Re: [ccp4bb] Hampton's adjustable cryoloop
Hi Zhijie --
With all manipulations on the goniometer, I strongly advise what I
learnt from Elspeth Garman: practice, practice, practice... but not
with your real crystal! Take it down, put up a dummy pin, and take the
time play around. I imagine even a non-hollow pin can be bent without
throwing it off with sufficient practice -- though Weikai is right, with
those pins it'll be REALLY tough, the special Hampton pins are much
recommended, because they have a weak point, making them far easier to
bend. A little tool is also supplied.
I do not agree however that you need a beamline with Kappa -- indeed, if
you were at such a beamline, there would be no need to bend the loop!
(How often I've wished for it...) The un-bent loops fit perfectly well
into cryotongs, as long as you affix them to the base at the right
length; once bent, the pins may not fit anymore, but you can always
straighten them again before retrieving them.
Of course, if you've already harvested your crystal on a non-bendable
pin, this doesn't help; but we routinely bend the loop itself, by
pushing on the stem of the loop (close to where it attaches to the pin),
with a pipette tip cut into a sharp point simply with scissors (you want
something non-metal, so as not to conduct heat onto the sample.) It's
not exact, of course, and (again) takes some practice. But very
effective -- it's rescued umpteen datasets for us. But BEWARE: DO NOT
BREATHE WHILE DOING THIS! (Go figure.)
HTH
phx
On 07/06/2011 23:33, Li, Weikai wrote:
Hi Zhijie,
This loop is good if you have a long unit cell on one dimension and you can
align your crystal in a particular direction. You basically need a beamline
equipped with Kappa, which allows you to directly put the crystal on with the
plastic tube. A normal cryotong does not hold the bent loop.
Regards,
Weikai
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] On Behalf Of Zhijie Li
[zhijie...@utoronto.ca]
Sent: Tuesday, June 07, 2011 5:30 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Hampton's adjustable cryoloop
Hello,
I just noticed that Hampton Research carries this adjustable mounted cryoloop
(HR5-900):
http://hamptonresearch.com/product_detail.aspx?cid=24sid=136pid=385wlmailhtml:{35C92305-260C-4820-B40D-05B0D91A0A8F}mid://0065/!x-usc:http://hamptonresearch.com/product_detail.aspx?cid=24sid=136pid=385
This looks quite interesting to me, as it seems that not every synchrotron
station's configuration can allow the use of an extended arc.
I wonder if somebody here can share some insights or experiences about this
adjustable cryoloop. I once tried to bend my non-hollow stainless steel pin in
liquid nitrogen with tweezers. It didn't work - the pin was too stiff then I
lost my crystal in the end. I wonder if this cryoloop was designed such that
bending it would be easier.
Thanks in advance!
Zhijie
Re: [ccp4bb] nVidia Quadro 4000 and the stereo bracket
On 06/08/11 08:53, Joe Watts wrote: I don't know about the Quadro 4000, but with the FX3800 I had a hell of a time tracking down a 3 pin stereo bracket. I eventually was directed to a vendor that sold a bracket by an engineer from NVIDIA. PNY Technologies PNQFX3800 Stereo Bracket for Quadro FX 3800. This will plug directly into the board for the 3800, it probably will for the 4000, but I'd check the graphics card diagram first. PNY item # 900-50762--000 is available from various vendors. I bought mine from BH Photo. I do not have a 4000 to verify, but it seems like a decent bet that the same adapter would work for it. Also, it took forever to find out how to get it to work with NVIDIA 3D vision. As it turns out, you have to set stereo mode to 10 in the config file. I know it doesn't say that anywhere; they always say to set to 3 for hardware stereo. This will not work if you buy the 3 pin DIN and plug it into the board yourself. -Joe Watts This is covered in the README file for the Linux Quadro FX driver: http://us.download.nvidia.com/XFree86/Linux-x86_64/270.41.19/README/index.html Appendix B. X Config Options: http://us.download.nvidia.com/XFree86/Linux-x86_64/270.41.19/README/xconfigoptions.html Includes descriptions of the 11 different stereo options, along with a description of which graphics cards are required for compatibility. 10) NVIDIA 3D Vision mode for use with NVIDIA 3D Vision glasses. The NVIDIA 3D Vision infrared emitter must be connected to a USB port of your computer, and to the 3-pin DIN connector of a Quadro graphics board (based on G8xGL or higher GPU) before starting the X server. Hot-plugging the USB infrared stereo emitter is not yet supported. Also, 3D Vision Stereo Linux support requires a Linux kernel built with USB device filesystem (usbfs) and USB 2.0 support. Not presently supported on FreeBSD or Solaris. (For stereo mode 10, Quadro graphics cards with G8xGL or higher GPUs) -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] unsubscription request
On Wed, Jun 08, 2011 at 10:41:03AM -0400, Angela (Shaoxu) Li wrote: I wish to unsubscribe to the mailing list. But I'm unsure as to how I can do that. Your help will be greatly appreciated. In the headers of every email sent from the list are some helpful reminders: List-Help: http://jiscmail.ac.uk/cgi-bin/webadmin?LIST=CCP4BB, mailto:lists...@jiscmail.ac.uk?body=INFO%20CCP4BB List-Unsubscribe: mailto:ccp4bb-unsubscribe-requ...@jiscmail.ac.uk List-Subscribe: mailto:ccp4bb-subscribe-requ...@jiscmail.ac.uk List-Owner: mailto:ccp4bb-requ...@jiscmail.ac.uk List-Archive: http://jiscmail.ac.uk/cgi-bin/webadmin?LIST=CCP4BB -ben -- | Ben Eisenbraun | SBGrid Consortium | http://sbgrid.org | | Harvard Medical School | http://hms.harvard.edu |
Re: [ccp4bb] unsubscription request
Hi, What about the ccp4 web page, from which you can follow the link to http://www.ccp4.ac.uk/ccp4bb.php ? HTH, Fred. Angela (Shaoxu) Li wrote: Hi there, I wish to unsubscribe to the mailing list. But I'm unsure as to how I can do that. Your help will be greatly appreciated. Best wishes, Angela
[ccp4bb] Change cell parameter
Dear all, I have a P2 derivative dataset with beta=89.6. I try to change the beta to 90.4 to be consistent with the native dataset. Should I do sth with the HKL, like applying a matrix? Thanks a million! Best, Zhiyi
Re: [ccp4bb] Change cell parameter
Zhiyi Wei wrote: Dear all, I have a P2 derivative dataset with beta=89.6. I try to change the beta to 90.4 to be consistent with the native dataset. Should I do sth with the HKL, like applying a matrix? Thanks a million! Best, Zhiyi Hi, Personally I would use sftools (no ccp4i GUI), to be run in a terminal sftools read mymtz.mtz set cell [then you specify the new cell] write mynewmtz.mtz stop However, before changing cell parameters I would think twice... Further, each data set in an mtz file can have its own cell dimensions. Differences in unit cell parameters of less that 1% (I think this is the consensus) are still isomorphous, over this you have non-isomorphism. There is a paper on this (Crick ?). Fred.
Re: [ccp4bb] Change cell parameter
Hi Zhiyi, This is very easily done using Pointless. From the gui, click Match index to reference, enter your two mtz files and run. ERic Eric T. Larson, PhD Biomolecular Structure Center Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 email: larso...@u.washington.edu On Wed, 8 Jun 2011, Vellieux Frederic wrote: Zhiyi Wei wrote: Dear all, I have a P2 derivative dataset with beta=89.6. I try to change the beta to 90.4 to be consistent with the native dataset. Should I do sth with the HKL, like applying a matrix? Thanks a million! Best, Zhiyi Hi, Personally I would use sftools (no ccp4i GUI), to be run in a terminal sftools read mymtz.mtz set cell [then you specify the new cell] write mynewmtz.mtz stop However, before changing cell parameters I would think twice... Further, each data set in an mtz file can have its own cell dimensions. Differences in unit cell parameters of less that 1% (I think this is the consensus) are still isomorphous, over this you have non-isomorphism. There is a paper on this (Crick ?). Fred.
Re: [ccp4bb] Change cell parameter
Thx Clemens, - my indexing gives the same setting, correct is -a -b c BR -Original Message- From: Clemens Vonrhein [mailto:vonrh...@globalphasing.com] Sent: Wednesday, June 08, 2011 9:06 AM To: Bernhard Rupp (Hofkristallrat a.D.) Subject: Re: [ccp4bb] Change cell parameter Hi Bernhard, On Wed, Jun 08, 2011 at 08:59:11AM -0700, Bernhard Rupp (Hofkristallrat a.D.) wrote: 2) this could well be the same cell differently set up (89.6 = 90.4) abc - c -b a Isn't that actually the same? I think if you want to change the 89.6 to 90.4 beta angle you should do abc - -a -b c (ie. 2-fold along c). Or in reciprocal space (reindex program): -h,-k,l Or am I missing something? Cheers Clemens BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Vellieux Frederic Sent: Wednesday, June 08, 2011 8:11 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Change cell parameter Zhiyi Wei wrote: Dear all, I have a P2 derivative dataset with beta=89.6. I try to change the beta to 90.4 to be consistent with the native dataset. Should I do sth with the HKL, like applying a matrix? Thanks a million! Best, Zhiyi Hi, Personally I would use sftools (no ccp4i GUI), to be run in a terminal sftools read mymtz.mtz set cell [then you specify the new cell] write mynewmtz.mtz stop However, before changing cell parameters I would think twice... Further, each data set in an mtz file can have its own cell dimensions. Differences in unit cell parameters of less that 1% (I think this is the consensus) are still isomorphous, over this you have non-isomorphism. There is a paper on this (Crick ?). Fred. -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
Re: [ccp4bb] Change cell parameter
you probably need to reindex your data. h - h k - -k l - -l by using the command hkl matrix 1 0 0 0 -1 0 0 0 -1 in scalepack In HKL2000 you should use reindex menu or data set macro (not the overall scaling macro). Dataset macro exists only in the newest version of HKL2000. The reindexing will change the beta angle automatically. Dear all, I have a P2 derivative dataset with beta=89.6. I try to change the beta to 90.4 to be consistent with the native dataset. Should I do sth with the HKL, like applying a matrix? Thanks a million! Best, Zhiyi Zbyszek Otwinowski UT Southwestern Medical Center at Dallas 5323 Harry Hines Blvd. Dallas, TX 75390-8816 Tel. 214-645-6385 Fax. 214-645-6353
Re: [ccp4bb] Change cell parameter
Thx Clemens, - my indexing gives the same setting, correct is -a -b c BR -Original Message- From: Clemens Vonrhein [mailto:vonrh...@globalphasing.com] Sent: Wednesday, June 08, 2011 9:06 AM To: Bernhard Rupp (Hofkristallrat a.D.) Subject: Re: [ccp4bb] Change cell parameter Hi Bernhard, On Wed, Jun 08, 2011 at 08:59:11AM -0700, Bernhard Rupp (Hofkristallrat a.D.) wrote: 2) this could well be the same cell differently set up (89.6 = 90.4) abc - c -b a Isn't that actually the same? I think if you want to change the 89.6 to 90.4 beta angle you should do abc - -a -b c (ie. 2-fold along c). Or in reciprocal space (reindex program): -h,-k,l Or am I missing something? Cheers Clemens BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Vellieux Frederic Sent: Wednesday, June 08, 2011 8:11 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Change cell parameter Zhiyi Wei wrote: Dear all, I have a P2 derivative dataset with beta=89.6. I try to change the beta to 90.4 to be consistent with the native dataset. Should I do sth with the HKL, like applying a matrix? Thanks a million! Best, Zhiyi Hi, Personally I would use sftools (no ccp4i GUI), to be run in a terminal sftools read mymtz.mtz set cell [then you specify the new cell] write mynewmtz.mtz stop However, before changing cell parameters I would think twice... Further, each data set in an mtz file can have its own cell dimensions. Differences in unit cell parameters of less that 1% (I think this is the consensus) are still isomorphous, over this you have non-isomorphism. There is a paper on this (Crick ?). Fred. -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
[ccp4bb] Two different asymmetric units from two different crystallization conditions
Dear All, I am working on a protein structure that yielded comparable diffraction quality crystals from two different crystallization condition. One of the crystallization condition conatins high conc. of salt pptant whereas the oher one contains high conc. of organic pptant. There are some minor differences in the stucture with respect to the backbone but what most surprising is the oligomeric structure. AnSEC study suggest the protein to be a tetramer in solution and a tetrameric assembly is observed in the asymmetric unit of the space group of the crystal obtained from high conc. of organic pptant. However, the crystal structure from the high conc. of salt pptant does not reveal any oligomeric assembly - symmetry operations of the space group does not suggest any oligomeric assembly. I believe the high salt conc. disrupted the tetrameric assembly and enabled crystallization of the protein as a monomer. Curious to know if there has been any similar precedence before. Cheers, Shiva
Re: [ccp4bb] Change cell parameter
Reindex your data as -h -k l or h -k -l - this will automatically change the cell to berta = 90.4 eleanor On 06/08/2011 04:10 PM, Vellieux Frederic wrote: Zhiyi Wei wrote: Dear all, I have a P2 derivative dataset with beta=89.6. I try to change the beta to 90.4 to be consistent with the native dataset. Should I do sth with the HKL, like applying a matrix? Thanks a million! Best, Zhiyi Hi, Personally I would use sftools (no ccp4i GUI), to be run in a terminal sftools read mymtz.mtz set cell [then you specify the new cell] write mynewmtz.mtz stop However, before changing cell parameters I would think twice... Further, each data set in an mtz file can have its own cell dimensions. Differences in unit cell parameters of less that 1% (I think this is the consensus) are still isomorphous, over this you have non-isomorphism. There is a paper on this (Crick ?). Fred.
[ccp4bb] Fwd: Re: Question about the statistical analysis-might be a bit off topic
Dear all, just to show what I mean where the problem is: I've produced 1 million Gaussian random numbers with a mean of 1 and a standard deviation of 1. I attach a plot showing both the Gaussian itself, and the distribution of the numbers obtained by taking the inverse. The latter looks quite non-Gaussian to me. According to the formulas in Wikipedia and John Taylor's book the inverse distribution should also have a mean of 1 and a sigma of 1. But this is not the case. Its standard deviation is 437 (a different random number would give a different number here!), due to its long tails that arise from those values of the original distribution that are close to 0. The Wikipedia's error propagation article in its Caveats and Warnings paragraph calls this a Cauchy distribution. This is clearly an example where the first-order approximation breaks down, and common sense tells me that this happens because we may divide by numbers close to zero. And it shows that it might be useful to think about error propagation, and not blindly apply the formulas. thanks, Kay Original Message Subject:Re: Question about the statistical analysis-might be a bit off topic Date: Tue, 7 Jun 2011 11:28:50 +0100 From: Ian Tickle ianj...@gmail.com Kay, the usual propagation-of-uncertainty formulae are based on a first-order approximation of the Taylor series expansion, i.e. assuming that 2nd and higher order terms in the series are can be neglected. This is clearly not the case if B is small relative to its uncertainty: you would need to include higher order terms. See the 'Caveats and Warnings' section in the Wikipedia article that Bernhard quoted. Cheers -- Ian On Tue, Jun 7, 2011 at 8:59 AM, Kay Diederichs kay.diederi...@uni-konstanz.de mailto:kay.diederi...@uni-konstanz.de wrote: what I'm missing in those formulas, and in the Wikipedia, is a discussion of the prerequisites - it seems to me that, roughly speaking, if the standard deviation of B is as large or larger than the absolute value of the mean of B, then we might divide by 0 when calculating A/B . This should influence the standard deviation of the calculated A/B, I think, and seems not to be captured by the formulas cited so far. best, Kay Am 20:59, schrieb James Stroud: The short answer can be found in item 2 in this link: http://science.widener.edu/svb/stats/error.html The long answer is I highly recommend Error Analysis by John Taylor: http://science.widener.edu/svb/stats/error.html If you can find the first edition (which can fit in your pocket) then consider yourself lucky. Later editions suffer book bloat. James On Jun 4, 2011, at 10:44 AM, capricy gao wrote: If means and standard deviations of A and B are known, how to estimate the variance of A/B? Thanks. -- Kay Diederichshttp://strucbio.biologie.uni-konstanz.de email: kay.diederi...@uni-konstanz.de mailto:kay.diederi...@uni-konstanz.de �Tel +49 7531 88 4049 Fax 3183 Fachbereich Biologie, Universit�t Konstanz, Box 647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature smime.p7s. attachment: A=sigA=1.png smime.p7s Description: S/MIME Cryptographic Signature
[ccp4bb] March 15, 2010 deadline- User proposal submission for Collaborative Crystallography at BCSB
Dear Users, Please note: Due to an extended shutdown, proposals will not be solicited in May for the July-August 2011 beamtime. The next cycle will be September-October 2011. The deadline to submit proposals will be July 15th. Regards Banu
[ccp4bb] FreeR_flag
HI, I am a beginer in crystallography. I have carried out molecular replacement in 'phenix' and now want to refine the structure in ccp4. Could anyone tell me what the proper Rfree_flag value to put in while using Refmac5(ccp4). I have used 1 and output seems to be fine but I want am not sure if am going in the right direction. Regards, Madhu
Re: [ccp4bb] FreeR_flag
On Wed, Jun 8, 2011 at 4:44 PM, Madhu shankar Madhu shankar mad07...@student.otago.ac.nz wrote: I am a beginer in crystallography. I have carried out molecular replacement in 'phenix' and now want to refine the structure in ccp4. Could anyone tell me what the proper Rfree_flag value to put in while using Refmac5(ccp4). I have used 1 and output seems to be fine but I want am not sure if am going in the right direction. What program did you use to create the R-free flags? If you used Phenix, this is correct - the rest of the flags will be 0. If you used a CCP4 program, the flags will be a range of integers (depending on what percent of reflections are flagged - if you use 5%, the range will be 0-19), and 0 is usually the test set. In that case, you could still use 1, but I'd recommend sticking to 0, because CCP4 programs will default to using that, and Phenix will recognize that convention in your MTZ file and use 0 too. -Nat PS. If Phenix generated the flags, you can also use the reflection file editor in the Phenix GUI to export them to the CCP4 convention, so CCP4 programs will use the correct set by default.
Re: [ccp4bb] Two different asymmetric units from two different crystallization conditions
Dear Shiva, It has happened many times. This paper (not about crystallography) is one example: http://onlinelibrary.wiley.com/doi/10./j.1742-4658.2005.05047.x/abstract;jsessionid=864D79CC1089210C6A3CDDAC3AFE25DB.d03t04 Why don't you try SEC with high salt concentration? Yours, Clement On Jun 9, 2011, at 3:19 AM, Shiva Bhowmik wrote: Dear All, I am working on a protein structure that yielded comparable diffraction quality crystals from two different crystallization condition. One of the crystallization condition conatins high conc. of salt pptant whereas the oher one contains high conc. of organic pptant. There are some minor differences in the stucture with respect to the backbone but what most surprising is the oligomeric structure. AnSEC study suggest the protein to be a tetramer in solution and a tetrameric assembly is observed in the asymmetric unit of the space group of the crystal obtained from high conc. of organic pptant. However, the crystal structure from the high conc. of salt pptant does not reveal any oligomeric assembly - symmetry operations of the space group does not suggest any oligomeric assembly. I believe the high salt conc. disrupted the tetrameric assembly and enabled crystallization of the protein as a monomer. Curious to know if there has been any similar precedence before. Cheers, Shiva Clement Angkawidjaja, PhD. G30 Assistant Professor --- Chemistry-Biology Combined Major Program International College, Osaka University 1-30 Machikaneyama-cho Toyonaka, Osaka 560-0043, Japan http://cmp.sci.osaka-u.ac.jp/CMP/ Tel. +81-6-6850-5952 Fax +81-6-6850-5961 --- Laboratory of Molecular Biotechnology Graduate School of Engineering Osaka University 2-1 Yamadaoka U1E-804 Suita, Osaka 565-0871, japan http://www.mls.eng.osaka-u.ac.jp/~bio_ext/mlsbe123/clement.html Tel/Fax +81-6-6879-4157
Re: [ccp4bb] Change cell parameter
Dear all, Thank you all! There are so many useful replies. The problem has been solved by using the way introduced by Clemens (see below, I dont have an access to SCALEPACK). BTW, although beta is close to 90, it is not a orthorhombic crystal (Rmerge goes up to ~0.3 after scaling). Thanks again! Zhiyi On Wed, Jun 8, 2011 at 11:20 AM, Clemens Vonrhein vonrh...@globalphasing.com wrote: Hi, try reindex hklin in.mtz hklout out.mtz e REIN HKL -h,-k,l END e Cheers Clemens On Wed, Jun 08, 2011 at 11:14:03AM -0400, Zhiyi Wei wrote: Dear all, I have a P2 derivative dataset with beta=89.6. I try to change the beta to 90.4 to be consistent with the native dataset. Should I do sth with the HKL, like applying a matrix? Thanks a million! Best, Zhiyi -- *** * Clemens Vonrhein, Ph.D. vonrhein AT GlobalPhasing DOT com * * Global Phasing Ltd. * Sheraton House, Castle Park * Cambridge CB3 0AX, UK *-- * BUSTER Development Group (http://www.globalphasing.com) ***
