[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.

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

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

[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

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

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=30sid=189pid=30 William Ho

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

[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

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 and

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 http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=CCP4i_diffraction_image_display_%28idiffdisp%29 Cheers David

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

[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

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

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

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.

[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!!!

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 . I like this