[ccp4bb] PhD-studentship for Structure Mining at EMBL Hamburg

2011-06-08 Thread Thomas R. Schneider
*** PhD-studentship for Structure Mining *** A PhD-fellowship is available in the group of Thomas Schneider at EMBL-Hamburg to develop methods for mining structural data in terms of fragments and ensembles to be used in the interpretation of electron density maps in low-resolution crystallogr

[ccp4bb] map format conversion

2011-06-08 Thread Masaki UNNO
Dear all I am sorry that I have posted the same question in March 11, 2011. However, unfortunately, the mail sever suffered extensive damage from a major earthquake. Thus I did not receive the answers, suggestions, or advices at that time. Please give me any suggestions, again. The questions a

Re: [ccp4bb] nVidia Quadro 4000 and the stereo bracket

2011-06-08 Thread Joe Watts
I don't know about the Quado 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 t

Re: [ccp4bb] anomalous difference map?

2011-06-08 Thread Herman . Schreuder
Dear Haytham, I do not think your unknown density is DTT. As far as I can judge from the pictures you sent it looks like an Asp or a Glu binding to a large spherical density which may be a metal ion (tin?). You can calculate an anomalous map in ccp4i with the program FFT, using model phases and s

Re: [ccp4bb] nVidia Quadro 4000 and the stereo bracket

2011-06-08 Thread David Schuller
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 F

[ccp4bb] PhD studentships for October 2011, University of Essex

2011-06-08 Thread Hough, Michael A
Dear CCP4bb, I would be grateful if you could forward this opportunity to potential PhD applicants. Thanks, Mike ---

[ccp4bb] unsubscription request

2011-06-08 Thread Angela (Shaoxu) Li
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

Re: [ccp4bb] unsubscription request

2011-06-08 Thread Ben Eisenbraun
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:

Re: [ccp4bb] unsubscription request

2011-06-08 Thread Vellieux Frederic
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

[ccp4bb] Change cell parameter

2011-06-08 Thread Zhiyi Wei
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

2011-06-08 Thread Vellieux Frederic
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 b

Re: [ccp4bb] Change cell parameter

2011-06-08 Thread Dale Tronrud
Since this is a change in cell convention from an acute monoclinic to an obtuse monoclinic indexing, I suspect that more than a change in the mtz header is required. The reciprocal lattice needs to be reindexed. Will pointless perform this task? Dale Tronrud On 06/08/11 08:10, Vellieux Frede

Re: [ccp4bb] Change cell parameter

2011-06-08 Thread Eric Larson
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,

Re: [ccp4bb] Change cell parameter

2011-06-08 Thread Bernhard Rupp (Hofkristallrat a.D.)
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,

Re: [ccp4bb] Change cell parameter

2011-06-08 Thread Zbyszek Otwinowski
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

Re: [ccp4bb] Change cell parameter

2011-06-08 Thread Richard Bunker
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,

[ccp4bb] Two different asymmetric units from two different crystallization conditions

2011-06-08 Thread Shiva Bhowmik
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

Re: [ccp4bb] Change cell parameter

2011-06-08 Thread Eleanor Dodson
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 t

[ccp4bb] Fwd: Re: Question about the statistical analysis-might be a bit off topic

2011-06-08 Thread Kay Diederichs
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-

[ccp4bb] March 15, 2010 deadline- User proposal submission for Collaborative Crystallography at BCSB

2011-06-08 Thread Banumathi Sankaran
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

2011-06-08 Thread Madhu shankar Madhu shankar
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

Re: [ccp4bb] FreeR_flag

2011-06-08 Thread Nat Echols
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 valu

Re: [ccp4bb] Two different asymmetric units from two different crystallization conditions

2011-06-08 Thread Clement Angkawidjaja
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

Re: [ccp4bb] Change cell parameter

2011-06-08 Thread Zhiyi Wei
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!