[ccp4bb] Ask for recommendation: crystal screening kit

. Morpheus (Molecular Dimensions) 8. Midas (Molecular Dimensions) Kind regards, Wenhe

Re: [ccp4bb] Protein behaves as dimers in 2M NaCl and as high oligomers with 300mM NaCl

highly charged pocket/site. The mutation of these residues possibly against the aggregation. Kind regards, Wenhe Sent from my iPad > On 27 Feb, 2014, at 3:47 pm, Tom Wong wrote: > > > Hello everyone! > > I have run into a problem in a 55kD recombinant human prote

[ccp4bb] Convert DSSP to PDB format

. Kind regards, Wenhe

[ccp4bb] Phosphorylated and un-phosphorylated protein structures

Dear members, Does anyone have an example of a pair of protein structures in phosphorylated (natural phosphorylation and mutation mimic) and un-phosphorylated states? —— particularly they have distinct conformational difference. Thank you. Kind regards, Wenhe

[ccp4bb] Rename chain ID of water molecules

name A (or B). Any tool in CCP4 can do this? I remembered that when we deposited our coordinates to PDB, the server can do this automatically. Thank you. Kind regards, Wenhe

Re: [ccp4bb] off-topic;Crystal cannot dissolved in buffer

but will try later. Kind regards, Wenhe On 26 Sep, 2014, at 7:53 am, Xiao Xiao wrote: > Hi everyone, > > Sorry for an off-topic question. > > I got a problem with crystal dissolving. Basically I got crystals of my > protein in various conditions, most conditions contain

[ccp4bb] Superpose tool in CCP4_some residues missing in RMS output list

nd residue number and the same toally residues number, they are 100% sequence identity as well. Anybody knows why some residues are missing in the RMS output list? Thank you. King regards, Wenhe

[ccp4bb] [CCP4] identify a rotation centre: domain rotation

D" it mentioned above, such as (157.251 151.877 -70.874), is possibly near to the "rotation centre". I would like to have your opinion though. Thank you. King regards, Wenhe

[ccp4bb] off-topic: "special" format for multiple sequence (protein) alignment

the conserved amino acids by colored blocks as shown in the attached file. Maybe some of you have seen some programs can do this? Thank you. King regards, Wenhe <>

[ccp4bb] off-topic:schematic representations for secondary structure

secondary structure from PDB database website (please see the attached figure). Does anyone know whether there is a program to draw these schematics? Thank you. King regards, Wenhe <><>

[ccp4bb] Any calculation function in CCP4 to analyze coordinate file?

/ligand, the average b-factor of protein/water/ligand, the number of residues which have alternative side chians, and so on. Thank you. King regards, Wenhe

[ccp4bb] [CCP4] movie for side chain flip

regards, Wenhe

[ccp4bb] [CCP4]data processing I222 vs pointless I121

t is body-centred monoclinic (Cell: 104.1 108.6 264.890 90 90) I couldn't see the difference between I222 and I121. May I ask do I need to go back to the Mosflm process step and choose other space group for the processing? Thank you. King regards, Wenhe

[ccp4bb] Morph with Chimera: how to make visible connection/interaction in Morph

Dear all, I would like to show the visible metal-residue interaction during the Morph movie. Anyone knows how to do that in Chimera? Thank you. King regards, Wenhe

[ccp4bb] Efforts been made to solve protein (soluble) aggregation

full-length aggregated protein is still functional in Gel-shift assay, which indicates the protein is corrected folding. I guess "soluble aggregation" is a common problem for tough proteins. If anyone has experience on it and can share with us, please drop an email. Kind regards, Wenhe

[ccp4bb] Compound with flexible conformation but nM Kd

out interacting with the target? Thanks. Kind regards, Wenhe

Re: [ccp4bb] Compound with flexible conformation but nM Kd

-pi interaction between the scaffold structure and the protein (tyrosine ring). Is it possible that the hydrophobic substituent could facilitate the formation of this pi-pi interaction but not necessary to involve in the interaction? Thanks. Kind regards, Wenhe > On Apr 27, 2018, at 1:50 AM,

Re: [ccp4bb] Compound with flexible conformation but nM Kd

ed to run the ITC to see what information I can get. Wenhe > On 27 Apr 2018, at 8:51 pm, vincent Chaptal wrote: > > Dear Wenhe, > > A thought came to mind after having read all the other threads, for which I > generally agree. > An alkyl chain on a molecule (charged? h

[ccp4bb] Glycoprotein expression strategy

regards, Wenhe To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1

[ccp4bb] Superpose program in CCP4

program for this purpose? Thank you! Kind regards, Wenhe

[ccp4bb] Structure example request for large domain movement "in crystallo" soaking

helpful for me to relate my result to other similar examples. Thank you very much. King regards, Wenhe

[ccp4bb] CCP4superpose_only superpose interesting residues

can not really use CCP4 Superpose to do it. May I ask do you have any idea managing to do it? Thank you. King regards, Wenhe

[ccp4bb] RNA-PROTEIN purification on FPLC

Dear members, We are planing to purify RNA only or/and RNA-protein complex on FPLC. The application of the purified materials is for crystallization. However, our concern is that our FPLC has been frequently used in bacterial expressing protein purification including purifying proteins from crude

[ccp4bb] COOT running on Macbook Pro M1 chip

Dear CCP4 community, The COOT is not running smoothly on my M1 chip Macbook. For example, when both model and the electron density map are displayed, the moving from one residue to the next (pressing SPACE bar) is lagging/slow (>2s). This only happened to my old computer, but I am surprised to fin

Re: [ccp4bb] COOT running on Macbook Pro M1 chip

> > Dear Wim, > > on my M1 Macbook Air, coot 0.9.6 (latest from CCP4) works smoothly/fast. > What is your XQuartz version? I have 2.8.1 . > > HTH, > Kay > > On Thu, 16 Sep 2021 15:40:53 +0800, WENHE ZHONG GMAIL.COM> wrote: > > >Dear CCP4 community, > &

[ccp4bb] Co-purified ligand present in protein crystal

digest protein with protease such as trypsin. Or use urea to denature the protein. However, these methods require relatively long processing time which is not optimal when the ligand that we want to analyse is unstable (degrade overtime). Anyone has more suggestions? Thank you! Kind regards, Wenhe

[ccp4bb] Predict effects of mutations on protein stability and protein-protein interaction

down the candidates. We only know that SDM is good server to predict the protein stability. Do you have other servers or softwares can recommend? We can do a cross comparison. Thanks. Kind regards, Wenhe