Re: [ccp4bb] Off-topic - Domain termini for construct design
Hi - I do not think there are rules. There is a logic, to never truncate within secondary structure elements, and to prefer to delete regions that have a high probability to be disordered. With excuses for the non-ccp4 plugin, you can use our web server to help you design these. http://xtal.nki.nl/ccd/Welcome.html A. On Mar 10, 2010, at 12:45, Claudia Scotti wrote: Dear All, I'd like to espress a protein for crystallisation as a whole, but also to try separate expression of its two domains. Although prediciting domain boundaires is not difficult, I know that it is worthwhile testing several constructs to improve espression in soluble form. In several works I've seen that the choice is to keep or give up some aminoacids (for example 4 or 5) at the N and/or C- termini and to test them to see which expresses best. I was wondering if there are defined rules to choose these variants and/or to modify the N and C termini of a protein of interest when it is not important to keep them true (=native) in order to optimise expression levels. Is there any good reference about this, please? Personal experiences are welcome. Many thanks, Claudia Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 Hotmail: Free, trusted and rich email service. Get it now. P please don't print this e-mail unless you really need to Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791
[ccp4bb] arp_warp 7.1 and CCP4 6.1.3
Hi. I don't know whether other people had this problem, but I've tried to install arp_warp 7.1 with CCP4 6.1.3 and the installation failed because the refmac version is 5.5.0109. There's a conditional branch in the installation script that extracts the 0109 from this and does not like the leading zero. Solution (to be tried): re-compile refmac5 changing the version number to 5.5.109 Pedro Matias
Re: [ccp4bb] Off-topic - Domain termini for construct design
Hello Claudia, have you thought of, instead of rules, using restricted proteolysis combined with N-terminal sequencing in order to better estimate a good position at least for the N-terminal part of your protein? Tim On Thu, Mar 11, 2010 at 09:26:53AM +0100, Anastassis Perrakis wrote: Hi - I do not think there are rules. There is a logic, to never truncate within secondary structure elements, and to prefer to delete regions that have a high probability to be disordered. With excuses for the non-ccp4 plugin, you can use our web server to help you design these. http://xtal.nki.nl/ccd/Welcome.html A. On Mar 10, 2010, at 12:45, Claudia Scotti wrote: Dear All, I'd like to espress a protein for crystallisation as a whole, but also to try separate expression of its two domains. Although prediciting domain boundaires is not difficult, I know that it is worthwhile testing several constructs to improve espression in soluble form. In several works I've seen that the choice is to keep or give up some aminoacids (for example 4 or 5) at the N and/or C-termini and to test them to see which expresses best. I was wondering if there are defined rules to choose these variants and/or to modify the N and C termini of a protein of interest when it is not important to keep them true (=native) in order to optimise expression levels. Is there any good reference about this, please? Personal experiences are welcome. Many thanks, Claudia Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 Hotmail: Free, trusted and rich email service. Get it now. P please don't print this e-mail unless you really need to Anastassis (Tassos) Perrakis, Principal Investigator / Staff Member Department of Biochemistry (B8) Netherlands Cancer Institute, Dept. B8, 1066 CX Amsterdam, The Netherlands Tel: +31 20 512 1951 Fax: +31 20 512 1954 Mobile / SMS: +31 6 28 597791 -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
Re: [ccp4bb] arp_warp 7.1 and CCP4 6.1.3
know-it-all Oh dear, arp warp still has not learned counting then? /know-it-all On Thu, Mar 11, 2010 at 08:42:38AM +, Pedro M. Matias wrote: Hi. I don't know whether other people had this problem, but I've tried to install arp_warp 7.1 with CCP4 6.1.3 and the installation failed because the refmac version is 5.5.0109. There's a conditional branch in the installation script that extracts the 0109 from this and does not like the leading zero. Solution (to be tried): re-compile refmac5 changing the version number to 5.5.109 Pedro Matias -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A signature.asc Description: Digital signature
Re: [ccp4bb] arp_warp 7.1 and CCP4 6.1.3
The attached modified install script strips off leading zeroes Phil (change name -sh to .sh) install_csh-sh Description: Binary data On 11 Mar 2010, at 08:42, Pedro M. Matias wrote: Hi. I don't know whether other people had this problem, but I've tried to install arp_warp 7.1 with CCP4 6.1.3 and the installation failed because the refmac version is 5.5.0109. There's a conditional branch in the installation script that extracts the 0109 from this and does not like the leading zero. Solution (to be tried): re-compile refmac5 changing the version number to 5.5.109 Pedro Matias
Re: [ccp4bb] crystallization plates and robotics
Hi, I have used the Art Robbins hydra to transfer reagents from deep well block to crystallisation plate, prior to using a mosquito to setup the drops. Assuming they are still available (this was about 4 yrs ago) the hydra was robust and easy to use. HTH, Dave -- Delivered via an Android. On Mar 11, 2010 5:55 AM, Engin Ozkan eoz...@stanford.edu wrote: Hi, everybody, We recently recognized a problem with our Innovaplate SD-2 (a.k.a. MRC 2-Well) plates from Hampton. Our last batch of Innovaplates have an inconsistent well height such that our crystallization robot (a Mosquito) cannot put protein in all the wells. When tested with an older Innovaplate or a hanging drop cover, everything was fine. Is anybody else observing this? I heard that European customers might be getting the same plates from a different source/manufacturing facility. If that is the case, from which company do you buy these plates? Another question is about 96-channel pipetting equipment: For experiments unrelated to crystallography I am in need of getting a 96-channel pipetting machine, such as Rainin's Liquidator. I am also hoping to use this for transferring crystallization screens from blocks into crystallization trays (Our robot sets up only the drops, but does not transfer large volumes of crystallization solutions). Does anybody use the Liquidator for crystallization reagent transfers, and if you do so, would you recommend it? I am open to any brand/model, so all suggestions are welcome. Thanks, Engin -- Engin Özkan Post-doctoral Scholar Laboratory of K. Christopher Garcia Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111
Re: [ccp4bb] arp_warp 7.1 and CCP4 6.1.3
Dear Pedro, This was fixed in ARP/wARP version 7.1 in January this year. We informed all who downloaded the software before the fix, but perhaps missed you. Just go now to www.arp-warp.org, download the package and install - everything should be fine. Best regards, Victor Pedro M. Matias wrote: Hi. I don't know whether other people had this problem, but I've tried to install arp_warp 7.1 with CCP4 6.1.3 and the installation failed because the refmac version is 5.5.0109. There's a conditional branch in the installation script that extracts the 0109 from this and does not like the leading zero. Solution (to be tried): re-compile refmac5 changing the version number to 5.5.109 Pedro Matias
[ccp4bb] Help regarding installation of CCP4 package
Dear all, I want to install the CCP4 package for our research studies in our lab system( 2GB RAM, 250 HD, windows server). But confused about the various versions like CCP4 for Linux OS and Windows OS . Please inform about the details of both versions. I have queries like, which one have all the modules and which one have user friendly nature. Please clear my doubts and inform me as soon as possible. It will help me to install in server. waiting for your valuable reply. Thanks in advance. With Regards, Gowriishankar Raju
[ccp4bb] AW: [ccp4bb] Off-topic - Domain termini for construct design
Dear Claudia, Though not a fixed rule, here are a few general things that we consider: - N- and C-termini of homologs (eg from BLAST) - Secondary structure predictions - Disorder prediction (eg disembl or grooms servers) - Limited proteolysis to experimentally detect floppy ends Try to accumulate as much information as possible to guide your construct design. In case of limited proteolysis: sometimes the truncated pieces are too short to be revealed on an SDS-PAGE. You may need mass spec to reveal cutting. Mit freundlichen Grüßen / Kind regards, Dr. Alexander Pautsch Boehringer Ingelheim Pharma GmbH Co. KG A Leitstrukturfindung Tel.: +49 (7351) 54-4683 Fax: +49 (7351) 54-97924 mailto:alexander.paut...@boehringer-ingelheim.com mailto:alexander.paut...@boehringer-ingelheim.com Boehringer Ingelheim Pharma GmbH Co. KG, Sitz: Ingelheim am Rhein; Registergericht Mainz: HR A 22206; Komplementär Boehringer Ingelheim Deutschland GmbH; Geschäftsführung: Dr. Engelbert Günster (Vorsitzender), Ralf Gorniak, Felix Gutsche, Mark Hagmann, Dr. Martin Wanning; Vorsitzender des Aufsichtsrates: Engelbert Tjeenk Willink; Sitz: Ingelheim am Rhein; Registergericht Mainz: HR B 23260 Diese E-Mail ist vertraulich zu behandeln. Sie kann besonderem rechtlichen Schutz unterliegen. Wenn Sie nicht der richtige Adressat sind, senden Sie bitte diese E-Mail an den Absender zurück, löschen die eingegangene E-Mail und geben den Inhalt der E-Mail nicht weiter. Jegliche unbefugte Bearbeitung, Nutzung, Vervielfältigung oder Verbreitung ist verboten. / This e-mail is confidential and may also be legally privileged. If you are not the intended recipient please reply to sender, delete the e-mail and do not disclose its contents to any person. Any unauthorized review, use, disclosure, copying or distribution is strictly prohibited. Von: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] Im Auftrag von Claudia Scotti Gesendet: Mittwoch, 10. März 2010 12:46 An: CCP4BB@JISCMAIL.AC.UK Betreff: [ccp4bb] Off-topic - Domain termini for construct design Dear All, I'd like to espress a protein for crystallisation as a whole, but also to try separate expression of its two domains. Although prediciting domain boundaires is not difficult, I know that it is worthwhile testing several constructs to improve espression in soluble form. In several works I've seen that the choice is to keep or give up some aminoacids (for example 4 or 5) at the N and/or C-termini and to test them to see which expresses best. I was wondering if there are defined rules to choose these variants and/or to modify the N and C termini of a protein of interest when it is not important to keep them true (=native) in order to optimise expression levels. Is there any good reference about this, please? Personal experiences are welcome. Many thanks, Claudia Claudia Scotti Dipartimento di Medicina Sperimentale Sezione di Patologia Generale Universita' di Pavia Piazza Botta, 10 27100 Pavia Italia Tel. 0039 0382 986335/8/1 Facs 0039 0382 303673 Hotmail: Free, trusted and rich email service. Get it now. https://signup.live.com/signup.aspx?id=60969
Re: [ccp4bb] crystallization plates and robotics
Engin-- We have used the Cybi-Well robot for daughtering from the deep well masterblocks into our crystallization trays for several years and really like it. It is made by Cy-Bio. HTH! annie Annie Hassell Glaxo Smithkline 5 Moore Drive RTP, NC 27709 919/483-3228 919/483-0368 (FAX) annie.m.hass...@gsk.com Engin Ozkan eoz...@stanford.edu Sent by: CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK 11-Mar-2010 00:55 Please respond to Engin Ozkan eoz...@stanford.edu To CCP4BB@JISCMAIL.AC.UK cc Subject [ccp4bb] crystallization plates and robotics Hi, everybody, We recently recognized a problem with our Innovaplate SD-2 (a.k.a. MRC 2-Well) plates from Hampton. Our last batch of Innovaplates have an inconsistent well height such that our crystallization robot (a Mosquito) cannot put protein in all the wells. When tested with an older Innovaplate or a hanging drop cover, everything was fine. Is anybody else observing this? I heard that European customers might be getting the same plates from a different source/manufacturing facility. If that is the case, from which company do you buy these plates? Another question is about 96-channel pipetting equipment: For experiments unrelated to crystallography I am in need of getting a 96-channel pipetting machine, such as Rainin's Liquidator. I am also hoping to use this for transferring crystallization screens from blocks into crystallization trays (Our robot sets up only the drops, but does not transfer large volumes of crystallization solutions). Does anybody use the Liquidator for crystallization reagent transfers, and if you do so, would you recommend it? I am open to any brand/model, so all suggestions are welcome. Thanks, Engin -- Engin Özkan Post-doctoral Scholar Laboratory of K. Christopher Garcia Howard Hughes Medical Institute Dept of Molecular and Cellular Physiology 279 Campus Drive, Beckman Center B173 Stanford School of Medicine Stanford, CA 94305 ph: (650)-498-7111
[ccp4bb] Crystallography course
Dear All, Attached is information about a new X-ray crystallography training program being introduced at Pennsylvania State University. Kindly pass it along to anybody that may be interested in such an oppurtunity. Thank you Neela attachment: AD 3-10-10 Xray -2.gif
[ccp4bb] I 1 21 1 and C1 21 1 in CCP4
Dear All, I may be asking a dumb question and if so I apologize. I have a ~200 amino acid N-terminal 'arm' of a full protein (C-term already solved) that diffracts to ~2.1A. It integrates nicely in C2 and gives good molecular replacement models from Balbes in C121, 1I21, A121, C1211 and I1211 (90% certain). Phaser gives nice hits in C2 and I2 but I have not been able to get it to accept the C1211 or I1211. It appears from refining the data that my solution is either C1211 or more probably I1211 unfortunately I am having problems using these two groups. In addition to this I also have some evidence of twinning L Molrep and Refmac will accept the I1211 and C1211 groups but the freer and uniquify components after Scala will not. I've used reindex with the space group as is, in brackets, and in the 'I 1 21 1' notation all to no avail. My refinements have been forced to use the mtz files output by the Balbes server which loose 50% completeness in these two cases. My current R and Rfree with this data are 27% and 38% and the overall chain that I have built is in good agreement with one of the SAXS envelopes I have, but the data completeness issue is causing me problems. Has anyone come across this, do I need to add a symm group to the existing groups? I seem to remember some issues with these a few years back but that part of my brain is too dusty at present! Thanks for any help and hopefully I will not be hitting my head against the wall with the obvious. Cheers, Eddie Edward Snell Ph.D. Assistant Prof. Department of Structural Biology, SUNY Buffalo, Hauptman-Woodward Medical Research Institute 700 Ellicott Street, Buffalo, NY 14203-1102 Phone: (716) 898 8631 Fax: (716) 898 8660 Skype: eddie.snell Email: esn...@hwi.buffalo.edu Telepathy: 42.2 GHz Heisenberg was probably here!
Re: [ccp4bb] I 1 21 1 and C1 21 1 in CCP4
Hi Edward There's no difference between any of the space groups you mention in terms of which is right or wrong, they are all equivalent: for the purposes of solving refining the structure it makes absolutely no difference which one is chosen. A2, C2 and I2 differ only in the unit cell and the indexing. The convention is to choose the one that gives beta as close to 90 as possible (but =90). In all cases b is chosen as the unique axis and c = a. But that is only a convention which ensures that if you determine the structure of an isomorphous crystal you will always get the same setting, which just makes it easier to determine that they are isomorphous. 'C121' (or 'C 2' or 'C 1 2 1') and 'I121' (or 'I 2' or 'I 1 2 1') are simply alternative names for 'C2' and 'I2'; if the program doesn't accept them it just means the other names haven't been programmed. I've never understood the rationale for the longer names, I think it was supposed to make the names unique, but provided you stick with the conventional settings (and in the vast majority of cases there's no reason not to), the short names are already unique without having the extra '1's and spaces. It seems to me that having the option of adding '1' spaces just adds to the confusion and leads to the exact problem you have encountered! Finally, 'C21' or 'C1211' or 'I21' or 'I1211' (or the versions with embedded spaces) are just origin-shifted non-conventional settings of C2 and I2; again it's very unlikely you would have a good reason to use them. Personally I would just stick with C2 or I2! Cheers -- Ian On Thu, Mar 11, 2010 at 6:07 PM, Edward Snell esn...@hwi.buffalo.edu wrote: Dear All, I may be asking a dumb question and if so I apologize. I have a ~200 amino acid N-terminal ‘arm’ of a full protein (C-term already solved) that diffracts to ~2.1A. It integrates nicely in C2 and gives good molecular replacement models from Balbes in C121, 1I21, A121, C1211 and I1211 (90% certain). Phaser gives nice hits in C2 and I2 but I have not been able to get it to accept the C1211 or I1211. It appears from refining the data that my solution is either C1211 or more probably I1211 unfortunately I am having problems using these two groups. In addition to this I also have some evidence of twinning L Molrep and Refmac will accept the I1211 and C1211 groups but the freer and uniquify components after Scala will not. I’ve used reindex with the space group as is, in brackets, and in the ‘I 1 21 1’ notation all to no avail. My refinements have been forced to use the mtz files output by the Balbes server which loose 50% completeness in these two cases. My current R and Rfree with this data are 27% and 38% and the overall chain that I have built is in good agreement with one of the SAXS envelopes I have, but the data completeness issue is causing me problems. Has anyone come across this, do I need to add a symm group to the existing groups? I seem to remember some issues with these a few years back but that part of my brain is too dusty at present! Thanks for any help and hopefully I will not be hitting my head against the wall with the obvious. Cheers, Eddie Edward Snell Ph.D. Assistant Prof. Department of Structural Biology, SUNY Buffalo, Hauptman-Woodward Medical Research Institute 700 Ellicott Street, Buffalo, NY 14203-1102 Phone: (716) 898 8631 Fax: (716) 898 8660 Skype: eddie.snell Email: esn...@hwi.buffalo.edu Telepathy: 42.2 GHz Heisenberg was probably here!
Re: [ccp4bb] I 1 21 1 and C1 21 1 in CCP4
Hi Edward I don't understand, provided the MR program is doing its job, in this case there are no alternative choices for the space group; all the alternative space groups are equivalent and should refine equally well after MR - if they don't there's something badly wrong with your original data. There's no need to test for alternative space groups in this case for the simple reason that there aren't any alternatives! (it's not like orthorhombic where you may need to test for P222, P2221 etc). The space group should have already been determined when you processed the data and there's no need to change it, assuming of course the correct space group is not centered monoclinic at all, but is say P21, or some orthorhombic space group - maybe that is your problem? The only reason to change it would be if the MR program doesn't recognise the name because it hasn't been programmed, in which case you might have to change the name 'C121' or 'C 1 2 1' to 'C2' using mtzutils. However from what you say the space group was set to C2 in the processing so there's no need to change it for the MR or refinement. I don't understand why the MR program is trying alternative space groups in this case, since it's completely unnecessary! Shifting the origin only becomes an issue if you want to compare your structure with a previously determined isomorphous one: it sounds like this is not your problem (at least not yet!). Cheers -- Ian On Thu, Mar 11, 2010 at 7:40 PM, Edward Snell esn...@hwi.buffalo.edu wrote: Thanks Ian, It seems as if Balbes does something to the input data (mtz file) looking at the mtzdump. I think it runs reindex (with the 50% loss in completeness). Unfortunately my molecular replacement solution that refines well is one of these origin shifted groups With C2 I have 4 choices including the original (basically the ones you mentioned). I've been fortunate and never had to shift origin before and never come across this. Is there an easy way to do this with my data, i.e. what program should I make use of? Again, I apologize if this is a dumb question, it's embarrassing as I've been doing this for more years than I can remember and just hit the brick wall here. Cheers, Eddie -Original Message- From: Ian Tickle [mailto:ianj...@gmail.com] Sent: Thursday, March 11, 2010 2:10 PM To: Edward Snell Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] I 1 21 1 and C1 21 1 in CCP4 Hi Edward There's no difference between any of the space groups you mention in terms of which is right or wrong, they are all equivalent: for the purposes of solving refining the structure it makes absolutely no difference which one is chosen. A2, C2 and I2 differ only in the unit cell and the indexing. The convention is to choose the one that gives beta as close to 90 as possible (but =90). In all cases b is chosen as the unique axis and c = a. But that is only a convention which ensures that if you determine the structure of an isomorphous crystal you will always get the same setting, which just makes it easier to determine that they are isomorphous. 'C121' (or 'C 2' or 'C 1 2 1') and 'I121' (or 'I 2' or 'I 1 2 1') are simply alternative names for 'C2' and 'I2'; if the program doesn't accept them it just means the other names haven't been programmed. I've never understood the rationale for the longer names, I think it was supposed to make the names unique, but provided you stick with the conventional settings (and in the vast majority of cases there's no reason not to), the short names are already unique without having the extra '1's and spaces. It seems to me that having the option of adding '1' spaces just adds to the confusion and leads to the exact problem you have encountered! Finally, 'C21' or 'C1211' or 'I21' or 'I1211' (or the versions with embedded spaces) are just origin-shifted non-conventional settings of C2 and I2; again it's very unlikely you would have a good reason to use them. Personally I would just stick with C2 or I2! Cheers -- Ian On Thu, Mar 11, 2010 at 6:07 PM, Edward Snell esn...@hwi.buffalo.edu wrote: Dear All, I may be asking a dumb question and if so I apologize. I have a ~200 amino acid N-terminal 'arm' of a full protein (C-term already solved) that diffracts to ~2.1A. It integrates nicely in C2 and gives good molecular replacement models from Balbes in C121, 1I21, A121, C1211 and I1211 (90% certain). Phaser gives nice hits in C2 and I2 but I have not been able to get it to accept the C1211 or I1211. It appears from refining the data that my solution is either C1211 or more probably I1211 unfortunately I am having problems using these two groups. In addition to this I also have some evidence of twinning L Molrep and Refmac will accept the I1211 and C1211 groups but the freer and uniquify components after Scala will not. I've used reindex with the space group as is, in brackets, and in the 'I 1 21 1'
[ccp4bb] pdb file deposition
Dear All, In depositing a pdb file, after validation step, an error comes up: *Solvent Atoms* The following solvent molecules lie farther than expected from the protein. Can any one give me some advice about it? deleting these water molecules results in a large increase of R factor, by the way. Thank you in advance, A
Re: [ccp4bb] pdb file deposition
Probably, you have built water molecules that are associated with symmetry-related macromolecules rather than the host molecule. Turn symmetry on, check the nearest neighbors of the offending waters, and move the waters close to the host molecule if appropriate. I believe you can do this with the CCP4 program watertidy. kmj On Thu, Mar 11, 2010 at 12:15 PM, Azadeh Shahsavar azadeh.shahsa...@gmail.com wrote: Dear All, In depositing a pdb file, after validation step, an error comes up: *Solvent Atoms* The following solvent molecules lie farther than expected from the protein. Can any one give me some advice about it? deleting these water molecules results in a large increase of R factor, by the way. Thank you in advance, A
[ccp4bb] Graduate Course on Neutrons in Structural Biology - Dead line for application extended to March 31, 2010
Dear colleagues, We are organizing a course focusing on neutron techniques used in structural biology. The course is designed for graduate students with knowledge of protein function and structure but no or limited experience of neutron sciences. Date: June 7 - June 11, 2010 Location: Oak Ridge, Tennessee, USA Deadline for application: March 31, 2010 Subjects include: - Crystallography - Small Angle Scattering - Reflectometry - Spectroscopy - Imaging - Labeling techniques Invited speakers: - Zimei Bu, Fox Chase Cancer center, Philadelphia, Pa - Tonya Kuhl, University of California, Davis, Ca - Robert McKenna, University of Florida, Gainesville, Fl - Douglas Tobias, University of California, Irvine, Ca Lecturers include: - John Ankner - Hassina Bilheux - Leighton Coates - Ken Herwig - William Heller - For a Meilleur - Kevin Weiss A maximum of 15 participants will be selected to attend the course. For more details contact Flora Meilleur (meille...@ornl.govmailto:meille...@ornl.gov) or visit: http://neutrons.ornl.gov/conf/gcnb2010 Best regards, Flora Meilleur Flora Meilleur Assistant Professor Molecular Structural Biochemistry N C State University Neutron Scattering Sciences Division Oak Ridge National Laboratory Phone: 865-241-2897
[ccp4bb] March 15, 2010 deadline- User proposal submission for Collaborative Crystallography at BCSB
Dear Users, The deadline for May/June 2010 Collaborative Crystallography proposals will be *Mar 15, 2010. * 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/becomealsuser.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 May/June 2010 allocation period, proposals must be submitted by *March 15, 2010.* The deadline for CC proposals for the time period July/August 2010 will be May 15, 2010. Regards, Banumathi Sankaran
Re: [ccp4bb] Nvidia 3D vision + 1920x1080 Desktop Displays
I would like to draw your attention: Do not rush to set these up now. There are many problems with quadro card and 3D vision kit running on linux. We are wasting a lot of time to work out solutions. Cheers Aidong On Mar 3, 2010, at 11:50 PM, Christian Rausch wrote: Hello, is someone using Nvidia 3D vision + a compatible 1920x1080 23.5 Desktop Display e.g. ACER GD245HQ 120 Hz LCD display OR Alienware OptX AW2310 120 Hz LCD display? Is it running nicely with Linux + Nvidia's Linux driver? How is the stereo quality compared to Zalman's 3D-LCDs or the old CrystalEyes shutter glasses + CRT monitor? Thank you, Christian Rausch -- Dr. Christian Rausch rau...@wzw.tum.de Lehrstuhl f. Biologische Chemie Phone: +49 (0)8161 71-4050 Technische Universitaet MuenchenFax: -4352 85350 Freising-Weihenstephan Germany http://www.wzw.tum.de/bc
