Re: [ccp4bb] 16th Annual CCP4/APS Crystallographic School (2024) in the US

Please note that we are still accepting applications, interested students are encouraged to apply before the deadline. A draft program is available at the course website. Charles, Andrey and Qingping From: CCP4 bulletin board on behalf of Qingping Xu <292f

Re: [ccp4bb] CIF file Cannot Open by Coot

On 8/15/24 16:08, Hu, Wenhao wrote: Hi Paul, I’ve attached screenshots that show the error message from Coot, along with the contents of the line that the message refers to. Since this CIF file contains experimental data and restrains that would be difficult to rebuild in other software, I’

Re: [ccp4bb] libcheck

On 8/15/24 17:14, Petr Pachl wrote: Hi Paul, so there is not way how to generate cif file when we have precise ideal structure (given from quantum chemistry calculations)? [This part first] That's right (if by that you mean that you (only) have coordinates and elements) - not in the CCP4 Ec

Re: [ccp4bb] libcheck

Hi Paul, so there is not way how to generate cif file when we have precise ideal structure (given from quantum chemistry calculations)? Also two off topic questions regarding coot-1 and coot. I tried to transfer some of my keybindings and settings to coot-1 "language". However as I understand not

Re: [ccp4bb] CIF file Cannot Open by Coot

If you have not edited the file, the WebCSD file will contain the contents of the asymmetric unit of a small molecule structure, with reported geometry and esds, but no restraints, not least of all because small molecule refinements are (nearly always) unrestrained. This would be CIF format. C

Re: [ccp4bb] libcheck

On 8/15/24 09:01, Andrea Smith wrote: -- Dear all, Dear Andrea, I successfully used libcheck to generate libraries for my ligands a couple of months ago. Now I wanted to use it again and it is giving me an error. Moreover, even though I select COOR Y and LCOOR N, libcheck uses COOR N and

Re: [ccp4bb] CIF file Cannot Open by Coot

Hi Paul, Thank you for your reply. I’ve attached screenshots that show the error message from Coot, along with the contents of the line that the message refers to. Since this CIF file contains experimental data and restrains that would be difficult to rebuild in other software, I’m seeking sol

Re: [ccp4bb] CIF file Cannot Open by Coot

On 8/15/24 15:01, Tang, Jiazhi wrote: -- It happens sometimes when you can not open the downloaded cif files properly. One solution is to draw the compound yourself in Chemdraw, copy the smiles and generate the cif in Elbow within the phenix suit or other ligand software within ccp4. Just

Re: [ccp4bb] CIF file Cannot Open by Coot

It happens sometimes when you can not open the downloaded cif files properly. One solution is to draw the compound yourself in Chemdraw, copy the smiles and generate the cif in Elbow within the phenix suit or other ligand software within ccp4. Just be careful if the ligand contains ions, which c

Re: [ccp4bb] CIF file Cannot Open by Coot

On 8/15/24 14:44, Martin Hu wrote: Dear [Recipient's Name], Dear [Correspondent's Name], I have downloaded a CIF file of a ligand of interest directly from WebCSD, which was originally obtained from experimental crystallography research, and attempted to import it into Coot. However, Coot

[ccp4bb] CIF file Cannot Open by Coot

Dear [Recipient's Name], I have downloaded a CIF file of a ligand of interest directly from WebCSD, which was originally obtained from experimental crystallography research, and attempted to import it into Coot. However, Coot indicates that it cannot read the file for some reason. I've also tri

[ccp4bb] PhD position in ultrafast imaging with X-ray lasers

Dear colleagues, My group is looking for a PhD student to join my ERC-funded project FemtoPix to develop ultrafast imaging methods using X-ray free-electron lasers to study the dynamics of biological macromolecules. The project builds on our recent

[ccp4bb] libcheck

Dear all,   I successfully used libcheck to generate libraries for my ligands a couple of months ago. Now I wanted to use it again and it is giving me an error. Moreover, even though I select COOR Y and LCOOR N, libcheck uses COOR N and LCOOR Y.   Can someone tell me what am I doing wrong?   I

[ccp4bb] PDB Archive Serves Structures Determined by Integrative and Hybrid Methods (IHM)

Dear all, Structures determined by integrative and hybrid structure determination methods (IHM) are now available alongside experimental structures in the PDB archive. These structures are deposited into and processed by the PDB-Dev system. Each IHM structure is issued a PDB ID, reported in