Re: [ccp4bb] ccp4 release 7.0 update 023

[Mark van Raaij]

Same here on El Capitan 10.11.6.
Mutate & Auto Fit still works though, but Simple Mutate crashes.

Mark J van Raaij
CNB-CSIC
www.cnb.csic.es/~mjvanraaijOn 23 Nov 2016 16:57, Julian Nomme 
 wrote:
>
> Same here on masOS Sierra... 
> Julian 
>
> Le 11/23/16 4:55 PM, Isupov, Michail a écrit : 
> > Hi, 
> > I have already uninstalled the latest update (23), on Snow Leopard 
> > the new COOT was crushing 
> > on attempt to mutate residue in graphical interface. 
> > Regards, 
> > Misha 
> > 
> > 
> >  
> > From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of wtempel 
> > [wtem...@gmail.com] 
> > Sent: Wednesday, November 23, 2016 3:50 PM 
> > To: CCP4BB@JISCMAIL.AC.UK 
> > Subject: Re: [ccp4bb] ccp4 release 7.0 update 023 
> > 
> > Hello, 
> > after installing updates 22 and 23 on an Ubuntu-14.04 (x86_64) box, I have 
> > yet to successfully “mutate” any amino acid residue in COOT. 
> > (setup-mutate 1) is printed to the terminal, followed by a line confirming 
> > on which atom I have clicked, but the residue type selection dialog does 
> > not appear. Coot just hangs at this point. Has anyone else encountered this 
> > problem? 
> > Regards. 
> > Wolfram 
> > 
> > ​ 
> > 
> > On Wed, Nov 23, 2016 at 9:41 AM, Charles Ballard 
> > > wrote: 
> > Dear All 
> > 
> > ccp4 update 23 has just been released.  It contains 
> > 
> >    * coot: 
> >   - update to coot 0.8.7 on linux and os x 
> > 
> >    * phaser: 
> >  - Bug fixes: ccp4i and interaction with Arcimboldo 
> >  - Update: Improved treatment of systematically weak data (e.g. severe 
> >anisotropy) 
> > 
> >    * ccp4i 
> >   - bug fix: phaser, updated defaults for phaser tasks 
> >   - bug fix: mrbump, updated defaults for phaser 
> > 
> > All the best 
> > 
> > Charles  Ballard on behalf of CCP4 core team 
>
> -- 
> Julian Nommé 
> Institut de Pharmacologie et de Biologie Structurale (IPBS) 
> Equipe de biophysique structurale 
> CNRS UMR 5089 
> 205 route de Narbonne BP 64182 
> 31077 Toulouse Cedex 4 France 
> Tel : +335 61 17 54 40 
> Web:  http://www.ipbs.fr 

Re: [ccp4bb] Best (Suitable) Mac Laptop configuration for protein Xtallography

[Mark van Raaij]

Hi Ivan, 
Being in the same boat, I have investigated a bit. It seems to be a straight trade-off between more processing power, more RAM and less partability Macbook, Macbook Air, 13" Macbook Pro, 15" Macbook Pro. 
For running Rosetta I think you will be thankful for the faster processors and extra RAM of the Pro...and only the 15" has quadcore. You can put 16 Gb RAM in the 13" Pro but it has only dual-core.
The 15" is quite a bit bigger to lug around...nevertheless I'll probably go for that one. 
I don't know if there are any updates to the Macbook forthcoming, but I have to wait a bit anyway for financial reasons.
Mark J van Raaij
CNB-CSIC
www.cnb.csic.es/~mjvanraaij
On 2 Apr 2015 15:03, xaravich ivan xaravich.i...@gmail.com wrote:Hello everyone,I am planing to buy a new Mac laptop (price no bar) which will let me run all xtallographic (CCP4 and Phenix) and reasonable Rosetta Molecular Modelling (1000 to 1 decoys) softwares smoothly.What in your opinion is the best configuration. (RAM, memory, number and speed  of processors, graphics card etc.) Also I am buying a Mac display separately so that I have a big screen for easy visualization of models, COOT etc.I know that powerful Mac desktops can make life much easier but here I am specifically interested in Mac laptops only.As always thanks in advance and I will post all the suggestions anonymously for others with same query.ivan

Re: [ccp4bb] P3212--1's in Space Group Names?

[Mark van Raaij]

the same as the 1 in P1 ;-)

seriously, if you look at space group names:

143  P3
144  P31
145  P32

149  P312
151  P3112
153  P3212

150  P321
152  P3121
154  P3221

the 1s in 149 to 154 are necessary to differentiate them all.

On 18 Feb 2015, at 04:51, Keller, Jacob wrote:

 Dear Crystallographers,
 
 I don't understand what the 1's are doing in space group names like P3212 or 
 P3112--can someone fill me in? Not easy to google this one.
 
 JPK
 
 ***
 Jacob Pearson Keller, PhD
 Looger Lab/HHMI Janelia Research Campus
 19700 Helix Dr, Ashburn, VA 20147
 email: kell...@janelia.hhmi.org
 ***

Mark J van Raaij
Lab 20B
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij

Re: [ccp4bb] Absence of contact between layers in a crystal

[Mark van Raaij]

In our structures 1H6W (1.9Å) and 1OCY (1.5Å) we observed something similar, I 
suspect the domain that makes the crystal contacts is three-fold disordered, 
leading to layers of nothing. In our paper in JMB 314, 1137 (doi 
10.1006/jmbi.2000.5204) we tried to explain it a bit, and describe what was 
done to try and show up the missing domain.

The 2HR0 structure was clearly made up, as were the data, apparently the 
mathematical function used to calculate the sigmas could be derived from the 
deposited data...It is indeed a pity that neither the structure nor the paper 
have been rejected. Perhaps the PDB is waiting for Nature, and Nature for the 
PDB...a joint letter to both might be in order to get this sorted out.


On 6 Feb 2015, at 11:58, Kerff Fred wrote:

 Hello,
 
 Looking at structure 2HR0 (The structure of complement C3b provides insights 
 into complement activation and regulation. »,Abdul Ajees, A.,  Gunasekaran, 
 K.,  Volanakis, J.E.,  Narayana, S.V.,  Kotwal, G.J.,  Krishna Murthy, H.M.;  
 (2006) Nature 444: 221-225), I noticed the absence of contacts between layers 
 in the crystal. Is it something that has already been observed in other 
 crystals?
 
 Best regards,
 
 Fred
 -
 Frédéric Kerff
 Chercheur qualifié F.R.S.-FNRS
 Cristallographie des protéines
 Centre d'Ingénierie des Protéines
 Université de Liège
 17, Allée du 6 Août - Bat B5a
 4000 Liège (Belgium)
 Tel.: +32 (0)4 3663620
 Fax: +32 (0)4 3663772
 
 
 
 Le 6 févr. 2015 à 10:12, Tim Gruene t...@shelx.uni-ac.gwdg.de a écrit :
 
 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA1
 
 Dear Smith,
 
 The sca file most likely does not contain flags. pointless can read
 the sca file, standardise it to ccp4 standards and freerflag marks
 random reflections. You should use the maximum of 500 unique
 reflections or 5% of the unique reflections, whichever is larger.
 
 Best,
 Tim
 
 On 02/06/2015 09:49 AM, Smith Lee wrote:
 Dear All, I have a sca file. Will you please tell me by which
 software or how I can know whether the sca file contains R-free
 tags? If not, by which software or how I can add the R-free tags?
 And how much of the reflections I add the R-free tags? I am looking
 forward to getting your reply. Smith
 
 
 - -- 
 - --
 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)
 
 iD8DBQFU1IWVUxlJ7aRr7hoRAmZHAJ4+6wREnwkFN0EhfErAA0tPSopKKwCgiLdi
 j0JFZac4kAh8twpov71MG84=
 =XN57
 -END PGP SIGNATURE-

Mark J van Raaij
Lab 20B
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij

Re: [ccp4bb] Assess anomalous signal?

[Mark van Raaij]

sure, whether the structure can be solved is a good criterion.
but often, when trying different heavy atoms, the structure can NOT be solved, 
and then some criterion to judge whether to continue to try and solve it with 
that data, or whether to focus on other datasets, other derivatives, another 
crystal form, another construct or even another protein, is useful.
CCanom in scala/aimless is one of these criteria.

Fluorescence signal is obtained also if you have disordered metal, so even if 
you get it, it does not mean you have a good derivative, because the metal may 
be in the solvent or bound to a disordered region.

If you have an isomorphous native, Patterson diff maps are a way to judge the 
number of heavy atoms, for SAD perhaps the anomalous Patterson map, but that 
may be less clear (more noisy).
In the Hg-case, the number of Cys can be a first guess of the number of Hg 
sites.




On 16 Jan 2015, at 17:18, Keller, Jacob wrote:

 How about “whether the structure can be solved” as a criterion, i.e, maybe 
 just put it into your favorite software and see whether it works, trying 
 various parameters? Depends on your goals, I guess―most people just want to 
 solve the structure and move on.
  
 JPK
  
 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of luzuok
 Sent: Friday, January 16, 2015 9:33 AM
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: [ccp4bb] Assess anomalous signal?
  
  
 Dear all,
 I'm doing Hg SAD phasing for the first time, and I met some problem:
 1. How to assess the anomalous signal after I process the data and get my mtz 
 file?  
 My labmate doesn't scan the fluorescence signal. Actually, I don't quite 
 understand why we use fluorescence to detect anomalous signal.
 2. How to estimate the number of heave atom in one unit cell? by soaking 
 heavy atom derivatives.
  
 Best!
  
 Lu Zuokun
 Nankai University
  
 --
 卢作�j
 南开大学新生物站A202
  
 

Mark J van Raaij
Lab 20B
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij

Re: [ccp4bb] Phaser MR problem

[Mark van Raaij]

Or perhaps there is only 1 copy and more solvent than you expect? This is not 
that uncommon.

On 20 Sep 2014 12:09, Randy Read rj...@cam.ac.uk wrote:

 Just to add to what Herman said: 

 The statistics are good for placing the domain represented by ensemble 1 
 (TFZ=14.3) and the first copy of the domain represented by ensemble 2 
 (TFZ=11.9), but not for the two possible solutions for placing the second 
 copy of ensemble 2 (TFZs of 4.5 and 4.7).  So it’s possible that only the 
 placement of the first two components is correct.  If you turn on symmetry in 
 coot, do those two domains come together to form a sensible whole protein?  
 If so, you could try using that composite model to look for more copies of 
 the whole protein (keeping in mind Herman’s point about the possible numbers 
 of copies). 

 That said, it’s going to be a challenge to finish up the structure rebuilding 
 and refinement when you have limited resolution and relatively low sequence 
 identity starting models.  With 3-fold or greater NCS, averaging would help a 
 great deal (2-fold helps somewhat but is less powerful); otherwise, you’re 
 likely to need some additional phase information. 

 Best wishes, 

 Randy Read 

 - 
 Randy J. Read 
 Department of Haematology, University of Cambridge 
 Cambridge Institute for Medical Research    Tel: +44 1223 336500 
 Wellcome Trust/MRC Building Fax: +44 1223 336827 
 Hills Road    E-mail: 
 rj...@cam.ac.uk 
 Cambridge CB2 0XY, U.K.   
 www-structmed.cimr.cam.ac.uk 

 On 19 Sep 2014, at 10:33, Veerendra KUMAR (IMCB) 
 veerend...@imcb.a-star.edu.sg wrote: 

  Dear CCP4 members, 
  
  Recently I have collected native data at 3.3 A resolution. The structure of 
  the protein should have two domains. The structure of c terminal domain 
  from homologous (30 seq similarity) is known. I took n terminal domain from 
  another homologous protein. I ran the phaser using these two ensembles and 
  got the following solutions. 
  #   [No title given] 
  SOLU SET RFZ=3.9 TFZ=14.3 PAK=4 LLG=144 TFZ==10.5 RFZ=2.4 TFZ=11.9 PAK=9 
  LLG=259 TFZ==7.0 RFZ=4.0 TFZ=4.5 PAK=24 LLG=207 TFZ==7.4 
  SOLU SPAC I 41 3 2 
  SOLU 6DIM ENSE ensemble1 EULER 43.364 14.638 271.356 FRAC 0.81509 0.22245 
  0.92422 BFAC -7.23070 
  SOLU 6DIM ENSE ensemble2 EULER 173.495 55.758 234.557 FRAC 1.25797 -0.71934 
  0.10135 BFAC 1.81823 
  SOLU 6DIM ENSE ensemble2 EULER 351.235 68.606 254.802 FRAC 0.64931 0.81795 
  0.27592 BFAC 5.82534 
  SOLU ENSE ensemble1 VRMS 1.157 
  SOLU ENSE ensemble2 VRMS 1.540 
  SOLU SET RFZ=3.9 TFZ=14.3 PAK=4 LLG=144 TFZ==10.5 RFZ=2.4 TFZ=11.9 PAK=9 
  LLG=259 TFZ==7.0 RFZ=2.7 TFZ=4.7 PAK=19 LLG=202 
  SOLU SPAC I 41 3 2 
  SOLU 6DIM ENSE ensemble1 EULER 43.364 14.638 271.356 FRAC 0.81509 0.22245 
  0.92422 BFAC -7.23070 
  SOLU 6DIM ENSE ensemble2 EULER 173.495 55.758 234.557 FRAC 1.25797 -0.71934 
  0.10135 BFAC 1.81823 
  SOLU 6DIM ENSE ensemble2 EULER 41.452 118.850 315.630 FRAC 0.61025 0.05816 
  1.60902 BFAC 5.47988 
  SOLU ENSE ensemble1 VRMS 1.157 
  SOLU ENSE ensemble2 VRMS 1.540 
  
  The TFZ score 14.3 suggests a solution. Then I did refinement using Ploy 
  Ala phaser model. The R values are 0.590/0.62. I use the map to build the 
  model in Buccaneer but it did not build anything. 
  
  Is the pahser solution correct? Why are the R values so high despite the 
  good TFZ score? Any suggestions are greatly appreciated. 
  
  Thank you 
  
  Veerendra 
  
  
  
  Note: This message may contain confidential information. If this Email/Fax 
  has been sent to you by mistake, please notify the sender and delete it 
  immediately. Thank you. 

Re: [ccp4bb] CCP4-6.4.0 Update 018

[Mark van Raaij]

same happened to me yesterday evening, but when I retried this morning, the 
update installed fine.
Did not change anything in between.

On 14 Jun 2014, at 11:21, Felix Frolow wrote:

 CCP4BB list,
 Today I tried to install update 018, however I have lost the ability to do it 
 from the GUI. Menu for checking available installation have disappeared 
 mysteriously.
 Any clue not related to something I probably did between previous 
 installation and this one will be welcomed. I do brute force reinstallation 
 right now and hope it will work.
 
 FF
 
 Dr Felix Frolow   
 Professor of Structural Biology and Biotechnology, Department of Molecular 
 Microbiology and Biotechnology
 Tel Aviv University 69978, Israel
 
 Acta Crystallographica F, co-editor
 
 e-mail: mbfro...@post.tau.ac.il
 Tel:  ++972-3640-8723
 Fax: ++972-3640-9407
 Cellular: 0547 459 608
 
 On Jun 13, 2014, at 23:07 , Andrey Lebedev andrey.lebe...@stfc.ac.uk wrote:
 
 Dear CCP4 Users
 
 An update for the CCP4-6.4.0 series has just been released, consisting
 of the following changes
 
 • refmac5 (all platforms):
  – Fixed restraints for M- and P-peptides
  – Fixed SAD scaling issue
 
 • monomers (all):
  – Fixed description for M- and P-peptides and some other entries
 
 • pointless (all):
  – Update to 1.9.10 fixing a long-standing bug in reindexing files with 
 different (permuted) unit cells
 
 • aimless (all):
  – Fix to explicit run definitioin
 
 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.ukmailto:c...@stfc.ac.uk.
 
 Many thanks for using CCP4.
 
 The CCP4 Core Team
 
 
 
 -- 
 Scanned by iCritical.
 
 

Mark J van Raaij
Lab 20B
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij

Re: [ccp4bb] High Rwork/Rfree vs. Resolution

[Mark van Raaij]

As the excellent tips that you got indicate, lower R-factors can be obtained by 
getting better data (better crystals, better data collection, better data 
processing) or better fitting, i.e. refinement. In this respect, I am impressed 
by the automatic data processing protocols now being implemented. Also, the 
automatic local NCS refinement in REFMAC seems very good for our recent 
structures.
But I would really want to make a general comment - not ALL structures can be 
better than the average! There will always be structures with 5% higher R/Rfree 
than the average in the same resolution range. Sometimes this will be due to 
suboptimal refinement, but sometimes it may simply not be possible to get 
better crystals and better data. Better not necessarily in term of resolution, 
but in terms of disorders like you describe for your plate-shaped crystals.
What I mean is that one should make all efforts to get better crystals and data 
and refine structures as well as possible, but sometimes it may not be possible 
to beat the average of the pdb and one should not get too hung up by that. 
These structures should also be deposited and published.
On the other hand, these rules that R-factor should be a certain value at a 
certain resolution, may lead to suboptimal refinement. For example the thought 
my R-factor is already better than the average could be counterproductive and 
lead people to stop refinement prematurely.
Sometimes a structure will have Rs better than the average for the resolution, 
but still better refinement could lower it further and this should then be 
done. I can think of an MR solution using a very homologous model that was 
refined at higher resolution, structures with high NCS, or simply certain 
rock-solid proteins...
Another popular one is (was?) that Rfree should always be below 30%, while 
several important structures justifiably have Rfrees quite a bit higher (others 
perhaps have not been refined enough).
So while comparing R/Rfree to the average of existing structures is useful, it 
may not necessarily be a sign that a structure is bad if your Rs are 5 % 
higher, not should your Rs being at or below the average be an excuse for 
stopping refinement too early.
Fear that ones Rs are not low enough may even lead to certain forms of 
cheating, for example not keeping the Rfree reflections truly free.

On 22 Feb 2014, at 01:41, Chris Fage wrote:

 Dear CCP4BB Users,
 
 I recently collected a number of datasets from plate-shaped crystals
 that diffracted to 1.9-2.0 angstroms and yielded very nice electron
 density maps. There is no major density unaccounted for by the model;
 however, I am unable to decrease Rwork and Rfree beyond ~0.25 and
 ~0.30, respectively. Probably due to the more 2-dimensional nature of
 my crystals, there is a range of phi angles in which the reflections
 are smeared, and I am wondering if the problem lies therein.
 
 I would be grateful if anyone could provide advice for improving my
 refinement statistics, as I was under the impression that the
 R-factors should be ~5% lower for the given resolution.
 
 A few more pieces of information:
 -Space group = P21, with 2 monomers per asymmetric unit;
 -Chi square = 1.0-1.5;
 -Rmerge = 0.10-0.15;
 -Data were processed in HKL2000 and refined in Refmac5 and/or phenix.refine;
 -PHENIX Xtriage does not detect twinning, but hints at possible weak
 translational pseudosymmetry;
 -I was previously able to grow one atypically thick crystal which
 diffracted to 1.65 angstroms with Rwork/Rfree at 0.18/0.22.
 Unfortunately, the completeness of the dataset was only ~90%.
 
 Regards,
 Chris

Mark J van Raaij
Lab 20B
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij

[ccp4bb] Check waters for possibly being sodium ions and similar

[Mark van Raaij]

In the past I remember using a simple program or webserver to check whether 
modelled water molecules might be metal ions, especially sodium, magnesium etc. 
as they do not differ much in density to waters. Based on coordination.
However, I can't remember the name and can't find it in google or the ccp4bb 
archives. What_if seems to have something similar implemented, but I remember 
it as a stand-alone program with a rather simple name.
Anyone have better memory or searching skills than me?

Mark J van Raaij
Lab 20B
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij

Re: [ccp4bb] Check waters for possibly being sodium ions and similar

[Mark van Raaij]

turns out some people indeed have better memory than me:
WASP inside STAN server
http://xray.bmc.uu.se/cgi-bin/gerard/rama_server.pl
thanks!

On 14 Feb 2014, at 12:49, Mark van Raaij wrote:

 In the past I remember using a simple program or webserver to check whether 
 modelled water molecules might be metal ions, especially sodium, magnesium 
 etc. as they do not differ much in density to waters. Based on coordination.
 However, I can't remember the name and can't find it in google or the ccp4bb 
 archives. What_if seems to have something similar implemented, but I remember 
 it as a stand-alone program with a rather simple name.
 Anyone have better memory or searching skills than me?
 
 Mark J van Raaij
 Lab 20B
 Dpto de Estructura de Macromoleculas
 Centro Nacional de Biotecnologia - CSIC
 c/Darwin 3
 E-28049 Madrid, Spain
 tel. (+34) 91 585 4616
 http://www.cnb.csic.es/~mjvanraaij
 

Mark J van Raaij
Lab 20B
Dpto de Estructura de Macromoleculas
Centro Nacional de Biotecnologia - CSIC
c/Darwin 3
E-28049 Madrid, Spain
tel. (+34) 91 585 4616
http://www.cnb.csic.es/~mjvanraaij

Re: [ccp4bb] resubmission of pdb

[Mark van Raaij]

Well, like Folmer says, you don't have to withdraw the entry, you could just 
let it be released before the paper is accepted. While in some projects there 
may be a legitimate fear that other scientists use your unpublished entry for 
things you don't want them to, in many projects this doesn't matter too much.
Also, for the PDB staff it is rather annoying to have to re-check the entry 
later, so these withdrawals should only be done when there is a real 
justification.



On 1 Feb 2014, at 23:29, MARTYN SYMMONS wrote:

 I have recently had the same problem. But generally, the PDB will usually 
 allow a further 6 months hold for review or modifications to an already 
 submitted paper.
 
 But what I wanted to say was that the correct term is 'withdrawal' if the 
 entry is removed pre-release - 'retraction' carries a pejorative connotation. 
 Even after release, pulling an entry would be called obsoleting (status OBS) 
 without superseding. So some structures have been 'obsoleted' owing to 
 retraction of a published paper. (Superseding is when a better structure 
 replaces the original - this process is tracked by the PDB.)
 
 Most pre-release 'withdrawn' entries are of course subsequently released 
 after re-submission. But the PDB does not seem to track these connections - 
 although they maintain a list of withdrawn entries - which means ids cannot 
 really be recycled.
 
 Interestingly, before release entries can be 'replaced' which means a new 
 structure can take the place (and 4 letter code) of the old one - this would 
 have to have the same meta-data - so source and expression - but could have 
 different resolution, space group, coordinates, and small molecules. Changes 
 in these could for example be motivated by referees' comments on the 
 submitted paper or maybe the authors got lucky with a better crystal. But 
 this pre-release replacement could also be potentially used to 'sex up' a 
 structure - for example by adding a 'novel' small molecule 'overlooked' in 
 the original deposition. Such changes are tracked privately by the PDB but 
 are not publically available... even after release.
 
 Even more interestingly, the ligand definitions such as bond orders can be 
 modified _after_ release (as in the recent R12 case I noticed*)... I think 
 this is owing to the lack of clear rules on small molecule changes - which 
 means the PDB should be considered of limited value as a definitive record of 
 small molecule chemistry.
 
 Cheers - M
 *https://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg33403.html
  
 
 
 
 
 
 
 
 From: Robbie Joosten robbie_joos...@hotmail.com
 To: CCP4BB@JISCMAIL.AC.UK 
 Sent: Saturday, 1 February 2014, 12:48
 Subject: Re: [ccp4bb] resubmission of pdb
 
 Hi Folmer,
 
 Perhaps because of the one year limit of keeping PDB entries in the 'HPUB'
 status. 
 
 So when a PDB entry is retracted before release, is the PDBid recycled after
 a while? 
 
 Cheers,
 Robbie
 
  -Original Message-
  From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
  Folmer Fredslund
  Sent: Saturday, February 01, 2014 10:33
  To: CCP4BB@JISCMAIL.AC.UK
  Subject: Re: [ccp4bb] resubmission of pdb
  
  Hi Faisal,
  
  There is one thing I don't understand:
  
  Some time back i had submitted a coordinate in PDB but because of
  unacceptance of the manuscript we had to retract the submission
  
  Why would you need to retract your deposited structure just because the
  paper describing the structure didn't get accepted?
  
  
  Venlig hilsen
  Folmer Fredslund
  
  On Jan 31, 2014 10:04 PM, Faisal Tarique faisaltari...@gmail.com
 wrote:
  
  
  Dear all
  
  Dear Dr. PDB,
  
  Some time back i had submitted a coordinate in PDB but because of
  unacceptance of the manuscript we had to retract the submission. During
  this procedure i got few zipped file from the annotator such as 1.
  rcsb0.cif-public.gz,  2. rcsb0.pdb.gz and  3. rcsb0-
  sf.cif.gz..Now i want to submit the same ..My question is what is the best
  way to do it again..??
  Should we start  from the beginning through ADIT Deposition tool
  and resubmit it with a new PDB id or there is some way to submit again
 those
  zip files which the annotator sent us after retraction..May you please
 suggest
  what could be the easiest way to submit our structure to PDB without much
  efforts.
  
  
  --
  Regards
  
  Faisal
  School of Life Sciences
  JNU
  
  
 
 

Re: [ccp4bb] skin on crystal

[Mark van Raaij]

Usually the skin is precipitated protein when it comes into contact with air. 
In this case, avoiding contact with air may be the only way to avoid the skin, 
i.e. crystallise using a technique that is not vapour diffusion, but for 
instance microbatch, microdialysis or free interface diffusion.

On 13 Jan 2014, at 21:02, Debasish Chattopadhyay wrote:

 We crystallized a protein at 4 and 22 deg C in different conditions:
  
 from ammonium sulfate in acetate buffer pH 5
 and
 PEG4000 in Hepes buffer at pH 7.5
  
 In both cases the drops have a slimy skin (almost feels like DNA).  We 
 therefore think that the skin is generated from the protein.
  
 I am sure some of you have had similar experiences.  I would like your 
 suggestions about how to avoid the skin.  Please note that we are not asking 
 for suggestions on how to handle the skin (such as using various tools)  we 
 are only interested in knowing  if there is a way to prevent the formation of 
 the skin.
  
 Thank you so much
  
 Debasish
  
 Ph: (205)934-0124; Fax: (205)934-0480
  

Re: [ccp4bb] structural homologs as cross seeds

[Mark van Raaij]

the differences are likely to be on the protein surface, and these would make 
the crystal contacts, i.e. it would be unlikely the protein could crystallise 
in the same crystal habit.
Never say never in crystallisation (i.e. try anything), but I would go for 
other things first like additives, different crystallisation techniques, 
temperatures, concentrations etc.

On 27 Dec 2013, at 20:29, Mahesh Lingaraju wrote:

 Dear all, 
 
 I was wondering if it sounds logical to use the crystals from a possible 
 structural homolog as seeds to induce nucleation ? (in terms of overall 
 sequence, the proteins are considerably different but based on sequence 
 alignment and structures from other related proteins, it is highly likely the 
 protein would have the same structure.)
 
 Please comment if any of you had experience with this. 
 
 Thank you 
 
 Happy holidays :) 
 
 Mahesh

Re: [ccp4bb] A question on protein microheterogenity for crystalization

[Mark van Raaij]

Dear Brett, 
We have seen this behaviour several times for different adenovirus fibre head 
proteins and don't really have an explanation for it. We have always set the 
peaks up separately when we had enough protein.
For this purification, as you don't have enough protein to pool them 
separately, I would pool them together and do a first crystallisation screen. 
But I would also immediately start a larger scale purification so you in the 
next crystallisation trial you can set the peaks up separately. If you are 
lucky, by the time you have done the second prep, from the first screen you may 
have some conditions to optimise. If not, the first screen should at least give 
some ideas about which precipitants, pHs and perhaps additives are most 
suitable.
Mark

On 14 Dec 2013, at 13:16, Acoot Brett wrote:

 Dear All,
 
 When I purified my protein by ion exchange chromatography for 
 crystallization, there were several peaks containing the target protein as 
 analyzed by SDS-PAGE. All these peaks have the same MW as determined by gel 
 filtration coupled MALLS. 
 
 For crystallization purpose, can I merge the corresponding ion exchange 
 chromatography peaks together? Otherwise the protein yield will be too low. 
 And how to explain the heterogeneity by ion exchange chromatography in this 
 situation?
 
 I am looking forward  to getting a reply from you.
 
 Acoot

Re: [ccp4bb] [phenixbb] Appropriate number of reflections for FreeR

[Mark van Raaij]

But at higher resolution you would like to release the restraints and introduce 
more parameters in refinement, such as anisotropic Bs - ideally keeping the 
observation/parameter ration more or less constant...

On 3 Nov 2013, at 12:50, Edward Berry wrote:

 Looking at it from the other side- suppose we say for a robust refinement we 
 need a certain number of reflections- say 4 times the number of atoms, maybe 
 less, I don't know. Any more than that is not really going to affect the 
 structure, So if you have high resolution you can afford to use a large 
 percentage of free reflections, and the cross-validation and maximum 
 liklihood will go really well, even with thin shells. On the other hand at 
 low resolution, well, sorry, you really can't spare any reflections for 
 cross-validation. (I have no idea whether this makes sense or not, but it 
 would be another way of looking at it).
 
  Mark van Raaij mjvanra...@cnb.csic.es 11/01/13 7:39 PM 
 the limit of 2000 reflections I guess is just because it would be a waste to 
 throw away more reflections for refinement, once the statistical minima for 
 calculating a reliable Rfree have been met. I.e. if you have 100.000 
 reflections, it would be a waste to use 5 or 10% of the reflections instead 
 of just 2%. I'd rather use as many as possible reflections for refinement.
 
 On 31 Oct 2013, at 20:21, Pavel Afonine wrote:
 
  Hi Joe,
 
  flags should be selected such that there is enough of them in each 
  relatively thin resolution shell (thin enough so ML target parameters can 
  be considered constant in each such shell). Lower end is about 50 
  reflections per shell. All in all this usually translates into about 10% 
  overall.
 
  Yes, there is a limit parameter set to 2000 by default. I don't know what's 
  the rationale for having it, may be someone can explain.
 
  Pavel
 
  On 10/31/13 12:10 PM, Joseph Noel wrote:
  Hi All. I think I have asked this before but forgot. Old age. What is
  the appropriate number / percentage of reflections to flag for a
  statistically appropriate Free-R calculation? If I am correct, the
  reflection file editor in Phenix chooses by default either 10% of the
  measured reflections or 2000 whichever comes first.
  __
  Joseph P. Noel, Ph.D.
  Arthur and Julie Woodrow Chair
  Investigator, Howard Hughes Medical Institute
  Professor, The Jack H. Skirball Center for Chemical Biology and Proteomics
  The Salk Institute for Biological Studies
  10010 North Torrey Pines Road
  La Jolla, CA 92037 USA
 
  Phone: (858) 453-4100 extension 1442
  Cell: (858) 349-4700
  Fax: (858) 597-0855
  E-mail: n...@salk.edu mailto:n...@salk.edu
 
  Publications  Citations:
  http://scholar.google.com/citations?user=xiL1lscJ
 
  Homepage Salk: http://www.salk.edu/faculty/noel.html
  Homepage HHMI: http://hhmi.org/research/investigators/noel.html
  __
 
 
 
  ___
  phenixbb mailing list
  pheni...@phenix-online.org
  http://phenix-online.org/mailman/listinfo/phenixbb
 
  ___
  phenixbb mailing list
  pheni...@phenix-online.org
  http://phenix-online.org/mailman/listinfo/phenixbb
 
 ___
 phenixbb mailing list
 pheni...@phenix-online.org
 http://phenix-online.org/mailman/listinfo/phenixbb

Re: [ccp4bb] OT: Who's Afraid of Peer Review?

[Mark van Raaij]

Even if you remove the authors it is often easy to ascertain who they are by 
reading the paper and reference list.

Marco Lolicato chimbio...@gmail.com wrote: 

Hi scientists,
this interesting topic brought back to my mind a similar discussion I had with 
a colleague of mine and now I want to share it with you guys.
As Vale already pointed out, the peer-review process seems to be far from an 
ideal system: there are many papers in which one of the author is himself the 
editor of the journal in which the paper is published; the impact factor of a 
journal is becoming the only way to judge the quality of a paper (and of the 
authors) [example:  one of the European Commission grants has as mandatory 
eligibility criterium that the applicant should have at least one paper 
published in a high IF journal...I'm asking...Why?].
I have also the suspect (from my insignificant experience) that some papers 
are accepted in really high IF journals without a clear peer-review process, 
but basing the decision mostly on the authors listed in that paper.
Anyway, for those reasons and more, I was wondering if maybe is nowadays 
needed to revisit the peer-review process. One thing that immediately came out 
was: the authors of a papers should be hidden to both the reviewers and the 
editors, so that paper will be judged only on the intrinsic quality and not 
from the names on it or from the country.

I'm looking forward to see your opinion. 


Marco




Il giorno 09/ott/2013, alle ore 15.00, Miguel Ortiz Lombardia ha scritto:

 Hi denizens,
 
 Now that Biology has gone missing, at least in the programs of the
 funding agencies in this part of the world, the reflections that I'm
 going to expose concern at best that even smaller field of natural
 philosophy that we euphemistically call, not without a twist of candour,
 biomedicine. At worst, they only concern the world whose limits are
 the limits of my language.
 
 As I understand it, the main purpose of really existing peer-reviewing
 is to act as a filter. By selecting those papers deemed publishable it
 spares us the herculean task of reading every possible piece emanating
 from our overheated brains. This actually reveals a big problem of
 really existing research (with the caveat expressed in the first
 paragraph). But I'm not going to venture into that problem: more clever
 minds have drowned in its muddy waters. Back to the point, if the need
 of publishing were not such a strong source of inspiration and we
 researchers would feel the compelling necessity of publishing only when
 we could write well-structured and thoughtful papers, full of useful
 data and rich in new ideas and hypotheses, we could then read a
 reasonable percentage of the papers concerning our fields of interest.
 In that utopia, peer-reviewing could be a continuous, transparent and
 open process that would involve a relevant part of the community. Not
 likely to happen and probably for good: knowledge seems to progress by a
 combination of slow accretion of small steps and sudden
 (re)interpretations of those steps.
 
 But what is interesting to see in that utopian/dystopian possibility is
 that really existing peer-reviewing suffers from a fundamental problem:
 statistical significance. Because, what significance is to be deposited
 in the opinions, whether reasonably argued or not (another thorny
 Pandora box I won't dare to open), of two, three or at best four people
 acting as editors or reviewers? Anonymous people in the latter case, to
 complete the scene.
 
 In the tension between these requirements trust is suppose to build up
 and give us a reasonable path to pursue our noble endeavours. In my
 insignificant opinion, in the current state of matters, trust is
 seriously broken. Too much pressure to publish, too many journals, too
 much money to make from publishing, too restricted and opaque a
 peer-reviewing system... As a corollary, my impression is that while
 many of us suspect we live in a bubble, we all seem to tacitly expect
 that we will not see it explode. A good friend of mine once offered me a
 book about the Spanish Armada; no joke. Its title was The confident
 hope of a miracle.
 
 To rebuild trust we need, among other things, to rebuild our tools. And
 we better do it before the next big bang. Research is not the only human
 activity involving knowledge and its transmission, we could use some
 curiosity beyond our noses.
 
 Vale.
 
 Miguel Ortiz Lombardía
 
 Architecture et Fonction des Macromolécules Biologiques (UMR7257)
 CNRS, Aix-Marseille Université
 Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
 Tel: +33(0) 491 82 86 44
 Fax: +33(0) 491 26 67 20
 mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr
 http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia
 
 El 09/10/13 20:04, Navdeep Sidhu escribió:
 John Bohannon wrote about his experience writing a computer program to 
 generate hundreds of unique papers. Thought some of you might find it of 
 interest:
 
 

Re: [ccp4bb] Stuck rfree - possible non merohedral twinning ?

[Mark van Raaij]

Dear Mahesh,
from the images you showed a few days ago I am not convinced the issue is 
twinning, just overlaps due to the long c-axis. But of course, I do not have 
have as much info as you, just those images. 
Unless you are really convinced you have twinning, if you can see what you want 
to see in the density, perhaps just do not worry too much about it. Or try to 
collect some better data, with no overlaps, from a crystal mounted with the 
long axis along the rotation axis, others and us have collected some good data 
on these kinds of crystals this way.
XDS may have integrated your current images reasonably well, but if the crystal 
is mounted better (mini-kappa goniometer for instance, or a bent loop, or mount 
many crystals and trust on luck), it will be able to do an even better job.
Mark

On 26 Aug 2013, at 17:43, Mahesh Lingaraju wrote:

 Hi Juergen  other experts
 
 Thanks for the suggestions.  I was under the impression that the twin 
 laws/operators are to be used if the twinning is merohedral. In my case, it 
 appears as if the twinning is non-merohedral and more over the data i have is 
 processed as P422 which does not have twin operators ( probably because all 
 the axial pairs are same anyway). Probably because of the same reason, 
 xtriage did not give any operators for me to use. In such cases, do people 
 usually try to process the data in another space group of lower symmetry 
 which has a twin law and is there a definite way to distinguish twinning by 
 merohedry vs non-merohedry other than just looking at the diffraction pattern 
 ( is it crucial to make that differentiation ?) ? 
 
 Thanks 
 
 Mahesh
 
 
 On Sun, Aug 25, 2013 at 10:24 PM, Bosch, Juergen jubo...@jhsph.edu wrote:
 Hi Mahesh,
 
 if you use Refmac, then you can tell it to refine the twin fraction, no need 
 to tell it the twin law as Refmac will figure it out. If you use phenix, you 
 explicitly tell it the twin law and refine then with it. You can get the 
 possible twin laws by running phenix.xtriage and looking at the log file.
 
 For a 1.7 Å dataset you should see excellent holes in the Phe and Tyr, even 
 though your Rfactors are high. If that is the case then you are likely 
 correct with the twin (if nothing else is wrong, Cbeta, Ramas etc). And you 
 did add some waters to your structure already right ? if not the go water 
 picking via Coot.
 
 Have you been converted to XDS now ? Welcome to the club.
 
 Jürgen
 
 On Aug 25, 2013, at 8:35 PM, Mahesh Lingaraju wrote:
 
 Hello everyone, 
 
 I collected a dataset which looked like it is twinned ( or a really long 
 axis in the cell)  and did not process in HKL2000 and MOSFLM but with some 
 of help and suggestions from CCP4BB, XDS was able to process it. The data 
 looks good upto 1.7 Å. However, the rfree is stuck at 0.34 even though my 
 model is almost complete. I am beginning to wonder if the data is really 
 twinned as it has the characteristics of non- merohedral twinning:
 In the images some of the reflections are sharp while some are split and one 
 of the axis in the cell is usually long ( the cell is a= 46.78 b= 46.78 c= 
 400.34; 90 90 90) 
 
 is there anyway to work around this ? or collecting better data is the only 
 solution ? 
 
 Any help is deeply appreciated
 
 Thanks 
 
 Mahesh
 
 ..
 Jürgen Bosch
 Johns Hopkins University
 Bloomberg School of Public Health
 Department of Biochemistry  Molecular Biology
 Johns Hopkins Malaria Research Institute
 615 North Wolfe Street, W8708
 Baltimore, MD 21205
 Office: +1-410-614-4742
 Lab:  +1-410-614-4894
 Fax:  +1-410-955-2926
 http://lupo.jhsph.edu
 
 
 
 
 

Re: [ccp4bb] Data processing - twinned xtals

[Mark van Raaij]

doesn't necessarily looked twinned to me.
Rather it looks like you have a trigonal or hexagonal cell with a long c-axis.
On image 2 it seems you may have systematic absences along l, although it is 
hard to tell the order. Perhaps P31, P32, P62, P64 or spacegroups with these 
symmetries plus 2-folds perpendicular.

On 16 Aug 2013, at 16:38, Mahesh Lingaraju wrote:

 Hi CCP4 folks 
 
 I have a data set which is looks twinned ( see the image-1  - I zoomed on to 
 the image so that one can spot the twinning. Furthermore, the spots are very 
 smeary from ~ 30 - 120 degrees of data collection, see image 2) I tried using 
 HKL2000 and mosflm to process this data but i cannot process it. I was 
 wondering if anyone has any ideas as to how to process this data or comments 
 on whether this data is even useful. Also, I would really appreciate if 
 someone could share their experiences on solving twinning issues during 
 crystal growth 
 
 Thanks in advance !
 
 Maheshimage 1.pngimage 2.png

Re: [ccp4bb] Data processing - twinned xtals

[Mark van Raaij]

PS For future data collections, try to get the long c-axis roughly along the 
crystal rotation axis if possible.

On 16 Aug 2013, at 16:38, Mahesh Lingaraju wrote:

 Hi CCP4 folks 
 
 I have a data set which is looks twinned ( see the image-1  - I zoomed on to 
 the image so that one can spot the twinning. Furthermore, the spots are very 
 smeary from ~ 30 - 120 degrees of data collection, see image 2) I tried using 
 HKL2000 and mosflm to process this data but i cannot process it. I was 
 wondering if anyone has any ideas as to how to process this data or comments 
 on whether this data is even useful. Also, I would really appreciate if 
 someone could share their experiences on solving twinning issues during 
 crystal growth 
 
 Thanks in advance !
 
 Maheshimage 1.pngimage 2.png

Re: [ccp4bb] Off-topic: NMR and crystallography

[Mark van Raaij]

Well, if you do NMR you avoid the possible bottlenecks of having to obtain 
well-diffracting crystals, and having to phase the protein (i.e. obtain SeMet 
protein crystals or suitable heavy atom derivatives; or a suitable MR model).
But instead, you'll need to prepare labelled protein (15N and/or 13C), which is 
expensive and for which your protein needs to be able to be expressed in 
minimal medium, and your protein will need to be very soluble, monodisperse (in 
general monomeric) and stable in a minimal NMR-compatible buffer for data 
collections lasting for hours. Assigning all the protons and calculating the 
final structure can also be months of work, while a high-resolution crystal 
structure can be finished in days, if the above-mentioned bottle-necks can be 
overcome.


On 9 Jun 2013, at 17:36, Theresa Hsu wrote:

 Dear all
 
 A question for the cross-trained members of this forum - for small sized 
 proteins, is NMR better than crystallography in terms of data collection 
 (having crystals in the first place) and data processing? How about membrane 
 proteins?
 
 I would appreciate replies to the board, instead of off-board, to allow for a 
 good discussion.
 
 Thank you.
 
 Theresa

Re: [ccp4bb] Why the name aimless

[Mark van Raaij]

i.e. the next program will be Graceless or Feckless?

On 2 May 2013, at 12:10, Phil Evans wrote:

 Reference:
 Gibbons, S. (1932) Cold Comfort Farm, Longmans, London
 
 On 2 May 2013, at 11:07, Roberto Battistutta roberto.battistu...@unipd.it 
 wrote:
 
 Hi everyone,
 just a curiosity, why the name aimless for the recent data reduction and 
 analysis program in CCP4? You know, my students are curious ...
 Thank you,
 Roberto.
 
 
 Roberto Battistutta
 Associate Professor
 Department of Chemistry
 University of Padua
 via Marzolo 1, 35131 Padova - ITALY
 tel. +39.049.827.5262
 fax. +39.049.827.5829
 roberto.battistu...@unipd.it
 www.chimica.unipd.it/roberto.battistutta/
 VIMM (Venetian Institute of Molecular Medicine)
 via Orus 2, 35129 Padova - ITALY
 tel. +39.049.7923.236
 fax +39.049.7923.250
 www.vimm.it

Re: [ccp4bb] Poor electron density in some of the chains in an asymmetric unit

[Mark van Raaij]

and 2VAK...average Bs for the twelve, sequence identical, chains vary from 28 
to 53.


On 29 Apr 2013, at 22:09, David Schuller wrote:

 On 04/29/13 12:26, Roger Rowlett wrote:
 FYI, I do know of one example of a solved structure where some of the 
 molecules in the ASU are poorly defined. In 1EKJ, 4 of the 8 molecules in 
 the ASU have low B-factors (mid 30s) and 4 have high B-factors (50s-60s). In 
 the unit cell these layers alternate. It is possible, if everything else has 
 been excluded, that your   crystal has a similar crystal-packing issue.
 
 Another is 3HDH. 
 Pig short chain L-3-hydroxyacyl-CoA dehydrongenase revisited: sequence 
 analysis and crystal structure determination.
 Barycki, et al (1999) Protein Science 8: 2010-2018.
 
 Examination of the map in the region of subunit C revealed that
 the electron density was considerably weaker for the third subunit
 compared to the other subunits...
 -- 
 ===
 All Things Serve the Beam
 ===
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
schul...@cornell.edu

Re: [ccp4bb] gelification of a pure protein

[Mark van Raaij]

reminds me of structure 1NEU, although here the gelation was reversible, see 
ref and abstract below - the paper has a photo of a tube of soluble protein and 
gelled protein

we have also had a couple of cold-sensitive proteins in our hands, that 
precipitated at 4 degrees when concentrated, but were soluble at room temp to 
quite high concentrations (and we got structures for both)


Neuron. 1996 Sep;17(3):435-49.
Crystal structure of the extracellular domain from P0, the major structural 
protein of peripheralnerve myelin.
Shapiro L, Doyle JP, Hensley P, Colman DR, Hendrickson WA.
P0, the major protein of peripheral nerve myelin, mediates membrane adhesion in 
the spiral wraps of the myelin sheath. We have determined the crystal structure 
of the extracellular domain from P0 (P0ex) at 1.9 A resolution. P0ex is folded 
like a typical immunoglobulin variable-like domain; five residues at the 
C-terminus are disordered, suggesting a flexible linkage to the membrane. The 
requirements for crystallization of P0ex are similar to those for maintaining 
the native extracellular spacing of adjacent myelin lamellae; thus, given the 
self-adhesive character of P0ex, the crystal itself may reveal some of the 
natural interactions that occur between P0 molecules in myelin. The structure 
leads to the suggestion that P0 extracellular domains may emanate from the 
membrane surface as tetramers that link to tetramers on the opposing membrane 
surface, to result in the formation of networks of molecules. We report 
analytical ultracentrifugation data for P0ex that support this idea.
PMID: 8816707


On 23 Apr 2013, at 00:36, Pascal Egea wrote:

 Dear All,
 
 I am presently faced with a peculiar case in the lab. We are expressing a 
 protein in E. coli and we are able to express it as a fusion protein without 
 problems . Fusion cleavage goes well and the final product looks homogenous 
 by size-exclusion chromatography with the expected molecular weight. There 
 are no signs of aggregation. However when we lower the salt concentration by 
 dialysis then the protein forms a gel. transparent , optically clear, with no 
 fluffy material (in the cold room).
 
 Gelification seems to occur when we lower the concentration below 100 mM 
 NaCl. This protein has a fairly high pI (~9.0). Attempts to reverse the 
 process by gentle heating or salt addition have been so far unsuccessful. It 
 is not a thermophilic protein. We have not been able to obtain crystals so 
 far.
 
 Has anyone already observed this kind of behavior and/or have any suggestions?
 
 Many thanks in advance .
 
 -- 
 Pascal F. Egea, PhD
 Assistant Professor
 UCLA, David Geffen School of Medicine
 Department of Biological Chemistry
 Boyer Hall room 356
 611 Charles E Young Drive East
 Los Angeles CA 90095
 office (310)-983-3515
 lab  (310)-983-3516
 email pe...@mednet.ucla.edu