[ccp4bb] Phaser: removing H in PDB increases the RFZ ?!
Hello, I have 4 molecules. If I use Phaser's AUTO_MR with all default parameters on them, I get the following scores: no_modif remove_H molecule RFZ TFZ RFZ TFZ 16.9 9.6 7.0 9.4 25.2 5.9 5.4 6.2 34.2 4.5 4.7 5.2 44.9 6.8 5.2 6.7 Hence, here are my existential questions, given that I heard many times "H is transparent for X-rays": * should I always remove H before running Phaser? * why? Here are a few lines of one of my PDBs containing H, in case it is misinterpreted by Phaser: --- ATOM 6 1H ALA A 1 18.629 -3.443 12.782 1.00 0.00 ATOM 7 2H ALA A 1 18.427 -2.484 13.918 1.00 0.00 ATOM 8 3H ALA A 1 17.496 -2.462 12.742 1.00 0.00 ATOM 9 HA ALA A 1 19.811 -0.866 13.013 1.00 0.00 ATOM 10 1HB ALA A 1 21.071 -1.469 10.982 1.00 0.00 ATOM 11 2HB ALA A 1 21.038 -2.809 12.152 1.00 0.00 ATOM 12 3HB ALA A 1 19.983 -2.852 10.720 1.00 0.00 --- Thanks a lot, Francois.
Re: [ccp4bb] Phaser: removing H in PDB increases the RFZ ?!
Markus Rudolph wrote: Hello, long ago I had a case when HG1 etc. were interpreted as mercury by phaser. Could that be relevant to your case? I hope not. However, as I have already seen EPMR handle some Hydrogen as Carbon, I am ready to see anything happening! :( I will have a quick look to see if I can make Phaser output atom numbers from what was read from the PDB. Regards, F. Regards, Markus On Tue, 12 Jan 2010, Francois Berenger wrote: Hello, I have 4 molecules. If I use Phaser's AUTO_MR with all default parameters on them, I get the following scores: no_modif remove_H molecule RFZ TFZ RFZ TFZ 16.9 9.6 7.0 9.4 25.2 5.9 5.4 6.2 34.2 4.5 4.7 5.2 44.9 6.8 5.2 6.7 Hence, here are my existential questions, given that I heard many times "H is transparent for X-rays": * should I always remove H before running Phaser? * why? Here are a few lines of one of my PDBs containing H, in case it is misinterpreted by Phaser: --- ATOM 6 1H ALA A 1 18.629 -3.443 12.782 1.00 0.00 ATOM 7 2H ALA A 1 18.427 -2.484 13.918 1.00 0.00 ATOM 8 3H ALA A 1 17.496 -2.462 12.742 1.00 0.00 ATOM 9 HA ALA A 1 19.811 -0.866 13.013 1.00 0.00 ATOM 10 1HB ALA A 1 21.071 -1.469 10.982 1.00 0.00 ATOM 11 2HB ALA A 1 21.038 -2.809 12.152 1.00 0.00 ATOM 12 3HB ALA A 1 19.983 -2.852 10.720 1.00 0.00 --- Thanks a lot, Francois.
Re: [ccp4bb] Phaser: removing H in PDB increases the RFZ ?!
Just to avoid any problem pdbcur xyzin X.pdb xyzout X-nohyd.pdb DELHYD END Eleanor Francois Berenger wrote: Markus Rudolph wrote: Hello, long ago I had a case when HG1 etc. were interpreted as mercury by phaser. Could that be relevant to your case? I hope not. However, as I have already seen EPMR handle some Hydrogen as Carbon, I am ready to see anything happening! :( I will have a quick look to see if I can make Phaser output atom numbers from what was read from the PDB. Regards, F. Regards, Markus On Tue, 12 Jan 2010, Francois Berenger wrote: Hello, I have 4 molecules. If I use Phaser's AUTO_MR with all default parameters on them, I get the following scores: no_modif remove_H molecule RFZ TFZ RFZ TFZ 16.9 9.6 7.0 9.4 25.2 5.9 5.4 6.2 34.2 4.5 4.7 5.2 44.9 6.8 5.2 6.7 Hence, here are my existential questions, given that I heard many times "H is transparent for X-rays": * should I always remove H before running Phaser? * why? Here are a few lines of one of my PDBs containing H, in case it is misinterpreted by Phaser: --- ATOM 6 1H ALA A 1 18.629 -3.443 12.782 1.00 0.00 ATOM 7 2H ALA A 1 18.427 -2.484 13.918 1.00 0.00 ATOM 8 3H ALA A 1 17.496 -2.462 12.742 1.00 0.00 ATOM 9 HA ALA A 1 19.811 -0.866 13.013 1.00 0.00 ATOM 10 1HB ALA A 1 21.071 -1.469 10.982 1.00 0.00 ATOM 11 2HB ALA A 1 21.038 -2.809 12.152 1.00 0.00 ATOM 12 3HB ALA A 1 19.983 -2.852 10.720 1.00 0.00 --- Thanks a lot, Francois.
[ccp4bb] off topic: multiple structural sequence alignment
Dear all, A bit off the topic question perhaps. I am trying to find a program which can do multiple structural sequence alignments. What I would like is a program which can take as input PDB codes (or files), and which will output a multiple sequence alignment in FASTA format with the full sequences of the supplied proteins intact. Preferably said server/program should be able to handle at least 20 input pdbs at once. I've been looking around, but have so far failed to find a program which does this. If anyone knows of a program or server which could handle this, I would be very grateful. Cheers, Ronnie Berntsson
Re: [ccp4bb] off topic: multiple structural sequence alignment
I ended up using multiprot and staccato recently http://bioinfo3d.cs.tau.ac.il/MultiProt/ There is a server for multiprot, but I downloaded the applications. I still ended up doing quite a bit manual editing in filling the gaps in the structures etc. I stumbled also over a link about the matter comparing different programs (by Dr Elaine Meng): http://www.cgl.ucsf.edu/home/meng/grpmt/structalign-content.html ~L~ __ Lari Lehtiö Pharmacy, Department of Biochemistry and Pharmacy Åbo Akademi University, BioCity, FIN-20520 Turku Finland +358 2 215 4270 http://www.users.abo.fi/llehtio/ __ Quoting Ronnie Berntsson : Dear all, A bit off the topic question perhaps. I am trying to find a program which can do multiple structural sequence alignments. What I would like is a program which can take as input PDB codes (or files), and which will output a multiple sequence alignment in FASTA format with the full sequences of the supplied proteins intact. Preferably said server/program should be able to handle at least 20 input pdbs at once. I've been looking around, but have so far failed to find a program which does this. If anyone knows of a program or server which could handle this, I would be very grateful. Cheers, Ronnie Berntsson
Re: [ccp4bb] Using SHARP to phase multiple different Sulphur-SAD datasets
Hi Jeremiah,
On Sat, Jan 09, 2010 at 05:01:07AM +, Jeremiah Farelli wrote:
> Does anyone know of an example where SHARP was used to phase
> multiple sulphur-SAD datasets and combine all of the data into one
> map?
I'm not aware of exactly such an example - but there shouldn't be any
problem with that at all. SHARP can easily handle that. Since it
doesn't need that distinction of 'native' and 'derivative' it would
just be a case of several compounds with different S-sites.
> I have multiple crystals of the same protein, but each crystal form
> has a different LtoM mutation (the sulfur content of the native
> construct is too low for phasing without the mutations). The
> crystals are sensitive to oxidaton, so I cannot make one construct
> with all of the mutations, and selenomethionine incorporation is out
> due to the oxidaton issues. Each crystal form from all mutants is
> isomorphous.
>
> I would like to collect highly redundant datasets of each form, and
> then use SHARP to find all the Sulphurs, and combine the initial
> phases from all datasets with the native data and build the model.
Remember that SHARP doesn't find the sites - autoSHARP could try
finding them by using SHELXC and SHELXD (from G. Sheldrick).
> The protein has two domains, and I know the structure of one of them
> (~40% of the total), so I should be able to use the intial MR phases
> to help with finding the sulphurs
That might be a good starting point: it is very easy to include the MR
phases into a SHARP run ('external phase information') and if those MR
phases are half decent your S-sites should be visible in the
log-likelihood gradient maps.
This is a feature available in SHARP for a very long time - see
http://www.globalphasing.com/sharp/manual/chapter2.html#external
> Is this feasible?
Depends on your signal, non-isomorphism, radiation damage etc.
> Are there any examples like this out there?
Well, we've used the MR-phases plus experimental phasing for more than
a decade now - seems such an obvious idea that we never thought of
writing a 'proper' paper about it.
Cheers
Clemens
--
***
* Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com
*
* Global Phasing Ltd.
* Sheraton House, Castle Park
* Cambridge CB3 0AX, UK
*--
* BUSTER Development Group (http://www.globalphasing.com)
***
Re: [ccp4bb] off topic: multiple structural sequence alignment
Both MUSTANG and MATT are good choices: http://www.cs.mu.oz.au/~arun/mustang/ http://groups.csail.mit.edu/cb/matt/ On Jan 12, 2010, at 7:17 AM, Ronnie Berntsson wrote: > Dear all, > > A bit off the topic question perhaps. > I am trying to find a program which can do multiple structural sequence > alignments. What I would like is a program which can take as input PDB codes > (or files), and which will output a multiple sequence alignment in FASTA > format with the full sequences of the supplied proteins intact. Preferably > said server/program should be able to handle at least 20 input pdbs at once. > I've been looking around, but have so far failed to find a program which does > this. If anyone knows of a program or server which could handle this, I would > be very grateful. > > Cheers, > Ronnie Berntsson
Re: [ccp4bb] Phaser: removing H in PDB increases the RFZ ?!
The increase in RFZ is relatively small and not entirely unexpected. While hydrogens only contribute one electron (as opposed to carbon (6), nitrogen(7), oxygen(8) and sulfur (16)), there are many hydrogens (in fact, almost as many as all the other atoms combined). For instance, in lysozyme you have (I used 3a67) 613 carbons, 193 nitrogens, 185 oxygens, 10 sulfurs and 959 hydrogens. Electron-wise this translates into ~13% of electrons being supplied by hydrogens. I certainly do not know how many hydrogens your model contains, but from the snippet you present it seems that you may have full set. Also, the "problem" will be exacerbated by the fact that you have B-factors of the hydrogens set to zero. Assuming that your non-hydrogen atoms have B-factors set to, say, 20, this will approximately double the relative contribution of hydrogens at the higher resolution end. True, contribution of hydrogens is not exactly additive, but it's probably not surprising to see roughly 5 percent change in RFZ. What is very interesting is that it seems to be general *improvement*, so maybe we ought to include hydrogens when doing MR. I don't know if PHASER generates riding hydrogens automatically. I think that characterize hydrogens as "transparent" to x-rays is somewhat misleading. There are plenty of examples where hydrogens are seen in ultrahigh resolution structures. Modern refinement programs all use riding hydrogens and it improves models. More precise statement is that at not-ultrahigh (non-atomic) resolution (i.e. worse than 1.2A) optical resolution is too low to distinguish two atoms separated by ~1A (typical value of X-H covalent bond). Cheers, Ed. On Tue, 2010-01-12 at 17:42 +0900, Francois Berenger wrote: > Hello, > > I have 4 molecules. > If I use Phaser's AUTO_MR with all default parameters on them, > I get the following scores: > > no_modif remove_H > molecule RFZ TFZ RFZ TFZ > 16.9 9.6 7.0 9.4 > 25.2 5.9 5.4 6.2 > 34.2 4.5 4.7 5.2 > 44.9 6.8 5.2 6.7 > > Hence, here are my existential questions, given that I heard > many times "H is transparent for X-rays": > * should I always remove H before running Phaser? > * why? > > Here are a few lines of one of my PDBs containing H, in case it is > misinterpreted by Phaser: > --- > ATOM 6 1H ALA A 1 18.629 -3.443 12.782 1.00 0.00 > > ATOM 7 2H ALA A 1 18.427 -2.484 13.918 1.00 0.00 > > ATOM 8 3H ALA A 1 17.496 -2.462 12.742 1.00 0.00 > > ATOM 9 HA ALA A 1 19.811 -0.866 13.013 1.00 0.00 > > ATOM 10 1HB ALA A 1 21.071 -1.469 10.982 1.00 0.00 > > ATOM 11 2HB ALA A 1 21.038 -2.809 12.152 1.00 0.00 > > ATOM 12 3HB ALA A 1 19.983 -2.852 10.720 1.00 0.00 > > --- > > Thanks a lot, > Francois. -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore -- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. -- / Lao Tse /
[ccp4bb] strange error in superpose
Hi, When I use the superpose program for SSM alignment with these two structures in the following command line: superpose 3BT1.pdb -s B 1OC0.pdb -s B superposed.pdb The screen output reads: PDB file 3BT1.pdb has been read in. ... 312 atoms selected using CID 'B' PDB file 1OC0.pdb has been read in. ... 289 atoms selected using CID 'B' Transformed coordinates will be written to file superposed.pdb *** empty graph for 1OC0.pdb. If I try loading the same structures (or just use the PDB codes) in the SSM server http://www.ebi.ac.uk/msd-srv/ssm/cgi-bin/ssmserver it seems to work just fine. Does anybody know how to avoid this error? Many thanks, Rob -- Robert Oeffner, Ph.D. Research Associate Department of Haematology, University of Cambridge Cambridge Institute of Medical Research Wellcome Trust / MRC Building, Hills Road, Cambridge, CB2 0XY www-structmed.cimr.cam.ac.uk, tel:01223763234, mobile:07712 887162
[ccp4bb] AW: [ccp4bb] off topic: multiple structural sequence alignment
Hi Ronnie, the (a) Mammoth tool might also work (but I just tried 6 structures or so when I used it a couple years ago - not 20). Jan --- Ronnie Berntsson schrieb am Di, 12.1.2010: Von: Ronnie Berntsson Betreff: [ccp4bb] off topic: multiple structural sequence alignment An: CCP4BB@JISCMAIL.AC.UK Datum: Dienstag, 12. Januar 2010, 13:17 Dear all, A bit off the topic question perhaps. I am trying to find a program which can do multiple structural sequence alignments. What I would like is a program which can take as input PDB codes (or files), and which will output a multiple sequence alignment in FASTA format with the full sequences of the supplied proteins intact. Preferably said server/program should be able to handle at least 20 input pdbs at once. I've been looking around, but have so far failed to find a program which does this. If anyone knows of a program or server which could handle this, I would be very grateful. Cheers, Ronnie Berntsson __ Do You Yahoo!? Sie sind Spam leid? Yahoo! Mail verfügt über einen herausragenden Schutz gegen Massenmails. http://mail.yahoo.com
Re: [ccp4bb] Phaser: removing H in PDB increases the RFZ ?!
Dear CCP4ers, I think that characterize hydrogens as "transparent" to x-rays is somewhat misleading. There are plenty of examples where hydrogens are seen in ultrahigh resolution structures. Modern refinement programs all use riding hydrogens and it improves models. More precise statement is that at not-ultrahigh (non-atomic) resolution (i.e. worse than 1.2A) optical resolution is too low to distinguish two atoms separated by ~1A (typical value of X-H covalent bond). if one looks at atomic scattering curves, hydrogens contribute to X-ray scattering mainly at low resolution, which makes them so difficult to detect even at atomic resolution. I think, it is generally a good idea to include hydrogens as riding atoms in all crystallographic tasks, and especially during refinement, both because of their scattering contribution and because of their geometrical contribution, if the latter is considered in form of anti-bumping restraints and even more important in form of hydrogen bonds. Best regards, Dirk. -- *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
[ccp4bb] strange error in superpose
Hi all, When I use the superpose program for SSM aligning these two structures in the following command line: superpose 3BT1.pdb -s B 1OC0.pdb -s B superposed.pdb The screen output reads: PDB file 3BT1.pdb has been read in. ... 312 atoms selected using CID 'B' PDB file 1OC0.pdb has been read in. ... 289 atoms selected using CID 'B' Transformed coordinates will be written to file superposed.pdb *** empty graph for 1OC0.pdb. If I try loading the same structures (or just use the PDB codes) in the SSM server http://www.ebi.ac.uk/msd-srv/ssm/cgi-bin/ssmserver it seems to work just fine. Does anybody know how to avoid this error? Many thanks, Rob
[ccp4bb] Adding H in refinement
Dear CCP4bb, since the discussion about H-atoms is on, I wanted to ask about what I saw during my refinements: I did refinement with phenix of my 1.9-2.0 Angstroem structures and included the hydrogens (riding). However, when I checked on the statistics (refinement close to the end), the average B-factor was extremely high (in phenix.polygon it was higher than with any other structure in similar resolution range). It makes sense though that this happens, if you have a residue which has a high B-factor and carries a lot of hydrogens the average B-factor will raise quite a lot (since the B-factor of hydrogens is calculated 1-1.5x of B-factor from the atom it sits on), right? (When I removed the hydrogens again, the average B-factor was fine...) My question is now did I do something wrong in my refinement (-> do I have to change something that this does not happen), or is this something everybody sees? If this is common, what would happen (during evaluation) if you want to publish a structure and the statistics show such a high average B-factor? Is it better to have hydrogens on, but a bad average B, or no hydrogens on and a good average B... Obviously, I never published a structure ;) Thanks for sharing your opinion! Sara -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] Im Auftrag von Dirk Kostrewa Gesendet: Dienstag, 12. Januar 2010 16:38 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Phaser: removing H in PDB increases the RFZ ?! Dear CCP4ers, > I think that characterize hydrogens as "transparent" to x-rays is > somewhat misleading. There are plenty of examples where hydrogens are > seen in ultrahigh resolution structures. Modern refinement programs all > use riding hydrogens and it improves models. More precise statement is > that at not-ultrahigh (non-atomic) resolution (i.e. worse than 1.2A) > optical resolution is too low to distinguish two atoms separated by ~1A > (typical value of X-H covalent bond). > if one looks at atomic scattering curves, hydrogens contribute to X-ray scattering mainly at low resolution, which makes them so difficult to detect even at atomic resolution. I think, it is generally a good idea to include hydrogens as riding atoms in all crystallographic tasks, and especially during refinement, both because of their scattering contribution and because of their geometrical contribution, if the latter is considered in form of anti-bumping restraints and even more important in form of hydrogen bonds. Best regards, Dirk. -- *** Dirk Kostrewa Gene Center, A 5.07 Ludwig-Maximilians-University Feodor-Lynen-Str. 25 81377 Munich Germany Phone: +49-89-2180-76845 Fax:+49-89-2180-76999 E-mail: kostr...@genzentrum.lmu.de WWW:www.genzentrum.lmu.de ***
Re: [ccp4bb] Adding H in refinement
Hi Sara, I don't know what "a good average B" is (or what "a bad average B" is). I know that the for the refined structure should fall in the same ball-park range than the temperature factor of the data computed from the Wilson plot. I am not saying that they should match exactly though. If they really differ wildly (e.g. 10 A**2 vs 140**2) then you double check things. Like the resolution range used to compute the Wilson B. And at 1.9-2.0 A resolution you should be able to compute a proper Wilson B. Fred Sara Züger wrote: Dear CCP4bb, since the discussion about H-atoms is on, I wanted to ask about what I saw during my refinements: I did refinement with phenix of my 1.9-2.0 Angstroem structures and included the hydrogens (riding). However, when I checked on the statistics (refinement close to the end), the average B-factor was extremely high (in phenix.polygon it was higher than with any other structure in similar resolution range). It makes sense though that this happens, if you have a residue which has a high B-factor and carries a lot of hydrogens the average B-factor will raise quite a lot (since the B-factor of hydrogens is calculated 1-1.5x of B-factor from the atom it sits on), right? (When I removed the hydrogens again, the average B-factor was fine...) My question is now did I do something wrong in my refinement (-> do I have to change something that this does not happen), or is this something everybody sees? If this is common, what would happen (during evaluation) if you want to publish a structure and the statistics show such a high average B-factor? Is it better to have hydrogens on, but a bad average B, or no hydrogens on and a good average B... Obviously, I never published a structure ;) Thanks for sharing your opinion! Sara
Re: [ccp4bb] Adding H in refinement
Hi Sara, - what you observe should not happen since phenix.refine uses riding model for H atoms. The hydrogen's B-factors are automatically inherited from the atoms these hydrogens are bonded to. For example, in X-H bond the B-factor of X should be equal to B-factor of H. - make sure you are using the latest version of PHENIX: http://www.phenix-online.org/download/ - if this does not help, please contact me directly, and send the data and model so I can tell you what exactly is not right (all the files will be handled confidentially). - there is PHENIX bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb Pavel. I did refinement with phenix of my 1.9-2.0 Angstroem structures and included the hydrogens (riding). However, when I checked on the statistics (refinement close to the end), the average B-factor was extremely high (in phenix.polygon it was higher than with any other structure in similar resolution range). It makes sense though that this happens, if you have a residue which has a high B-factor and carries a lot of hydrogens the average B-factor will raise quite a lot (since the B-factor of hydrogens is calculated 1-1.5x of B-factor from the atom it sits on), right? (When I removed the hydrogens again, the average B-factor was fine...) My question is now did I do something wrong in my refinement (-> do I have to change something that this does not happen), or is this something everybody sees? If this is common, what would happen (during evaluation) if you want to publish a structure and the statistics show such a high average B-factor? Is it better to have hydrogens on, but a bad average B, or no hydrogens on and a good average B... Obviously, I never published a structure ;)
Re: [ccp4bb] off topic: multiple structural sequence alignment
This server and/or standalone program may be useful as well because of speed, being that 20 structures will take a while on most servers: http://ub.cbm.uam.es/mammoth/mult/ At 05:17 AM 1/12/2010, Ronnie Berntsson wrote: Dear all, A bit off the topic question perhaps. I am trying to find a program which can do multiple structural sequence alignments. What I would like is a program which can take as input PDB codes (or files), and which will output a multiple sequence alignment in FASTA format with the full sequences of the supplied proteins intact. Preferably said server/program should be able to handle at least 20 input pdbs at once. I've been looking around, but have so far failed to find a program which does this. If anyone knows of a program or server which could handle this, I would be very grateful. Cheers, Ronnie Berntsson == | Mensur Dlakic, PhD| Tel: (406) 994-6576| | Department of Microbiology| Fax: (406) 994-4926| | Montana State University | Lab: (406) 994-6237| | 109 Lewis Hall, P.O. Box 173520 | http://myprofile.cos.com/mensur| | Bozeman, MT 59717-3520| E-mail: mdla...@montana.edu| ==
[ccp4bb] January 15, 2009 deadline- User proposal submission for Collaborative Crystallography at BCSB
Dear Users, The deadline for Mar/April 2010 Collaborative Crystallography proposals will be *January 15, 2009. * Through the Collaborative Crystallography Program (CC) at the Advanced Light Source (ALS), scientists can send protein crystals to Berkeley Center for Structural Biology (BCSB) staff researchers for data collection and analysis. The CC Program can provide a number of benefits to researchers: * Obtain high quality data and analysis through collaborating with expert beamline researchers; * Rapid turn around on projects; and * Reduced travel costs. To apply, please submit a proposal through the ALS General User proposal review process for beamtime allocation. Proposals are reviewed and ranked by the Proposal Study Panel, and beamtime is allocated accordingly. BCSB staff schedule the CC projects on Beamlines 5.0.1 and 5.0.2 to fit into the available resources. Only non-proprietary projects will be accepted. As a condition of participation, BCSB staff researchers who participate in data collection and/or analysis must be appropriately acknowledged - typically being included as authors on publications and in PDB depositions. Please consult the website for additional information at: http://bcsb.als.lbl.gov/wiki/index.php/Collaborative_Crystallography - How To Apply: To learn more, go to: http://www-als.lbl.gov/als/quickguide/independinvest.html To submit a proposal, go to: http://alsusweb.lbl.gov/. Scroll down to "*Structural Biology beamlines (includes protein SAXS)*" and click on "New Proposal." Enter your proposal information, with attention to the following details: * For question 3/First choice, select "5.0.1 (Monochromatic);" for question 3/Second choice, select "5.0.2 (MAD)." * Check box (yes) in response to question (7) "Do you want collaborative crystallography (beamline 5.0.1 or 5.0.2 only) * In question 4, please describe a specific research project with a clear end point. In order to request CC time for Mar/April 2010 allocation period, proposals must be submitted by *January 15, 2009.* The deadline for CC proposals for the time period May/June 2010 will be March 15, 2010. Regards, Banumathi Sankaran
[ccp4bb] Beamtime at the ALS
Dear All, January 15, 2010 is the deadline for the March/April 2010 Rapid Access Proposal cycle. All Berkeley Center for Structural Biology(BCSB) beamlines are equipped with ADSC Q315/Q315R detectors, automated sample changers and data collection software enabling high-throughput crystal screening and data collection. Remote data collection is available on all BCSB beamlines, providing the user with the full complement of sample visualization, sample manipulation, beamline control, data acquisition and data analysis tools exactly as they would see them if they were stationed at the beamline. This enhanced remote operation capability is coupled with 22hr onsite support by BCSB staff who are able to assist immediately with loading additional samples for remote users or troubleshoot any issues that might arise. Remote users can furthermore be kept up-to-date on changes in ring status via an SMS service (http://bcsb.als.lbl.gov/wiki/index.php/Ring_Status_Notifications_to_Cell_Phone) Specific features are summarized below. Beamlines 8.2.1 and 8.2.2: To facilitate studies on small crystals, a microdiffractometer was installed in the beamline 8.2.1 endstation. The new equipment allows precise sample positioning to within 2 microns, excellent sample viewing of very small crystals, and an off-axis crystal positioning stage. Both beamlines 8.2.1 and 8.2.2 feature a Rigaku sample changer (Actor), allowing remote operations to now be a routine mode of access for these beamlines. Beamlines 5.0.1, 5.0.2, 5.0.3: The Berkeley Automounter sample handling system has a routine capacity of 96 samples (6 pucks). In a typical high-throughput screening mode, the mount-to-mount time is around 2.5 minutes per sample, allowing users to screen a full puck within 45 minutes. The sector 5 beamline user stations are equipped with fully high-adjustable, ergonomically friendly work stations. Data analyses in the BCSB is facilitated by software maintained by sbgrid (http://www.sbgrid.org). A 16 core linux machine is available for our users to process their data and solve/refine their structure. An additional mode of access to the BCSB beamlines is through the Collaborative Crystallography (CC) Program. Users apply for beamtime via the general user program, and collaborate with an expert crystallographer who will conduct the experiments and data reduction on behalf of the researchers. Depending on the users, structure solution, model building and refinement can be carried out as well. Please contact bcsbbeamt...@lbl.gov for more information. Please visit http://bcsb.lbl.gov/ for more details about the Center and its beamlines. To find out more, click on: http://www.als.lbl.gov/als/quickguide/independinvest.html We invite you to submit a proposal at: http://alsusweb.lbl.gov/ Scroll down to "Structural Biology beamines (includes protein SAXS)." Click on "New Proposal." If you'd like to apply for May/June 2010 beamtime at the Advanced Light Source, please submit a General User proposal by March 15, 2010. If you have any questions or would like to request open beamtime, please e-mail bcsbbeamt...@lbl.gov. Please note that executed user agreements must be received by LBNL prior to beamtime. Proprietary fees, if applicable, must be received by LBNL at least five working days prior to scheduled beamtime. -- - P.H. Zwart Beamline Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org CCTBX: http://cctbx.sf.net -
