[ccp4bb] Problem with macOS Catalina

Hi Guys I recently updated my macOS to the latest Catalina and here the problem begins. A number of my structural biology softwares like Coot, CCP4i2 and CCP4 are not working. Are you facing the same problem? Any solution please Kahkashan

Re: [ccp4bb] Problem with macOS Catalina

Hi Paul No, I haven't. Now I am going to. Faisal On Tue, Dec 24, 2019 at 1:02 PM Paul Emsley wrote: > On 24/12/2019 15:23, Firdous Tarique wrote: > > > > I recently updated my macOS to the latest Catalina and here the problem > begins. A number of my structural > >

[ccp4bb] best program for merging the two datasets

Hi. I have collected multiple datasets for my crystals and now want to merge them. Iwanted to know that between Blend and pointless, which programme is better to merge two or more data sets? Thanks Kahkashan To unsubscrib

[ccp4bb] Molecular Dynamics

Hello everyone I am trying to run a molecular dynamics simulation of a protein which has a Zn atom and few phosphorylated PTMs (Thr is phosphorylated). PTMs and Zn play essential roles to maintain the structural integrity and therefore cannot be removed rather I want to keep both of them for my ru

[ccp4bb] incorporating disulfide linkage

Hi I have a weird question. Is it possible to incorporate or mutate amino acid residues at the interface of two interacting surfaces in a multi subunit protein complexes hoping it to form a disulfide bond making the over all complex more stable for downstream structural studies ? Is there any sor

Re: [ccp4bb] incorporating disulfide linkage

; > Guillaume > > > On 16 Mar 2020, at 08:58, Firdous Tarique > wrote: > > Hi > > I have a weird question. Is it possible to incorporate or mutate amino > acid residues at the interface of two interacting surfaces in a multi > subunit protein complexes hoping it

[ccp4bb] server to predict structural stability

Hi I am trying to incorporate novel disulfide bond by introducing Cys mutants at the interface of a protein complex (A+B) and (C+B) whose crystal structure are already known. The idea is to introduce novel disulfide bonds in these individual complexes which does not dissociate and can be tried fo

[ccp4bb] Lost extension bar in Coot

Hi Just downloaded the new CCP4-7.1. Wondering where the extension bar in Coot 0.9 has gone. Please help me to find it. I think it is hidden somewhere. Best Kahkashan To unsubscribe from the CCP4BB list, click the followi

[ccp4bb] taking information from a deposited structure

Dear CCP4 community members. I have solved a crystal structure of a protein and am now trying to get a structure with a ligand bound to it, but so far unsuccessful. A homologous structure with the same ligand is present in the RCSB PDB (un published). Is it permissible to fetch structural informa

Re: [ccp4bb] taking information from a deposited structure

dge Institute for Medical Research Tel: +44 1223 336500 > The Keith Peters Building Fax: +44 1223 > 336827 > Hills Road E-mail: > rj...@cam.ac.uk > Cambridge CB2 0XY, U.K. > www-structmed.c

[ccp4bb] How to fix residual B value problem in pdbredo

*Hello everyoneI have a structure whose quality improves a lot when submitting it to PDB-Redo server. But when I am trying to put the output coordinates for validation it is not taking up and comes with message that: Structure contains Residual B values and TLS records are present but required ANIS

[ccp4bb] Can H-clashes be ignored ?

Hello everyone. I have a basic question. When a validation report of a coordinate is generated we often come across a term known as "Too-Close Contacts". First of all can somebody please explain me what is the shortest interatomic distance between the two atoms which is permissible ? Next, in thi

Re: [ccp4bb] Can H-clashes be ignored ?

w in our full quantum refinement of a small >> structure done as part of quantum refinement project (www.qrefine.com): >> >> http://scripts.iucr.org/cgi-bin/paper?S2059798317016746 >> >> All the best, >> Pavel >> >> On Fri, Aug 17, 2018 at 6:27 PM, Firdo

[ccp4bb] suggestions for cryoprotectant

Dear members I have got beautiful crystal hits in SaltRx screens which are not diffracting to a good resoultion. All of them are salt based condition and I am not able to formulate a good cryoprotectant for these crystals. I also think that in my case the poor resolution is due to a poor cryoprote

[ccp4bb] Coot shortcut key for Mutate

Hello everyone Can anybody tell me the Coot shortcut key for mutate or mutate and refine. Is there any way to turn it on or to assign a particular key if it is disabled ? Regards Firdous To unsubscribe from the CCP4BB lis

Re: [ccp4bb] Coot shortcut key for Mutate

Emsley wrote: > On Thu, 2021-06-10 at 00:20 +0530, Firdous Tarique wrote: > > Hello everyone > > > > Can anybody tell me the Coot shortcut key for mutate or mutate and > refine. Is there any way to turn it on or to assign > > a particular key if it is disabled ? &g

[ccp4bb] Solubility of Aluminum Fluoride

Hi Sorry for the off topic question but can anybody please suggest how to dissolve Aluminium Fluoride in water ? I know it has little solubility in water but have seen people using AF3 for their structural studies (ADP + AF3 as ATP analogue). Is there any other solvent where they have made AF3 sol

Re: [ccp4bb] Solubility of Aluminum Fluoride

uate protective measures (PPE, hood, etc.). > > Good luck, > > Guillaume > > > On 21 Jun 2022, at 19:38, Firdous Tarique > wrote: > > Hi > > Sorry for the off topic question but can anybody please suggest how to > dissolve Aluminium Fluoride in water ? I k

Re: [ccp4bb] Solubility of Aluminum Fluoride

Thanks everyone for their wonderful suggestions. Best F On Wed, Jun 22, 2022 at 11:42 AM Patrick Loll wrote: > Kevin and Guillaume said it all quite well. I just want to stress one > thing, namely that these solutions are metastable, and will eventually > precipitate (hours to days). > > In th

[ccp4bb] difficulties in crystallizing Fe-S containing proteins

Hi I am trying to crystallize a Fe-S cluster containing protein which is sensitive to oxygen present in the air. In the presence of air due to 'fenton reaction' the Fe-S breaks to give heterogeneous population of different Fe-S cluster and free Fe species. I also faced lots of difficulties in the

[ccp4bb] Protein toxicity or low expression

Hello everyone. I am struggling with the solubility or expression of my proteins in BL21DE3 E.coli expression cells. In one of my construct I have a Sumo-His fusion at the n-terminal of my protein. After induction what I see is the expression of the Sumo tag only. My sequencing results are fine an

[ccp4bb] domain prediction of a membrane protein

Hello everyone I am trying to clone some domains of a transmembrane protein. I have used an online server "Phobius" for the prediction of sequences which is showing it to be a membrane protein with cytoplasmic, non cytoplasmic and transmembrane regions. Attached is the image of that prediction. Re

Re: [ccp4bb] Mac M2 chip

Hi I too have an issue with my latest M2 Mac mini where the Phaser in Phenix runs extremely slow in comparision to my intel Mac laptop. I had also posted it on the phenix bulletin board but so far did not receive any suggestions how to fix it. By any chance if you guys have the previous email thr

[ccp4bb] Error doing automatic select 2D classes job in Relion-4.0.0

Hi I am getting the following error while running the class ranker program for automatically selecting the 2D classes. Can anybody please suggest where the issue is ? PYTHON ERROR: The required python module 'torch' was not found. in: /usr/local/relion-4.0-source/src/class_ranker.cpp, line 1954

Re: [ccp4bb] About model building

Do the mass spec of your crystal to identify the other protein. Once done solve your structure and build the complete model. This should be straight forward and quick. Best Wishes On Sat, 4 Nov 2023, 09:05 Sam Tang, wrote: > Dear community, > > I am solving the structure of a complex between pr

[ccp4bb] Making thioester bond in Chimera/ChimeraX

Hi Does anybody know how to make thioester bonds in Chimera or ChimeraX ? I am unable to make a bond between Cys321 in mol A with Gly1 in mol B (S-glycyl-L-cysteine) using Chimera or ChimeraX. I tried Isolde in ChimeraX and Build Structure in Chimera to make a bond between selected atoms but so

[ccp4bb] Not able to see Glycine in stick form

Hi everyone In ChimeraX I am not able to show Gly simultaneously as a stick and cartoon. If I am trying to show Gly as a stick then the cartoon line breaks up at this position. And this is for all structures if you see. By showing a cartoon and stick together, the sticks for all amino acids show u

[ccp4bb] How to make GDP.BeF3 solution ?

Hi I would appreciate it if someone could share with me a step by step protocol for making a stable GDP.BeF3 solution which is often used as a transition state analogue for structural studies of a protein complex ? Or a vendor from where it can be purchased directly. Regards Firdous ##

[ccp4bb] Showing Stick Representation In Coot

Hello everyone. Is there any way to show stick representation of the selected amino acid residues in Coot while everything else is represented in the form of C-alphas/Backbone. I want to show the amino acids of the catalytic centre in the stick form and not alter the C-alphas/Backbone conformation

Re: [ccp4bb] Showing Stick Representation In Coot

That makes sense. Thanks On Tue, Aug 27, 2024 at 2:46 PM Edwin Pozharski wrote: > I don't know the explicit answer to your question, but you can always copy > active site residues into a separate model and use different representation > for that. > > On Tue, Aug 27, 202

Re: [ccp4bb] Showing Stick Representation In Coot

Thanks Parijat This is exactly what I wanted. Best wishes Firdous On Tue, Aug 27, 2024 at 3:00 PM Parijat Das wrote: > You can use the Draw>Additional representation to do that in coot. > > Regards, > > Parijat > > > On Tue, Aug 27, 2024 at 6:22 PM Firdou

[ccp4bb] 3D classification of a small membrane protein.

Dear all I have a question about the 3D classification of a membrane protein using Relion 3.1, where I aim to remove some junk particles. The protein is relatively small (180 kDa), and its structure has already been resolved by cryoEM. It has minimal features outside the micelle ring and is primar

Re: [ccp4bb] Could Pottasium sodium tartarate diffract?

Hi. Yes, this is a diffraction pattern of a salt crystal. Best On Fri, 31 Jan 2025, 06:59 syed ibrahim, < 048c02cac012-dmarc-requ...@jiscmail.ac.uk> wrote: > Hi All > > I have a protein crystal (thin plate crystal) diffracted to high > resolution. The crystallisation condition is 200mM Pott

[ccp4bb] Installation of XDSGUI

Hello everyone I'm looking to install XDSGUI on my Linux computer but haven't been able to find clear instructions so far. I've checked the website (https://wiki.uni -konstanz.de/xds/index.php/XDSGUI), but the steps are a bit difficult to follow.. I would really appreciate a straightforward, hassl

[ccp4bb] Refinement in ISOLDE failing

Dear everyone I am trying to refine my protein using ISOLDE in ChimeraX which is failing with the following error. "At least one residue in your model does not match any templates in the MD forcefield. This may be due to missing or superfluous atoms, or an unusual residue that has not yet been

Re: [ccp4bb] Refinement in ISOLDE failing

Problem solved. Thanks On Wed, Apr 9, 2025 at 1:17 PM Firdous Tarique wrote: > Dear everyone > > > I am trying to refine my protein using ISOLDE in ChimeraX which is failing > with the following error. > > > "At least one residue in your model does not match any tem

[ccp4bb] Designing Cryo-ET teaching module for students

Hello everyone I am planning to teach a Cryo-ET course module for undergraduate students at an introductory to intermediate level next year. The course will cover image processing and 3D reconstruction, including tilt series alignment, segmentation, and subtomogram averaging, aiming to achieve a r

Re: [ccp4bb] BRIL as a Chaperone

Hi BRIL is attached to the C-terminal not in the N-terminal. Best On Fri, May 23, 2025 at 11:46 AM Firdous Tarique wrote: > Hi everyone > > I am encountering an issue during data processing of a membrane protein > construct fused to BRIL (apocytochrome b562RIL) at the N-termi