[ccp4bb] Following up on fragment hits

Hi all, I have started generating hits from a fragment library that has been screened by SPR, thermal shift and crystallography. We have a few potential allosteric binders that would, for selectivity reasons, be quite interesting if they show modulation of enzyme activity. I am thinking about per

[ccp4bb] Challenging Mol.Rep. Problem

Hi all, I’m stuck on a rather complex molecular replacement problem. The crystals are of an antigen-Fab complex totaling ~67 kDa (waiting to confirm using PAGE gel). They diffract to ~3.5A at the synchrotron and process in C2 with dimensions 220x130x230 and beta at 103 so it looks like there are r

[ccp4bb] Question 2/2: Internal deletions of construct

Hi all, I am expressing a construct in e. coli (BL21-CodonPlus(DE3)-*RIL*) that corresponds to a truncated form of a lower eukaryotic protein. I inherited this construct (though I did do some additional SDM), but DNA sequencing of the insert confirms it is as expected. Without protease inhibitors

[ccp4bb] Question 1/2: Ethanol-tight seals for 96-well racks

Hi all, I'm looking for a suitable SBS footprint plate that has 96 wells and can be sealed (and resealed), one column (8 wells) at a time, using a system that won't allow volatile organic solvents to escape or dissolve the seal. Racks will be stored at -20oC, so that is a consideration too. I've

Re: [ccp4bb] Peptide solubility issues

wrote: > Hello Mo Wong, > Some points below are good, but don't underestimate custom peptides > sometimes... can be much harder/expensive than recombinant proteins. > If you ordered the peptides it is good to know how they synthesized them, > and how the elution profiles during purifi

[ccp4bb] Peptide solubility issues

Hi all, Slightly off topic - but I'm having trouble solubilizing some peptides for SPR and hoped someone on the BB might have some other suggestions. The peptides are intra-chain S-S cross-linked 12mers with pIs of ~3. 10 residues are hydrophobic and 2 are acidic. Peptides have been tested with a

Re: [ccp4bb] Keeping sequence alignments in register

some PDB files don't have this information, and also, if you have the structure of say the C-terminal domain of a protein the N-terminal residues will not be present in the header. Many thanks in advance for any further tips/advice! On Sat, Sep 21, 2013 at 8:42 AM, Mo Wong wrote: > Hi, &

[ccp4bb] Keeping sequence alignments in register

Hi, I'm trying to do sequence alignments that are generated using PDB files as the sequence source so are often missing residues with the sequence. Is there any way to run BLAST (or related server - not a local program) that accepts wildcards so I can keep the numbering in the resulting alignment

Re: [ccp4bb] Placing coordinates and mtz reflections file on a common new origin

atch should do the job. I presume you did a structure factor > calculation for one or both models? > > I'm not clear what the problem is with that. Is it that it is giving you > the wrong shift? > > > On 30 July 2013 14:33, Mo Wong wrote: > >> Hi all, >>

[ccp4bb] Placing coordinates and mtz reflections file on a common new origin

Hi all, I am trying to get multiple molecular replacement solutions on the same origin. I know this has been asked before, however, in my case I want to stick to CCP4 programmes (I am aware PHENIX can do this). I have tried to get this to work using csymmatch which outputs the origin-shifted coor

[ccp4bb] Delete waters within radius of defined space

Hi all, I'd like to be able to automatically remove modeled/refined water molecules that overlap regions of space that have been flagged as potential "blobs" of interest in an initial difference density map. My questions are: 1) Can I get Coot to output to a file the coordinates it spits out whe

[ccp4bb] Off topic: SYPRO Orange

Hi all, Does anyone know if SYPRO orange can be purchased in any form other than a DMSO stock? If not, has anyone successfully removed DMSO from a concentrated stock of SYPRO orange (i.e., via centrifugal evaporation)? Thanks

[ccp4bb] Accessing CCP4MG applications via python scripts

Hi, I can't see any documentation on the CCP4MG web site that shows how to access applications using python scripts. If someone could e-mail me basic script that uses SSM to automatically superimpose all loaded PDBs I'd be very grateful. Thanks!

Re: [ccp4bb] Scaling up from an Intelliplate to Linbro Plate

hl=en > > > > patr...@douglas.co.ukDouglas Instruments Ltd. > > DouglasHouse, EastGarston, Hungerford, Berkshire, RG177HD, UK > > Directors: Peter Baldock, Patrick Shaw Stewart > > http://www.douglas.co.uk/ > > Tel: 44 (0) 148-864-9090US toll-free

[ccp4bb] Scaling up from an Intelliplate to Linbro Plate

Hi all, I know scaling up from a hit found from a high throughput screen is an empirical process, but does anyone have a good rule of thumb as a starting point when it comes to scaling up from a hit observed in an Intelliplate to a Linbro plate (i.e., change in volume ratios, amount to add to rese

[ccp4bb] Refs. for alpha-helical propensity of varying homopolymer lengths

Hi all, I'm looking for a paper which has a figure that plots alpha-helical propensity against homopolymer length for various types of amino acids (i.e., alanine, glutamate, and leucine) - with or without an N-terminal cap (experimental or theoretical is fine). I've not found anything that is laye

Re: [ccp4bb] .phs file conversion

Hi, Not the quickest way, but you can easily convert PHS files to MTZ files using CCP4i ("Convert to/modify/extend MTZ" - via the f2mtz programme). Then generate the map as you would a normal MTZ file. Since PHS files come in 2 flavours, check the following web site to see which format your's is

Re: [ccp4bb] Off topic: Mammalian gene expression in E. coli

tephen Weeks, Ph. D. > Drexel University College of Medicine > Department of Biochemistry and Molecular Biology > Room 10102 New College Building > 245 N. 15th St. > Philadelphia, PA 19102 > > Phone: (+) 215-762-7316 > Fax: (+) 215-762-4452 > > > > Mo

Re: [ccp4bb] Off topic: Mammalian gene expression in E. coli

Thanks for the reply. I've checked my sequence for rare codons; however, what would be useful to a pseudo-molecular biologist like me is a web server which will look at your input DNA sequence and guesstimate the success of expression in E. coli (i.e., consider codon frequency). Does one exist? Ev

[ccp4bb] Off topic: Mammalian gene expression in E. coli

I thought I'd post this to the CCP4bb, as judging by previous posts, it seems I could get some useful insight into my problem... This is question has probably been asked by people for a long as molecular biology has been around, but hopefully my question isn't a complete rehash of other peoples: I

[ccp4bb] Molecular replacement using a partial molecular replacement solution

Hello, My problem: I have poorly phased 3.5A data which suggests 6 molecules per ASU, and using MolRep with the experimental phases ("search for model in the map") I have good solutions 3 of them. There is a lot of empty electron density which needs to be filled with more copies of the molecule. I

[ccp4bb] Search nucleotide database "in-frame"

Hi all, I'm trying to find a website where I can seach a nucleotide database with a relatively short (say 12 bases) in-frame sequence (i.e; -GGA--CAG-etc), and have the results in the same frame (so the resulting hits include regions which code for the same amino acid sequence). I'm sure this can