Re: [ccp4bb] The Good and the Bad crystal contact?

On 06/29/2011 10:22 PM, Paul Lindblom wrote: Hi everybody, can anybody tell me how crystal contacts are defined? Are there good and bad crystal contacts? They are the most important interactions with impact on the crystal quality, but they are not of covalent nature, aren´t they? With best

Re: [ccp4bb] International Symbol for sin(theta)/lambda‏

Hi James, Well, I think there's q (or s) which depending on where you're coming from can be 4*pi* sin(theta)/lambda, or 2*sin(theta)/lambda, or . * sin(theta)/lambda) or or * sin(theta)/lambda. Small-angle X-ray scattering (and other fields) uses those as symbols for the

Re: [ccp4bb] The Good and the Bad crystal contact?

On 30 Jun 2011, at 01:42, Michael Thompson wrote: the introduction of a disulfide can create artificial crystal contacts, which also aid in crystallization Another example of this is described here: The structural and energetic basis for high selectivity in a high-affinity protein-protein

[ccp4bb] generate large symmetry model

Does anyone have a rigorous method (or script) for generating an extended lattice e.g 3x3x3 unit cells from any pdb file? Any help gratefully received, Dave David Hargreaves Associate Principal Scientist _ AstraZeneca

Re: [ccp4bb] generate large symmetry model

Hi Dave, as first step you apply all symmetry operators of the space group to the pdb-file in order to fill the unit cell, and store all copies in the same PDB-file. You can do this with pdbset and the symgen keyword, see http://www.ccp4.ac.uk/dist/html/pdbset.html#symgen Check with coot that all

Re: [ccp4bb] generate large symmetry model

Well - you have a problem of chain IDS, but pdbset xyzin asymm.pdb xyzout whole-cell.pdb symgen P212121 (say) end will generate a whole unit cell, then pdbset xyzin whole-cell.pdb xyzout whole-cell-+100 symgen x+1,y,z end etc will move that unitcell.pdb You would have to put them all

Re: [ccp4bb] generate large symmetry model

As well as pdbset, you can use pdbcur. A combination of keywords genunit, symop and symcommit. I’d probably use genunit (applicable to whatever spacegroup you have), followed by a second call using symop/symcommit to apply unit cell translations. Cheers Martyn From: CCP4 bulletin board

Re: [ccp4bb] generate large symmetry model

Apologies for suggesting a non-CCP4 solution, but UCSF Chimera can do that and more (interactively!): Tools - Higher Order Structure - Unit cell Petr On Jun 30, 2011, at 2:52 PM, Hargreaves, David wrote: Does anyone have a rigorous method (or script) for generating an extended lattice

Re: [ccp4bb] generate large symmetry model

Its obviously not going to be possible to give a unique chain letter for every chain in 27 cells, but forget renaminmg the chains and its very easy to generate the models to look at- might even do it in a triple-nested foreach loop in csh. After generating the whole cell as suggested by David or

Re: [ccp4bb] generate large symmetry model

PDBCur (CCP4) should be able to generate the unit cell at once, which then should be translated to 3x3x3 cube. All may be done within a single run of PDBCur, a simple keyword input is required. Same job is doable with PDBSet. Eugene On 30 Jun 2011, at 15:36, Petr Leiman wrote: Apologies for

Re: [ccp4bb] generate large symmetry model

You can do this with PyMOL with the supercell script: http://pymolwiki.org/index.php/Supercell Cheers, Thomas On 06/30/2011 02:52 PM, Hargreaves, David wrote: Does anyone have a rigorous method (or script) for generating an extended lattice e.g 3x3x3 unit cells from any pdb file? Any help

Re: [ccp4bb] International Symbol for sin(theta)/lambda

This has been a point of confusion Here are the conventions used in a few of the classic SAXS text vs. recent reviews: -- I believe Guinier actually used the variable u in his thesis, but must have changed at some point (I don't have it handy to check at the moment). Guinier

Re: [ccp4bb] International Symbol for sin(theta)/lambda

The most extreme degree of confusion (or at least of requirement for fast mental arithmetic) I have come across in relation to this topic is the habit of small-molecule crystallographers working on accurate density studies to characterise the resolution limit of their datasets by quoting the

[ccp4bb] nmr question

Dear members, I know that it is not possible to solve a structure by nmr of more than approx. 30 kda. But I have to admit that I dont know why. What exactly is overlapping? With best regards, Lena

Re: [ccp4bb] nmr question

There are about 20 structures solved by NMR with chain lengths above 300 residues. Some of them are solved by combination of restraints and modeling (e.g. 2010 Nature paper describing implementation of Rosetta modeling coupled with backbone-only data, by Raman/Montelione/Baker et al.). Principal