Tagged Questions

0
votes
1answer
87 views

Lysine methylation for proteins containing disulfide bonds?

Hi all, I am currently attempting to crystallise a two domain protein which contains several structurally important disulfides. We have a high resolution structure of one domain ( …
1
vote
6answers
307 views

Using Windows PCs for crystallography?

I recently asked about the state of Macs in crystallography, and now I thought I'd ask about the state of Windows PCs. Windows 7 looks to be pretty good. I know that CCP4, Coot, …
1
vote
2answers
76 views

Find the best model for molecular replacement.

Hi everybody, I just crystallized a new project protein. How can I find a possible model for using molecular replacement? I have the sequence of my protein. Is it enough to make a …
5
votes
6answers
353 views

Are Linux workstations still necessary for crystallography, or will Macs suffice?

Are Linux workstations still required these days to do crystallography, or can everything be done on a Mac? While roughly twice as expensive, perhaps Macs are more useful as they …
3
votes
1answer
135 views

GPU computing in structural biology?

I'm aware of GPU computing making great strides in tomography, but are there any projects which use GPGPUs in structural biology? Or, are the algorithms from, for example, crystal …
2
votes
1answer
82 views

refmac 5.5.0092 not writing pdb/mtz files

Howdy, One of our users was trying to re-run some Refmac jobs originally run with version 5.5.0088 under version 5.5.0092, and he noticed that although the logfile shows Refmac co …
1
vote
1answer
130 views

Ligand fitting with coot

I have been trying to fit the ligand in electron density since a long time. I could place it in the right place by simply using 'rotate/translate zone'. Now i am facing difficulty …
3
votes
1answer
66 views

Recommendation for dynamic/static light scattering unit?

We are thinking of buying a dynamic/static light scattering unit to analyze our samples. The Nanostar from Wyatt (previously from Dynapro) seems to combine both DLS and static ligh …
4
votes
6answers
262 views

Crystallography Books: What order?

What order do you recommend reading crystallography books? Two parts: 1) Suggestion a book if it is not listed 2) Vote up books that should be read first (are a good starting po …
2
votes
2answers
262 views

Best/favorite ways to calculate rmsd of 2 structures?

When calculating rmsd values, are some methods more rigorous/correct than others? I have used super and align in PyMOL and just taken the readout from the terminal window, but eac …
3
votes
2answers
112 views

mounting, freezing thin needle crystals

I have quite thin needle crystals. They break or bend when I try to mount and freeze them in small loops. If I use larger loops, the solvent in the loop causes a lot of background …
1
vote
2answers
38 views

Is MODIP still available? Any alternatives?

Does anyone know if the program MODIP is still available? Anyone know any other programs that will do what MODIP does? Thanks! Mark
3
votes
3answers
806 views

How to add a ligand to a model?

I have a question regarding adding a ligand to my model. I'm not quite sure how to do it. I have obtained the ligand in two different ways, either in SMILES format from the drugban …
4
votes
1answer
52 views

non consecutive atom selection in coot

I am trying to assemble my model (after molecular replacement and automatic rebuilding) from smaller parts of different models. To avoid hand editing of pdb files I tried the "copy …
3
votes
3answers
154 views

2D plot of active site?

Can anybody recommend a program to plot a couple of amino acid residues of a active site/cavity in 2D? A screenshot of the active site is to confusing. Thanks, P. edit: As far as …

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