Re: [ccp4bb] BLT wish
Hi Bill Sorry, I was tired! Yes, I agree entirely. Trying to maintain one's own working TclTk from source is not straightforward, and best avoided. CCP4 know this and are working hard to remedy the situation! On 17 Aug 2011, at 23:31, William Scott wrote: On Aug 17, 2011, at 3:25 PM, Harry wrote: Hi Bill I don't think this includes BLT, does it? No. That was what I was trying to say (apparently not very well, sorry!): On 17 Aug 2011, at 22:33, William Scott wrote: if CCP4 could free itself of this dependency... …then it could make use of the no-BLT version of tcl/tk provided with OS X 10.6 and 10.7. Harry -- Dr Harry Powell, MRC Laboratory of Molecular Biology, MRC Centre, Hills Road, Cambridge, CB2 0QH
Re: [ccp4bb] Computer encryption matters
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear John, encrypted disks are completely transparent once the system is up and running. The only issue will be a slow-down for disk I/O intense operations, e.g. copying a large amount of data takes noticably longer on an encrypted disk - but not too much longer, especially with a fast machine. You might want to keep a separate local partition e.g. for data parallel integration (XDS). Other than that your worries are indeed completely misplaced since as user you only see and notice the unencrypted files and when you send data to colleagues, you send them unencrypted. Cheers, Tim On 08/17/2011 09:13 PM, Jrh wrote: Dear Colleagues, My institution is introducing concerted measures for improved security via encryption of files. A laudable plan in case of loss or theft of a computer with official files eg exams or student records type of information stored on it. Files, folders or a whole disk drive can be encrypted. Whilst I can target specific files, this could get messy and time consuming to target them and keep track of new to-be-encrypted files. It is tempting therefore to agree to complete encryption. However, as my laptop is my calculations' workbench, as well as office tasks, I am concerned that unexpected runtime errors may occur from encryption and there may be difficulties of transferability of data files to colleagues and students, and to eg PDB. Does anyone have experience of encryption? Are my anxieties misplaced? If not, will I need to plan to separate office files, which could then all be encrypted, from crystallographic data files/calculations, which could be left unencrypted. If separate treatment is the best plan does one need two computers once more, rather than the one laptop? A different solution would be to try to insist on an institutional repository keeping such files. In anticipation, Thankyou, John Prof John R Helliwell DSc - -- - -- 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/ iD8DBQFOTL2ZUxlJ7aRr7hoRAifHAKDrHShwwtDdC3ANKzdlT7DuQ/tN9wCeJM/x mwWNdk4dxGKW7OjymMgT3+c= =bISG -END PGP SIGNATURE-
Re: [ccp4bb] Computer encryption matters
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Or a USB-stick with the key, but in this case don't get your laptop being stolen with the USB-stick near-by ;-) Tim On 08/18/2011 03:26 AM, Francois Berenger wrote: [...] Another minor drawback is that you will possibly need a password to boot your machine (on Linux at least). Regards, F. - -- - -- 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/ iD8DBQFOTL5QUxlJ7aRr7hoRAgXnAKCm5JhkvIGPRI72u1iX7sRhofw41QCgk0hq eJtkVY5wmMV1BIBSUoV7dNM= =Hfnz -END PGP SIGNATURE-
Re: [ccp4bb] COOT library
Thanks Huw. Unfortunately I have the same problem when using the new libraries. Maybe it has something to do with the pdb file (output from Phaser) I'm trying to refine. Do I have to rename the residues in the pdb file or is there another trick?
[ccp4bb] crystal Packing
Dear All I was working two domain protein and i have an hexagonal look like crystals from additive screen, now i am facing problem these crystal are growing in 2 minutes even in cold room even at lower protein concentration @2mg/ml . and i have an smeary data of 7 Å, and we thinking one domain might be flexible and other is stable is there anyway to increase the crystal packing Any suggestions are welcome. Eswar Reddy
Re: [ccp4bb] crystal Packing
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Eswar, you can not only alter the protein concentration but also the precipitant concentration. If your protein really is soluble before you set up the crystallisation trials, you are bound to find a condition without crystals by lowering the precipitant concentration (provided they are not growing by salting-in, but in that case, water would be the precipitant in a way...). Once you are there (just before you get crystals) this is a good condition to try micro-seeding. And think about the nature of the protein. Maybe increasing the temperature is more promising than decreasing? You can also use an additive screen. Good luck, Tim On 08/18/2011 10:24 AM, eswar reddy wrote: Dear All I was working two domain protein and i have an hexagonal look like crystals from additive screen, now i am facing problem these crystal are growing in 2 minutes even in cold room even at lower protein concentration @2mg/ml . and i have an smeary data of 7 Å, and we thinking one domain might be flexible and other is stable is there anyway to increase the crystal packing Any suggestions are welcome. Eswar Reddy - -- - -- 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/ iD8DBQFOTNQgUxlJ7aRr7hoRAsFrAKDc0n+BCdqhzCXiU5rSpDSWHmonDwCglMwX yqb8be8DnnoAO0CVv05oQ9c= =BieH -END PGP SIGNATURE-
[ccp4bb] structure based superposition
Dear all, I would like to know the tools/servers/programs that can be used for structure based superposition of two or more proteins. Please help me out..!! Thanks, -Suda
Re: [ccp4bb] structure based superposition
normaly you can do it in the pymol. In the main interface, on the left menu, there is a:A button, click it, then looking for Aliagn. Then you can do it. But I prefer to use CCP4, in CCp4 there is a tool : Superpose. You can fine any region you want to do superpose.
Re: [ccp4bb] structure based superposition
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hello Suda, You can use - - lsqkap - - lsqman - - tools available in coot - - pymol - - probably something like phenix.superpose ... Cheers, Tim On 08/18/2011 11:10 AM, Suda Ravindran wrote: Dear all, I would like to know the tools/servers/programs that can be used for structure based superposition of two or more proteins. Please help me out..!! Thanks, -Suda - -- - -- 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/ iD8DBQFOTOKYUxlJ7aRr7hoRAoh8AJ9Kx2qWJAXEDvyxnSt7bnAk54rfPwCg15AN +yV/DvZS4+oVGUkQfTufIOs= =zj1/ -END PGP SIGNATURE-
Re: [ccp4bb] structure based superposition
... and in ccp4mg On 18 Aug 2011, at 10:55, Shilong Fan wrote: normaly you can do it in the pymol. In the main interface, on the left menu, there is a:A button, click it, then looking for Aliagn. Then you can do it. But I prefer to use CCP4, in CCp4 there is a tool : Superpose. You can fine any region you want to do superpose.
Re: [ccp4bb] COOT library
On 18 Aug 2011, at 09:29, Eric Karg wrote: Thanks Huw. Unfortunately I have the same problem when using the new libraries. Maybe it has something to do with the pdb file (output from Phaser) I'm trying to refine. Do I have to rename the residues in the pdb file or is there another trick? Yes RNA with the old syntax won't work with the new dictionary - but then it would have worked with the old one (I've just checked that). Can you paste a nucleotide from the problem PDB into an email to the BB and also say what atoms coot is failing to match in real-space refinement. The versions of Phaser and Coot would be useful too! Thanks, Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular Biology University of Leeds
[ccp4bb] Postdoc Positions at EMBL Grenoble
The Schaffitzel laboratory at the European Molecular Biology Laboratory (EMBL) Grenoble, France seeks to recruit outstanding postdoctoral scientists in structural biology. We study the structure and function of large macromolecular complexes in gene expression. The project involves structure determination by single-particle cryo-electron microscopy of large multicomponent complexes produced in insect cells (MultiBac technology, collaboration with Imre Berger), their purification and biophysical and biochemical characterization. http://www.embl.fr/research/unit/schaffitzel/index.html The positions require a Ph.D. in biochemistry, structural biology or a related field. Outstanding applicants have experience in guiding structure determination projects from start to finish, experience in electron microscopy would be advantageous. Candidates are highly motivated individuals who enjoy working as part of a young, dynamic, collaborative and multidisciplinary team. The laboratory is well-situated in a structural biology environment at the Polygone Scientifique in Grenoble. We are equipped with a state-of-the-art electron microscope (Polara, FEI). Access to modern biophysical instrumentation (analytical ultracentrifugation, surface plasmon resonance, dynamic light scattering, isothermal calorimetry, CD and fluorescence spectrometers) is provided. The positions are available from January 2012 and funded for 3 years. Contracts may be extended depending on performance. Please send your CV, a statement of research interests, and names (including email address) of at least two referees by email to Dr. Christiane Schaffitzel (schaffit...@embl.fr). Applications will be accepted until the positions are filled.
Re: [ccp4bb] COOT library
On 18 Aug 2011, at 09:29, Eric Karg wrote: Thanks Huw. Unfortunately I have the same problem when using the new libraries. Maybe it has something to do with the pdb file (output from Phaser) I'm trying to refine. Do I have to rename the residues in the pdb file or is there another trick? This was indeed a problem with the pdb file from Phaser which contained U and G but *s not 's and O1P not OP1 etc. I guess this means that to minimise conversion woes it's important to make sure any nucleic search model input to Phaser is v3.2 syntax and then everything downstream will work. Hopefully someday this mess will be a distant memory! Huw -- Dr Huw Jenkins Astbury Centre for Structural Molecular Biology University of Leeds
Re: [ccp4bb] Computer encryption matters
John, Since so many people have said it's flawless, I'd like to point out this is not always the case. The particular version of the particular package that we have installs some system libraries that caused a program I use on a moderately frequent basis to crash every time I tried to open a file on a network drive. It took me about 9 months to figure out what the cause was, during which time I had to manually copy things to the local drive before I could open them in that particular program. The vendor of the encryption software has a newer version but our IT department is using an older version. There is another workaround but it's kind of a hack. So I'd say problems are very rare, but if you run into strange behavior, don't rule out encryption as a possible cause. -Eric On Aug 17, 2011, at 3:13 PM, Jrh wrote: Dear Colleagues, My institution is introducing concerted measures for improved security via encryption of files. A laudable plan in case of loss or theft of a computer with official files eg exams or student records type of information stored on it. Files, folders or a whole disk drive can be encrypted. Whilst I can target specific files, this could get messy and time consuming to target them and keep track of new to-be-encrypted files. It is tempting therefore to agree to complete encryption. However, as my laptop is my calculations' workbench, as well as office tasks, I am concerned that unexpected runtime errors may occur from encryption and there may be difficulties of transferability of data files to colleagues and students, and to eg PDB. Does anyone have experience of encryption? Are my anxieties misplaced? If not, will I need to plan to separate office files, which could then all be encrypted, from crystallographic data files/calculations, which could be left unencrypted. If separate treatment is the best plan does one need two computers once more, rather than the one laptop? A different solution would be to try to insist on an institutional repository keeping such files. In anticipation, Thankyou, John Prof John R Helliwell DSc
[ccp4bb] more Computer encryption matters
Since we're on the subject... I've been tempted on and off to encrypt my hard drive, but after getting burned once a hundred years ago when encrypted data turned into garbled bytes all of a sudden I've been hesitant. I've gone so far as to install TrueCrypt (on a MacBook), but I haven't put it into action. Before I do, the big question: What software do people on the bb use for encryption? What can be recommended without hesitation? Thanks. Andreas On 18/08/2011 1:19, Eric Bennett wrote: John, Since so many people have said it's flawless, I'd like to point out this is not always the case. The particular version of the particular package that we have installs some system libraries that caused a program I use on a moderately frequent basis to crash every time I tried to open a file on a network drive. It took me about 9 months to figure out what the cause was, during which time I had to manually copy things to the local drive before I could open them in that particular program. The vendor of the encryption software has a newer version but our IT department is using an older version. There is another workaround but it's kind of a hack. So I'd say problems are very rare, but if you run into strange behavior, don't rule out encryption as a possible cause. -Eric -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
Re: [ccp4bb] more Computer encryption matters
What software do people on the bb use for encryption? What can be recommended without hesitation? I've had no problems with TrueCrypt, which I've been using on linux and OS X for ~4 years (for personal systems, not lab ones). But I haven't used it for storing files I've been doing anything I/O intensive with, so I can't give any feedback on that. As far as having encrypted data turn into unrecoverable junk, it's always worth having backups (either un-encrypted, or using a different encryption scheme) - especially since encryption makes low-level recovery difficult to impossible. Pete Thanks. Andreas On 18/08/2011 1:19, Eric Bennett wrote: John, Since so many people have said it's flawless, I'd like to point out this is not always the case. The particular version of the particular package that we have installs some system libraries that caused a program I use on a moderately frequent basis to crash every time I tried to open a file on a network drive. It took me about 9 months to figure out what the cause was, during which time I had to manually copy things to the local drive before I could open them in that particular program. The vendor of the encryption software has a newer version but our IT department is using an older version. There is another workaround but it's kind of a hack. So I'd say problems are very rare, but if you run into strange behavior, don't rule out encryption as a possible cause. -Eric
[ccp4bb] question about SIGF
Dear all, I am a student in crystallography. So not quite familiar with some even basic concepts. In shelx .hkl file or ccp4 .mtz file there is a column SIGF which is related to standard deviation of the structure factor. I read through many text book for crystallography, there are many formulas about this topic. Sometimes it is a square of sigma, sometimes it is not. My question is: 1. What is the exact mathematical formula for SIGF or SIGFP in ccp4 or shelx format file? 2. If it can be calculated from F, why it is necessary to include it in ccp4 or shelx reflection file (they have F already) ? 3. Is this value really important in structure determination? Why and how? As I understood, during data collection each reflection measured several times, so there is a deviation from the average F. That is the meaning of SIGF. But how to use this value in structure determination? Is there some kind of correction or refinement on F according to SIGF? And also when multiplicity during data collection is low, the SIGF would not be so interested. So is that means the SIGF would not be so important in some measurements? Any kind reply from you guys would be greatly appreciated. Many thanks! Best regards, G
Re: [ccp4bb] structure based superposition
Hi Shilong, On Thu, Aug 18, 2011 at 5:55 AM, Shilong Fan fanshil...@hotmail.com wrote: normaly you can do it in the pymol. In the main interface, on the left menu, there is a:A button, click it, then looking for Aliagn. Then you can do it. But I prefer to use CCP4, in CCp4 there is a tool : Superpose. You can fine any region you want to do superpose. PyMOL can indeed perform alignments. It has three different methods and I'd like to take a second to clear up the differences. First, the align command (A Align ) performs a sequence alignment followed by a few rounds of fitting throw away outliers to improve the fit. The super command is similar to align, but if you indicate seq=0 then PyMOL will ignore the sequence. It then uses a dynamic programming strategy to find the best fit. Last, PyMOL also offers access to the structure-only cealign method as well. Of course, if you already know your paired atoms you can just use any of the 'fit' commands to do the fitting. Here are links to the PyMOLWiki pages for reference: * -- http://www.pymolwiki.org/index.php/Align * -- http://www.pymolwiki.org/index.php/Super * -- http://www.pymolwiki.org/index.php/Cealign * -- http://www.pymolwiki.org/index.php/Fit Hope this helps. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120
Re: [ccp4bb] structure based superposition
You can do structure based sequence alignments using STRAP. It's java based and free. On Aug 18, 2011 5:20 AM, Suda Ravindran biobud...@gmail.com wrote: Dear all, I would like to know the tools/servers/programs that can be used for structure based superposition of two or more proteins. Please help me out..!! Thanks, -Suda
[ccp4bb] Prodrug bugs
Dear CCP4 There is a bug in the ccp4i interface to prodrug on both linux and windows. There is a title line that is read in to the command file which means the software does not run Unrecognised keyword. This can be removed using the run and view com file option However on windows I then get the error Cannot find PRODRG data file (prodrg.param). Turns out share/prodrg/prodrg.param is not bundled in the distribution Works if I copy that over from linux. Best wishes Nick -- Prof Nicholas H. Keep Executive Dean of School of Science Professor of Biomolecular Science Crystallography, Institute for Structural and Molecular Biology, Department of Biological Sciences Birkbeck, University of London, Malet Street, Bloomsbury LONDON WC1E 7HX email n.k...@mail.cryst.bbk.ac.uk Telephone 020-7631-6852 (Room G57 Office) 020-7631-6800 (Department Office) Fax 020-7631-6803 If you want to access me in person you have to come to the crystallography entrance and ring me or the department office from the internal phone by the door
Re: [ccp4bb] structure based superposition
Check out Theseus: http://www.theseus3d.org/ You will need a sequence based alignment. This alignment can be provided automatically by muscle if you have it installed (http://www.drive5.com/muscle/)--this is different from pymol. Pymol seems to do an SVD to obtain the alignment. I'm not up to date on what all the other programs are using, but I think most use least-squares, so you need to provide a sequence based alignment for these programs Theseus results are always as good or better (subjectively speaking) than straight least-squares superposition. I don't know how the Theseus/muscle combo compares to pymol's use of SVD in terms of alignment quality because I haven't compared them directly. James On Aug 18, 2011, at 3:10 AM, Suda Ravindran wrote: Dear all, I would like to know the tools/servers/programs that can be used for structure based superposition of two or more proteins. Please help me out..!! Thanks, -Suda
[ccp4bb] Morph with Chimera: how to make visible connection/interaction in Morph
Dear all, I would like to show the visible metal-residue interaction during the Morph movie. Anyone knows how to do that in Chimera? Thank you. King regards, Wenhe
Re: [ccp4bb] Morph with Chimera: how to make visible connection/interaction in Morph
Hi, You'd be better off sending this query to the Chimera BB: chimera-us...@cgl.ucsf.edu Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel E-mail: bshaa...@bgu.ac.il Phone: 972-8-647-2220 Skype: boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of WENHE ZHONG [wenhezhong.xmu@gmail.com] Sent: Thursday, August 18, 2011 7:23 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Morph with Chimera: how to make visible connection/interaction in Morph Dear all, I would like to show the visible metal-residue interaction during the Morph movie. Anyone knows how to do that in Chimera? Thank you. King regards, Wenhe
Re: [ccp4bb] Morph with Chimera: how to make visible connection/interaction in Morph
On Thu, 2011-08-18 at 17:23 +0100, WENHE ZHONG wrote: Dear all, I would like to show the visible metal-residue interaction during the Morph movie. Anyone knows how to do that in Chimera? Thank you. King regards, Wenhe IIUC, you have worked out how to generate the morph trajectory itself with chimera. While I am sure that chimera itself has all the capabilities, my own take on making pointless morph movies is to output the result as the multimodel pdb file and then make a movie with pymol as described here http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Morph_with_Chimera PyMOL will definitely make metal bonds if you use ball-and-stick representation, otherwise the bond command http://www.pymolwiki.org/index.php/Bond is a good way to exert more detailed control over your imagery. -- After much deep and profound brain things inside my head, I have decided to thank you for bringing peace to our home. Julian, King of Lemurs
Re: [ccp4bb] question about SIGF
On Thursday, August 18, 2011 08:19:13 am G Y wrote: Dear all, I am a student in crystallography. So not quite familiar with some even basic concepts. In shelx .hkl file or ccp4 .mtz file there is a column SIGF which is related to standard deviation of the structure factor. I read through many text book for crystallography, there are many formulas about this topic. Sometimes it is a square of sigma, sometimes it is not. My question is: 1. What is the exact mathematical formula for SIGF or SIGFP in ccp4 or shelx format file? There is none. The column in the file simply holds whatever value was input from some data-processing program. You need to take a step back and ask how each individual program calculates, or estimates, sigma(F). 2. If it can be calculated from F, why it is necessary to include it in ccp4 or shelx reflection file (they have F already) ? It cannot be calculated from F. 3. Is this value really important in structure determination? Why and how? As I understood, during data collection each reflection measured several times, so there is a deviation from the average F. That is the meaning of SIGF. But how to use this value in structure determination? Is there some kind of correction or refinement on F according to SIGF? It tells you how much faith to put in that particular Fobs. If the sigma value is small (compared to Fobs) then you would tend to have confidence that the Fobs value is accurate, and therefore rate your current model better if it correctly predicts Fobs. Conversely, if the sigma value is large then you would tend to think that Fobs is unreliable and therefore not penalize your current model if Fcalc != Fobs. This line of reasoning explains why the primary use of sigma is to weight the various residuals during refinement. Typically the weight assigned to each observation is (1 / sigma^2). Although it goes a step or two beyond the specific question you asked, I suggest that you work through Randy Read's notes on maximum likelihood, weighting, and least-squares. http://www-structmed.cimr.cam.ac.uk/Course/Likelihood/likelihood.html This may lead to a deeper understanding of how accounting for sigma leads to a better model. Ethan And also when multiplicity during data collection is low, the SIGF would not be so interested. So is that means the SIGF would not be so important in some measurements? Any kind reply from you guys would be greatly appreciated. Many thanks! Best regards, G -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg University of Washington, Seattle 98195-7742
[ccp4bb] PDBe introduces PDBeXpress - easy-to-use yet powerful PDB analysis tools
Hi all, As part of its recent summer update, the Protein Data Bank in Europe (PDBe; http://pdbe.org) introduced PDBeXpress (http://pdbe.org/express), an umbrella name for a set of easy-to-use yet powerful PDB analysis tools. The first two modules can be used to answer questions such as what residues are found in the binding sites of vitamin B1? and given that I have a cavity lined with Asp, Trp, Ile, Val and His, what compounds are known to bind to such a set of residues? - There are many advanced tools and resources available worldwide to search, browse and analyse the contents of the PDB at the level of entire entries or molecules. However, when it comes to the nitty-gritty of analysing the core structural data contained in the PDB, i.e. atoms and their interactions, the situation is different. PDBeMotif (http://pdbe.org/motif) is one of the most powerful services available (freely) for analysing PDB entries in terms of detailed structure, sequence and chemistry. A practical example is described here: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Structural_motifs_in_the_PDB However, PDBeMotif is also quite complex to use. For this reason, PDBe has begun to develop small modules of PDBeMotif (and other) analysis functionality that are presented in such a way that they are very easy to use by non-experts and provide answers to common but complex questions. The first two PDBeXpress modules were released in the recent PDBe summer update; both provide information and statistics about ligands in the PDB. They can be accessed from http://pdbe.org/express (help and documentation are available from there as well). What residues interact? --- For any ligand in the PDB that you specify, this tool (using PDBeMotif behind the scenes) will retrieve the residues with which this ligand interacts, as observed in current PDB entries. The results are plotted on an interactive graph, which can be used to further view the PDB entries in which the interactions occur, or to perform further analyses using PDBeMotif. When you start the service, all you need to provide is the name or 3-letter code of the compound of interest (or do a search at PDBeChem - http://pdbe.org/chem - if you are unsure). You can select your favourite compound, or compare closely related compounds such as GBC, GLC and GLO. The results page contains a graph that shows the relative occurrence of the amino acids in the binding sites of the compound (extracted from the PDBeMotif database). If you hover your mouse over the bars, you see the total number of interactions between a residue type and your compound. If you click on a bar, you will get more details (e.g., 15.6% of the total interactions are with ASP (16 interactions with 9 occurrences of GLO in 7 PDB entries)). Below this are links that take you to the corresponding PDB entries or further analyses using PDBeMotif. What binds here? This tool enables you to search for ligands in the PDB that interact with a given set of residues and the results are also shown in an interactive graph. When you use this tool, you simply click on the amino-acid types that are present in the binding site. If you require that a residue occurs twice, click it twice, etc. For instance, what do you think is the most frequently found compound to interact with ARG ARG ARG LYS LYS LYS? - We hope that you will find PDBeXpress useful. As always, we welcome constructive criticism, comments, suggestions, bug reports, etc. through the feedback button at the top of any PDBe web page. We also welcome your suggestions for future PDBeXpress modules! --Gerard --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
[ccp4bb] Thankyou re encryption matters
Dear Colleagues, Thankyou for your detailed, and prompt, helpful advice on this issue, which I much appreciate. I see that I have overestimated my anxieties but should probably still move a little cautiously. Thus I will first suggest to my IT encryptors' taskforce, for want of a better term, that as I promise to delete any past 'sensitive files' , and in future will only consult data of this type if held in a university repository, I propose not to have encryption for the time being. Best regards, John Prof John R Helliwell DSc
Re: [ccp4bb] more Computer encryption matters
OS X 10.7 enables you to do whole-drive encryption. Here is a description from Arse Technica: http://arstechnica.com/apple/reviews/2011/07/mac-os-x-10-7.ars/13 I ain't never tried it myself. 10.7 seems to run slow enough as it is. -- Bill On Aug 18, 2011, at 5:34 AM, Andreas Förster wrote: Since we're on the subject... I've been tempted on and off to encrypt my hard drive, but after getting burned once a hundred years ago when encrypted data turned into garbled bytes all of a sudden I've been hesitant. I've gone so far as to install TrueCrypt (on a MacBook), but I haven't put it into action. Before I do, the big question: What software do people on the bb use for encryption? What can be recommended without hesitation? Thanks. Andreas On 18/08/2011 1:19, Eric Bennett wrote: John, Since so many people have said it's flawless, I'd like to point out this is not always the case. The particular version of the particular package that we have installs some system libraries that caused a program I use on a moderately frequent basis to crash every time I tried to open a file on a network drive. It took me about 9 months to figure out what the cause was, during which time I had to manually copy things to the local drive before I could open them in that particular program. The vendor of the encryption software has a newer version but our IT department is using an older version. There is another workaround but it's kind of a hack. So I'd say problems are very rare, but if you run into strange behavior, don't rule out encryption as a possible cause. -Eric -- Andreas Förster, Research Associate Paul Freemont Xiaodong Zhang Labs Department of Biochemistry, Imperial College London http://www.msf.bio.ic.ac.uk
[ccp4bb] Sequence Alignment Question
Hello Everyone, A little off topic but, what is a good way to show (publication quality) multiple sequence alignment? I am trying to show conserved regions in related proteins from different organisms. Thank you -- Yuri Pompeu
Re: [ccp4bb] more Computer encryption matters
On 08/18/2011 09:34 PM, Andreas Förster wrote: Since we're on the subject... I've been tempted on and off to encrypt my hard drive, but after getting burned once a hundred years ago when encrypted data turned into garbled bytes all of a sudden I've been hesitant. I've gone so far as to install TrueCrypt (on a MacBook), but I haven't put it into action. Before I do, the big question: What software do people on the bb use for encryption? What can be recommended without hesitation? For Linux: checking the encrypted disk option of the installer (if I remember well I did this with a Ubuntu Linux once). Regards, F. Thanks. Andreas On 18/08/2011 1:19, Eric Bennett wrote: John, Since so many people have said it's flawless, I'd like to point out this is not always the case. The particular version of the particular package that we have installs some system libraries that caused a program I use on a moderately frequent basis to crash every time I tried to open a file on a network drive. It took me about 9 months to figure out what the cause was, during which time I had to manually copy things to the local drive before I could open them in that particular program. The vendor of the encryption software has a newer version but our IT department is using an older version. There is another workaround but it's kind of a hack. So I'd say problems are very rare, but if you run into strange behavior, don't rule out encryption as a possible cause. -Eric
Re: [ccp4bb] Sequence Alignment Question
You can try this site: http://espript.ibcp.fr/ESPript/cgi-bin/ESPript.cgi If you have .pdb for one of your sequences, you'll be able to show secondary structure also. vitali On Thu, Aug 18, 2011 at 6:31 PM, Yuri yuri.pom...@ufl.edu wrote: Hello Everyone, A little off topic but, what is a good way to show (publication quality) multiple sequence alignment? I am trying to show conserved regions in related proteins from different organisms. Thank you -- Yuri Pompeu
[ccp4bb] Microcrystal cryo
Hi all, I was wondering with the all of the advances in microbeam technology and hardware, what is the best methods for cryoprotecting microcrystals? Are oils better than solutions? How do you address the excess liquid issues? Is there a way to test the conditions prior to shipping it off to the synchrotron? Tips and tricks would be appreciated and I'll make a summary of the replies for future archive searchers like myself. Thanks in advance, Katherine
Re: [ccp4bb] more Computer encryption matters
For anything other than the most intensive I/O operations, recent processors will give you very respectable performance. I don't encrypt whole drives but I do have some AES-encrypted disk images in Snow Leopard, and I get about 38 MB/sec throughput copying (using cp) and 60 MB/sec reading (while also calculating cksum) for files of several hundred megabytes in size. I only have one drive, so the write test includes the time it takes to read the data from the unencrypted hard drive before writing back to the disk image on the same volume. The process that handles the encryption only hits about 30% CPU use while writing and 40% while reading so I assume my hard drive is the limiting factor. If I repeat the read test, so presumably the encrypted data is already cached, it hits over 90 MB/sec throughput and about 60% of a single core is busy. These numbers are for a 2.93 GHz core i7 iMac with the HDS722020ALA330 Hitachi drive. I believe this is the 870 series chip which does _not_ have the new AES instruction set on-chip. -Eric On Aug 18, 2011, at 5:50 PM, William G. Scott wrote: OS X 10.7 enables you to do whole-drive encryption. Here is a description from Arse Technica: http://arstechnica.com/apple/reviews/2011/07/mac-os-x-10-7.ars/13 I ain't never tried it myself. 10.7 seems to run slow enough as it is. -- Bill
[ccp4bb] Off topic_protein degradation.
Dear all, I am trying to crystallize a protein for which the yield and solubility were both fine. However, this protein has a severe problem of degradation. When stored at RT, the protein will degrade madly into pieces, while stored at 4 degree, the degradation is much slower and a relatively stable truncate form can be get. I am going to try to crystallize the protein at 4 degree, however I still want to understand what's going on there at RT because this protein was supposed to be very stable, it is Cys rich, and the 6 Cys were predicted to form 3 disulfide bonds which hold the protein as a globule, how can a protein with 3 stabilizing disulfide bond be fully degraded like this? Is there a possibility of spontaneous disulfide bond breakage at pH 8 ? Another question is I tried limited proteolysis with this protein, however even at 1:1000(w/w, chymotrypsin), the protein is degraded into pieces in about 2 hrs (again, a relatively stable truncated form can be get between 10 min and 30 min). I am wondering how is the crystallization probability correlated with proteolysis stability? Does this phenomenon indicate that the crystallization probability of my protein is pretty low? Any comments would be greatly appreciated. Bei 2011-08-15
Re: [ccp4bb] Sequence Alignment Question
Use ALINE sequence editor. if you multiple sequence alignment file from clustalW, you can open in ALINE software and generate publication quality of image. http://crystal.bcs.uwa.edu.au/px/charlie/software/aline/ --- On Thu, 18/8/11, Yuri yuri.pom...@ufl.edu wrote: From: Yuri yuri.pom...@ufl.edu Subject: [ccp4bb] Sequence Alignment Question To: CCP4BB@JISCMAIL.AC.UK Date: Thursday, 18 August, 2011, 5:31 PM Hello Everyone, A little off topic but, what is a good way to show (publication quality) multiple sequence alignment? I am trying to show conserved regions in related proteins from different organisms. Thank you -- Yuri Pompeu
Re: [ccp4bb] structure based superposition
Hi Suda, You can do this in Coot by loading the two structures, then using the tool Calculate- SSM superpose. The rmsd value and sequence identity should be reported within your terminal window. Hope that helps. -Joe Date: Thu, 18 Aug 2011 14:40:32 +0530 From: biobud...@gmail.com Subject: [ccp4bb] structure based superposition To: CCP4BB@JISCMAIL.AC.UK Dear all, I would like to know the tools/servers/programs that can be used for structure based superposition of two or more proteins. Please help me out..!! Thanks, -Suda
Re: [ccp4bb] Sequence Alignment Question
Yuri wrote: Hello Everyone, A little off topic but, what is a good way to show (publication quality) multiple sequence alignment? I am trying to show conserved regions in related proteins from different organisms. Thank you -- Yuri Pompeu or clustalw, e.g. http://npsa-pbil.ibcp.fr/cgi-bin/align_clustalw.pl You can save the HTML to your disk and edit it with mozilla (seamonkey), print to pdf, or grab screenshot for a gif. Color is limited to characters not background, which in my opinion looks better anyway. One could use photoshop on the gif to color background - but then maybe easier to use ESPript
