[ccp4bb] on NaCl and Tris for crystallization
Dear All, For the protein buffer for the crystallization purpose, if we buy from Sigma-Aldrich, which types of NaCl and Tris are much suitable? I am looking forward to getting your reply. Cheers, Acoot
Re: [ccp4bb] Copying R-free flags - possibly daft question.
Well there's a funny thing. It seems that this is already in xia2 (strange moment when I wade in there to make the change and found it already made, it seems from my logs in May) However, it seems that I have not actually released this version. My bad. An updated release will appear shortly. best wishes, Graeme On 5 Nov 2012, at 15:13, Graeme Winter wrote: > Thanks indeed Eleanor, when I get a moment I will add this too to the xia2 > cad script! > > Best wishes, > > Graeme > > > On 5 November 2012 11:37, Antony Oliver wrote: > Thanks Eleanor - guess I should have plumbed the depths of the CAD manual a > little further. > > Works perfectly. > > Antony. > > --- > Dr Antony W Oliver > Senior Research Fellow > CR-UK DNA Repair Enzymes Group > Genome Damage and Stability Centre > Science Park Road > University of Sussex > Falmer, Brighton, BN1 9RQ > > email: antony.oli...@sussex.ac.uk > tel (office): +44 (0)1273 678349 > tel (lab): +44 (0)1273 677512 > > On Nov 5, 2012, at 11:24 AM, Eleanor Dodson wrote: > > > Just give CAD the resolution cut off of the new data set.. > > Eleanor > > From the CAD documentation.. > > RESOLUTION [ RESOLUTION OVERALL ] | [RESOLUTION FILE_NUMBER > >] > > > > Use either: > > > > RESOLUTION OVERALL > > for overall resolution limits, or: > > RESOLUTION FILE_NUMBER > > to set input limit for FILE_NUMBER . > > , are the resolution limits for the data to be included, i.e. > > data are included for which > > (1/)**2 >= 4 sin**2theta/lambda**2 >=(1/)**2 > > NOTE: Defaults are 0.1 and 1000.0 Angstrom. > > > > > > On 5 Nov 2012, at 09:53, Antony Oliver wrote: > > > >> Am I worrying about something unnecessarily? > >> > >> I have several protein-drug datasets, all in the same spacegroup, but > >> wildly varying resolutions. > >> I wish to use the same reflections for calculating R-free in all cases. > >> > >> Using xia2 with a reference dataset for both indexing and R-free seems to > >> work fine, apart from the fact that the resulting mtz file, now contains > >> R-free labels for reflections that have no observations… i.e. taken from > >> the higher resolution "reference dataset"; see output below. > >> > >> I get essentially the same results using CAD to copy the R-free column > >> between mtzfiles…. > >> > >> Is this actually a problem - or is it just my innate sense of tidiness > >> that wants the resolution values to be the same? > >> > >> > >> Many thanks, > >> > >> Antony. > >> > >> Col SortMinMaxNum % Mean Mean Resolution > >> Type Column > >> num order Missing complete abs. LowHigh > >> label > >> > >>1 ASC 0 36 0 100.00 14.2 14.2 57.66 2.02 H > >> H > >>2 NONE 0 36 0 100.00 14.6 14.6 57.66 2.02 H > >> K > >>3 NONE 0 38 0 100.00 14.8 14.8 57.66 2.02 H > >> L > >>4 NONE0.019.0 132 99.18 9.52 9.52 57.40 2.02 I > >> FreeR_flag > >>5 NONE -30.6 10855.5 11647 28.03 202.72 203.43 57.66 3.17 J > >> IMEAN > >>6 NONE1.5 356.4 11647 28.0311.5211.52 57.66 3.17 Q > >> SIGIMEAN > >>7 NONE7.8 1040.0 11647 28.03 109.05 109.05 57.66 3.17 F > >> F > >>8 NONE1.423.8 11647 28.03 6.59 6.59 57.66 3.17 Q > >> SIGF > >> > >> > >> No. of reflections used in FILE STATISTICS16183 > >> > >> > >> > >> > >> > >> --- > >> Dr Antony W Oliver > >> Senior Research Fellow > >> CR-UK DNA Repair Enzymes Group > >> Genome Damage and Stability Centre > >> Science Park Road > >> University of Sussex > >> Falmer, Brighton, BN1 9RQ > >> > >> email: antony.oli...@sussex.ac.uk > >> tel (office): +44 (0)1273 678349 > >> tel (lab): +44 (0)1273 677512 > >> > > >
[ccp4bb] low resolution molecular replacement with partial model
Hi all, I was wondering if there are examples of successful MR with low resolution data (~7A). Our protein crystallized in the P21 (a= 111; b= 211, c=126; beta=99.7). We only have a partial search model (267 amino acids) that accounts for ~6% of the AU (however at 100% identity). Has anybody been successful in such situations? Thanks, Daniel
Re: [ccp4bb] low resolution molecular replacement with partial model
Dear Daniel, here is an example of MR at 7 A: http://www.pdb.org/pdb/explore/explore.do?structureId=4GZA http://www.ncbi.nlm.nih.gov/pubmed/23104057 Best wishes, Tomas On Tue, Nov 6, 2012 at 11:06 AM, Panne Daniel wrote: > Hi all, > > I was wondering if there are examples of successful MR with low resolution > data (~7A). Our protein crystallized in the P21 (a= 111; b= 211, c=126; > beta=99.7). We only have a partial search model (267 amino acids) that > accounts for ~6% of the AU (however at 100% identity). > > Has anybody been successful in such situations? > > Thanks, > Daniel
Re: [ccp4bb] low resolution molecular replacement with partial model
Dear Daniel, There are two questions here. First, is there likely to be enough signal to get a clear solution for the molecular replacement; second, will getting a solution for the molecular replacement be of any use to you? On the first point, we have some new ways of estimating the signal of a molecular replacement search in Phaser. These depend on the completeness of the model, the estimated error of the model (relative to the resolution of the data) and the number of reflections. With 100% identity, your model should be almost perfect at 7A resolution, which is in your favour, but 6% of the a.u. is very much against you. In any case, the calculations indicate that there would be a marginal signal in this case (predicting an LLG of about 16 for a correct solution). If you were lucky and the part of the structure you can model were the best-ordered part of the crystal, then you could do somewhat better and may even get a clear solution, which usually requires an LLG of about 50 or more. In contrast, molecular replacement calculations with ribosomes can give very clear solutions at resolutions below 10A, because there are so many reflections in a large problem and the models can be reasonably complete. So it's very case dependent. On the second point, it's hard to imagine what you would learn from this. There are no methods to complete a very incomplete model at such low resolution, and you're not modeling a complex so you wouldn't learn about interactions. However, if you had some kind of heavy atom derivative or anomalous scatterer bound, then there might just be enough information from this to help to find the sites, and thus bootstrap the structure solution. Best wishes, Randy Read On 6 Nov 2012, at 11:06, Panne Daniel wrote: > Hi all, > > I was wondering if there are examples of successful MR with low resolution > data (~7A). Our protein crystallized in the P21 (a= 111; b= 211, c=126; > beta=99.7). We only have a partial search model (267 amino acids) that > accounts for ~6% of the AU (however at 100% identity). > > Has anybody been successful in such situations? > > Thanks, > Daniel -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
[ccp4bb] shelx c/d/e from ccp4i
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear all, since there were more than one remark about the shelx c/d/e interface in ccp4 6.3.0 crashing I just tried myself. I DO get output from shelxc, unlike e.g. Shanti Pal Gangwar who opened one corresponding thread on this bb, but shelxc crashes because of improper conversion of the mtz-file to sca-format. Since sca-format is fixed format, the data ought to be rescaled to 9.99, something e.g. the program mtz2sca (http://shelx.uni-ac.gwdg.de/~tg/research/programs/mtz2x/mtz2sca/index.php) does by default. I know that several pipelines have had this problem with mtz2various, but I am not aware of a fix (I ran the ccp4 auto-update just now). I can recommend, however, that people either use Thomas Schneider's GUI hkl2map or run shelx c/d/e from the command line - it is really not difficult and explained e.g. in the tutorial available from my web-site. http://shelx.uni-ac.gwdg.de/~tg/teaching/anl-ccp4/index.php I copy this to ccp4-dev hoping that the ccp4i GUI gets fixed soon. I case there is a fix I am not aware of, I am sorry, no offence meant. There have just been many comments (also personal, off-board) and I hope this gives an answer to many of those who asked. Best, Tim - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iD8DBQFQmSSaUxlJ7aRr7hoRAlb3AJ49M4a3wS7invlq2eMgI9NseWMXDACguZgL 4B8Ghh3ifIafPDD9OdW4GlI= =kfmx -END PGP SIGNATURE-
Re: [ccp4bb] shelx c/d/e from ccp4i
In my hands shelxc/d/e pipeline as it is implemented in ccp4 is working perfectly. After slowing structure yesterday using hkl2map I resolved it using ccp4 to have faster access to buccaneer or ARP/wARP. Needless to say that I used data I have measured in the form of output.sca from SCALEPACK. So it is probably really only converting of MTZ to SCA that induces problem. Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 6, 2012, at 16:54 , Tim Gruene wrote: > -BEGIN PGP SIGNED MESSAGE- > Hash: SHA1 > > Dear all, > > since there were more than one remark about the shelx c/d/e interface > in ccp4 6.3.0 crashing I just tried myself. > > I DO get output from shelxc, unlike e.g. Shanti Pal Gangwar who opened > one corresponding thread on this bb, but shelxc crashes because of > improper conversion of the mtz-file to sca-format. > > Since sca-format is fixed format, the data ought to be rescaled to > 9.99, something e.g. the program mtz2sca > (http://shelx.uni-ac.gwdg.de/~tg/research/programs/mtz2x/mtz2sca/index.php) > does by default. > > I know that several pipelines have had this problem with mtz2various, > but I am not aware of a fix (I ran the ccp4 auto-update just now). > > I can recommend, however, that people either use Thomas Schneider's > GUI hkl2map or run shelx c/d/e from the command line - it is really > not difficult and explained e.g. in the tutorial available from my > web-site. > > http://shelx.uni-ac.gwdg.de/~tg/teaching/anl-ccp4/index.php > > I copy this to ccp4-dev hoping that the ccp4i GUI gets fixed soon. > I case there is a fix I am not aware of, I am sorry, no offence meant. > There have just been many comments (also personal, off-board) and I > hope this gives an answer to many of those who asked. > > Best, > Tim > > - -- > - -- > Dr Tim Gruene > Institut fuer anorganische Chemie > Tammannstr. 4 > D-37077 Goettingen > > GPG Key ID = A46BEE1A > > -BEGIN PGP SIGNATURE- > Version: GnuPG v1.4.12 (GNU/Linux) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ > > iD8DBQFQmSSaUxlJ7aRr7hoRAlb3AJ49M4a3wS7invlq2eMgI9NseWMXDACguZgL > 4B8Ghh3ifIafPDD9OdW4GlI= > =kfmx > -END PGP SIGNATURE-
Re: [ccp4bb] PhD position Diabetes
Hello, I would like if this job still is disponible and how do I apply. Thanls, Leonardo
Re: [ccp4bb] Coot 0.7 Saving Dialog opens behind main window
I agree, this is a frustrating "feature." I tend to work around this by pressing Cmd-` (back-tick) to cycle through the X11 windows (this works for other applications as well), or by running Coot from within the directory containing the PDB file and using Ctrl-S to save with auto-incremented (e.g. -coot-0.pdb) filenames without having to open the Save dialog. Cheers, Jared Jared Sampson Xiangpeng Kong Lab NYU Langone Medical Center kong.med.nyu.edu From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Eike Schulz [eike.sch...@embl.de] Sent: Tuesday, October 30, 2012 11:32 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Coot 0.7 Saving Dialog opens behind main window Dear Coot-users, I am running Coot-0.7 on OSX 10.6.8. Installation from the 'Scott'-package was no problem at all it runs very smoothly. However, whenever I want to save the coordinates the saving dialog open -behind- the main window. To be more precise: the coordinate molecule selector opens in front of it but the -file name selector- opens behind the main window. This is over the time a bit frustrating when you have to minimize/move the main window every time you want to save your structure. Does it happen to others as well, or is this specific to my system? If its possible, how could it be changed to open in front of the main window? Best regards Eike
[ccp4bb] how to find and add water molecules in electron density map in coot??
I have to put water molecules in my model but It's difficult to judge that electron density is for water of something else. How to differentiate How the electron density look like for metal ions like Ca and Na??? regards saleem
Re: [ccp4bb] how to find and add water molecules in electron density map in coot??
On Tue, Nov 6, 2012 at 12:06 PM, saleem raza wrote: > I have to put water molecules in my model but It's difficult to judge that > electron density is for water of something else. How to differentiate > > How the electron density look like for metal ions like Ca and Na??? Sodium can't be distinguished from water on the basis of electron density. You can use the bond valence method (e.g. a program like WASP) to identify likely sodium ions, but this requires good data and relatively high resolution. Calcium has nearly twice as many electrons as water, and should be very obvious in the Fo-Fc map (assuming you've built in a water to start with) unless it's only present at half occupancy. Depending on the wavelength you collected at and the quality of the data, you may also be able to see a peak in the anomalous difference map. The chemical environment tends to be more distinctive than sodium too. -Nat
[ccp4bb] What to put on Custom Declaration for shipped samples?
I was asked by our shipping folks what we should put on the Customs Declaration so that samples that we ship or that are shipped to us (in dewars, styrofoam boxes, and/or padded envelopes) would not be held up in Customs. I had them put: "Scientific samples of less than 1 mg of non-infectious, non-hazardous protein. No health hazard." but it has been so long that I have had to do so. I suppose I could name the exact protein, (e.g. hen egg white lysozyme), but maybe that is not a good idea. What wording do folks put on these forms nowadays? What works? Do I need to put the buffer components? Thanks for responses. Jim
Re: [ccp4bb] What to put on Custom Declaration for shipped samples?
Hi Jim, If there are magic words that always get items through customs, please let me know! In our experience, it is very hard to predict what will or won't be held up. Lucky the vast majority of items go through without an issue. We've had better luck using FedEx instead of TNT shipping although it shouldn't matter. Depending on the country, they may want the origin of the material (synthetic, animal derived, etc.). I would be as complete as possible in your description. I suspect this doesn't apply, but it's sometimes worth dividing samples as larger sizes can be more tightly regulated. Regards, Sean Seaver, PhD P212121 http://store.p212121.com/
Re: [ccp4bb] What to put on Custom Declaration for shipped samples?
Jim, dottore... Starting back traveling to synchrotrons in the beginning of 80 I say, do not volunteer information, more magic words you say, more papers you fetch, more faxes you send in advance more they will torture you. You do not need custom declaration anywhere (at least in Europe), in states I would drive We have send a fax with a full description of Polaroid 3000ASA in 1992 in Heathrow, and they ( security, I was ready to take them apart) burn these sensitive films on the purpose by X-rays on our way to Photon Factory. Many years after that in 2008, one of these people (I have very good memory) again in Heathrow told me - you have two choices - either irradiation or invasive check, and we will not be gentle. I choose irradiation. I will met him next time in a bar or a pub and will take very nice care of him :-) DO NOT VOLUNTEER INFORMATION, IT WILL BE AGAINST YOU…. If it is written non-infectious, they will read infectious, you will write non-hazardous - they will read hazardous, you will say lysozyme - they will read anthrax…. And the most terrible thing for you will be if they will apply frontal check, not selection which you may snick, but total check. Just go forward, take another person with you, takes doubles, go to different check-in points, system is working sporadically, increase your chance by multiplication FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 6, 2012, at 22:25 , Jim Pflugrath wrote: > I was asked by our shipping folks what we should put on the Customs > Declaration so that samples that we ship or that are shipped to us (in > dewars, styrofoam boxes, and/or padded envelopes) would not be held up in > Customs. > > I had them put: > > "Scientific samples of less than 1 mg of non-infectious, non-hazardous > protein. No health hazard." > > but it has been so long that I have had to do so. I suppose I could name the > exact protein, (e.g. hen egg white lysozyme), but maybe that is not a good > idea. > > What wording do folks put on these forms nowadays? What works? Do I need to > put the buffer components? > > Thanks for responses. > > Jim
[ccp4bb] Fwd: [ccp4bb] What to put on Custom Declaration for shipped samples?
May I add a little note: "Dewar" reads as a destructive device. "Thermos" reads as thermos, which the dewar is except for no relation to the Thermos trademark. Good luck, Boris Brumshtein -- Forwarded message -- From: Felix Frolow Date: Tue, Nov 6, 2012 at 1:32 PM Subject: Re: [ccp4bb] What to put on Custom Declaration for shipped samples? To: CCP4BB@jiscmail.ac.uk Jim, dottore... Starting back traveling to synchrotrons in the beginning of 80 I say, do not volunteer information, more magic words you say, more papers you fetch, more faxes you send in advance more they will torture you. You do not need custom declaration anywhere (at least in Europe), in states I would drive We have send a fax with a full description of Polaroid 3000ASA in 1992 in Heathrow, and they ( security, I was ready to take them apart) burn these sensitive films on the purpose by X-rays on our way to Photon Factory. Many years after that in 2008, one of these people (I have very good memory) again in Heathrow told me - you have two choices - either irradiation or invasive check, and we will not be gentle. I choose irradiation. I will met him next time in a bar or a pub and will take very nice care of him :-) DO NOT VOLUNTEER INFORMATION, IT WILL BE AGAINST YOU…. If it is written non-infectious, they will read infectious, you will write non-hazardous - they will read hazardous, you will say lysozyme - they will read anthrax…. And the most terrible thing for you will be if they will apply frontal check, not selection which you may snick, but total check. Just go forward, take another person with you, takes doubles, go to different check-in points, system is working sporadically, increase your chance by multiplication FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 6, 2012, at 22:25 , Jim Pflugrath wrote: > I was asked by our shipping folks what we should put on the Customs > Declaration so that samples that we ship or that are shipped to us (in > dewars, styrofoam boxes, and/or padded envelopes) would not be held up in > Customs. > > I had them put: > > "Scientific samples of less than 1 mg of non-infectious, non-hazardous > protein. No health hazard." > > but it has been so long that I have had to do so. I suppose I could name the > exact protein, (e.g. hen egg white lysozyme), but maybe that is not a good > idea. > > What wording do folks put on these forms nowadays? What works? Do I need to > put the buffer components? > > Thanks for responses. > > Jim
Re: [ccp4bb] What to put on Custom Declaration for shipped samples?
Can't say I've made Felix's experiences: I've never had problems and rarely funny looks -- a bit of patient explanation does the job. That's when flying with the dry shipper myself, so not quite what you asked; but I carry along a letter with nice departmental & university letter-head and important-looking signature, along the lines pasted at the bottom. phx On 06/11/2012 21:32, Felix Frolow wrote: Jim, dottore... Starting back traveling to synchrotrons in the beginning of 80 I say, do not volunteer information, more magic words you say, more papers you fetch, more faxes you send in advance more they will torture you. You do not need custom declaration anywhere (at least in Europe), in states I would drive We have send a fax with a full description of Polaroid 3000ASA in 1992 in Heathrow, and they ( security, I was ready to take them apart) burn these sensitive films on the purpose by X-rays on our way to Photon Factory. Many years after that in 2008, one of these people (I have very good memory) again in Heathrow told me - you have two choices - either irradiation or invasive check, and we will not be gentle. I choose irradiation. I will met him next time in a bar or a pub and will take very nice care of him :-) DO NOT VOLUNTEER INFORMATION, IT WILL BE AGAINST YOU…. If it is written non-infectious, they will read infectious, you will write non-hazardous - they will read hazardous, you will say lysozyme - they will read anthrax…. And the most terrible thing for you will be if they will apply frontal check, not selection which you may snick, but total check. Just go forward, take another person with you, takes doubles, go to different check-in points, system is working sporadically, increase your chance by multiplication FF Dr Felix Frolow Professor of Structural Biology and Biotechnology, Department of Molecular Microbiology and Biotechnology Tel Aviv University 69978, Israel Acta Crystallographica F, co-editor e-mail: mbfro...@post.tau.ac.il Tel: ++972-3640-8723 Fax: ++972-3640-9407 Cellular: 0547 459 608 On Nov 6, 2012, at 22:25 , Jim Pflugrath wrote: I was asked by our shipping folks what we should put on the Customs Declaration so that samples that we ship or that are shipped to us (in dewars, styrofoam boxes, and/or padded envelopes) would not be held up in Customs. I had them put: "Scientific samples of less than 1 mg of non-infectious, non-hazardous protein. No health hazard." but it has been so long that I have had to do so. I suppose I could name the exact protein, (e.g. hen egg white lysozyme), but maybe that is not a good idea. What wording do folks put on these forms nowadays? What works? Do I need to put the buffer components? Thanks for responses. Jim - This letter relates to the Dry Shipper being transported by on flight to/from the , from the . The package contains frozen protein crystals produced by the as part of a . These *non-toxic and non-hazardous proteins *were isolated from*/Escherichia coli/* using molecular biology recombinant techniques**as research samples for structural studies. *The samples DO NOT contain any animal or viral products in accordance with NCIE guidelines (reference: GUIDELINES FOR IMPORTATION #1114) and DO NOT have any biological activity*. In order to maintain the integrity and scientific value of the samples, they *SHOULD NOT* be removed from the container or left at room temperature, as this will change the temperature balance in the samples.Failure to follow these guidelines will result in the destruction of several months of scientific work.The container has been designed to maintain the samples at low temperature for the duration of the flight
