[ccp4bb] looking for people interested in fast (0.8 ms) x-ray shutter

Dear CCP4 community, please excuse the off topic question. I'm currently looking into buying a fast shutter for X-ray use from nmlaser (www.nmlaser.com). They had a model LS500, marked as discontinued on their web page. It has a minimum opening time of 800 us, an aperture of 2.5 mm and the cro

Re: [ccp4bb] Display x-ray images in windows

And in the "paid for" version the keyword is AgentExtraOptions = "-defer 0" Thomas On 03/24/2010 12:39 AM, Kay Diederichs wrote: > As I recently learnt from Andy Arvai, the "-nopixmap" is not needed if > the (free) NX server has > AGENT_EXTRA_OPTIONS_X="-defer 0" > in its node.conf . >

[ccp4bb] Positions available: Enzyme Function Initiative

Protein Production Core in the Enzyme Function Initiative - We are looking to recruit individuals with extensive experience in molecular biology, protein purification, crystallization and automation to join the Protein Production Core of t

[ccp4bb] R merge and R init

Dear All; I have a crystal structure collected on in house X-ray facility from Bruker using Xprep. I submitted the paper but the reviewer ask for the R merge. As I can't access to the computer at the moment its crashed out. But I have the prp file which have the R init values. My question is!!! 1

Re: [ccp4bb] update on SeMet production

Hello, Here is our lab's work with HEK293T in bioreactor: Pak JE, Rini JM., X-ray crystal structure determination of mammalian glycosyltransferases., Methods Enzymol. 2006;416:30-48. http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B7CV2-4MCC01F-3&_user=994540&_coverDate=12%2F31%2F200

Re: [ccp4bb] Butandiol as Cryoprotectant 2.

[nosy] The one that your crystal likes less. I guess that's the idea of this screen, isn't it? [/nosy] Their product http://hamptonresearch.com/documents/product/30-000221.pdf description dedicate a full paragraph to 2,3 Butanediol. Tim On Wed, Mar 24, 2010 at 02:27:37PM -0400, Oganes

Re: [ccp4bb] 2,3-butanediol

Dear all, I would like to know which is the more suitable method of using 2,3-Butanediol as cryoprotectant? Addition in to reservoir buffer or crystal soaking or both can be tried? Cheers Gauri -- I am sure both could be tried, but have found quite few papers mentioning brief soaking with 2

Re: [ccp4bb] Full B Factor

Daniel Bonsor wrote: How do I convert the B-factors from my final structure to full B factors if I did not use TLS refinement? I have been refining isotropic B-factors. Do I switch to overall B-factor refinement, do something else, or have I missed the point altogether? It may be a dumb questio

[ccp4bb] 2,3-butanediol

Dear all, I would like to know which is the more suitable method of using 2,3-Butanediol as cryoprotectant? Addition in to reservoir buffer or crystal soaking or both can be tried? Cheers Gauri

Re: [ccp4bb] Full B Factor

Hi Daniel, How do I convert the B-factors from my final structure to full B factors if I did not use TLS refinement? a non-ccp4 tool: if you have PHENIX installed then: 1) if your PDB file has TLS matrices in its header and residual B-factors in ATOM records, then: phenix.tls model.pdb c

Re: [ccp4bb] Display x-ray images in windows

Dear Paul, You can also use idiffdisp, which might do what you want. See http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=CCP4i_diffraction_image_display_%28idiffdisp%29 Cheers David _

Re: [ccp4bb] Butandiol as Cryoprotectant 2.

> > thanks so far for sharing your experience with Butanediol. But is it > important to use a specific enantiomer ? Are you all only using 2R3R- > Butanediol which is quite expensive ? Sigma Cat. # 18970 2,3-Butanediol puriss., mixture of racemic and meso forms, ≥99.0% (GC) (Fluka) works well

[ccp4bb] Full B Factor

How do I convert the B-factors from my final structure to full B factors if I did not use TLS refinement? I have been refining isotropic B-factors. Do I switch to overall B-factor refinement, do something else, or have I missed the point altogether? It may be a dumb question but best to be saf

Re: [ccp4bb] orthogonal limits of a protein

I have a program that would calculate the limits of the protein along it's axes of inertia (besides doing many other things). If you are interested, please let me know. Thanks Abhinav j...@ssrl Phone: (650) 926-2992 Fax: (650) 926-3292 Francois Berenger wrote: Hello, Is there a ccp4

Re: [ccp4bb] Butandiol as Cryoprotectant 2.

There are three diastereomers, two of which I think work. The meso compound, however supposedly does not freeze clear. Hampton sells two of these in their kit, but doesn't specify the stereochemistry of one of them. http://hamptonresearch.com/product_detail.aspx?cid=30&sid=189&pid=30 William Ho

[ccp4bb] Butandiol as Cryoprotectant 2.

Dear CCP4BB-users, thanks so far for sharing your experience with Butanediol. But is it important to use a specific enantiomer ? Are you all only using 2R3R-Butanediol which is quite expensive ? Ulrike

Re: [ccp4bb] orthogonal limits of a protein

Strictly speaking even Tim's solution may not give the true 'smallest box', by which I assume is meant 'minimal volume box'. I suspect moleman does this calculation (my apologies to Gerard if I'm wrong!) by determining the axes of inertia, then rotating the molecule by the matrix of eigenvectors a

[ccp4bb] Job opportunity in structure-based ligand design in Dundee (UK)

Hi, I have a job opportunity for a highly motivated individual in the area of structure-based ligand design design in my group. Check out our University web page for more information about the job and on how to apply (http://www.jobs.dundee.ac.uk/vacancies/20100407_1-y.html). Cheers Ruth

Re: [ccp4bb] orthogonal limits of a protein

Dear Francois, I don't know if the pdbset command Clemens and Eleanor suggested actually gives you the answer you are looking. Take for example this case: --- | /| |/ | --- assume the diagonal line is the protein as it is inside the unit cell, the unit cell dimensions are not the smallest b

Re: [ccp4bb] orthogonal limits of a protein

Francois Berenger wrote: Hello, Is there a ccp4 tool to find automatically the smallest virtual orthogonal "box" that contain a given PDB ? Even if your favorite tool is not part of ccp4, I would be happy to know about it. ;) Thanks, Francois. pdbset xyzin thisprotein.pdb end This prints out

Re: [ccp4bb] orthogonal limits of a protein

Hi, On Wed, Mar 24, 2010 at 04:18:04PM +0900, Francois Berenger wrote: > Hello, > > Is there a ccp4 tool to find automatically the smallest virtual > orthogonal "box" that contain a given PDB ? echo END | pdbset xyzin your.pdb xyzout /dev/null | \ awk '/Orthogonal Coordinate limits/,/On Z/'

Re: [ccp4bb] Display x-ray images in windows

As I recently learnt from Andy Arvai, the "-nopixmap" is not needed if the (free) NX server has AGENT_EXTRA_OPTIONS_X="-defer 0" in its node.conf . I like this a lot because I tend to forget about the -nopixmap option, _and_ it does not work for the zoom window. HTH, Kay Am 20:59, schrieb J

Re: [ccp4bb] orthogonal limits of a protein

Hi Francois, a non-ccp4 tool: if you have PHENIX installed then: iotbx.pdb.box_around_molecule model.pdb will do it (if I correctly understood you question). You can also specify a buffer region around a molecule: iotbx.pdb.box_around_molecule model.pdb --buffer-layer=5 Pavel. On 3/24/10

[ccp4bb] orthogonal limits of a protein

Hello, Is there a ccp4 tool to find automatically the smallest virtual orthogonal "box" that contain a given PDB ? Even if your favorite tool is not part of ccp4, I would be happy to know about it. ;) Thanks, Francois.