[ccp4bb] Center for Biomolecular Structure Lecture Series

Dear CCP4 researchers, You are cordially invited to the Center for Biomolecular Structure (virtual) lecture series, Structure Function of Lipid Metabolism Dr. Michael Airola Stony Brook University May 26, 2021, 13:30 (EST) Registration Link: https://bnl.zoomgov.com/meeting/register/v

[ccp4bb] Postdoc opening to study mechanisms of CRISPR-Cas

Dear All, A NIH-funded postdoc position is available in Ailong Ke’s Lab at Cornell University, Ithaca, USA. The main theme of the lab is to understand the underlying mechanism of RNA-guided processes inside cell. Projects for postdoctoral training typically involve nucleic acid biochemistry, cr

[ccp4bb] American Crystallographic Association Virtual Meeting, Structural Biology of Infectious Diseases

The 71th annual meeting of the American Crystallographic Association Annual Meeting will be held virtually from July 30-August 5, 2021. A session on the Structural Biology of Infectious Diseases will be held on Tuesday, August 3. We invite scientists to submit abstracts for oral presentations i

Re: [ccp4bb] generate symmetry mates of EM structures

Hi, Stefano, Thanks. I use Pymol 2.4. I figured out that if I downloaded the PDB (5L93) RCSB website (biological assembly 1 PDB file), Pymol would show each state of the structure (3 chains) individually, if I execute the "set all_states, on" command, I can see the assembly. Best, Xiao On Fri,

Re: [ccp4bb] Does anyone know of a "CHARMM bulletin board" ?

Hi Not sure why ACE didn't work, but if you change the nomenclature of HIS to HSD it should work. However, if it's getting too troublesome, you can always use CHARMM-GUI online server for input generation. See if it helps. Arunabh Get Outlook for Android __

Re: [ccp4bb] Does anyone know of a "CHARMM bulletin board" ?

On Fri, May 21, 2021, Fred Vellieux wrote: CHARMM bulletin board similar to CCP4BB ? The discussion site is called a "forum" in CHARMM-lingo. Try visiting https://www.charmm.org/. Note also the CHARMM-GUI (under Tools), which can be of considerable help in setting up a system. ...dac #

Re: [ccp4bb] generate symmetry mates of EM structures

Dear David, Thank you for your help. It seems the problem is due to the Pymol program. I could only see 3 chains in Pymol from the assembly PDB downloaded from the RCSB website (biological assembly 1 PDB file). If I use UCSF Chimera, I can see 18 chains. With others' help, I can also use "sym" com

[ccp4bb] Does anyone know of a "CHARMM bulletin board" ?

Hi folks, Sorry about the non-ccp4 question. I don't know where to ask. I have to perform MD simulations but I am totally on my own here. The one program that appears to be free (in terms of license) seems to be CHARMM. GROMACS (testing with the examples found in the internet) did not work in

Re: [ccp4bb] generate symmetry mates of EM structures

Dear Xiao, For public entries in the PDB archive, it is possible to download the coordinates of the assemblies defined in the PDB entry. If you visit the page for the entry at PDBe (pdbe.org/5l93) and select 'Downloads' you have the option to download various data, including mmCIF files cont

[ccp4bb] generate symmetry mates of EM structures

Dear Community, I wonder if there is a way to generate symmetry mates of EM structures? For example for PDB code 5L93, I tried PISA assembly server and Pymol to generate assembly (18 chains) but failed because it is not a crystal structure. I tried to download assembly directly from RCSB databank

Re: [ccp4bb] Converting data set to another format?

There is a  Nonius/Bruker software that converts the images and writes out the undistorted frames. Many years ago we also tried to use MOSFLM and XDS to process our Proteum images (Bruker) but even with this transformation we could not do it, so in the end we gave up. Regards, Pedro Às 09:

Re: [ccp4bb] Converting data set to another format?

Hi Dirk Converting to a form that Mosflm can read is not too much of a problem - the problem arises because Kappa CCD images are not corrected for spatial distortions, which can be significant. I think you would need a correction table (or similar - maybe “brass plate” images if you have them