Re: [ccp4bb] Adding metal ions

Dear Jose, I want to simulate the copper/protein complex to track the movement of copper ion from the surface to its binding site. Best Veerendra -Original Message- From: CCP4 bulletin board On Behalf Of Jose Brandao-Neto Sent: Tuesday, June 20, 2023 11:23 AM To:

Re: [ccp4bb] Adding metal ions

Sent: Friday, June 16, 2023 5:40 PM To: Veerendra Kumar Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] Adding metal ions Take a protein structure with waters, replace surface waters with Cu++ and run some very basic MD to optimize distances. Many of the atoms will move since Cu++ will find

[ccp4bb] Adding metal ions

Dear All, I want to add about 200 copper ions on protein surface randomly. Is there any program available to serve the purpose? Thank you Best regards Veerendra Get Outlook for Android To

Re: [ccp4bb] India EMBO Lecture course on Tumour Metabolism-Dealine extended 28th February 2023

Dear All, Deadline for registration and abstract submission extended till 28th February, 2023. Registration link- https://meetings.embo.org/event/23-tumour-metabolism Thank you Best Regards Veerendra Kumar, PhD Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows

Re: [ccp4bb] E.coli cell lysis using glass beads

Veerendra Kumar, PhD Associate Professor & Ramalingaswami Fellow Amity Institute of Molecular Medicine & Stem Cell Research (AIMMSCR) J-3 108, Amity University Campus Sector-125, Noida-201303 UP, INDIA http://amity.edu/aimmscr/Faculty.asp Google Scholar: https://scholar.google.com/citati

[ccp4bb] E.coli cell lysis using glass beads

Dear All, Sorry for the off topic. May I ask your experience about bacterial cell lysis using glass beads beating? How is the cell lysis compared with sonication and French press? Does the glass beads affect the protein quality? Thank you in advance. Best Regards Veerendra Kumar, PhD Associate

Re: [ccp4bb] relative domain motion calculation...

Hi Mintu You can use Chimera to calculate rotation angel. http://www.cgl.ucsf.edu/chimera/videodoc/AlignDomains/ Veerendra On 21/4/15 3:39 PM, Mintu Chandra mi...@iiserb.ac.in wrote: Dear All, I am working with a protein containing tandem domains, connected with 3-4 residue linker. I want

[ccp4bb] Phaser MR problem

Dear CCP4 members, Recently I have collected native data at 3.3 A resolution. The structure of the protein should have two domains. The structure of c terminal domain from homologous (30 seq similarity) is known. I took n terminal domain from another homologous protein. I ran the phaser using

[ccp4bb] DNA structures superimpose

Dear CCP4 members, Is there any program to superimpose the DNA structures? I also want to measure the relative domain rotation angle. I tried using DynDom but it does not work for me. Can someone suggest a program which can output the rotation angles? Thank you Best Regards Veerendra kumar