Re: [ccp4bb] WaterTidy fails in windows ccp4i
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Jacob, to semi-answer your question: coot runs under windows, as far as I know, but it may not be in the gui. Tim On 10/19/2011 08:41 PM, Jacob Keller wrote: Well, I see that it fixes/edits waters, but it seems to add them too, according to the documentation Add/Tidy Waters - Watertidy This task rationalises waters at the end of refinement. See program documentation: Watertidy, Distang. Is there a program in the gui that adds waters, if not this one? There is of course arp/warp, but not in windows... Jacob On Wed, Oct 19, 2011 at 1:32 PM, Ed Pozharski epozh...@umaryland.edu wrote: On Wed, 2011-10-19 at 12:45 -0500, Jacob Keller wrote: Is there an alternative water-picker in the gui? watertidy is not a water-picker -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFOn8jaUxlJ7aRr7hoRAtOiAKDHhyG1Vj4sZ0ohCOLqR2r0lfCrDgCcCwBI zTRQvZCUj4sFcN6RdduBj7U= =h0Fy -END PGP SIGNATURE-
Re: [ccp4bb] WaterTidy fails in windows ccp4i
Adding to Tim's comment. In Coot use: Extensions-Modelling-Arrange Waters Around Protein... B -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Jacob, to semi-answer your question: coot runs under windows, as far as I know, but it may not be in the gui. Tim On 10/19/2011 08:41 PM, Jacob Keller wrote: Well, I see that it fixes/edits waters, but it seems to add them too, according to the documentation Add/Tidy Waters - Watertidy This task rationalises waters at the end of refinement. See program documentation: Watertidy, Distang. Is there a program in the gui that adds waters, if not this one? There is of course arp/warp, but not in windows... Jacob On Wed, Oct 19, 2011 at 1:32 PM, Ed Pozharskiepozh...@umaryland.edu wrote: On Wed, 2011-10-19 at 12:45 -0500, Jacob Keller wrote: Is there an alternative water-picker in the gui? watertidy is not a water-picker -- I'd jump in myself, if I weren't so good at whistling. Julian, King of Lemurs - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFOn8jaUxlJ7aRr7hoRAtOiAKDHhyG1Vj4sZ0ohCOLqR2r0lfCrDgCcCwBI zTRQvZCUj4sFcN6RdduBj7U= =h0Fy -END PGP SIGNATURE- - No virus found in this message. Checked by AVG - www.avg.com Version: 2012.0.1831 / Virus Database: 2092/4562 - Release Date: 10/19/11
Re: [ccp4bb] Biological assembly
Hi, If, in your case, no possible asymmetric unit can contain A1-B2, then you deposit A1-B1 (or I suppose A2-B2...) and indicate to the PDB (like placing cards in the header cards) the operator to be used (and the subunit it applies to) in order to generate the most likely biological dimer. Normally the PDB can take care of that. Fred. Kayashree M wrote: Respected Sir, The space group is H3. if I generate the symmetry, it appears to be a dimer of trimers stacked one above the other with a rotation of 60 deg wrt each other, like this - A1, A2, A3 (in one trimer) stacked upon B1, B2, B3 (second trimer). So structure that is in the ASU is with A1-B1 while PISA predicts A1-B2. Thank you With Reagrds Kavya -CCP4 bulletin board CCP4BB@JISCMAIL.AC.UK wrote: - To: CCP4BB@JISCMAIL.AC.UK From: James Stroud Sent by: CCP4 bulletin board Date: 10/19/2011 10:41PM Subject: Re: [ccp4bb] Biological assembly On Oct 19, 2011, at 4:36 AM, Kayashree M wrote: We have a structure which is a homodimer in the asymmetric unit. PISA predicts most probable assembly as a dimer but this dimeric assembly is different from what is solved (offcourse we can generate the symmetry equivalent molecule and get that). This last sentence is a bit vague. Can you take the just dimer that PISA predicts, fit this dimer to the lattice (i.e. each monomer sitting correctly in density but retaining the dimeric relationship predicted by PISA), and then generate the complete lattice using just this fitted dimer and crystallographic symmetries? If so, that means that the PISA dimer is equivalent to the ASU you can deposit the PISA dimer as the ASU. James -- This message has been scanned for viruses and dangerous content by *MailScanner* http://www.mailscanner.info/, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by *MailScanner* http://www.mailscanner.info/, and is believed to be clean.
Re: [ccp4bb] Biological assembly
Thank you Sir for the suggestions. Hi,If, in your case, no possible asymmetric unit can contain A1-B2, then you deposit A1-B1 (or I suppose A2-B2...) and indicate to the PDB (like placing cards in the header cards) the operator to be used (and the subunit it applies to) in order to generate the most likely biological dimer. Normally the PDB can take care of that.The protein looks like the letter "C", So in one of the trimer it is arrangedas "C" while in the other trimer (stacked) it is arranged like "inverted C", SoThe dimer A1-B1 and A2-B2 are same while A1-B1 and A1-B2 are different.Thanking you With RegardsKavya-- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
Re: [ccp4bb] Biological assembly
I am sure someone has suggested this - you can submit your coordinates to the PISA server which will give you a detailed analysis of contacts, then you choose which grouping you think makes the most reasonable assemblyn and take the asymmetric unit from that . I actually like to do that while still refining - it makes coot a lot easier to use if you are working with a compact molecule! Eleanor t On 10/20/2011 05:25 AM, Kayashree M wrote: Respected Sir, The space group is H3. if I generate the symmetry, it appears to be a dimer of trimers stacked one above the other with a rotation of 60 deg wrt each other, like this - A1, A2, A3 (in one trimer) stacked upon B1, B2, B3 (second trimer). So structure that is in the ASU is with A1-B1 while PISA predicts A1-B2. Thank you With Reagrds Kavya -CCP4 bulletin boardCCP4BB@JISCMAIL.AC.UK wrote: - To: CCP4BB@JISCMAIL.AC.UK From: James Stroud Sent by: CCP4 bulletin board Date: 10/19/2011 10:41PM Subject: Re: [ccp4bb] Biological assembly On Oct 19, 2011, at 4:36 AM, Kayashree M wrote: We have a structure which is a homodimer in the asymmetric unit. PISA predicts most probable assembly as a dimer but this dimeric assembly is different from what is solved (offcourse we can generate the symmetry equivalent molecule and get that). This last sentence is a bit vague. Can you take the just dimer that PISA predicts, fit this dimer to the lattice (i.e. each monomer sitting correctly in density but retaining the dimeric relationship predicted by PISA), and then generate the complete lattice using just this fitted dimer and crystallographic symmetries? If so, that means that the PISA dimer is equivalent to the ASU you can deposit the PISA dimer as the ASU. James -- This message has been scanned for viruses and dangerous content by *MailScanner*http://www.mailscanner.info/, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by *MailScanner*http://www.mailscanner.info/, and is believed to be clean.
Re: [ccp4bb] Biological assembly
Respected Madam, Actually I was not aware of the fact that we have to deposit the structure which is most probablebiological assembly (since in PDB there are seperate representations for the asymmetric unit and biological unit).Also Since I dint have any experimental evidences other than PISA predictions and comparison with the structures from different organisms, I continues to refine the model PHASER predicted.In addition the PHASER refined model has 3 Cadmium ions inbetween the monomers stronglycoordinated by both the monomers. Hence I did not have any doubts upon this assembly. FinallyI submitted this assembly itself. and by mistake I mentioned most probably biological assemblysection while submitting the PDB, Which gave rise to all confusions.Thanking youWith RegardsM. Kavyashree-Eleanor Dodson c...@ysbl.york.ac.uk wrote: -To: Kayashree M ka...@ssl.serc.iisc.inFrom: Eleanor Dodson c...@ysbl.york.ac.ukDate: 10/20/2011 03:23PMCc: CCP4BB@JISCMAIL.AC.UKSubject: Re: [ccp4bb] Biological assemblyI am sure someone has suggested this - you can submit your coordinates to the PISA server which will give you a detailed analysis of contacts, then you choose which grouping you think makes the most reasonable assemblyn and take the asymmetric unit from that .I actually like to do that while still refining - it makes coot a lot easier to use if you are working with a compact molecule!Eleanort On 10/20/2011 05:25 AM, Kayashree M wrote: Respected Sir, The space group is H3. if I generate the symmetry, it appears to be a dimer of trimers stacked one above the other with a rotation of 60 deg wrt each other, like this - A1, A2, A3 (in one trimer) stacked upon B1, B2, B3 (second trimer). So structure that is in the ASU is with A1-B1 while PISA predicts A1-B2. Thank you With Reagrds Kavya -CCP4 bulletin boardCCP4BB@JISCMAIL.AC.UK wrote: - To: CCP4BB@JISCMAIL.AC.UK From: James Stroud Sent by: CCP4 bulletin board Date: 10/19/2011 10:41PM Subject: Re: [ccp4bb] Biological assembly On Oct 19, 2011, at 4:36 AM, Kayashree M wrote: We have a structure which is a homodimer in the asymmetric unit. PISA predicts most probable assembly as a dimer but this dimeric assembly is different from what is solved (offcourse we can generate the symmetry equivalent molecule and get that). This last sentence is a bit vague. Can you take the just dimer that PISA predicts, fit this dimer to the lattice (i.e. each monomer sitting correctly in density but retaining the dimeric relationship predicted by PISA), and then generate the complete lattice using just this fitted dimer and crystallographic symmetries? If so, that means that the PISA dimer is equivalent to the ASU you can deposit the PISA dimer as the ASU. James -- This message has been scanned for viruses and dangerous content by *MailScanner*http://www.mailscanner.info/, and is believed to be clean. -- This message has been scanned for viruses and dangerous content by *MailScanner*http://www.mailscanner.info/, and is believed to be clean.-- This message has been scanned for viruses anddangerous content by MailScanner, and isbelieved to be clean.-- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
Re: [ccp4bb] Biological assembly
Dear Bostjan, In case when ASU has the same multiplicity (number of chains) as the probable biological assembly, the latter is an ASU as well. In such a case, the PDB suggests to choose ASU in the form of that assembly, purely for simplicity. It seems to me that this is not an unreasonable suggestion and it would be nice if that were a common practice. Maybe I am misunderstanding what you are saying Eugene, but the ASU interface may not necessarily be the biological interface. Not at all. But if anticipated biological assembly has the same size as ASU, then one should be able to choose ASU such that it is biological assembly. Consider that, when there is more than 1 chain in ASU, its configuration may be chosen in many different ways (but not completely arbitrarily, of course). E.g., in case of heterodimeric ASU, _any_ hetero-pair of molecules in crystal is a valid ASU (even if they do not make a contact :)). By this I mean that, by applying all crystal symmetry operations and unit cell translations, one can reconstruct the whole crystal from an arbitrary hetero-pair. In case of homodimers it is slightly more complex, e.g. one has to exclude monomers in parallel orientations. I think it is perfectly possible that two subunits in a biological dimer, for example, may be related by crystallographic axis, but the NCS may be a different non-physiological crystal contact, therefore the ASU won't be the same as the biological dimer. So I am not sure if the above applies in general. I would think (am I wrong here?) that NCS-reduced PDB entries do not represent crystal's ASU (simply because they are reduced by _non-crystallographic_ symmetry operations). In order to get the ASU, one needs to apply NCS to the content of the entry. E.g., PDB entry 1stm has 5 chains, but they do not make an ASU: applying all space group symmetry operations would not reconstruct the crystal. NCS-expansion, however, gives a 60-chain viral capsid, which is the ASU. For fun, you may state that your ASU in this case is 2 complementing parts of neighbouring capsids, and this would be crystallographically correct. It is a matter of common sense (and sense of beauty perhaps) that we choose to deposit a complete viral capsid as an ASU here. Eugene. Bostjan Bostjan Kobe NHMRC Research Fellow Professor of Structural Biology School of Chemistry and Molecular Biosciences and Institute for Molecular Bioscience (Division of Chemistry and Structural Biology) and Centre for Infectious Disease Research Cooper Road University of Queensland Brisbane, Queensland 4072 Australia Phone: +61 7 3365 2132 Fax: +61 7 3365 4699 E-mail: b.k...@uq.edu.au URL: http://www.scmb.uq.edu.au/staff/bostjan-kobe Office: Building 76 Room 329 Notice: If you receive this e-mail by mistake, please notify me, and do not make any use of its contents. I do not waive any privilege, confidentiality or copyright associated with it. Unless stated otherwise, this e-mail represents only the views of the Sender and not the views of The University of Queensland.
[ccp4bb] Post-doc Position - Columbia University
A Postdoctoral Research Associate position is available for the structural studies on enzymes involved in fatty acid metabolism or proteins involved in pre-mRNA 3'-end processing. We have extensive experience in these areas, and have generated many high-impact publications. Please see my home page for more information- http://como.bio.columbia.edu/tong Strong experience in protein biochemistry is required. Prior experience with X-ray crystallography is desirable. Please send CV and names of three references to me by email. Prof. Liang Tong Department of Biological Sciences Columbia University New York, NY 10027 Email: lt...@columbia.edu
[ccp4bb] Laptop stereo
Dear All, I just bought a new laptop with the graphics card NVIDIA GeForce GTX 460M with 1.5GB memory. Unfortunately the stereo does not work with Coot (Windows or Linux). Can Anyone help me ? Thanks in advance, Claude.
Re: [ccp4bb] Laptop stereo
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Claude, why do you expect stereo to work with a laptop? Usually it requires special equipment, e.g. a shutter system or polarizing screen and goggles, like the Zalman 3D monitors. Maybe you want to let us know more about your setup. Tim On 10/20/2011 02:33 PM, Claude Didierjean wrote: Dear All, I just bought a new laptop with the graphics card NVIDIA GeForce GTX 460M with 1.5GB memory. Unfortunately the stereo does not work with Coot (Windows or Linux). Can Anyone help me ? Thanks in advance, Claude. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFOoBYKUxlJ7aRr7hoRAmTvAJ9pC5tPvhps3wL+jrf8O2F1Dpx3nwCgvVZD Ks5+gjvRMYeffNX1sYsobXg= =vEsw -END PGP SIGNATURE-
Re: [ccp4bb] Laptop stereo
There are a some models of laptop which contain a stereo-capable screen, but since the make model of the laptop were not mentioned, it is not clear that Claude's equipment is on that list. http://www.nvidia.com/object/3d-vision-system-requirements.html He also does not mention which OS he is running, which is the next question. On 10/20/11 08:37, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Claude, why do you expect stereo to work with a laptop? Usually it requires special equipment, e.g. a shutter system or polarizing screen and goggles, like the Zalman 3D monitors. Maybe you want to let us know more about your setup. Tim On 10/20/2011 02:33 PM, Claude Didierjean wrote: Dear All, I just bought a new laptop with the graphics card NVIDIA GeForce GTX 460M with 1.5GB memory. Unfortunately the stereo does not work with Coot (Windows or Linux). Can Anyone help me ? Thanks in advance, Claude. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFOoBYKUxlJ7aRr7hoRAmTvAJ9pC5tPvhps3wL+jrf8O2F1Dpx3nwCgvVZD Ks5+gjvRMYeffNX1sYsobXg= =vEsw -END PGP SIGNATURE- -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
[ccp4bb] OIST-CCP4 Final announcement
Dear Colleagues, This is the final call for applicants for the CCP4/OIST School on protein structure solution taking place in Okinawa, Japan from the 5th - 9th of December 2011. The closing deadline for applications is this coming Tuesday October 25th. There is no registration fee for the school. The students will be responsible for their own travel but lodging and food will be provided by the hosts. These and other details (The program, the list of speakers, the application process, accommodations, site access, contacts etc) can be found at the school website at: http://www.ccp4.ac.uk/schools/OIST-2011/ The program for the school can be directly viewed here: http://www.ccp4.ac.uk/schools/OIST-2011/OIST2011-program.pdf The school will include data processing, structure solution, model building, refinement, validation, automation of many steps etc. Participants are encouraged to bring their own raw data or processed data for hands-on problem solving under the guidance of software developers and other experts. Kind regards, Fadel, Garib and Charles
Re: [ccp4bb] Laptop stereo
There are several laptops which are compatible with the Nvidia 3D vision system. However, I only know of laptops with GeForce type cards, whereas Coot and Pymol require OpenGL and a Quadro graphics card to work in stereo. In fact, the hardware requirements for Windows (Vista and 7) are less strict than for Linux in that you can buy a less expensive card, but it still needs to be a Quadro. I've tried to interest the Coot windows developer to make a port of Coot from OpenGL stereo to DirectX stereo but that apparently it is not a straightforward proposition. So, for the moment (and until NVIDIA releases compatible drivers) that option is grayed out... Pedro At 14:01 20-10-2011, David Schuller wrote: There are a some models of laptop which contain a stereo-capable screen, but since the make model of the laptop were not mentioned, it is not clear that Claude's equipment is on that list. http://www.nvidia.com/object/3d-vision-system-requirements.html He also does not mention which OS he is running, which is the next question. On 10/20/11 08:37, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Claude, why do you expect stereo to work with a laptop? Usually it requires special equipment, e.g. a shutter system or polarizing screen and goggles, like the Zalman 3D monitors. Maybe you want to let us know more about your setup. Tim On 10/20/2011 02:33 PM, Claude Didierjean wrote: Dear All, I just bought a new laptop with the graphics card NVIDIA GeForce GTX 460M with 1.5GB memory. Unfortunately the stereo does not work with Coot (Windows or Linux). Can Anyone help me ? Thanks in advance, Claude. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFOoBYKUxlJ7aRr7hoRAmTvAJ9pC5tPvhps3wL+jrf8O2F1Dpx3nwCgvVZD Ks5+gjvRMYeffNX1sYsobXg= =vEsw -END PGP SIGNATURE- -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu Industry and Medicine Applied Crystallography Macromolecular Crystallography Unit ___ Phones : (351-21) 446-9100 Ext. 1669 (351-21) 446-9669 (direct) Fax : (351-21) 441-1277 or 443-3644 email : mat...@itqb.unl.pt http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit Mailing address : Instituto de Tecnologia Quimica e Biologica Apartado 127 2781-901 OEIRAS Portugal
Re: [ccp4bb] Laptop stereo
Hi Claude (and others), I guess you have an Stereo capable laptop (Geforce + 120hz Monitor)? At least the GeForce 460M is on the list for 3D-Vision. However, as the GeForce graphics cards are not able to support quad-buffered OpenGL (vierfach gebufferte OpenGL-Anwendungen), I don't think they will ever work with Coot and the same might be true for PyMol (http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg11320.html) and other 3D crystallographic programs. As far as I understand it's mostly, because the GeForce can only display 3D in fullscreen and not in single windows... (most likey due to driver restrictions). So, AFIAK there is no mobile 3D-platform available for crystallographers. Regards, Jan PS: If I'm wrong I would be happy to know! Am 20.10.2011, 15:01 Uhr, schrieb David Schuller dj...@cornell.edu: There are a some models of laptop which contain a stereo-capable screen, but since the make model of the laptop were not mentioned, it is not clear that Claude's equipment is on that list. http://www.nvidia.com/object/3d-vision-system-requirements.html He also does not mention which OS he is running, which is the next question. On 10/20/11 08:37, Tim Gruene wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Claude, why do you expect stereo to work with a laptop? Usually it requires special equipment, e.g. a shutter system or polarizing screen and goggles, like the Zalman 3D monitors. Maybe you want to let us know more about your setup. Tim On 10/20/2011 02:33 PM, Claude Didierjean wrote: Dear All, I just bought a new laptop with the graphics card NVIDIA GeForce GTX 460M with 1.5GB memory. Unfortunately the stereo does not work with Coot (Windows or Linux). Can Anyone help me ? Thanks in advance, Claude. - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.10 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFOoBYKUxlJ7aRr7hoRAmTvAJ9pC5tPvhps3wL+jrf8O2F1Dpx3nwCgvVZD Ks5+gjvRMYeffNX1sYsobXg= =vEsw -END PGP SIGNATURE- -- Dr. Jan Gebauer AG Prof. Baumann Institut für Biochemie / Uni-Köln Otto-Fischer-Str. 12-14 / 50674 Köln Fon: +49 (221) 470 3212 Fax: +49 (221) 470 5066
[ccp4bb] BioStruct-X Call for proposal submission for Transnational Access funding
On behalf of the BioStruct-X management team I would like to draw your attention to the following call for proposals: BioStruct – X Call for proposal submission for Transnational Access funding BioStruct-X is a state-of-the-art, coordinated, multi-site platform that supports access to established and emerging key methods in structural biology. Eleven facilities from across Europe provide installations for applications in small angle X-ray scattering (SAXS), macromolecular X-ray crystallography (MX), biological X-ray imaging (XI), and protein production and high-throughput crystallisation (PP and HTX). Participating facilities are: EMBL Hamburg, Hamburg, Germany (SAXS, MX, PP and HTX) EMBL Grenoble, Grenoble, France (MX, PP and HTX) SOLEIL, Saint Aubain, France (SAXS, MX, XI) Max-lab, Lund, Sweden (SAXS and MX) ALBA, Barcelona, Spain (MX and XI) DESY, Hamburg, Germany (MX and XI) Diamond, Didcot, United Kingdom (SAXS, MX, XI, PP and HTX) ELETTRA, Trieste, Italy (MX) HZB, Berlin, Germany (MX and XI) PSI, Villigen, Switzerland (MX, PP and HTX) UOXF, Oxford, United Kingdom (PP and HTX) BioStruct-X offers a unified portal for Block Allocation Group (BAG) project proposal application and evaluation. We encourage the formation of BAG consortia interested in using multiple technology platforms offered in BioStruct-X. The complete BioStruct-X proposal application will be carried out online. Electronic proposal application forms and detailed description of the facilities are available on BioStruct-X website (http://www.biostruct-x.eu/). * Note: Proposal submission will be possible after November 1st. BioStruct-X cooperates with the ESRFI project Instruct in providing an integrated and coordinated technology platform to all relevant methods in structural biology. BioStruct-X is funded by the Seventh Framework Programme (FP7) of the European Commission. For further information contact: Ivana Custic, BioStruct-X project manager tel: +49-40-89902-124 e-mail: biostru...@embl-hamburg.de
[ccp4bb] Dyndom errors
For some reason, Dyndom all of a sudden does not work (or the error lies between the monitor and keyboard). When I submit 2 PDB codes of nearly equal sequence identity, I get the sequence identity 40%. Now, if I try to upload my own files, I get the File not found error (when I know for sure that they are). Also, when the server doesn't give either of the above errors, I am left with an apache error. I've used this server many times to do the same type of analysis that I am having so much trouble with now. I also tried running the CCP4 embedded version, but get a segmentation fault error, and the program won't advance. Has anyone else encountered these errors? Perhaps the server is under maintenance? Any help is greatly appreciated! Best, jason porta
Re: [ccp4bb] Biological assembly
Since a crystallographic 3-fold generates the trimer (of dimers) then A1-B2 can be the ASU in this case.Just generate the symmetry mates with the A1-B1 dimer and then make a new PDB of A1-B2 then generate the symmetry mates of A1-B2 to see that the lattice is complete.I compulsively made and attached an illustration to show what I mean.James H3.pdf Description: Adobe PDF document On Oct 20, 2011, at 3:40 AM, Kayashree M wrote:Thank you Sir for the suggestions. Hi,If, in your case, no possible asymmetric unit can contain A1-B2, then you deposit A1-B1 (or I suppose A2-B2...) and indicate to the PDB (like placing cards in the header cards) the operator to be used (and the subunit it applies to) in order to generate the most likely biological dimer. Normally the PDB can take care of that.The protein looks like the letter "C", So in one of the trimer it is arrangedas "C" while in the other trimer (stacked) it is arranged like "inverted C", SoThe dimer A1-B1 and A2-B2 are same while A1-B1 and A1-B2 are different.Thanking you With RegardsKavya-- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.
Re: [ccp4bb] IUCr committees, depositing images
John Helliwell points out to me that it might be useful to know what MX crystallographic data researchers in different countries are already expected to deposit or save. He notes that research funding agencies in the UK expect researchers to preserve their raw experimental data for at least 5 years. Can people comment on what data they are already expected to save in their countries, and what mechanisms they already have for facilitating this (for example the Australian Research Council TARDIS initiative which helps store raw diffraction images)? If you want to see or post comments on this thread on the IUCR Forum you can do that at: http://forums.iucr.org/viewforum.php?f=21 Also of course posts here on this mailing list are fine. -Tom T
Re: [ccp4bb] How can improve diffraction quality
An excellent review of this subject was published not long ago: http://dx.doi.org/10.1107/S0907444905032130 It is even open access! But, in general the trick to improving diffraction is to get your molecules clean, get them to all adopt the same conformation, and then sit still. Adding a column (even if you think your prep is clean) can help, as can fractional recrystallization. Not many people know this, but even the much maligned hen egg white lysozyme doesn't diffract very well if the prep is contaminated with lysozyme dimers, which is why commercial lysozyme is purified by fractional recrystallization. There is a heat-shock treatment described in the above paper, and of course additive screens. The reason why additive screens work seems to be because if you can get something to stick to the protein, it is more likely to sit still. -James Holton MAD Scientist On 10/18/2011 4:45 AM, Afshan Begum wrote: Dear ccp4 user I am facing one crucial problem regarding diffraction. Actually the size of my crystal is good enough 0.5mm but it was diffracted only 4 A. The conditions of crystallization recipes are 4.5% PEG 1000, 0.1M Tris and 25mM Na citrate. I really need your suggestions regarding how can i improve my diffraction quality? Your support is highly appreciable. Best Regards AFSHAN
