[ccp4bb] Defining an ellipse around a protein structure

2011-05-27 Thread Vandu Murugan
Dear all, Is there a program or server that would define a ellipsoid around a given protein molecule? I would also like to calculate the axis components of the defined ellipse. Thanks in advance.. cheers, wandu

Re: [ccp4bb] software for generate or display DNA central axis

2011-05-27 Thread Wataru Kagawa
Hi Xu, Curves+ (http://gbio-pbil.ibcp.fr/Curves_plus/Curves+.html) can generate helical axis of DNA. Wataru On 2011/05/28, at 7:51, xu xiang wrote: > Hi all, > > Sorry for this off-topic question. Does anyone know how to generate or > display DNA central axis? I want to measure the distance

[ccp4bb] software for generate or display DNA central axis

2011-05-27 Thread xu xiang
Hi all, Sorry for this off-topic question. Does anyone know how to generate or display DNA central axis? I want to measure the distance between my protein and the central axis. Best, Sean

[ccp4bb] confused about ncs in this xtal and local correlation maps with maprot.

2011-05-27 Thread Francis E Reyes
Hi all I was just fiddling around with ncs and maps, so I tried to use maprot a 2fofc map (refined model) of a crystal that has two molecules related by the NCS: (given by LSQKAB over the CA's) CROWTHER (Euler) ALPHA BETA GAMMA 95.8381478.49123 145.66571 TRANSLATION VECTOR

Re: [ccp4bb] expression of membrane proteins as GST fusions

2011-05-27 Thread Anna Maria Tochowicz
Hi Pascal, The GST helps a lot with expression, but unfortunately it's very difficult to purify it away after cleavage. I would strongly recommended to try MBP tag. Good luck! Anna On Fri, May 27, 2011 at 1:50 PM, Pascal Egea wrote: > > Dear All, > > This is not strictly a crystallography rel

[ccp4bb] expression of membrane proteins as GST fusions

2011-05-27 Thread Pascal Egea
Dear All, This is not strictly a crystallography related question. We are trying to express several membrane proteins and were considering the use of GST as a fusion partner instead of the HIS or FLAG purification tags. I would like to know if anyone had any experience (positive or negative) to sh

Re: [ccp4bb] Problems in refinement

2011-05-27 Thread Dale Tronrud
There has been a serious problem in Refmac which apparently Garib has fixed in this new release. When calculating structure factors for models in space group P1 Refmac would "lose" some of the atoms. I first ran into the problem by looking at the Electron Density Server map for entry 3LEN.

Re: [ccp4bb] Buster

2011-05-27 Thread Gerard Bricogne
Dear Xavier, I am very sorry that I didn't respond instantly to your query about this strange observation at the beginning of the month. After that, it was sitting rather invisibly in my mailbox, given that its subject line said "Re: [ccp4bb] Dehydration treatments" :-) . We are just ab

[ccp4bb] digilab honeybee96 alignment tools

2011-05-27 Thread Christian Biertuempfel
Dear all, We have a Digilab Honeybee96 pipetting robot with a few broken needles in the lab. I have got replacement needles from Digilab but their alignment tools are on backorder. Does anybody (preferably nearby) have these tools and would be willing to lend them to us? We would pay for shipping a

[ccp4bb] strange fortran error in refmac

2011-05-27 Thread Christian Roth
Dear CCP4ler, I have a strange fortran error attached below when I started a restrained refinement with Refmac. I tried also for the beginning a simple rigid body refinmet for comparison and except that it complains about the Hessian B Array, which ist too big, it runs to completion. Has anyone

Re: [ccp4bb] larger molecular weight shown by analytic ultracentrifugation

2011-05-27 Thread Kushol Gupta
Hi Jerry - By AUC, do you mean sedimentation velocity (SV)? Both gel filtration and SV are not terribly great ways to determine precise molecular mass, especially if the macromolecule of interest is anisotropic in shape. In your SV values, do you see a large f/fo, or a broad distributio

Re: [ccp4bb] need proper suggestion

2011-05-27 Thread Patrick Shaw Stewart
Afshan Radaev and Sun published a paper a few years ago showing that crystallization conditions for complexes are strongly biased towards PEG conditions (rather than e.g. high salt conditions). The reference is below. I would use microseeding into random screens [2], using the crystals that you

Re: [ccp4bb] need proper suggestion http://scripts.iucr.org/cgi-bin/paper?ms0234

2011-05-27 Thread Miller, Mitchell D.
Another reference with a detailed method for transferring crystals to new conditions prior to soaking is Ray WJ Jr, Bolin JT, Puvathingal JM, Minor W, Liu YW, Muchmore SW. Removal of salt from a salt-induced protein crystal without cross-linking. Preliminary examination of "desalted" crystals of

[ccp4bb] larger molecular weight shown by analytic ultracentrifugation

2011-05-27 Thread Jerry McCully
Dear ALL; I am sorry for this off-topic question about analytic ultracentrifugation (AUC). We recently solved one structure from crystals grown out of PEG4000 plus buffer. Since the crystal was grown from PEG, we think the protein would maintain its native oligomerization state as in

[ccp4bb] post-doc possition at BNL

2011-05-27 Thread Orville, Allen
Job Title: Postdoctoral Research Associate - Protein Crystallography, Macromolecular Single-Crystal Spectroscopy, X-ray Diffraction Job ID: 15788 To apply, please visit: http://www.bnl.gov/HR/careers/ Requires a Ph.D. in biochemistry, chemistry, biology, biophysics, or related areas, and s

Re: [ccp4bb] need proper suggestion

2011-05-27 Thread Herman . Schreuder
Dear Afshan, As Fred suggested, you may try to get rid of the ammonium phosphate by transferring it to a PEG solution. However, it may be that you get the nice crystals because your protein is stabilized by the phosphate in the active site. Crystal packing may prevent the phosphate from leavin

[ccp4bb] Call for papers for a special issue on Cryo-EM-based modeling

2011-05-27 Thread Gerard DVD Kleywegt
Hi all, This may be of interest to those methods developers amongst us who are ogling the rich potential bounties to be reaped by applying low-resolution X-ray model-building and refinement methods to EM maps... --Gerard -- Forwarded message -- Date: Thu, 12 May 2011 07:52:48

Re: [ccp4bb] need proper suggestion http://scripts.iucr.org/cgi-bin/paper?ms0234

2011-05-27 Thread Vellieux Frederic
Afshan Begum wrote: Dear All, I have a severe prob lam to performed my ligand binding study with corresponding protein. I have taking the native diffraction data at 1.75 A and after that i have performed soaking as well co-crystallization experiment with my inhibitors. Problem is that at the

[ccp4bb] need proper suggestion

2011-05-27 Thread Afshan Begum
Dear All, I have a severe prob lam to performed my ligand binding study with corresponding protein. I have taking the native diffraction data at 1.75 A and after that i have performed soaking as well co-crystallization experiment with my inhibitors. Problem is that at the active site phosphate

Re: [ccp4bb] Problems in refinement

2011-05-27 Thread Petr Kolenko
Dear colleagues, Q2 is solved by new installation of Refmac. Many thanks for your time and effort. I appreciate all your comments. Petr 2011/5/27 David Cobessi : > Dear Petr, > Before running Refmac, you have to remove the ANISOU line using pdbset for > example. In fact you should not add the T

[ccp4bb] Postdoctoral Position - University of Oxford

2011-05-27 Thread Chris O'Callaghan
*Postdoctoral Position in the University of Oxford * A postdoctoral research scientist position is available in the Wellcome Trust Centre in the University of Oxford, UK. The post is funded for 3 years Salary range £29,099 to £35,788 p.a (approximately 33,-41,000 Euros) Our work focuses

Re: [ccp4bb] Problems in refinement

2011-05-27 Thread Garib N Murshudov
Dear Petr Newer version of refmac is 5.6 and it should be available from ccp4 soon. Meanwhile you can try this version from this website http://www.ysbl.york.ac.uk/refmac/data/refmac_experimental/refmac5.6_linux.tar.gz There are versions for mac etc also. regards and I hope you will sort it

Re: [ccp4bb] Problems in refinement

2011-05-27 Thread Petr Kolenko
Dear colleagues, regarding Q2: I do not use TLS parameters, the space group is P1, and yesterday I tried to refine the structure with anisotropic ADP (60,000 reflections against 50,000 parameters) - no positive maximums. Then I used the anisotropic model as input and refined isotropically, the ma