/d/issues/2007/03/00/dz5094/index.html

Cheers, Manfred

On 07.03.2014 11:12, Murray, James W wrote:

Dear all,

It is well known that  you can look at anomalous difference maps to see heavier 
atoms - although I think not enough people do it. One technique that I think is 
powerful, but under-used is to calculate element-specific maps by taking the 
difference of anomalous difference data from just above and below the 
absorption edge. This paper introduces the technique and explains it well 
http://journals.iucr.org/d/issues/2005/05/00/he5321/index.html. I suspect if 
this method were more used, many mis-labeled metals in proteins would come to 
light.

James

--
Dr. James W. Murray
Lecturer in Biotechnology
Dept. Life Sciences
Imperial College, London
Tel: +44 (0)20 759 48895

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Tim Gruene 
[t...@shelx.uni-ac.gwdg.de]
Sent: Friday, March 07, 2014 9:44 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Validity of Ion Sites in PDB

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Jacob,

the 'check-my-metal' server at http://csgid.org/csgid/metal_sites/
lists a couple of references which might be of interest.

As usual in crytallography one must understand the science in order to
understand the reliability of the models from the PDB. They are not
the truth but only models to explain the data from a diffraction
experiment.

Best,
Tim



On 03/06/2014 08:45 PM, Keller, Jacob wrote:

Dear Crystallographers,

I was curious whether there has been a rigorous evaluation of ion
binding sites in the structures in the pdb, by PDB-REDO or
otherwise. I imagine that there is a considerably broad spectrum of
habits and rigor in assigning solute blobs to ion X or water, and
in fact it would be difficult in many cases to determine which ion
a given blob really is, but there should be at least some fraction
of ions/waters which can be shown from the x-ray data and known
geometry to be X and not Y. This could be by small anomalous
signals (Cl and H2O for example), geometric considerations, or
something else. Maybe this does not even matter in most cases, but
it might be important in others...

All the best,

Jacob Keller


*** Jacob Pearson Keller,
PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr,
Ashburn, VA 20147 email: kell...@janelia.hhmi.org
***


- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Icedove - http://www.enigmail.net/

iD8DBQFTGZUEUxlJ7aRr7hoRAtC+AKDr6cJzgWgUAWPO6AYmDHMlFs6gbwCg8+E/
Yj2NVdKiYBq9O28v9eCQWDA=
=YkXc
-END PGP SIGNATURE-


--
Dr. Manfred. S. Weiss
Helmholtz-Zentrum Berlin für Materialien und Energie
Macromolecular Crystallography (HZB-MX)
Albert-Einstein-Str. 15
D-12489 Berlin
GERMANY
Fon:   +49-30-806213149
Fax:   +49-30-806214975
Web:   http://www.helmholtz-berlin.de/bessy-mx
Email: mswe...@helmholtz-berlin.de




Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. 
Vorsitzende Dr. Beatrix Vierkorn-Rudolph
Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
D-14109 Berlin

http://www.helmholtz-berlin.de

Re: [ccp4bb] CCP4 lib file

2014-03-07 Thread Eleanor Dodson

Have you run refmac with the Review restraints option - that generates
LINKs if they seem necessary.
Or can you use the SUGAR links already set upin the library?
Eleanor




On 7 March 2014 11:51, Remie  wrote:

> Thanks Eleanor,
> I ended up using a glucose ligand lib file from a different protein that
> my friend used and refinement Refmac5 worked out.
> However I need to add the LINK Command in PDB so CCP4 recognizes that
> glucoses connected.
> Can I get help please?
> Thank you,
> Remie
>
>
> On Mar 5, 2014, at 10:49 AM, Eleanor Dodson 
> wrote:
>
> There are lots of GLUCOSE type lib files for different sugars.
> One way to find what is available is:
> From the REfinement GUI click Monomer library sketcher
>
> You get a window with File in the top LH corner
> Click on that and ask for Read monomer from library
>
> Then enter a key word GLUCOSE and you get this list
> ADQ etc etc
>
> Select what you want and go from there..
>
> Or do this crude method to get a complete list!:
>
> [ccp4@roo timm]$ grep -i glucose $CLIBD/monomers/*/*
>
>
>
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/a/ADQ.cif:ADQ  ADQ
> 'ADENOSINE-5'-DIPHOSPHATE-GLUCOSE' non-polymer61  38 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/a/AGL.cif:AGL  AGL
> '4,6-DIDEOXY-4-AMINO-ALPHA-D-GLUCOSE ' pyranose   24  11 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/b/BG6.cif:BG6  BG6
> 'BETA-D-GLUCOSE-6-PHOSPHATE  ' non-polymer27  16 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/b/BGC.cif:BGC  BGC
> 'BETA-D-GLUCOSE  ' pyranose   24  12 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/d/D6G.cif:D6G  D6G
> '2-DEOXY-GLUCOSE-6-PHOSPHATE ' pyranose   26  15 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/d/DDA.cif:DDA  DDA
> '2,6-DIDEOXY-BETA-D-GLUCOSE  ' pyranose   22  10 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/G16.cif:G16  G16
> 'ALPHA-D-GLUCOSE 1,6-BISPHOSPHATE' pyranose   30  20 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/G1P.cif:G1P  G1P
> 'ALPHA-D-GLUCOSE-1-PHOSPHATE ' pyranose   27  16 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/G2F.cif:G2F  G2F
> '2-DEOXY-2FLUORO-GLUCOSE ' pyranose   23  12 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/G4D.cif:G4D  G4D
> '4-DEOXY-ALPHA-D-GLUCOSE ' pyranose   23  11 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/G6D.cif:G6D  G6D
> '6-DEOXY-ALPHA-D-GLUCOSE ' non-polymer23  11 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/G6P.cif:G6P  G6P
> 'ALPHA-D-GLUCOSE-6-PHOSPHATE ' pyranose   27  16 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/G6Q.cif:G6Q  G6Q
> 'GLUCOSE-6-PHOSPHATE ' non-polymer27  16 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GDA.cif:GDA  GDA
> '4-DEOXY-4-AMINO-BETA-D-GLUCOSE  ' non-polymer25  12 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GFP.cif:GFP  GFP
> '2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE-1-P' pyranose   26  16 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GLC-B-D.cif:GLC-b-D  GLC
> 'beta_D_glucose  ' D-pyranose 24  12 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GLC.cif:GLC  GLC
> 'ALPHA-D-GLUCOSE ' pyranose   24  12 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GLD.cif:GLD  GLD
> '4,6-DIDEOXYGLUCOSE  ' pyranose   22  10 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GLF.cif:GLF  GLF
> '1-FLUORO-ALPHA-1-DEOXY-D-GLUCOSE' pyranose   23  12 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GLO.cif:GLO  GLO
> 'D-GLUCOSE IN LINEAR FORM' non-polymer24  12 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GLT.cif:GLT  GLT
> '5-DEOXY-5-THIO-ALPHA-D-GLUCOSE  ' non-polymer24  12 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GMM.cif:GMM  GMM
> 'GLUCOSE MONOMYCOLATE' non-polymer   200  74 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GUD.cif:GUD  GUD
> 'GLUCOSE-URIDINE-C1,5'-DIPHOSPHATE   ' non-polymer58  36 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/i/ISX.cif:ISX  ISX
> 'GLUCOSE BETA-1,3-ISOFAGAMINE' non-polymer44  21 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/k/KBG.cif:KBG  KBG
> '2-KETO-BETA-D-GLUCOSE   ' non-polymer22  12 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:ADQ
> ADQ 'ADENOSINE-5'-DIPHOSPHATE-GLUCOSE' non-polymer61  38 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:AGL
> AGL '4,6-DIDEOXY-4-AMINO-ALPHA-D-GLUCOSE ' pyranose   24  11 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:BG6
> BG6 'BETA-D-GLUCOSE-6-PHOSPHATE  ' non-polymer27  16 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/m

Re: [ccp4bb] CCP4 lib file

2014-03-07 Thread Remie

Thanks Eleanor,
I ended up using a glucose ligand lib file from a different protein that my 
friend used and refinement Refmac5 worked out.
However I need to add the LINK Command in PDB so CCP4 recognizes that glucoses 
connected. 
Can I get help please?
Thank you,
Remie


> On Mar 5, 2014, at 10:49 AM, Eleanor Dodson  wrote:
> 
> There are lots of GLUCOSE type lib files for different sugars.
> One way to find what is available is:
> From the REfinement GUI click Monomer library sketcher
> 
> You get a window with File in the top LH corner
> Click on that and ask for Read monomer from library
> 
> Then enter a key word GLUCOSE and you get this list
> ADQ etc etc
> 
> Select what you want and go from there..
> 
> Or do this crude method to get a complete list!:
> 
> [ccp4@roo timm]$ grep -i glucose $CLIBD/monomers/*/*
> 
> 
> 
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/a/ADQ.cif:ADQ  ADQ 
> 'ADENOSINE-5'-DIPHOSPHATE-GLUCOSE' non-polymer61  38 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/a/AGL.cif:AGL  AGL 
> '4,6-DIDEOXY-4-AMINO-ALPHA-D-GLUCOSE ' pyranose   24  11 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/b/BG6.cif:BG6  BG6 
> 'BETA-D-GLUCOSE-6-PHOSPHATE  ' non-polymer27  16 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/b/BGC.cif:BGC  BGC 
> 'BETA-D-GLUCOSE  ' pyranose   24  12 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/d/D6G.cif:D6G  D6G 
> '2-DEOXY-GLUCOSE-6-PHOSPHATE ' pyranose   26  15 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/d/DDA.cif:DDA  DDA 
> '2,6-DIDEOXY-BETA-D-GLUCOSE  ' pyranose   22  10 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/G16.cif:G16  G16 
> 'ALPHA-D-GLUCOSE 1,6-BISPHOSPHATE' pyranose   30  20 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/G1P.cif:G1P  G1P 
> 'ALPHA-D-GLUCOSE-1-PHOSPHATE ' pyranose   27  16 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/G2F.cif:G2F  G2F 
> '2-DEOXY-2FLUORO-GLUCOSE ' pyranose   23  12 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/G4D.cif:G4D  G4D 
> '4-DEOXY-ALPHA-D-GLUCOSE ' pyranose   23  11 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/G6D.cif:G6D  G6D 
> '6-DEOXY-ALPHA-D-GLUCOSE ' non-polymer23  11 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/G6P.cif:G6P  G6P 
> 'ALPHA-D-GLUCOSE-6-PHOSPHATE ' pyranose   27  16 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/G6Q.cif:G6Q  G6Q 
> 'GLUCOSE-6-PHOSPHATE ' non-polymer27  16 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GDA.cif:GDA  GDA 
> '4-DEOXY-4-AMINO-BETA-D-GLUCOSE  ' non-polymer25  12 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GFP.cif:GFP  GFP 
> '2-DEOXY-2-FLUORO-ALPHA-D-GLUCOSE-1-P' pyranose   26  16 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GLC-B-D.cif:GLC-b-D  GLC 
> 'beta_D_glucose  ' D-pyranose 24  12 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GLC.cif:GLC  GLC 
> 'ALPHA-D-GLUCOSE ' pyranose   24  12 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GLD.cif:GLD  GLD 
> '4,6-DIDEOXYGLUCOSE  ' pyranose   22  10 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GLF.cif:GLF  GLF 
> '1-FLUORO-ALPHA-1-DEOXY-D-GLUCOSE' pyranose   23  12 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GLO.cif:GLO  GLO 'D-GLUCOSE 
> IN LINEAR FORM' non-polymer24  12 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GLT.cif:GLT  GLT 
> '5-DEOXY-5-THIO-ALPHA-D-GLUCOSE  ' non-polymer24  12 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GMM.cif:GMM  GMM 'GLUCOSE 
> MONOMYCOLATE' non-polymer   200  74 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/g/GUD.cif:GUD  GUD 
> 'GLUCOSE-URIDINE-C1,5'-DIPHOSPHATE   ' non-polymer58  36 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/i/ISX.cif:ISX  ISX 'GLUCOSE 
> BETA-1,3-ISOFAGAMINE' non-polymer44  21 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/k/KBG.cif:KBG  KBG 
> '2-KETO-BETA-D-GLUCOSE   ' non-polymer22  12 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:ADQ  
> ADQ 'ADENOSINE-5'-DIPHOSPHATE-GLUCOSE' non-polymer61  38 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:AGL  
> AGL '4,6-DIDEOXY-4-AMINO-ALPHA-D-GLUCOSE ' pyranose   24  11 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:BG6  
> BG6 'BETA-D-GLUCOSE-6-PHOSPHATE  ' non-polymer27  16 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:BGC  
> BGC 'BETA-D-GLUCOSE  ' pyranose   24  12 .
> /y/people/ccp4/ccp4-6.4.0/lib/data/monomers/list/mon_lib_list.cif:D6G

[ccp4bb] CCP4-6.4.0 Update 010

2014-03-07 Thread Charles Ballard

Dear CCP4 Users,

An update for the CCP4-6.4.0 series has just been released, consisting of the 
following changes

◆ ARP/wARP (Mac, Linux)
1. Fix in the use of free R flag in the ARP/wARP CCP4i interface for solvent 
building
2. Fix in the identification of non-crystallographic symmetry that in some 
cases led to zero target number of residues
3. Fix in recognition of secondary structural elements that in rare cases led 
to a 'bus error'
* Many thanks to Marcin Cymborowski, Carmelo Giacovazzo, Ulrich Gohlke and Vito 
Calderone for reporting these problem cases.

◆ imosflm (update to 7.1.0 for all platforms)
- Multi-lattice implementation
- Parallel processing of wedges

◆ feckless (0.0.2, all)
- Fixes several major bugs

◆ pointless (1.9.2, all)
- General update for multi-lattice

◆ ctruncate (1.13.13, all)
- Fixes negative eigenvalue exit during anisotropy analysis

◆ cnautilus (0.4, all)
- Some basic output markup and numbering of output sequences

◆ refmac5 (5.8.006, all)
- Fixes for ARP/wARP and forthcoming release of Crank2




Note that auto-updates work only with CCP4 6.4.0 series, therefore please 
upgrade if necessary.
The Update Manager is now included in the package so you do not need to install 
it separately.
In addition, all available updates will be installed automatically if you are 
using Setup Manager for CCP4 installation.

Please report any bugs to c...@stfc.ac.uk.

Many thanks for using CCP4.

the CCP4 core team.
-- 
Scanned by iCritical.

Re: [ccp4bb] Validity of Ion Sites in PDB

2014-03-07 Thread Murray, James W

Dear all, 

It is well known that  you can look at anomalous difference maps to see heavier 
atoms - although I think not enough people do it. One technique that I think is 
powerful, but under-used is to calculate element-specific maps by taking the 
difference of anomalous difference data from just above and below the 
absorption edge. This paper introduces the technique and explains it well 
http://journals.iucr.org/d/issues/2005/05/00/he5321/index.html. I suspect if 
this method were more used, many mis-labeled metals in proteins would come to 
light.

James

--
Dr. James W. Murray
Lecturer in Biotechnology
Dept. Life Sciences
Imperial College, London
Tel: +44 (0)20 759 48895

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Tim Gruene 
[t...@shelx.uni-ac.gwdg.de]
Sent: Friday, March 07, 2014 9:44 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Validity of Ion Sites in PDB

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Jacob,

the 'check-my-metal' server at http://csgid.org/csgid/metal_sites/
lists a couple of references which might be of interest.

As usual in crytallography one must understand the science in order to
understand the reliability of the models from the PDB. They are not
the truth but only models to explain the data from a diffraction
experiment.

Best,
Tim

On 03/06/2014 08:45 PM, Keller, Jacob wrote:
> Dear Crystallographers,
>
> I was curious whether there has been a rigorous evaluation of ion
> binding sites in the structures in the pdb, by PDB-REDO or
> otherwise. I imagine that there is a considerably broad spectrum of
> habits and rigor in assigning solute blobs to ion X or water, and
> in fact it would be difficult in many cases to determine which ion
> a given blob really is, but there should be at least some fraction
> of ions/waters which can be shown from the x-ray data and known
> geometry to be X and not Y. This could be by small anomalous
> signals (Cl and H2O for example), geometric considerations, or
> something else. Maybe this does not even matter in most cases, but
> it might be important in others...
>
> All the best,
>
> Jacob Keller
>
>
> *** Jacob Pearson Keller,
> PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr,
> Ashburn, VA 20147 email: kell...@janelia.hhmi.org
> ***
>

- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

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Re: [ccp4bb] Validity of Ion Sites in PDB

2014-03-07 Thread Tim Gruene

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Hash: SHA1

Dear Jacob,

the 'check-my-metal' server at http://csgid.org/csgid/metal_sites/
lists a couple of references which might be of interest.

As usual in crytallography one must understand the science in order to
understand the reliability of the models from the PDB. They are not
the truth but only models to explain the data from a diffraction
experiment.

Best,
Tim



On 03/06/2014 08:45 PM, Keller, Jacob wrote:
> Dear Crystallographers,
> 
> I was curious whether there has been a rigorous evaluation of ion
> binding sites in the structures in the pdb, by PDB-REDO or
> otherwise. I imagine that there is a considerably broad spectrum of
> habits and rigor in assigning solute blobs to ion X or water, and
> in fact it would be difficult in many cases to determine which ion
> a given blob really is, but there should be at least some fraction
> of ions/waters which can be shown from the x-ray data and known
> geometry to be X and not Y. This could be by small anomalous
> signals (Cl and H2O for example), geometric considerations, or
> something else. Maybe this does not even matter in most cases, but
> it might be important in others...
> 
> All the best,
> 
> Jacob Keller
> 
> 
> *** Jacob Pearson Keller,
> PhD Looger Lab/HHMI Janelia Farms Research Campus 19700 Helix Dr,
> Ashburn, VA 20147 email: kell...@janelia.hhmi.org 
> ***
> 

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

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Yj2NVdKiYBq9O28v9eCQWDA=
=YkXc
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Re: [ccp4bb] Validity of Ion Sites in PDB

2014-03-07 Thread Jan Dohnalek

Given the average resolution of protein structures, reliability of ion site
identification is almost always in question.
Realistically, I think that only a combination of approaches and evaluation
of several factors (including other experimental methods) leads to good
answers (as I am trying to teach in my lectures). Therefore also an easy
and uniformly reliable evaluation of ion sites in the PDB is not possible
(too many details to be included in the analysis which are not part of the
PDB record). In many cases though it is fairly easy to say "wrong ion".

Jan Dohnalek
IBT Prague



On Fri, Mar 7, 2014 at 7:09 AM, Robbie Joosten
wrote:

>  Dear Jacob,
>
> There are a lot of potential problems with ion validation, that make
> obtaining a reliable answer difficult. If you want to datamine ion
> validation results, you can use the ready-made WHAT_CHECK files in the
> PDBREPORT databank for original PDB files or in the PDB_REDO databank for
> their re-refined or rebuilt counterparts (note that PDB_REDO does not
> explicitly do anything with ions,  yet).
> WHAT_CHECK uses the bond valence method to check for waters that should be
> ions and ions that should be other ions or water and mines the
> crystallisation conditions for hints of what could be there.
>
> HTH,
> Robbie
>
> Sent from my Windows Phone
>  --
> Van: Keller, Jacob
> Verzonden: 6-3-2014 20:45
> Aan: CCP4BB@JISCMAIL.AC.UK
> Onderwerp: [ccp4bb] Validity of Ion Sites in PDB
>
>  Dear Crystallographers,
>
>
> I was curious whether there has been a rigorous evaluation of ion binding
> sites in the structures in the pdb, by PDB-REDO or otherwise. I imagine
> that there is a considerably broad spectrum of habits and rigor in
> assigning solute blobs to ion X or water, and in fact it would be difficult
> in many cases to determine which ion a given blob really is, but there
> should be at least some fraction of ions/waters which can be shown from the
> x-ray data and known geometry to be X and not Y. This could be by small
> anomalous signals (Cl and H2O for example), geometric considerations, or
> something else. Maybe this does not even matter in most cases, but it might
> be important in others...
>
> All the best,
>
> Jacob Keller
>
>
> ***
> Jacob Pearson Keller, PhD
> Looger Lab/HHMI Janelia Farms Research Campus
> 19700 Helix Dr, Ashburn, VA 20147
> email: kell...@janelia.hhmi.org
> ***
>



-- 
Jan Dohnalek, Ph.D
Institute of Biotechnology
Institute of Macromolecular Chemistry
Academy of Sciences of the Czech Republic
Heyrovskeho nam. 2
16206 Praha 6
Czech Republic

Tel: +420 296 809 340
   +420 226 201 571
Fax: +420 296 809 410

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