Re: [ccp4bb] Off Topic: Web or e-tools for booking instrument time
Hi All, I have used MRBS http://mrbs.sourceforge.net/ to manage booking of a large number of instruments for a few years. Free, open source, simple, local installation, works very well. regards, Dmitry -- Dr. Dmitry Veprintsev Biomolecular Research Laboratory, OFLC/103 Paul Scherrer Institut 5232 Villigen PSI Switzerland Tel +41 (0) 56 310 5246; Fax +41 (0)56 310 5288 dmitry.veprint...@psi.ch http://www.psi.ch/~veprintsev_d
Re: [ccp4bb] crystallizing a complex that's sensitive to ionic strength
Dear Hua, adding water as suggested by Jan Kern could also be accomplished in a more sophisticated way by using dialysis buttons. They require large volumes, though, 5mul is the minimum as far as I know. At the fancy end of this you could try the TOPAZ system by fluidigm. At the ECM in Darmstadt one of the companies presented a cheap, plasitc based version of this which looked quite appealing to me. Maybe it was the CrystalHarp from Molecular Dimensions, but I am not sure. Cheers, Tim On Sat, Feb 26, 2011 at 09:13:49PM -0500, Hua Yuan wrote: Dear CCP4 community members, I've been trying to crystallize a protein complex that's very sensitive to ionic strength, i.e., lower salt (~0.3M) will cause precipitation of the complex but higher salt (~0.5 M) breaks the complex apart. The interaction that holds the complex is probably mainly ionic type. The crystals I got so far has only one component of the complex from which all the crystallization conditions have high salt such as 2M Ammonium Sulfate in them. Besides repeatly screening many crystallization conditions, I was wondering whether is any way to work around this problem. Your suggestions would be greatly appreciated! Thanks, Hua -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A signature.asc Description: Digital signature
[ccp4bb] coot
Hello everybody, Currently I am refining my 6 x 220 amino acid structure and I was wondering if COOT is automatically writing a kind of protocol what I am changing in my pdb file when I am fitting-in new residues or mutate amino acids. If so where can I find it? Thanks a lot, Stefanie Dr. Stefanie Freitag-Pohl Durham University Chemistry Dept South Road Durham. DH1 3LE Tel: 0191 3342143 Email: stefanie.freitag-p...@durham.ac.uk
Re: [ccp4bb] Density sharpening with Truncate?
Hi, I'm on Garib's side here. The way the maximum likelihood targets work, the variances are defined relative to the average intensity in a resolution shell, so if you change the falloff the variances will change in the same way. In fact, one way to implement maximum likelihood refinement is in terms of E-values, from which the falloff has been removed. If your B-factors didn't run into hard limits (which, as Garib points out, they will when you make the data non-physical) you would end up with the same model if you refined against sharpened data, except the B-factors would be lower. The other thing that will change if you sharpen the data is that the R-factors will be higher, because the poorly-fit higher-resolution terms will contribute more to the sums. And that's probably not what you want when you might already have a hard time getting a low resolution structure past the freeR police! This is a case where intuition can lead you astray. Intuition might suggest that, if you sharpen the data, the refinement program should pay more attention to fitting the high resolution detail, but the likelihood target doesn't look at the data the same way you do when you look at a map. The fact that you can define the target in terms of E-values means that, if your model and data are both good, the likelihood target can be thought of as sharpening the data anyway. Best wishes, Randy Read On 28 Feb 2011, at 09:02, Dirk Kostrewa wrote: Dear CCP4ers, I really would sharpen the structure factors, not only the electron density maps. The simple reason is: if sharpening emphasizes enough information at higher resolution to help interpreting the electron density maps, refinement will also benefit from this information. Of course, the mean B-factor of the refined structure will be lower by the sharpening B-factor, but since B-factor sharpening is usually done with lower resolution data, the Wilson B-factor is usually very high, and thus far, I didn't run into problems with B-factors crashing at the lower limit. The sharpening B-factor can easily reach values in the -100s A**2, not only -10 to -50 A**2. Axel Brunger has published several papers about how to estimate a good sharpening B-factor (a recent one with references is Brunger et al. Acta Cryst D65, 128-133). He usually describes map sharpening, but B-factor sharpening of structure factors seems to be done routinely for virus structures in Steve Harrisons lab. One word of caution: the B-factor sharpening should be correctly described not only in the publication but also in the PDB deposition (if refinement was done against sharpened structure factors, the refinement statistics can only be reproduced using these structure factors). The original structure factors can be easily reproduced by applying back the negative sharpening B-factor. Best regards, Dirk. Am 26.02.11 01:09, schrieb Garib N Murshudov: I would not sharpen structure factors before refinement. It may cause problems with B value refinement (a lot of B values may stuck around 2 or minimum B). One must remember that not all atoms in crystal have same Bvalue. There is a distribution of Bvalues. However maps can be sharpened after refinement. It can be done directly in coot (I hope this version of coot is now widely available). Or if you are using refmac for refinement you can use: mapc sharpen # regularised map sharpening. Bvalues and regularisation parameters are calculated automatically or mapc sharpenBvalue # regularised map sharpening with specified Bvalue or mapc sharpenBvalue mapc sharpen alphavalue=0.1 # regularisation paramater. alpha=0 is simple sharpening. I am sure other programs have similar options. (I know CNS has and it has been used successfully by many people) regards Garib P.S. These options available from refmac v5.6 available from; www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac5.6_linux.tar.gz On 25 Feb 2011, at 23:57, Dima Klenchin wrote: At 05:39 PM 2/25/2011, Pete Meyer wrote: Or could anyone suggest a program that would be of help? CAD scaling with a scale factor of 1.0 and negative B-factor (isotropic or anisotropic) should do the trick. I haven't had much luck with density sharpening (at least at ~4-5 Angstroms), but others have apparently had some success with it. Alternatively, CCP4i task Run FFT does the job: 1. Take MTZ from Refmac output 2. Run FFT to create simple map with SigmaA-weighted phases (i.e., PHWT label). 3. In Infrequently used options, Apply B-factor scaling to F1, specify negative B-factor scaling value, usually within -10 to -50. - Dima -- *** Dirk Kostrewa Gene Center Munich, A5.07 Department of Biochemistry Ludwig-Maximilians-Universität München Feodor-Lynen-Str. 25 D-81377 Munich Germany Phone:+49-89-2180-76845
Re: [ccp4bb] coot
Hi, Stefanie Are those 6 molecules related by NCS? If so, you can model one first, and use transform_coords_molecule (imol, rtop) to generate others. I used to do this five times for a pentamer: output_pdb='template' for i in range (2,6): transform_coords_molecule (1, [[x1, y1, z1, x2, y2, z2, x3, y3, z3], [a, b, c]]) filename=output_pdb+str(i)+'.pdb' save_coordinates (1, filename) I think you can write all the the tranformation matrix out instead of the loop if they differ significantly. Others may have more experience. Best, Joe On Mon, Feb 28, 2011 at 6:32 PM, FREITAG-POHL S. stefanie.freitag-p...@durham.ac.uk wrote: Hello everybody, Currently I am refining my 6 x 220 amino acid structure and I was wondering if COOT is automatically writing a kind of protocol what I am changing in my pdb file when I am fitting-in new residues or mutate amino acids. If so where can I find it? Thanks a lot, Stefanie Dr. Stefanie Freitag-Pohl Durham University Chemistry Dept South Road Durham. DH1 3LE Tel: 0191 3342143 Email: stefanie.freitag-p...@durham.ac.uk
Re: [ccp4bb] Density sharpening with Truncate?
Dear Randy, thanks for your comment - a good point with the likelihood target estimated from E-values! So, in principle, there shouldn't be any difference in maximum-likelihood refinement using sharpened data or not. However, for curiosity, in one case at 4.3 A resolution and a sharpening B-factor of ~100 A**2, I compared ML refinement against the sharpened data with ML refinement against the original data and subsequent map sharpening: the R-factors were almost identical, and so were the electron density maps in most places. But in a some places, the maps were slightly different, with slightly less (!) model-bias and slightly clearer densities for the refinement against sharpened data. But those judgements were very subjective, and since a true structure at really high resolution is not available, I never could quantify this. Either, this was only anecdotal evidence, or there is still room for improvement in existing ML refinement programs. Best regards, Dirk. Am 28.02.11 11:40, schrieb Randy Read: Hi, I'm on Garib's side here. The way the maximum likelihood targets work, the variances are defined relative to the average intensity in a resolution shell, so if you change the falloff the variances will change in the same way. In fact, one way to implement maximum likelihood refinement is in terms of E-values, from which the falloff has been removed. If your B-factors didn't run into hard limits (which, as Garib points out, they will when you make the data non-physical) you would end up with the same model if you refined against sharpened data, except the B-factors would be lower. The other thing that will change if you sharpen the data is that the R-factors will be higher, because the poorly-fit higher-resolution terms will contribute more to the sums. And that's probably not what you want when you might already have a hard time getting a low resolution structure past the freeR police! This is a case where intuition can lead you astray. Intuition might suggest that, if you sharpen the data, the refinement program should pay more attention to fitting the high resolution detail, but the likelihood target doesn't look at the data the same way you do when you look at a map. The fact that you can define the target in terms of E-values means that, if your model and data are both good, the likelihood target can be thought of as sharpening the data anyway. Best wishes, Randy Read On 28 Feb 2011, at 09:02, Dirk Kostrewa wrote: Dear CCP4ers, I really would sharpen the structure factors, not only the electron density maps. The simple reason is: if sharpening emphasizes enough information at higher resolution to help interpreting the electron density maps, refinement will also benefit from this information. Of course, the mean B-factor of the refined structure will be lower by the sharpening B-factor, but since B-factor sharpening is usually done with lower resolution data, the Wilson B-factor is usually very high, and thus far, I didn't run into problems with B-factors crashing at the lower limit. The sharpening B-factor can easily reach values in the -100s A**2, not only -10 to -50 A**2. Axel Brunger has published several papers about how to estimate a good sharpening B-factor (a recent one with references is Brunger et al. Acta Cryst D65, 128-133). He usually describes map sharpening, but B-factor sharpening of structure factors seems to be done routinely for virus structures in Steve Harrisons lab. One word of caution: the B-factor sharpening should be correctly described not only in the publication but also in the PDB deposition (if refinement was done against sharpened structure factors, the refinement statistics can only be reproduced using these structure factors). The original structure factors can be easily reproduced by applying back the negative sharpening B-factor. Best regards, Dirk. Am 26.02.11 01:09, schrieb Garib N Murshudov: I would not sharpen structure factors before refinement. It may cause problems with B value refinement (a lot of B values may stuck around 2 or minimum B). One must remember that not all atoms in crystal have same Bvalue. There is a distribution of Bvalues. However maps can be sharpened after refinement. It can be done directly in coot (I hope this version of coot is now widely available). Or if you are using refmac for refinement you can use: mapc sharpen # regularised map sharpening. Bvalues and regularisation parameters are calculated automatically or mapc sharpenBvalue # regularised map sharpening with specified Bvalue or mapc sharpenBvalue mapc sharpen alphavalue=0.1# regularisation paramater. alpha=0 is simple sharpening. I am sure other programs have similar options. (I know CNS has and it has been used successfully by many people) regards Garib P.S. These options available from refmac v5.6 available from;
[ccp4bb] Postdoc position available, University of Bristol, UK
Dear all, I have a 3 yr postdoc position available in my lab (Biochemistry, Bristol), starting early/mid April. Please see below for further particulars. Informal enquires welcome, though full applications MUST be made via the University of Bristol website (http://www.bris.ac.uk/boris/jobs/feeds/ads?ID=93852). Cheers, Paul Research Assistant (ref. 16077) School of Biochemistry Contract: Fixed Term Contract (36 months) Salary:£29,972 - £33,734 Grade:Level a in Pathway 2 Closing date for applications:9:00am 22 Mar 2011 Anticipated interview date:01 Apr 2011 Description Working in the group of Dr Paul Race, you will undertake a BBSRC funded research project investigating the structural basis of natural product biosynthesis in terrestrial bacteria. You will have (or shortly have) a PhD in chemistry, biochemistry or a related discipline, and a proven track record in recombinant protein expression, purification and crystallisation, allied to significant experience in the determination of protein structures using macromolecular X-ray crystallography. Previous experience in electron and/or cryo-electron microscopy and a background in structural enzymology would be considered advantageous. You should be an enthusiastic and innovative scientist, a good team worker and an excellent communicator. The position is full-time and funding is available for three years currently. If successful, you may be appointed either on a fixed term or a permanent contract depending on the extent of your previous relevant research experience. Further information can be found at www.bristol.ac.uk/personnel/ftc/ Dr Paul Race Royal Society URF School of Biochemistry University of Bristol BS8 1TD paul.r...@bristol.ac.uk Tel. +44 (0)117 331 2150 Fax. +44 (0)117 331 2168 http://www.bris.ac.uk/biochemistry/research/pr.html
[ccp4bb] AW: [ccp4bb] coot
Hi Zheng I think, it's much easier to go this way: Coot - Extensions - NCS - Copy NCS Chain or Copy NCS Residue Range Cheers Stefan -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Zheng Zhou Gesendet: Montag, 28. Februar 2011 12:13 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] coot Hi, Stefanie Are those 6 molecules related by NCS? If so, you can model one first, and use transform_coords_molecule (imol, rtop) to generate others. I used to do this five times for a pentamer: output_pdb='template' for i in range (2,6): transform_coords_molecule (1, [[x1, y1, z1, x2, y2, z2, x3, y3, z3], [a, b, c]]) filename=output_pdb+str(i)+'.pdb' save_coordinates (1, filename) I think you can write all the the tranformation matrix out instead of the loop if they differ significantly. Others may have more experience. Best, Joe On Mon, Feb 28, 2011 at 6:32 PM, FREITAG-POHL S. stefanie.freitag-p...@durham.ac.uk wrote: Hello everybody, Currently I am refining my 6 x 220 amino acid structure and I was wondering if COOT is automatically writing a kind of protocol what I am changing in my pdb file when I am fitting-in new residues or mutate amino acids. If so where can I find it? Thanks a lot, Stefanie Dr. Stefanie Freitag-Pohl Durham University Chemistry Dept South Road Durham. DH1 3LE Tel: 0191 3342143 Email: stefanie.freitag-p...@durham.ac.uk
Re: [ccp4bb] Teaching powerpoints
I have brought my collection of teaching powerpoints etc. up to date. They are available free for educational purposes. Please send me an email if you wish to receive the password for accessing them. If you previously obtained this password from me it should still be valid. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-39-3021 or -3068 Fax. +49-551-39-22582
Re: [ccp4bb] CCP4 for iphones
In a sentence, primarily due to cost and power constraints mobile devices don't (currently) have the horsepower to do any serious *generic* number crunching, as would be required for anything of interest to this community. On the topic of using otherwise-idle compute time, our group has a publicly available service for doing molecular replacement which accesses a federation of computing centers across the US (through Open Science Grid): https://portal.nebiogrid.org/secure/apps/wsmr/ We regularly secure 50-150,000 hours per day of computing time from OSG. We're in the process of improving this and adding in additional services. Watch this space. For those with more of an interest on this topic, you can read on below. Regards, Ian This thread raises some interesting questions, but indicates a lack of understanding of the difference between what a mobile device like an iPhone, iPad, or Android can do compared to a rack-mounted server, desktop computer, or even laptop.The number crunching mobile devices are capable of is for specific sorts of data like audio and video codecs which are offloaded to specialized hardware and which can't (currently) be reused for other applications (like protein structure studies). GPUs are showing how this can change, but I wouldn't hold your breath. I think power and battery life will continue to be challenges for mobile devices for a long time, so even if generic computing ability catches up with conventional desktop/server capabilities, few people will want their batteries drained by their device running continuously doing an MD simulation or structure refinement. On 2/25/11 5:01 PM, Xiaoguang Xue wrote: Well, maybe building a distributed computing network （Like Fold@Home) by iphone is an improvement of the clusters. Let's think about a phenomenon, the most common functions of our iphone are calling, playing music, and maybe gaming, so most of the time the phone is idle. Why don't we try to use these idle computing time to help us doing some more important and interesting things, like determining the proteins structures US-based non-commercial researchers can access Open Science Grid (http://www.opensciencegrid.org/), which consists of a federation of about 80,000 compute cores, by registering for a certificate and joining (or forming) a Virtual Organization. We host a Virtual Organization in OSG called SBGrid which is open to all SBGrid consortium members (http://sbgrid.org/). We regularly get 2000-4000 compute cores from OSG for extended periods (12-96 hours), so it is a very powerful resource. Another alternative for structural biologists who could benefit from 1000s of compute cores is to get an allocation at a national supercomputing center. In the US, NERSC or TeraGrid are good routes for this, and many options exist. In Europe EGI and DEISA provide a similar one stop shop for federated grid computing and supercomputing center access. http://www.nersc.gov/ https://www.teragrid.org/ http://www.egi.eu/ http://www.deisa.eu/ Finally, you can benefit from the millions of desktop computers out there with super-powerful compute cores and GPUs that spend most of the time (often 90%) completely idle using screen saver computing. Here there is really only one option which is BOINC, developed by the group that created SETI@Home. Rosetta is (sort-of) available this way through Rosetta@home, developed by the Baker Lab. http://boinc.berkeley.edu/ http://boinc.bakerlab.org/ I also noticed that there is some progress in grid computing on iphone and PS3. So I think it's possible to apply this technique to structural biology. http://www.sciencedaily.com/releases/2010/04/100413072040.htm I think adding iPhone to the title of that article was just to attract readers. They are only using the standard web-browsing features available on pretty much any smart phone or mobile device to view web-portal views of computational infrastructure. All the actual computing was done on PS3s (and only 16 of them). In other words, if you consider browsing to EBI or RCSB to access some sequence alignment program or view some protein structures, then you can say I've used an iPhone for grid computing. Most people, however, would question the accuracy of this association.
Re: [ccp4bb] CCP4 for iphones
On 2/25/11 5:41 PM, Nat Echols wrote: On Fri, Feb 25, 2011 at 2:10 PM, Sean Seaver s...@p212121.com wrote: I've been curious if there has been discussion about moving data processing and refinement to a software as a service (SaaS) deployment. If programs were web accessible then it may save researchers time and trouble (maintaining and installing software). In turn, one could then process data via their iphone. The computational demand would be enormous and personally have a hard time even doing a back of the envelope calculation. The demand could be offset such as by limiting jobs or the number of users, etc... It will be interesting to see how mobile plays a role in crystallography. SBGrid has done something like this for massively parallel MR searches: https://portal.nebiogrid.org/secure/apps/wsmr/ But that's a massively parallel and highly distributed calculation, which isn't what crystallographers do most of the time. Nor do they need to be particularly mobile in an era of remote synchrotron data collection. Nat, thanks for commenting on this. As the person who has developed it, I'm glad someone has noticed the connection between the web-based application (well, really just an application wrapper, since it uses CCP4 software underneath) and what it is actually doing behind the scenes. It seems to us (within SBGrid) that there are quite a few applications that can benefit from access to large scale computational infrastructure. Sometimes having that resource available will allow people to ask new questions or pose old questions in a new way. We're always happy to talk to people who have ideas for new computational workflows or applications that can benefit from 10s of thousands of compute cores or that process TB of data. And of course the underlying resources are available to others to access themselves (see another post I made on this same thread about an hour ago). I have a lot of other objections to the idea of doing everything as a webapp, but that's a separate rant. I do, however, like the idea of using multi-touch interfaces for model-building, but you need something at least the size of an iPad for that to be more productive than using a traditional computer with a mouse. I agree that not everything should be done as a web app. When high-functionality UI features are required, developing these with CSS, jQuery, AJAX, HTML5, Java, etc. is super time consuming, compared with conventional integrated UI toolkits (Tcl/TK, Qt, Cocoa, .NET, etc.). Similarly when significant "real-time" data processing is required, or if multiple applications are interacting with the same data, then the UI (graphical or otherwise) needs to be "close" to the user data, and not stuck messing around with web browsers (which can't really be scripted) and web forms. I got a 21" HP multi-touch screen last year to explore improved touch-based interfaces for structural biology applications, however it doesn't work (properly) under OS X, and I'm not inclined to shift to a Windows based environment to develop for it. Hopefully some standard USB interfaces/drivers/libraries (events) will appear soon so the iPad and other tablets aren't the exclusive domain for touch-based applications. Ian
[ccp4bb] Calculating Difference Maps Between an RCSB data set and an mtz (Different Ligand)
Trying to calculate a difference map from a dataset downloaded from the RCSB and one I have. The following applies: Object find the difference between two bound ligands of the same structure in the same space group. My following work path has been: 1) Convert mmCIF to mtz (RCSB data set) 2) Use CAD to combine them 3) Use FFT to generate the diff map If I remember correctly, I think I am missing a scaling step somewhere. Any thoughts? Scott -- Scott D. Pegan, Ph.D. Assistant Professor Chemistry Biochemistry University of Denver Office: 303 871 2533 Fax: 303 871 2254
Re: [ccp4bb] Calculating Difference Maps Between an RCSB data set and an mtz (Different Ligand)
I just looked at a previous thread by Dale Tronrud that explains this. here it is: Re: [ccp4bb] Fo-Fo Difference Map Dale Tronrud Mon, 03 May 2010 16:19:46 -0700 I've struggled with getting CCP4 to calculate Fo-Fo maps, since I usually use other software. The tricks are that the data sets have to be scaled to each other in reciprocal space, and the maps calculated with the same cell constants (which will be a lie for at least one of them). The procedure I used the last time I did this was 1) Create a master mtz file with F-holo, F-apo, Fc-apo, Phic-apo. UseReflection Data Utilities, Merge Mtz Files (Cad). Don't includethe H, K, and L columns explicitly, despite the default. 2) Scale F-holo and F-apo. Use Experimental Phasing, Data Preparation,Scale and Analyse Data Sets, Scale refinement using Scaleit. Don'tinclude anomalous differences unless your interest is in changinganomalous scatterers. My notes indicate that Fhscal works better butdoes not have anisotropic scaling. If your two data sets do not differanisotropically try Fhscal. 3) Enter Coot. a) Load apo coordinates. b) Open mtz, calculate map F-holo, phic-apo. This is done with File.Open Mtz,mmCIF, fcf or phs... c) Open mtz, calculate map F-apo, phic-apo d) Calculate difference map. Extensions.Maps... . Make a Difference Map... e) Find difference map peaks. The greater the difference in cell constants the greater the noise in the map. I think the high resolution cutoff for the maps should be 2 A delta/(A+delta) where A is the cell edge with the largest change, and delta is the amount of change (in Angstrom). Basically a 1A change for a 100A edge would require a 2A resolution limit. A 5A change would imply a 10A cutoff and a very boring map. I would appreciate feedback on this procedure, if you find it hard to understand or it doesn't work. Certainly the Phenix solution looks simpler. Dale Tronrud Replacing the Coot step by FFT works too. vincent Le 2/28/11 5:26 PM, Scott Pegan a écrit : Trying to calculate a difference map from a dataset downloaded from the RCSB and one I have. The following applies: Object find the difference between two bound ligands of the same structure in the same space group. My following work path has been: 1) Convert mmCIF to mtz (RCSB data set) 2) Use CAD to combine them 3) Use FFT to generate the diff map If I remember correctly, I think I am missing a scaling step somewhere. Any thoughts? Scott -- Scott D. Pegan, Ph.D. Assistant Professor Chemistry Biochemistry University of Denver Office: 303 871 2533 Fax: 303 871 2254 -- Vincent Chaptal Institut de Biologie et Chimie des Protéines Drug Resistance modulation and mechanism 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 16
Re: [ccp4bb] crystallizing a complex that's sensitive to ionic strength
Have you tried adding water to your reservoir and allowing it to vapor diffuse into the drop? Kris Kris F. Tesh, Ph. D. Department of Biology and Biochemistry University of Houston - Original Message From: Tim Gruene t...@shelx.uni-ac.gwdg.de To: CCP4BB@JISCMAIL.AC.UK Sent: Mon, February 28, 2011 3:48:25 AM Subject: Re: [ccp4bb] crystallizing a complex that's sensitive to ionic strength Dear Hua, adding water as suggested by Jan Kern could also be accomplished in a more sophisticated way by using dialysis buttons. They require large volumes, though, 5mul is the minimum as far as I know. At the fancy end of this you could try the TOPAZ system by fluidigm. At the ECM in Darmstadt one of the companies presented a cheap, plasitc based version of this which looked quite appealing to me. Maybe it was the CrystalHarp from Molecular Dimensions, but I am not sure. Cheers, Tim On Sat, Feb 26, 2011 at 09:13:49PM -0500, Hua Yuan wrote: Dear CCP4 community members, I've been trying to crystallize a protein complex that's very sensitive to ionic strength, i.e., lower salt (~0.3M) will cause precipitation of the complex but higher salt (~0.5 M) breaks the complex apart. The interaction that holds the complex is probably mainly ionic type. The crystals I got so far has only one component of the complex from which all the crystallization conditions have high salt such as 2M Ammonium Sulfate in them. Besides repeatly screening many crystallization conditions, I was wondering whether is any way to work around this problem. Your suggestions would be greatly appreciated! Thanks, Hua -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A
Re: [ccp4bb] Calculating Difference Maps Between an RCSB data set and an mtz (Different Ligand)
Replacing the Coot step by FFT works too. An additional benefit of the Coot approach is that you can use LSQ-matched maps and maps on different grids and space groups. (I was under the impression that that was not quite so easy with FFT.) Also worth noting, Coot does not (yet) do auto-scaling. Paul.
Re: [ccp4bb] Calculating Difference Maps Between an RCSB data set and an mtz (Different Ligand)
Yes - you are. - There are some extra steps. Download pdbs and mtz files csymmmatch -pdbin-ref 1.pdb -pdbin 2.pdb -origin-hand -pdbout 2-to-1.pdb That checks they are on same origin and symmetry equivalent. refmac for 1.pdb refmac for 2-to-1.pdb cad to merge two refmac outputs. You will have to rename columns you want Then each Fobs will be scaled to the matching FC and that may be good enough. But you may need to worry about different B values. You can use SCALEIT to match everything to one of the FPs Then fft Eleanor I merge data - calculate my own On 02/28/2011 04:26 PM, Scott Pegan wrote: Trying to calculate a difference map from a dataset downloaded from the RCSB and one I have. The following applies: Object find the difference between two bound ligands of the same structure in the same space group. My following work path has been: 1) Convert mmCIF to mtz (RCSB data set) 2) Use CAD to combine them 3) Use FFT to generate the diff map If I remember correctly, I think I am missing a scaling step somewhere. Any thoughts? Scott
Re: [ccp4bb] Calculating Difference Maps Between an RCSB data set and an mtz (Different Ligand)
2) Scale F-holo and F-apo. Use Experimental Phasing, Data Preparation, Scale and Analyse Data Sets, Scale refinement using Scaleit. Don't include anomalous differences unless your interest is in changing anomalous scatterers. My notes indicate that Fhscal works better but does not have anisotropic scaling. If your two data sets do not differ anisotropically try Fhscal. This is not a problem. First scale anisotropically with your favourite program. Then the Kraut scaling correction using FHSCAL is a small correction on top of this, so just rescale the anisotropically-scaled output using FHSCAL. I didn't include an anisotropic scaling option in FHSCAL for the simple reason that this option was already available in other programs. The greater the difference in cell constants the greater the noise in the map. I think the high resolution cutoff for the maps should be 2 A delta/(A+delta) where A is the cell edge with the largest change, and delta is the amount of change (in Angstrom). Basically a 1A change for a 100A edge would require a 2A resolution limit. A 5A change would imply a 10A cutoff and a very boring map. I would appreciate feedback on this procedure, if you find it hard to understand or it doesn't work. Certainly the Phenix solution looks simpler. Dale See this thread: http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg15533.html -- Ian
[ccp4bb] stuck with COOT installation in openSUSE 11.3
Hello, I could not open the COOT GUI after installing either from 'coot-0.6.1-binary-Linux-x86_64-centos-5-gtk2.tar.gz' or from 'coot-0.6.2-pre-1-revision-3205-binary-Linux-x86_64-centos-5-gtk2.tar.gz' I used the following commands: 1. from /usr/loca/src sudo tar xvzf *.gz as suggested in http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/COOT#Installing_Coot_on_Linux 2. I created the following link by typing sudo ln -s /usr/local/src/coot-Linux-x86_64-centos-5-gtk2/bin/coot /usr/local/bin/coot After I run the command 'coot' I got the following error: hena@dl403a-2:~ coot COOT_PREFIX is /usr/local /usr/local/bin/coot-real /usr/local/bin/coot: line 247: /usr/local/bin/coot-real: No such file or directory /usr/local/bin/coot: line 253: /usr/local/bin/guile: No such file or directory hena@dl403a-2:~ Then I link the whole 'bin' directory as follows: sudo ln -s /usr/local/src/coot-Linux-x86_64-centos-5-gtk2/bin/ /usr/local/bin/ and I got the following error after running 'coot': hena@dl403a-2:~ coot COOT_PREFIX is /usr/local/src/coot-Linux-x86_64-centos-5-gtk2 /usr/local/src/coot-Linux-x86_64-centos-5-gtk2/bin/coot-real /usr/local/src/coot-Linux-x86_64-centos-5-gtk2/bin/coot-real: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory coot-exe: /usr/local/src/coot-Linux-x86_64-centos-5-gtk2/bin/coot-real coot-version: /usr/local/src/coot-Linux-x86_64-centos-5-gtk2/bin/coot-real /usr/local/src/coot-Linux-x86_64-centos-5-gtk2/bin/coot-real: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory platform: /bin/uname core: #f No core file found. No debugging This is not helpful. Please turn on core dumps before sending a crash report hena@dl403a-2:~ I checked that I have 'libpng12.so.0' file in different 'lib' folders. I successfully installed other programs like CCP4, CNS and PHENIX in my openSUSE 11.3 Can someone advise what's wrong I am doing? Many thanks... hena
Re: [ccp4bb] stuck with COOT installation in openSUSE 11.3
Hello Hena, maybe the libpng12.so.0 libraries on your system happen to be all 32-bit versions. You installed the 64-bit version (because of the x86_64 in the name of the tar-archive), therefore you also require a 64-bit version of the libpng12.so.0. Do you have such a file in /usr/lib, and if so, is it really a file or maybe only a link to a file which once existed on your system? Cheers, Tim On Mon, Feb 28, 2011 at 01:39:37PM -0800, Hena Dutta wrote: Hello, I could not open the COOT GUI after installing either from 'coot-0.6.1-binary-Linux-x86_64-centos-5-gtk2.tar.gz' or from 'coot-0.6.2-pre-1-revision-3205-binary-Linux-x86_64-centos-5-gtk2.tar.gz' I used the following commands: 1. from /usr/loca/src sudo tar xvzf *.gz as suggested in http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/COOT#Installing_Coot_on_Linux 2. I created the following link by typing sudo ln -s /usr/local/src/coot-Linux-x86_64-centos-5-gtk2/bin/coot /usr/local/bin/coot After I run the command 'coot' I got the following error: hena@dl403a-2:~ coot COOT_PREFIX is /usr/local /usr/local/bin/coot-real /usr/local/bin/coot: line 247: /usr/local/bin/coot-real: No such file or directory /usr/local/bin/coot: line 253: /usr/local/bin/guile: No such file or directory hena@dl403a-2:~ Then I link the whole 'bin' directory as follows: sudo ln -s /usr/local/src/coot-Linux-x86_64-centos-5-gtk2/bin/ /usr/local/bin/ and I got the following error after running 'coot': hena@dl403a-2:~ coot COOT_PREFIX is /usr/local/src/coot-Linux-x86_64-centos-5-gtk2 /usr/local/src/coot-Linux-x86_64-centos-5-gtk2/bin/coot-real /usr/local/src/coot-Linux-x86_64-centos-5-gtk2/bin/coot-real: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory coot-exe: /usr/local/src/coot-Linux-x86_64-centos-5-gtk2/bin/coot-real coot-version: /usr/local/src/coot-Linux-x86_64-centos-5-gtk2/bin/coot-real /usr/local/src/coot-Linux-x86_64-centos-5-gtk2/bin/coot-real: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory platform: /bin/uname core: #f No core file found. No debugging This is not helpful. Please turn on core dumps before sending a crash report hena@dl403a-2:~ I checked that I have 'libpng12.so.0' file in different 'lib' folders. I successfully installed other programs like CCP4, CNS and PHENIX in my openSUSE 11.3 Can someone advise what's wrong I am doing? Many thanks... hena -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A signature.asc Description: Digital signature
