[ccp4bb] detergent parameters

Hi , Sorry for the offtopic first. Could you provide any materials on line in terms of detergent parameters changing vs. temperature. I am very interested in how CMC, aggregation number,etc change from room temp. to 4 C. Thanks a lot and happy new year all! Deliang

Re: [ccp4bb] problem with 'generate' (cns_solve)

Hi Mareike, Did you also use Coot to fit the small molecule into the structure? If so, there might be some glitch at the stage of writing out the remodeled ligand... Do the coordinates for the small molecule look different within the input and output pdb files for the ligand when you look at

[ccp4bb] problem with 'generate' (cns_solve)

I am refining a structure in which I had to model a small molecule (done with Dundee PRODRG2 server). After fitting the small molecule into the structure I merged the pdb's and used the merged pdb file for "generate" (cns_solve). (Just in case: I did put the top and par file for the small m

Re: [ccp4bb] Difference Map in COOT - Possible lignad but clash with structure?

On Fri, 28 Dec 2007 15:55:39 + Brenda Patterson <[EMAIL PROTECTED]> wrote: Hello, I am fairly new to this lark No problem. With a name like Patterson, your future is guaranteed (unless of course you see everything in the world with intensity but no phase). I have a d

Re: [ccp4bb] Difference Map in COOT - Possible lignad but clash with structure?

There is another possibility that your ligand is not fully occupied, if the binding site of protein endures an apparent change when bound by ligand. Lijun On Dec 28, 2007, at 7:55 AM, Brenda Patterson wrote: Hello, I am fairly new to this lark so please forgive me if this question is un

[ccp4bb] Postdoctoral fellow position at NIH

A postdoctoral fellow position is immediately available at the Structural Immunobiology Unit, NIAID/NIH for a highly motivated individual to determine the structures of macromolecular complexes involved in innate immune responses. Our research program aims to elucidate how the pattern recognit

Re: [ccp4bb] Difference Map in COOT - Possible lignad but clash with structure?

What's the resolution? At low res it is possible to miss a subtle movement of e.g. some sidechains which are being replaced by the ligand. What quality parameters did the MR have? Can you omit the entire ligand binding site, refine, and re-generate the map - what does it look like after that? A pi

Re: [ccp4bb] Difference Map in COOT - Possible lignad but clash with structure?

Covalent modification?? Bias in 2fo-fc map? Can you show us a pic of offending density? Dave On 28/12/2007, Brenda Patterson <[EMAIL PROTECTED]> wrote: > > Hello, > > I am fairly new to this lark so please forgive me if this question is > unclear, > but it is really puzzling me. > > I have used

[ccp4bb] Difference Map in COOT - Possible lignad but clash with structure?

Hello, I am fairly new to this lark so please forgive me if this question is unclear, but it is really puzzling me. I have used phaser to generate a molecular replacement structure of my target (which has 100% identity to my template) and this particular crystal I had soaked with a ligand. I ha

[ccp4bb] problem in creation of symmetrycal molecules- thank you

Dear all, Thank you very much for all who are all responded to my query that problem in creation of symmetrycal molecules. I received all mails which contains valuable information. Finally I had created the symmetrical molecules using PISA server. Thanks for all and thank you very much. With Re

Re: [ccp4bb] setpaths.sh

If you did a binary install, did you remember to run the post-install script: install.sh? Does the $CEXAM/unix/runnable/run-all test work? Meyer, Peter wrote: Hi Li, setpaths.sh (and variants for other shells) are generated during the cctbx build process (with ccp4-6.0.2, this might happen o