[ccp4bb] Does MicroED (microcrystal electron diffraction) have phase problem ?

Hi, All, I am new to MicroED (microcrystal electron diffraction). I know that X-ray crystallography has phase problem, and I think MicroED has phase problem too (it is diffraction of electron instead of x-ray). However, when I read the Wikipedia, I could not understand the following description of

Re: [ccp4bb] [Offtopic] Protein stain in Coomassie Blue dyes

will > work. This is different from when you want to use the dye to do some > quantitative work such as the Bradford assay. It would be interesting to > know the effect of detergents on Bradford. > > Zhijie > > > > On Oct 4, 2018, at 9:26 PM, Alex Lee wrote: > > Dear

[ccp4bb] [Offtopic] Protein stain in Coomassie Blue dyes

Dear All, I am thinking that in an SDS-PAGE experiment, if protein samples are boiled in SDS containing loading dye, and supposedly SDS interacts with proteins, why the Coomassie Blue dyes could still interact with and stain the proteins? I am thinking SDS is covering the proteins, making no

Re: [ccp4bb] PDB ligand 3-letter code for TCEP?

ers > michael > > From: CCP4 bulletin board on behalf of Alex Lee < > alexlee198...@gmail.com> > Reply-To: Alex Lee > Date: Thursday, 19 October 2017 at 11:19 > To: "CCP4BB@JISCMAIL.AC.UK" > Subject: [ccp4bb] PDB ligand 3-letter code for TCEP? > > Hi

[ccp4bb] PDB ligand 3-letter code for TCEP?

Hi All, I tried to look for the 3-letter ligand for reducing reagent TCEP in PDB but I could not find one. I even search with "Tris(2-carboxyethyl)phosphine hydrochloride" in PDB but got right hit. How do I need to to to pull the TCEP code out?

Re: [ccp4bb] Pymol point mutagenesis turns out to be deletion of a residue

thanks. Coot works! On Wed, Apr 19, 2017 at 10:20 AM, Vipul Panchal wrote: > I am not experienced with pymol. However if you are familiarized with > coot, you can mutate and set rotamer. It is really simple. > > On 12-Apr-2017 12:15 AM, "Alex Lee" wrote: > >

Re: [ccp4bb] Refmac5 twin refinement pushing Rfree surprisingly down

It’s hard to interpret MR results otherwise. >> >> >> >> Also, since the higher-symmetry SG works in MR, you should try to refine >> the model in that SG, with only two twin domains, refining twin fraction. I >> can guarantee that a good reviewer will have you do t

Re: [ccp4bb] Refmac5 twin refinement pushing Rfree surprisingly down

ace groups of PG 321/312 using Phaser. >> Going from PG 3 to PG 32 should halve the number of copies per ASU. You may >> have to re-process your data in the higher point group to do this. >> >> >> >> Or you might actually have a tetartohedral twin, but

Re: [ccp4bb] Refmac5 twin refinement pushing Rfree surprisingly down

. > > > > The twin fractions indicate a high twin fraction—~46% if actually > hemihedral! > > > > Also take a look at the paper I referenced for more info. I can send you a > .pdf if you need me to. > > > > Please let me know how it works out—I am interested in t

Re: [ccp4bb] Refmac5 twin refinement pushing Rfree surprisingly down

il 2017 at 19:52, Robbie Joosten wrote: > > Hi Alex, > > > > You are not giving the number after refinement without the twin > refinement. Nevertheless, R-free drops like this are not unheard of. You > should check your Refmac log file, it would warn you of potent

[ccp4bb] Refmac5 twin refinement pushing Rfree surprisingly down

Dear All, I have a protein/dna complex crystal and data collected at 3A and another set at 2.8A, space group P32. L test shows twinning (fraction around 0.11). The structure solved by MR and model building of the complex finish (no solvent built yet, I do not think it's good to build solvent in su

[ccp4bb] Pymol point mutagenesis turns out to be deletion of a residue

Dear All, I am using MacPymol 1.8.6, I did Pymol point mutagenesis using Wizard, everytime after I choose a residue for mutation, choosing a mutated target residue and a rotamer and click apply, the text of the sequence on top of the main window shows my selected residue is mutated but the graphic

[ccp4bb] software or tool for Individual residue in a Ramachandran plot graph?

Dear All, Is there a tool or software which can give Ramachandran information of individual residues in a plot? I used Coot to check for Ramachandran plots, but it shows all the residues in a coordinate I put in Coot, not individual one. I also use "residue info" in coot, it tells Ramachandran "p

[ccp4bb] Pymol alignment command grammar help

Dear CCP4BB members, I tried to use pymol command to align two proteins, I read the pymol wiki and I could not understand the command grammars (I am not computer major and not familiar with machine language). For example pymol wiki says as below: Furthermore, you may wish to restrict the alignme

Re: [ccp4bb] How to determine the concentration of biotinylated peptide?

; Centre for DNA Fingerprinting and Diagnostics >> Hyderabad, INDIA >> >> Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com >> Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab) >> Lab URL: http://www.cdfd.org.in/labpages/computational_functional_ >> genomics.html &

[ccp4bb] How to determine the concentration of biotinylated peptide?

Dear All, Sorry for the off-topic question, I'd like to do Biacore SPR assay with N-terminal biotinylated peptide as ligand (to Biacore SA chip) and my protein as analyte. I have a question of how to determine the concentration of biotinylated peptide （synthetic peptide), if the peptide has no Tyr

Re: [ccp4bb] does Refmac5 do density modification in the refinement of a structure?

flattening, then > beginning the rebuild cycles with these phases. > > This approach is provided in CCP4I2 > Eleanor > > On 16 December 2016 at 19:44, Alex Lee wrote: > >> Hi All, >> >> I am using CCP4i 7.0.0.025 linux version. I am wondering if Refmac5 >

[ccp4bb] does Refmac5 do density modification in the refinement of a structure?

Hi All, I am using CCP4i 7.0.0.025 linux version. I am wondering if Refmac5 automatically does density modification (e.g. solvent flattening, NCS, etc..) in the refinement after I put a solution coordinate from Phaser MR molecular replacement and the experiment data (MTZ file)? If Refmac5 does n

Re: [ccp4bb] iMosflm: How to change gain and exclude frames

akes anywhere from 1 to 4 hours to > work through, depending on how carefully you do it. > > HTH > > Harry > -- > Dr Harry Powell > Chairman of International Union of Crystallography Commission > on Crystallographic Computing > Chairman of European Crystallographic

[ccp4bb] iMosflm: How to change gain and exclude frames

Dear CCP4bb members, I am new to iMosflm data processing (I use HKL2000 but I really want to learn iMosflm). After automatic index, cell refinement and integration in iMosflm, I got 2 warnings. 1. Error in detector gain. BGRATIO of my data lies outside the 0.7 to 1.3 range (mine is 0.64) Imosfl

[ccp4bb] MrBump and Balbes Molecular Replacement of multiple copies in ASU Failed even with high homology model

Hi All, I have a protein which contains 72 amino acids. The crystal of this protein diffracts to 2.5A with SG P31 (CELL Dimension 65.9590 65.9590 164.3900 90. 90. 120.). Pointless indicates no twinning. Mathew coefficient as below: For estimated molecular weight 7919. Nmol/asym Mat

Re: [ccp4bb] sodium thiocyanate as cryoprotectant

bhi > > > > Abhimanyu Kumar Singh, Ph.D. > School of Biosciences > University of Kent > Canterbury, UK. > > On 27 Sep 2016 23:43, "Alex Lee" wrote: > >> Hi CCP4bb members, >> >> I have a condition for my protein crystals at "0.2M sodium

[ccp4bb] sodium thiocyanate as cryoprotectant

Hi CCP4bb members, I have a condition for my protein crystals at "0.2M sodium thiocyanate, 25% PEG3350, pH6.9". I'd like to try cryoprotectant with just higher concentration of sodium thiocyanate, but I have no google hits of the range of concentration I should use. I wonder anyone in this forum