[ccp4bb] Coot 0.6: new binaries and NEW CITATION

2009-12-14 Thread Kevin Cowtan
Two things for Coot users... Firstly, I have just uplaoded the remaining Linux binaries for Coot 0.6, i.e. Fedora 8, Fedora 10 and Ubuntu 6.06 (with python and gtk2 gui). You can find them on the Coot website here: http://www.biop.ox.ac.uk/coot/software/binaries/releases/ Secondly, please c

Re: [ccp4bb] Error in CAD during ARP/wWARP run in sharp/autoSHARP - also posted in sharp discuss

2009-12-14 Thread Eleanor Dodson
Well - cad cant work with that script so somehow it is being generated wrongly, presumanly in Arp/warp stage.. It would need input such as: LABIN FILE 1 E1=FBshasol E2 = something - presumably SIGFBshasol Eleanor Narayanan Ramasubbu wrote: Hi: Sorry for the same posting in here as well b

Re: [ccp4bb] MR question

2009-12-14 Thread Eleanor Dodson
The 2nd peak is a shoulder of the origin peak at 1.0 0 0 so should be ignored.. The 3rd peak is 16% of the origin - rather marginal I would say. So I dont think there is clear evidence of translational NCS Eleanor Sylvia Fanucchi wrote: Morning all Apologies for the simple question.

[ccp4bb] question about refmac/coot findwater

2009-12-14 Thread Boaz Shaanan
Hi, This question may have been asked before, so please excuse me for re-posting it. I notice that when I do a round of 10 cycles of refmac combined with (5cycles, 3 sigma level, 1.4 A resolution) of findwaters in coot, some water molecules from the different coot cycles fall one on top of the

[ccp4bb] Postdoctoral position in NYC

2009-12-14 Thread Olga Boudker
A funded postdoctoral position is availableimmediately in Weill Cornell Medical College in New York City.  The research focus will be on thecrystallography-based study of the structure and function of membrane transporters.The laboratory is fully equipped and has regular access to crystallizati

[ccp4bb] 2010 Hybrid Methods Symposium Abstract Deadline Today

2009-12-14 Thread Wes Sundquist
Dear Colleagues: This is a reminder that today is the deadline for Early Registration and Abstract Submission for the 2010 Symposium on Structural Analysis of Supramolecular Assemblies by Hybrid Methods. The Symposium will be held at Granlibakken Conference Center, Lake Tahoe, California, and t

[ccp4bb] When can I say the refinement is done?

2009-12-14 Thread rui
Hi, All, I have a general question for refinement. I tried to refine a dataset that is about 2.3A and got R/Rfree is about o.18/0.24. RMS(angles): 0.77, RMS(bonds): 0.003 however, when I check with molprobity, There are still some outliers and some bad contact that is overlap > 0.4 A.

Re: [ccp4bb] When can I say the refinement is done?

2009-12-14 Thread Pavel Afonine
Hi, the exact answer to your question is here: http://cci.lbl.gov/~afonine/for_ak/validation.pdf In particular, your question below is spelled out is discussed staring from slide #2. Pavel. On 12/14/09 7:50 AM, rui wrote: Hi, All, I have a general question for refinement. I tried to refi

Re: [ccp4bb] When can I say the refinement is done?

2009-12-14 Thread Anastassis Perrakis
A less exact answer, albeit less precise and informative than the very nice PDF and the very useful Polygon ideas, is: "very well done, but have another look at this couple of Ramachandran outliers and also consider loosening up the geometry a bit". ;-) A. On Dec 14, 2009, at 17:04, Pavel

[ccp4bb] H32 or R 3 2 :H

2009-12-14 Thread Eleanor Dodson
hypFdemo_28.pdb: CRYST1 58.351 58.351 155.876 90.00 90.00 120.00 R 3 2 :H 1 I dont hold a candle for either of these SGs but Phaser is now outputting the R 3 2 :H and many many other CCP4 programs are then falling over Can the symlib be modified to accept both? Eleanor

[ccp4bb] CALL FOR ESRF SYNCHROTRON BEAM TIME WITH ONLINE MICOSPEC AT BEAMLINE ID14-2 (19th to 22nd of February 2010)

2009-12-14 Thread David FLOT
-- CALL FOR PROPOSALS FOR BEAMTIME WITH ONLINE MICROSPEC *Proposal Deadline 13th of January 2010* There will be beamtime available at the ESRF for MX data collection with a setup that allows online monitoring of UV/VIS spectral changes of the

Re: [ccp4bb] When can I say the refinement is done?

2009-12-14 Thread Pavel Afonine
This is pointed out (in absolutely unobvious way - I wish I can add voice to that PDF) at the slide #19 -:) (except loosening weights). P. On 12/14/09 8:35 AM, Anastassis Perrakis wrote: A less exact answer, albeit less precise and informative than the very nice PDF and the very useful Polyg

[ccp4bb] announcement EMBO Practical Course : Scientific Programming and Data Visualisation for Structural Biology

2009-12-14 Thread Panne Daniel
Course Announcement EMBO Practical Course : Scientific Programming and Data Visualisation for Structural Biology We are pleased to announce our practical course " Scientific Programming and Data Visualisation for Structural Biol

Re: [ccp4bb] H32 or R 3 2 :H

2009-12-14 Thread James Stroud
Disclaimer: Phaser is the greatest MR program I've ever seen. However: "The Hermann-Mauguin space group symbol is given without parenthesis, e.g., P 21 21 2 and using the full symbol, e.g., C 1 2 1 instead of C 2." -- The RCSB http://deposit.rcsb.org/adit/docs/pdb_atom_format.html I don'

[ccp4bb] 3D search for peptide conformers?

2009-12-14 Thread Patrick Loll
I have a 10-residue stretch of a protein that adopts an interesting conformation; I'd like to know if this conformation occurs in other proteins. I'd welcome suggestions for tools that will allow me to to search for this peptide conformation in the PDB. I naturally thought of DALI, but it s

Re: [ccp4bb] H32 or R 3 2 :H

2009-12-14 Thread Soisson, Stephen M
I believe that Coot also outputs R 3 2 :H (Paul can clarify). We need some standardization on the hexagonal setting for R32. Having just suffered through a fairly brutal structure determination in this space group, I can say that there are some 'issues' with this. For instance HKL outputs a lin

[ccp4bb] Postdoctoral position in structural studies of membrane proteins by electron crystallography (cryo-EM) and X-ray crystallography

2009-12-14 Thread Schmidt-Krey, Ingeborg
Postdoctoral position in structural studies of membrane proteins by electron crystallography (cryo-EM) and X-ray crystallography A postdoctoral position is available in the School of Biology at the Georgia Institute of Technology (Georgia Tech). The laboratory has a main focus on structure-fun

[ccp4bb] 3D search for peptide conformers? - SSM

2009-12-14 Thread Miri Hirshberg
Mon, Dec. 14th 2009 London Hello, I think you can you SSM Secondary Structure Matching at PDBe http://www.ebi.ac.uk/msd-srv/ssm/ you can upload your coordinate file and try to match to the whole of PDB. Hope it helps Miri On Mon, 14 Dec 2009, Patrick Loll wrote: I have a 10-residue stret

Re: [ccp4bb] H32 or R 3 2 :H

2009-12-14 Thread Peter Zwart
Hi Stephen, > R32 > H32 > R32 :H Correct. These are all hexagonal setting. As far as I know, the hexagonal setting of R32 (R32:H) is the first one that comes up in the ITvA as is listed a R32. The rhombohedral/primitive setting of R32 (R32:R) comes second in the ITvA, I guess the first setting ta

Re: [ccp4bb] H32 or R 3 2 :H

2009-12-14 Thread Soisson, Stephen M
Thanks Peter. The unfortunate thing is that not all of the programs are able to understand these different notations, and that they preferentially use different ones. It would be nice if we all agreed to standardize. I, personally, have no problem with R 3 2 :H since that is what it really is.

Re: [ccp4bb] Retraction of 12 Structures

2009-12-14 Thread Sean Seaver
On Thu, 10 Dec 2009 13:06:36 -0600, Tanner, John J. wrote: >Some of you might be curious about the "Ajees et al debacle" that Jacob mentioned in his message. Here are two links: > >Nature Brief Communication that questioned the validity of one of Murthy's structures: > >http://www.nature.com/na

[ccp4bb] configuration or install issue with tk

2009-12-14 Thread Stuart Endostreeter
Fellow users, I just installed v6.1.2 on Ubuntu 9.0.4 today and have run into the following problem when I try to run ccp4i for the first time as root to configure the program: r...@:/home//Documents# ccp4i No protocol specified Application initialization failed: couldn't con

Re: [ccp4bb] configuration or install issue with tk

2009-12-14 Thread Mark A. White
Stuart, Are you logged-in as root or are you working in a root shell ( using su or sudo)? Depending on your security settings X-windows may not permit a program that is run from a root shell to access the display, which belongs to the user logged-in through X-windows. I get around the administra

Re: [ccp4bb] configuration or install issue with tk

2009-12-14 Thread Tim Gruene
With 'sudo' you should not have this issue. I agree, though, that having a separate user account to install crystallographic programs is quite an advantage from an administrative point of view. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID =

Re: [ccp4bb] configuration or install issue with tk

2009-12-14 Thread Stuart Endo-Streeter
I was running from a root shell. Ubuntu does not let me login as root. That is normally a good thing, but if I remember correctly to finish the ccp4i setup last time I on a CentOS system I had to login as root. I will try to reinstall tomorrow using sudo, but frankly I hate using it. Stuart

Re: [ccp4bb] configuration or install issue with tk

2009-12-14 Thread Edward A. Berry
Mark A. White wrote: Stuart, Are you logged-in as root or are you working in a root shell ( using su or sudo)? Depending on your security settings X-windows may not permit a program that is run from a root shell to access the display, which belongs to the user logged-in through X-windows. Anot

Re: [ccp4bb] configuration or install issue with tk

2009-12-14 Thread Tim Gruene
On Mon, 14 Dec 2009, Edward A. Berry wrote: Mark A. White wrote: Stuart, Are you logged-in as root or are you working in a root shell ( using su or sudo)? Depending on your security settings X-windows may not permit a program that is run from a root shell to access the display, which belongs t