Re: [ccp4bb] Identify mysterious density in CryoEM map

ld not > make much difference if your "Fobs" come from X-ray or cryo-EM! > Please share your experience if you choose to give it a try. > Good luck! > Pavel > > P.S.: Phenix way to convert map to structure factors (example): > phenix.map_to_structure_factors map.mr

[ccp4bb] Identify mysterious density in CryoEM map

Dear all, We’re working on an unknown ligand density in our CryoEM structure. Is there a program that uses deep-learning to fill uncharacterized electron density similar to Checkmyblob but for CryoEM maps? Thanks, Jan

[ccp4bb] Search for a particular motif [off-topic]

Dear all, I apologize for the off-topic question. I’d like to search for a particular aa sequence motif inside the protein sequence data bank (Swiss-prot, Uniprot, etc…) with the following criteria: It should not be inside a secondary structure. Does anyone know a program that could do that?

[ccp4bb] Power supply for a Phillips CM10 Electron Microscope?

Dear all, We’re looking for a 24 h.t. and 24 fil. power supply for a Phillips CM10 Electron Microscope. Does anyone know how to get such component separately? Used is fine too. Thanks, J. To unsubscribe from the CCP4BB

[ccp4bb] Coot on Macosx Catalina

Hi everyone, I'm running into issues installing coot on Macosx Catalina. When install the system using BINARY.setup the following message shows up: Does anyone else faced this problem? Is there a way to work around it? Thanks, J.

Re: [ccp4bb] High Rfree in last Shell

ments of Biophysics and Biochemistry > UT Southwestern Medical Center > 5323 Harry Hines Blvd. > Rm. ND10.214A > Dallas, TX 75390-8816 > diana.tomch...@utsouthwestern.edu <mailto:diana.tomch...@utsouthwestern.edu> > (214) 645-6383 (phone) > (214) 645-6353 (fax) >

[ccp4bb] High Rfree in last Shell

Hi everyone, I’m trying to publish two structures at 3.1Å resolution with the following refinement statistics: Resolution range (Å) 49.2-3.1 49.3-3.1 Rfactor (%)24.0 (32.4)

Re: [ccp4bb] Salt or protein?

rp-ccp...@virginmedia.com> wrote: > > Hi Jan > > What happens if you use a program that can easily use spots from all images > to index, like DIALS or XDS? My recollection (which may be wrong) is that > this is not straigthforward in HKL3000. > > >> On 17 Feb

[ccp4bb] What is the easiest/cheapest way to obtain a library of proline derivatives?

Sorry for being a bit off-topic, but I’m looking to transform the catalytic properties of a protein I’m working on by adding an aromatic moiety on one of its prolines. However none of the proline derivatives I find commercially are really interesting. Does anyone know what would be the cheapest

Re: [ccp4bb] Proline derivatives

Thanks everyone for all the suggestion! I have plenty of options now! > On Mar 31, 2017, at 11:06 AM, Lakshmi SwarnaMukhi Pidugu > <swarna.pid...@gmail.com> wrote: > > You could try scifinder. > > Swarna > > On Wed, Mar 29, 2017 at 6:07 PM, Jan van Agthoven <

[ccp4bb] Proline derivatives

Hi Everyone, Does anyone know what’s the fastest way the find all commercially available proline derivatives on carbon gamma? Thanks, Jan

[ccp4bb] Coot on MacOsX undo button

Hi everyone, Looks like the undo button on Coot doesn't work. I installed Coot-0.8.6 on MacOsx El Capitan. Anyone knows what could be the problem? Or where to report the bug? Thanks,

[ccp4bb] Phenix refinement with modified amino acids

Dear all, I'm refining a structure with three modified amino, ccp4 code: CY3, DTR, and MPT respectively. However I don't know how to give phenix.refine the adequate libraries as to obtain the correct geometry for three amino acids. I tried to add the cif libraries downloaded from ccp4 to the

[ccp4bb] Table in NSMB

Dear all, I'm filling out my table for NSMB, about a structure of protein ligand bound to a receptor. They ask for 3 different lines regarding number of atoms bfactor. 1) Protein 2) Ligand/Ion 3) Water. Does my protein ligand belong to Protein or Ligand/Ion? Thanks,

Re: [ccp4bb] AW: [ccp4bb] Table in NSMB

looked at again. Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Nat Echols Gesendet: Dienstag, 18. Februar 2014 17:29 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Table in NSMB On Tue, Feb 18, 2014 at 8:19 AM, Jan van Agthoven janc...@gmail.commailto:janc

[ccp4bb] Low resolution and polyalanine mutation

I apologize for being a bit naive, but it turns out that I'm working an low resolution mode (3.6 A). A great part of the chains have previously been built with polyalanine, since there's obviously no density for the side chains. When using phenix, I obtain a model just as good with all residues

Re: [ccp4bb] repulsive effects of arginine

Thanks for your responses, Andrey, I had no idea about these arginine associations. In this case the arginines are facing each other guanidinium to guanidinium. I guess they wouldn't attract. Nadir, the asp is not entrapped between the two arginines. But Hermann is probably right by saying that

Re: [ccp4bb] repulsive effects of arginine

, Jan van Agthoven wrote: Thanks for your responses, Andrey, I had no idea about these arginine associations. In this case the arginines are facing each other guanidinium to guanidinium. I guess they wouldn't attract. Nadir, the asp is not entrapped between the two arginines. But Hermann

[ccp4bb] repulsive effects of arginine

Hi everyone, I'm working on structure of an antibody that inhibits a receptor. The antibody doesn't induce any conformational change in the receptor and doesn't bind the ligand binding site. If we superimpose the receptor with antibody and ligand the only hindrance we find is a electrostatic

[ccp4bb] imosflm, bad predictions

Hi everyone, I recently switched from HKL2000 to imosflm to get rid of ice rings. The group space and cell unit of the data set are known and perfectly recognized by HKL2000. The predictions are also correct. In imosflm, the unit cell and space group are recognized. However the predictions are

[ccp4bb] sugar and coot

Hi everyone! Does anyone know if there is a way of auto-refining a sugar in Coot? Jan

Re: [ccp4bb] spherulites and PEG3350

-- *From:* Jan van Agthoven janc...@gmail.com *To:* CCP4BB@JISCMAIL.AC.UK *Sent:* Wednesday, August 24, 2011 2:05 PM *Subject:* [ccp4bb] spherulites and PEG3350 Dear all, I recently obtained some spherulites while trying to crystallize my protein. The spherulites are manually reproducible