Re: [ccp4bb] 3D fitting
In ccp4i select Coordinate utilities/Superpose And then on the first menu select Superpose using secondary structure matching. It will automatically superpose based on fold rather than atom alignment. (This is the same software as used at the EBI for what used to be called MSDfold). Miri Hirshberg wrote: Sun., Jan. 17th 2010 EBI Greetings, I am looking for a 3D structure superposition program which takes two structures and superpose them based only on the coordinates X,Y,Z regardless of of residue/atoms name. (both files are in PDB format) Thanks Miri Dr Miri Hirshberg European Bioinformatics Institute UK PDBe - EBI -EMBL http://www.ebi.ac.uk/pdbe Phone: +44 (0) 1223 492647 FAX: +44 (0) 1223 494468
Re: [ccp4bb] verifying a molecular replacement solution (test case where the true structure is known)
reforigin http://www.ccp4.ac.uk/dist/html/reforigin.html Does exactly what you want, but requires that the 2 PDB files have the same atoms - the CAONLY option can help with missing atoms, but it still won't work unless you have mutated your search model to the target sequence. solution_check A utility from the Balbes package, included as a stand-alone binary in the latest ccp4. Alternative origins are documented in: http://www.ccp4.ac.uk/dist/html/alternate_origins.html HTH Martyn On Mon, 2010-01-18 at 11:47 +0900, Francois Berenger wrote: Hello, 1) In the case I know the true structure (I am verifying I use Phaser correctly), is there a program to do so? Some other questions, if I am to write this program by myself: 2) is there a list somewhere of the translation ambiguities for each spacegroup? For example, in P1 it would say me any translation on any axis is fine. 3) is there a list of permissible origins for each space group? For example, in P212121 it would say me there are 8 possible choices and list them for me. I already know of symop.lib, but I don't think it has some of the information I am looking for. I also know the csymmatch example program of the clipper library, it does part of what I intend to do. Thanks a lot, Francois. -- *** * * * Dr. Martyn Winn * * * * STFC Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, U.K. * * Tel: +44 1925 603455E-mail: martyn.w...@stfc.ac.uk* * Fax: +44 1925 603825Skype name: martyn.winn * * URL: http://www.ccp4.ac.uk/martyn/ * ***
[ccp4bb] SCA
Dear all, Does anyone have the current (or old) version of SCA? (SCA: statistical coupling analysis) It should be as a toolbox of Matlab software. Thank you in advance, Azadeh
Re: [ccp4bb] verifying a molecular replacement solution (test case where the true structure is known)
Alternative origins are documented in: http://www.ccp4.ac.uk/dist/html/alternate_origins.html Note that this list makes no distinction between alternate origins and symmetry-equivalent origins. In principle, for any space group, any completely arbitrary alternate origin is permissible, all you need to do is expand the structure to P1, shift the co-ords to any arbitrary origin and off you go. It will of course mean that the symmetry elements are no longer where you expect them to be from ITC-A! In many cases the structure factor program does a partial expansion to a sub-group (maybe P1) because the SF formulae that it has coded are for a limited selection of space groups (I'm thinking specifically about SFALL, possibly other programs have a much more complete set of SF formulae coded). We try to avoid doing the full expansion because we want to take advantage of the symmetry as far as possible to minimise the computation time (though that's hardly an issue with modern computers). What this means is that only the alternate origins listed are consistent with the SF formula that the program is using for the specific space group that it uses for the calculation. However in addition, for centred space groups (A,B,C,F,I,R) some of the alternate origins will be equivalent, in that the SFs calculated using those origin shifts will be identical in both amplitude and phase so that the electron density maps will be identical, and no origin shift is needed if you want to overlay them (it may be that you still need to apply a space-group symmetry operator in order to overlay the atomic co-ordinates, but this won't change the SFs). For non-equivalent alternate origins only the calculated amplitudes are invariant, the phases are not, so that the maps will look completely different unless you apply the appropriate origin shift. For example in P212121 (0,0,0) and (1/2,1/2,1/2) are non-equivalent alternate origins (there are 8 in all) if the program uses the standard factorised SF formula for P212121, whereas in I222 these two are equivalent (so there are only 4 non-equivalent). Similar considerations apply to C222 (4 non-equivalent origins) and F222 (2) but the table above makes no such distinction. Cheers -- Ian Disclaimer This communication is confidential and may contain privileged information intended solely for the named addressee(s). It may not be used or disclosed except for the purpose for which it has been sent. If you are not the intended recipient you must not review, use, disclose, copy, distribute or take any action in reliance upon it. If you have received this communication in error, please notify Astex Therapeutics Ltd by emailing i.tic...@astex-therapeutics.com and destroy all copies of the message and any attached documents. Astex Therapeutics Ltd monitors, controls and protects all its messaging traffic in compliance with its corporate email policy. The Company accepts no liability or responsibility for any onward transmission or use of emails and attachments having left the Astex Therapeutics domain. Unless expressly stated, opinions in this message are those of the individual sender and not of Astex Therapeutics Ltd. The recipient should check this email and any attachments for the presence of computer viruses. Astex Therapeutics Ltd accepts no liability for damage caused by any virus transmitted by this email. E-mail is susceptible to data corruption, interception, unauthorized amendment, and tampering, Astex Therapeutics Ltd only send and receive e-mails on the basis that the Company is not liable for any such alteration or any consequences thereof. Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, Cambridge CB4 0QA under number 3751674
Re: [ccp4bb] Reindexing P21.. the process?
Francis E Reyes wrote: Hi all I have data integrated and scaled to P21 via denzo/scalepack. I'm concerned about the workflow to obtain the alternate indexing arrangement (h,k,l) - (h,-k,-h-l). I was thinking .sca ( not specifying NO MERGE) - .mtz - reindex but the documentation for reindex says all my DANO columns are 'negated' ( I do not specify NOREDUCE). So I must run truncate on the reindexed intensities to recalculate F(+/-) and DANO/SIGDANO) ? Thanks FR I would not do any reindexing till all the processing is finished, then reindex the truncated output file. There are many ways to kill a pig as they say but that is the simplest.. Eleanor
Re: [ccp4bb] 3D fitting
PISA will do that - an EBI service or available less prettily from ccp4i Eleanot Miri Hirshberg wrote: Sun., Jan. 17th 2010 EBI Greetings, I am looking for a 3D structure superposition program which takes two structures and superpose them based only on the coordinates X,Y,Z regardless of of residue/atoms name. (both files are in PDB format) Thanks Miri Dr Miri Hirshberg European Bioinformatics Institute UK PDBe - EBI -EMBL http://www.ebi.ac.uk/pdbe Phone: +44 (0) 1223 492647 FAX: +44 (0) 1223 494468
Re: [ccp4bb] Stereo TF - VGA to 3-pin VESA Stereo Adapter
Hi, the following information might be of use for the ones that do not have a 3-pin mini connector and are working under linux http://www.int03.co.uk/crema/hardware/stereo/ - J. - Sabuj Pattanayek wrote: Hi, I thought FX3700 would work. Good to hear confirmation from you. It would be nice a Linux driver is available to allow USB based stereo sync. Yeah, it won't happen anytime soon. This details which cards are supported for 3D vision and which have a 3 pin mini-DIN stereo connector. That page says cards without the connector can be used via USB, but I am not sure if that applies to Linux or just to Windows. Again, USB stereo only works with Windows. They did not put the USB stereo code into the Linux binary driver :( . FX1400 and FX3500 not working - are you just saying that because they do not appear on the list, or have you personally verified it? Those happen to be the cards I currently have. We have also verified that both the 1400 and 3500 do not work and also that the Quadro 370 works with Windows using the USB stereo but does not work with Linux. Thus, the cheapest way to go on Linux for hardware stereo is with the Quadro 3700. Someone posted a link for the release notes of the 195.30 beta driver last week. I can't find the link right now, but I believe it said that to be supported for 3D vision, the card has to be G82XL or newer. The Core designations for Quadro cards can be found at Wikipedia: http://en.wikipedia.org/wiki/Nvidia_Quadro It only works with a G8x based card or better (see stereo option 10 in the 195.22 driver readme ftp://download.nvidia.com/XFree86/Linux-x86/195.22/README/README.txt). We've been using 195.22 with Stereo 10 without problems, here's an xorg.conf for Centos5: http://forums.nvidia.com/index.php?showtopic=91072st=0p=968627#entry968627 HTH, Sabuj Pattanayek -- Dr. Jeroen R. Mesters Gruppenleiter Strukturelle Neurobiologie und Kristallogenese Institut für Biochemie, Universität zu Lübeck Zentrum für Medizinische Struktur- und Zellbiologie Ratzeburger Allee 160, D-23538 Lübeck Tel: +49-451-5004065, Fax: +49-451-5004068 Http://www.biochem.uni-luebeck.de Http://www.iobcr.org Http://www.selfish-brain.org Http://www.opticryst.org -- If you can look into the seeds of time and say which grain will grow and which will not - speak then to me (Macbeth) --
[ccp4bb] parameters defining crystallographic model quality
Dear all, What are the standard methods for the crystallographic model judgment? What parameters should be included in the final refinement statistics in relation to the model error? What is Cruinkshank DPI and how can it be calculated and what information it gives about the quality of the model? Thanks in advance for the suggestions. J.
Re: [ccp4bb] parameters defining crystallographic model quality
I'd head to Gerard Kleywegt's Practical Model Validation web course post-haste: http://xray.bmc.uu.se/embo2001/modval/ http://xray.bmc.uu.se/embo2001/modval/Eric On Mon, Jan 18, 2010 at 11:00 AM, james09 pruza james09x...@gmail.comwrote: Dear all, What are the standard methods for the crystallographic model judgment? What parameters should be included in the final refinement statistics in relation to the model error? What is Cruinkshank DPI and how can it be calculated and what information it gives about the quality of the model? Thanks in advance for the suggestions. J.
Re: [ccp4bb] verifying a molecular replacement solution (test case where the true structure is known)
Looks like you have already gotten several good suggestions, but I also wrote a jiffy program for doing this that does not require the two PDB files to have the same atom names: http://bl831.als.lbl.gov/~jamesh/pickup/origins.com Which you run like this: origins.com right_origin.pdb wrong_origin.pdb P212121 correlate nochains The bottom of the script file contains a list of allowed origin shifts, which are each applied in turn and the resulting symmetry-expanded atom constellations compared. If you use the word correlate on the command line the atoms will be converted to an electron density map using sfall and the correlation coefficient used as the match score. By default, the program breaks up the PDBs into their chains (segids) and searches each one separately. You can turn this off by using the word nochains on the command line. I think emma should give you similar results, but the algorithms are certainly different. -James Holton MAD Scientist Francois Berenger wrote: Hello, 1) In the case I know the true structure (I am verifying I use Phaser correctly), is there a program to do so? Some other questions, if I am to write this program by myself: 2) is there a list somewhere of the translation ambiguities for each spacegroup? For example, in P1 it would say me any translation on any axis is fine. 3) is there a list of permissible origins for each space group? For example, in P212121 it would say me there are 8 possible choices and list them for me. I already know of symop.lib, but I don't think it has some of the information I am looking for. I also know the csymmatch example program of the clipper library, it does part of what I intend to do. Thanks a lot, Francois.
[ccp4bb] arp/warp: missing 'wilsonb'
Hello, we have been trying to run arp warp 7.1.0 from ccp4-6.1.2 starting from experimental phases. As we hit the run or 'run view comm script' button, a window appears saying Can't read 'wilsonb': no such variable followed by a polite apology and nothing else happens ever after. What might be the cause and the cure of such behaviour? Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
[ccp4bb] Molecular Replacement
Dear All; We have solved a crystal structrure of protein at 1.8 A. I have now another crystal of the same protein in aother unit cell,for the new crystal type resolution is 3.6 A but when I use our structure as a seach model It does't give any solution. Any suggestion would be highly appreciated. -- Muhammad Bashir Khan Department for Biomolecular Structural Chemistry Max F. Perutz Laboratories University of Vienna Campus Vienna Biocenter 5 A-1030 Vienna Austria Phone: +43(1)427752224 Fax: +43(1)42779522
Re: [ccp4bb] SCA
Hi Azadeh, I looked into this and other related methods extensively once, and came out with the understanding that SCA is not really the best of this type of analysis (you can read some of the papers out there which analyze the several methods). I found that the java package from Mark Gerstein's group at Yale does any/all of the analyses in parallel (if you want) and is relatively easy to set up. The best, as I recall, was the one based on: Gobel,U. et al. (1994) Correlated mutations and residue contacts in proteins. Proteins: Struct. Funct.Genet., 18, 309-317. I think you need an MTA for the actual SCA software, as well. Jacob *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** - Original Message - From: Azadeh Shahsavar To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, January 18, 2010 4:25 AM Subject: [ccp4bb] SCA Dear all, Does anyone have the current (or old) version of SCA? (SCA: statistical coupling analysis) It should be as a toolbox of Matlab software. Thank you in advance, Azadeh
Re: [ccp4bb] Stereo TF - VGA to 3-pin VESA Stereo Adapter
On Mon, Jan 18, 2010 at 7:33 AM, mesters mest...@biochem.uni-luebeck.de wrote: Hi, the following information might be of use for the ones that do not have a 3-pin mini connector and are working under linux http://www.int03.co.uk/crema/hardware/stereo/ Didn't really see anything linux specific on that website but doing searches for rivatuner linux or softquadro linux mentions the nvclock utility which one might be able to use to mod a geforce into a quadro before you try the hard hacks mentioned above.
Re: [ccp4bb] Molecular Replacement
Dear Muhammed, that's not uncommon. Your protein might undergo domain movements or contain flexible parts. if your structure contains any loops / floppy regions (with high B-values), you can exclude them from the search model. If it is composed of domains, chop it into pieces and search with one after the other, starting from the largest one. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Mon, 18 Jan 2010, Muhammed bashir Khan wrote: Dear All; We have solved a crystal structrure of protein at 1.8 A. I have now another crystal of the same protein in aother unit cell,for the new crystal type resolution is 3.6 A but when I use our structure as a seach model It does't give any solution. Any suggestion would be highly appreciated. -- Muhammad Bashir Khan Department for Biomolecular Structural Chemistry Max F. Perutz Laboratories University of Vienna Campus Vienna Biocenter 5 A-1030 Vienna Austria Phone: +43(1)427752224 Fax: +43(1)42779522
[ccp4bb] Postdoctoral position at the European Institute of Oncology, Milan
Post-doctoral research position at the European Institute of Oncology Milan, Italy A postdoctoral research position in structural biology is available in Marina Mapelli's group at the IFOM-IEO Campus, Milano. The group interests focuses on the structural and functional aspects of protein complexes governing spindle orientation during asymmetric cell divisions. We use a combination of biochemical, biophysical and structural methods to study the molecular mechanisms underlying spindle dynamics, and how they relate to the asymmetric outcome of a cell division (for more info please see http://www.ifom-ieo-campus.it/research/mapelli.php) . We are seeking a motivated and enthusiastic postdoctoral fellow interested in understanding how protein structures relate with their cellular activity. Applicants should have recently obtained a Ph.D. in biochemistry, structural biology or equivalent qualification in a relevant research area. Ideal candidates should have experience in multi-protein complex reconstitution, protein purification and engineering. Knowledge of x-ray crystallography will be an advantage. The Structural Biology Department of the IFOM-IEO Campus is equipped with the state-of-the-art apparatus for protein purification and crystallization, including a nanodrop crystallization robot and an automated imaging system, and has good access to the synchrotron beamlines. Successful candidates will benefit from a stimulating and collaborative environment within the Campus (http://www.ifom-ieo-campus.it/ ). The position is founded for three years starting from February 2010. It will remain open until filled. Postdoc applicants should send their enquiries by e-mail to Marina Mapelli (marina.mape...@ifom-ieo-campus.it), including a cover letter and their cv. They should also ask two referees to send letters of recommendation at the same electronic address. - Marina Mapelli, PhD Department of Experimental Oncology European Institute of Oncology Via Adamello 16, I-20139 Milan, Italy tel: ++39-02-9437-5018/5042 fax: ++39-02-94375990 email: marina.mape...@ifom-ieo-campus.it http://www.ifom-ieo-campus.it/research/mapelli.php -
[ccp4bb] DPI
Dear ccp4bbers, Can anyone suggests the acceptable range of DPI value as an coordinated error and except sfcheck, what other programs calculate it? Thanks in advance. James...
Re: [ccp4bb] parameters defining crystallographic model quality
Hi, for example, these qualities below will tell me something about your model: 1. Rfree, Rwork overall and shown in resolution shells; 2. Geometry statistics: - overall rmsd's bonds, angles, ...; - Molprobity statistics/scores; - histograms of deviations from ideal bonds, angels, ...; 3. Plot of local density correlation (map CC) reported per residue/atom, as well as mFo-DFc and 2mFo-DFc map values reported per residue/atom; 4. POLYGON picture showing where your model stands w.r.t. similar ones available in the database (Acta Cryst. D65, 297-300 (2009)). For example, all the above you can get in PHENIX using Comprehensive validation tool. Pavel. On 1/18/10 8:00 AM, james09 pruza wrote: Dear all, What are the standard methods for the crystallographic model judgment? What parameters should be included in the final refinement statistics in relation to the model error? What is Cruinkshank DPI and how can it be calculated and what information it gives about the quality of the model? Thanks in advance for the suggestions. J.
Re: [ccp4bb] Molecular Replacement
Dear Muhammed, In case you have used phaser for MR you could try to either decrease sequence identity or increase the rmsd of the search model (both ways are equivalent). This allows also to account for flexibility/movements in your target protein like Tim explained. Cheers, christian Muhammed bashir Khan wrote: Dear All; We have solved a crystal structrure of protein at 1.8 A. I have now another crystal of the same protein in aother unit cell,for the new crystal type resolution is 3.6 A but when I use our structure as a seach model It does't give any solution. Any suggestion would be highly appreciated. ___ Dr. Christian Biertümpfel Laboratory of Molecular Biology NIDDK/National Institutes of Health phone: +1 301 402 4647 9000 Rockville Pike, Bldg. 5, Rm. B1-03 fax: +1 301 496 0201 Bethesda, MD 20892-0580 USA ___
[ccp4bb] incorrect linkage definitions ?
Hi everybody, I have a question regarding glycosidic bonds. This relates to refmac, phenix and cns, so I thought the best forum to pose this was here. We have these very nifty link descriptions, such as BETA1-4, ALPHA1-6, etc. that come with refmac and phenix. These essentially describe a chiral center and torsion angles around position C1. However, the way a glycosidic linkage is defined as alpha or beta does not solely depend on the C1 chiral center (see below if interested, and see if I am right). An ALPHA1-3 link in refmac or phenix works for a alpha-D-mannose, but it forces my alpha-L-fucoses to become beta, no matter what I do. And by the way, secreted and membrane proteins you make in insect cells will have ALPHA1-3 and ALPHA1-6 linkages to fucose, and in mammals, ALPHA1-6 to fucose; this should be a very common occurrence (and problem). This seems to be a fucose-specific problem, since it is the only standard sugar residue, that's an L sugar, so the defined links will result in incorrect stereoisomers. I would be very happy if anyone can check the logic here, and please correct me (it has been 12 years since I learnt and soon forgot what an anomer is!). Best, Engin P.S. Alpha or beta: How a sugar is designated as an alpha or beta anomer is actually complicated, and requires one to draw a Fischer projection. IUPAC says: Relative stereodescriptors used in carbohydrate nomenclature to describe the configuration at the anomeric carbon by relating it to the anomeric reference atom. For simple cases the anomeric reference atom is the same as the configurational reference atom. Thus in ?-d-glucopyranose the reference atom is C-5 and the OH at C-1 is on the same side as the OH at C-5 in the Fischer projection. Simply checking wikipedia:anomer can show that an alpha or beta anomer can have opposite chiral centers depending on the identity of the sugar. Also, the current versions of FUC-a-L in the monomer libraries of refmac and phenix seem to be beta indeed. Garib Murshudov knows about this. See http://www.flickr.com/photos/46544...@n03/4274285327/ HIC-UP has it right: http://xray.bmc.uu.se/hicup/FUC/ -- 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] incorrect linkage definitions ?
On Monday 18 January 2010, Engin Ozkan wrote: Hi everybody, I have a question regarding glycosidic bonds. This relates to refmac, phenix and cns, so I thought the best forum to pose this was here. We have these very nifty link descriptions, such as BETA1-4, ALPHA1-6, etc. that come with refmac and phenix. These essentially describe a chiral center and torsion angles around position C1. However, the way a glycosidic linkage is defined as alpha or beta does not solely depend on the C1 chiral center (see below if interested, and see if I am right). An ALPHA1-3 link in refmac or phenix works for a alpha-D-mannose, but it forces my alpha-L-fucoses to become beta, no matter what I do. I do not know what options are available in phenix, but in the refmac dictionaries you have the option of specifying the chiral volume of the anomeric carbon as both rather than as negativ or postive. This will preserve the chirality of the model as input. So long as you provide the correct anomer in your input model, you should be OK. Caveat: I have used this successfully for to handle anomers of GLU, GAL, NAG, and SIA, but I can't rule out a bug of some sort that hits other sugars. Ethan And by the way, secreted and membrane proteins you make in insect cells will have ALPHA1-3 and ALPHA1-6 linkages to fucose, and in mammals, ALPHA1-6 to fucose; this should be a very common occurrence (and problem). This seems to be a fucose-specific problem, since it is the only standard sugar residue, that's an L sugar, so the defined links will result in incorrect stereoisomers. I would be very happy if anyone can check the logic here, and please correct me (it has been 12 years since I learnt and soon forgot what an anomer is!). Best, Engin P.S. Alpha or beta: How a sugar is designated as an alpha or beta anomer is actually complicated, and requires one to draw a Fischer projection. IUPAC says: Relative stereodescriptors used in carbohydrate nomenclature to describe the configuration at the anomeric carbon by relating it to the anomeric reference atom. For simple cases the anomeric reference atom is the same as the configurational reference atom. Thus in ?-d-glucopyranose the reference atom is C-5 and the OH at C-1 is on the same side as the OH at C-5 in the Fischer projection. Simply checking wikipedia:anomer can show that an alpha or beta anomer can have opposite chiral centers depending on the identity of the sugar. Also, the current versions of FUC-a-L in the monomer libraries of refmac and phenix seem to be beta indeed. Garib Murshudov knows about this. See http://www.flickr.com/photos/46544...@n03/4274285327/ HIC-UP has it right: http://xray.bmc.uu.se/hicup/FUC/
Re: [ccp4bb] SCA
yes, other people can comment probably but i think entropy based estimates are better (as i remember less dependent on sample set size). and indeed yale has a server. which may or may not do what you want. secondly its not proper to distributed ohter people's software w/o their permission (actuaally its abs wrong, if not illegal, availibility is anohter question of course...). i would advise to look at papers on entropy based measures of coupling and write to the authors. my two cents..., tommi Quoting Jacob Keller j-kell...@md.northwestern.edu: Hi Azadeh, I looked into this and other related methods extensively once, and came out with the understanding that SCA is not really the best of this type of analysis (you can read some of the papers out there which analyze the several methods). I found that the java package from Mark Gerstein's group at Yale does any/all of the analyses in parallel (if you want) and is relatively easy to set up. The best, as I recall, was the one based on: Gobel,U. et al. (1994) Correlated mutations and residue contacts in proteins. Proteins: Struct. Funct.Genet., 18, 309-317. I think you need an MTA for the actual SCA software, as well. Jacob *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** - Original Message - From: Azadeh Shahsavar To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, January 18, 2010 4:25 AM Subject: [ccp4bb] SCA Dear all, Does anyone have the current (or old) version of SCA? (SCA: statistical coupling analysis) It should be as a toolbox of Matlab software. Thank you in advance, Azadeh -- Tommi Kajander, Ph.D. Macromolecular X-ray Crystallography Research Program in Structural Biology and Biophysics Institute of Biotechnology P.O. Box 65 (Street address: Viikinkaari 1, 4th floor) University of Helsinki FIN-00014 Helsinki, Finland Tel. +358-9-191 58903 Fax +358-9-191 59940
Re: [ccp4bb] incorrect linkage definitions ?
That would be a partial solution to the alpha-L-fucose problem, except for the fact that currently, the monomer library description for alpha-L-fucose is a beta! So, unless one is extremely vigilant, they will get beta fucoses, which I believe do not exist in N-linked sugars. Currently, another solution is to modify the monomer library to have the correct alpha fucose (which is a must), and then define a bond and a few angle restraints (and possibly torsion), in phenix. Another one is to ask phenix to use a beta linkage, which imposes an alpha linkage on L-fucose! Apparently, two wrongs do make a right. The real problem is that every crystallographer I asked tells me that they use these linkages, without giving much of a thought. This is not surprising. Figuring out if an anomer is alpha or beta required me to spend a couple of hours digging up my organic chem notes, and reading several sections from an IUPAC publication (So, I would appreciate further confirmation of this). The real solution is to have another set of linkages for L sugars, in refmac and phenix. This will not work for every possible sugar, but should for the standard/common ones. Engin On 1/18/10 2:03 PM, Ethan Merritt wrote: On Monday 18 January 2010, Engin Ozkan wrote: Hi everybody, I have a question regarding glycosidic bonds. This relates to refmac, phenix and cns, so I thought the best forum to pose this was here. We have these very nifty link descriptions, such as BETA1-4, ALPHA1-6, etc. that come with refmac and phenix. These essentially describe a chiral center and torsion angles around position C1. However, the way a glycosidic linkage is defined as alpha or beta does not solely depend on the C1 chiral center (see below if interested, and see if I am right). An ALPHA1-3 link in refmac or phenix works for a alpha-D-mannose, but it forces my alpha-L-fucoses to become beta, no matter what I do. I do not know what options are available in phenix, but in the refmac dictionaries you have the option of specifying the chiral volume of the anomeric carbon as both rather than as negativ or postive. This will preserve the chirality of the model as input. So long as you provide the correct anomer in your input model, you should be OK. Caveat: I have used this successfully for to handle anomers of GLU, GAL, NAG, and SIA, but I can't rule out a bug of some sort that hits other sugars. Ethan And by the way, secreted and membrane proteins you make in insect cells will have ALPHA1-3 and ALPHA1-6 linkages to fucose, and in mammals, ALPHA1-6 to fucose; this should be a very common occurrence (and problem). This seems to be a fucose-specific problem, since it is the only standard sugar residue, that's an L sugar, so the defined links will result in incorrect stereoisomers. I would be very happy if anyone can check the logic here, and please correct me (it has been 12 years since I learnt and soon forgot what an anomer is!). Best, Engin P.S. Alpha or beta: How a sugar is designated as an alpha or beta anomer is actually complicated, and requires one to draw a Fischer projection. IUPAC says: Relative stereodescriptors used in carbohydrate nomenclature to describe the configuration at the anomeric carbon by relating it to the anomeric reference atom. For simple cases the anomeric reference atom is the same as the configurational reference atom. Thus in ?-d-glucopyranose the reference atom is C-5 and the OH at C-1 is on the same side as the OH at C-5 in the Fischer projection. Simply checking wikipedia:anomer can show that an alpha or beta anomer can have opposite chiral centers depending on the identity of the sugar. Also, the current versions of FUC-a-L in the monomer libraries of refmac and phenix seem to be beta indeed. Garib Murshudov knows about this. See http://www.flickr.com/photos/46544...@n03/4274285327/ HIC-UP has it right: http://xray.bmc.uu.se/hicup/FUC/ -- 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] Postdoctoral Position at Vanderbilt University
Postdoctoral and Staff Positions: Structural Biology and Biochemistry of Membrane Proteins The lab of Chuck Sanders at Vanderbilt University has openings for PhD-level staff and/or postdoctoral fellows to conduct studies of disease-related membrane protein structure, folding, and function. Proteins under study include the human amyloid precursor protein (Alzheimer’s disease), peripheral myelin protein 22 (Charcot-Marie- Tooth disease), integrins (kidney failure), the HERG and KCNQ1 potassium channels (cardiac arrhythmias), and diacylglycerol kinase (see Van Horn et al. SCIENCE 324, 1726-1729 (2009). More information on these projects is found at the lab web site listed below. While some projects involve much NMR spectroscopy, other projects are more biochemically focused. There are also opportunities to carry out X-ray crystallographic studies through our collaboration with Prof. Tina Iverson and computational studies through our collaboration with Prof. Jens Meiler. Candidates should have an interest in working with integral membrane proteins. The Vanderbilt Biomolecular NMR Spectroscopy Laboratory will soon install a 900 MHz instrument to complement current instrumentation. Vanderbilt University is listed as one of FORTUNE’s 2009 “100 Best Companies to Work For”. Start dates are flexible. Candidates should send a CV, including contact information for references, to: chuck.sand...@vanderbilt.edu Prof. Charles R. Sanders Dept. of Biochemistry and Center for Structural Biology Vanderbilt University Nashville, Tennessee 37232-8725 USA Phone: (615)-936-3756 Lab web site: http://structbio.vanderbilt.edu/sanders Vanderbilt University is an equal opportunity employer.
Re: [ccp4bb] ccp4bb unsubscribe
On Jan 17, 2010, at 9:35 PM, Sonya Sivaraj wrote: brThis message and any attachments may contain proprietary or confidential information. If you are not the intended recipient or you received the message in error, you must not use, copy or distribute the message. Please notify the sender immediately and destroy the original message. Thank you. Well, I would say a few thousand of us are not the intended recipient. If you google ccp4 unsubscribe the top hit is the link to the web interface: http://www.ccp4.ac.uk/ccp4bb.php#subscription
Re: [ccp4bb] SCA
There is a server at the Yale site, but if you want to play around more with the parameters, you can download the whole package and run it locally without too much trouble. There are some options which are not available through the server. The documentation is not great, however. The Gerstein package also contains the entropy-based methods (at least some). My problem is really knowing where to go once one gets the results... Jacob *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** - Original Message - From: Tommi Kajander tommi.kajan...@helsinki.fi To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, January 18, 2010 4:10 PM Subject: Re: [ccp4bb] SCA yes, other people can comment probably but i think entropy based estimates are better (as i remember less dependent on sample set size). and indeed yale has a server. which may or may not do what you want. secondly its not proper to distributed ohter people's software w/o their permission (actuaally its abs wrong, if not illegal, availibility is anohter question of course...). i would advise to look at papers on entropy based measures of coupling and write to the authors. my two cents..., tommi Quoting Jacob Keller j-kell...@md.northwestern.edu: Hi Azadeh, I looked into this and other related methods extensively once, and came out with the understanding that SCA is not really the best of this type of analysis (you can read some of the papers out there which analyze the several methods). I found that the java package from Mark Gerstein's group at Yale does any/all of the analyses in parallel (if you want) and is relatively easy to set up. The best, as I recall, was the one based on: Gobel,U. et al. (1994) Correlated mutations and residue contacts in proteins. Proteins: Struct. Funct.Genet., 18, 309-317. I think you need an MTA for the actual SCA software, as well. Jacob *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** - Original Message - From: Azadeh Shahsavar To: CCP4BB@JISCMAIL.AC.UK Sent: Monday, January 18, 2010 4:25 AM Subject: [ccp4bb] SCA Dear all, Does anyone have the current (or old) version of SCA? (SCA: statistical coupling analysis) It should be as a toolbox of Matlab software. Thank you in advance, Azadeh -- Tommi Kajander, Ph.D. Macromolecular X-ray Crystallography Research Program in Structural Biology and Biophysics Institute of Biotechnology P.O. Box 65 (Street address: Viikinkaari 1, 4th floor) University of Helsinki FIN-00014 Helsinki, Finland Tel. +358-9-191 58903 Fax +358-9-191 59940
