Re: [ccp4bb] replacement for Scientific Linux

Hi Harry, same here. Actually we skipped RHEL8 and its alternatives, so moved directly from CentOS7 to Rocky9. We are happy with that decision. Best wishes, Kay On Fri, 26 Apr 2024 15:57:46 +, Andy Purkiss wrote: >Hi Harry, > >We've been migrating to Rocky Linux as it is built on RHEL

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] add ligand with AceDRG

When you try to use LIG in Phenix it gives you an error message as it doesn’t know that LIG is obsoleted. Diana Sent from my iPhone > On Apr 26, 2024, at 10:08 AM, Yong Wang > <3c4fc05cc53b-dmarc-requ...@jiscmail.ac.uk> wrote: > > EXTERNAL MAIL > > Dear all, > > Perhaps the issue is that

Re: [ccp4bb] add ligand with AceDRG

Use the search tab at the RCSB web site, type in a 3 letter code, and if it has been used for a ligand then it will appear as a Chemical Component. Thanks to Phil, I am on vacation in Mexico and cut and pasting URLs is a pain on an iPhone. Diana Sent from my iPhone On Apr 26, 2024, at 9:07 

Re: [ccp4bb] replacement for Scientific Linux

Hi Harry, I started using Debian about 10-15 years ago, and never changed my opinion since. I had tested various others before, like redhat, suse, ubuntu etc. The stable version of Debian is indeed very stable, as there are no version changes, only bug fixes etc. The new release is about every

[ccp4bb] Staff Scientist Position to Manage Protein Purification Facility at Ohio State

Dear Colleagues, The Department of Biological Chemistry and Pharmacology at The Ohio State University has recently obtained 5 years of generous funding to equip and staff a facility for expression and purification of proteins for structural analysis by cryo-EM, x-ray crystallography, and NMR

Re: [ccp4bb] replacement for Scientific Linux

If you want to keep as close to scientific linux as possible, I would suggest Alma or Rocky Linux. Those were the two options my group considered when the writing was on the wall for scientific linux and we were ramping up our workstations. We ended up going with Alma, but I'm not sure it is any

[ccp4bb] Deadline extended - ECM34 - Symposium on Serial crystallography and dynamics/room temperature

Dear all, A gentle reminder for the ECM "M3 Serial crystallography and dynamics/room temperature" Please note that the general deadline for abstract submission has been extended to May 7th. Best regards Anna and Daniele On Tue, Apr 9, 2024 at 10:12 AM Daniele de Sanctis wrote: > Dear

Re: [ccp4bb] replacement for Scientific Linux

Hello Harry Any of the top 50 on distrowatch.com will basically be fine and the next 20 or so on the list will probably be fine. Then you start getting into the twilight zone. I am sure that will help greatly to narrow down your choice ;-0 Best wishes, Jon Cooper. jon.b.coo...@protonmail.com

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] add ligand with AceDRG

Dear all, Perhaps the issue is that the refinement program should be able to handle the priority of ligand dictionary, i.e. your custom ligand ID and dictionary overrides any existing in the default collection. I have not had any trouble with LIG or SX1, both existing in PDB ligands. I also

Re: [ccp4bb] replacement for Scientific Linux

Hi Harry, We've been migrating to Rocky Linux as it is built on RHEL in a similar way to Scientific Linux. Most things compiled on Centos 7 (our default for a while) work in Rocky Linux version 9. For compilers etc., I use the Software Collections / devtoolsets to run later versions than the

Re: [ccp4bb] add ligand with AceDRG

Dear Oliver and CCP4BB readers, This obsoleted LIG came from PDB entry 1JVP deposited in 2001 by Jean-Michel Rondeau working at Novartis. He must simply have been the first person to deposit a structure in which the ligand was called LIG ... . That molecule is now called 89E, but as Phil showed,

[ccp4bb] replacement for Scientific Linux

Hi folks For many years I’ve been using Scientific Linux as my OS of choice (when not using my Mac) - but it’s been discontinued. SL was based on RHEL, and had useful things like a less-buggy Fortran/C/C++ compiler than that released by RH. What do people here recommend as a replacement?

Re: [ccp4bb] add ligand with AceDRG

Hi Stefanie, If you want to try Grade2 (for a non-confidential ligand) then this is easy to do using the Grade Web Server https://grade.globalphasing.org/ We have altered our default "3-letter code” (aka PDB chemical component ID) to “LIG”. The reserved PDB two letter codes 01 to 99 are also

Re: [ccp4bb] add ligand with AceDRG

Thanks for the feedback, I will let PDBe developers know that this is causing confusion and that LIG should not return results. Kind regards, Deborah On 26/04/2024 16:11, Garib Murshudov wrote: On this website: https://www.ebi.ac.uk/pdbe-srv/pdbechem/ If you search for LIG it returns a

Re: [ccp4bb] add ligand with AceDRG

Indeed, as Diana points out: PDB's own components.cif defines LIG as: _chem_comp.id LIG _chem_comp.name "3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H11 N3" So they probably should fix that. Also that

Re: [ccp4bb] add ligand with AceDRG

On this website: https://www.ebi.ac.uk/pdbe-srv/pdbechem/ If you search for LIG it returns a ligand. With small letters it says: The chemical component you are trying to view (LIG) has been obsoleted. You have been redirected to the component

Re: [ccp4bb] add ligand with AceDRG

Hi Diana, Could you please clarify where you are searching? LIG is obsolete and definitely not in use. Cheers, Deborah On 26/04/2024 15:40, Diana Tomchick wrote: But I think that is a mistake, if you search for LIG in the PDB, it brings up a definite ligand that has that 3-letter code.

Re: [ccp4bb] add ligand with AceDRG

But I think that is a mistake, if you search for LIG in the PDB, it brings up a definite ligand that has that 3-letter code. Diana Sent from my iPhone On Apr 26, 2024, at 8:04 AM, Deborah Harrus wrote:  Dear all, Just to clarify, "LIG" is also a reserved code, so it's safe to use. See

Re: [ccp4bb] add ligand with AceDRG

Dear all, Just to clarify, "LIG" is also a reserved code, so it's safe to use. See https://www.wwpdb.org/news/news?year=2023#656f4404d78e004e766a96c6 Kind regards, Deborah Harrus PDBe On 25/04/2024 16:04, Diana Tomchick wrote: The PDB has reserved the following codes for unknown ligands:

Re: [ccp4bb] add ligand with AceDRG

Thank you Paul. I did not think about it. Stefanie, could you please send the log file to me? Regards Garib > On 26 Apr 2024, at 14:17, Paul Emsley wrote: > > > On 25/04/2024 13:01, FREITAG-POHL, STEFANIE wrote: >> >> >> >> I have trouble adding a ligand with AceDRG in CCP4i2 into my

Re: [ccp4bb] COOT 1.1 and DNA mutation

On 26/04/2024 02:44, Paul Emsley wrote: On 25/04/2024 16:07, Simon Vecchioni wrote: Paul, Many thanks for fixing the [simple mutate] button for DNA in v1.1.08--works like a charm! I would ask about two other DNA features-- 1) The [add terminal residue] button seems unresponsive for DNA,

Re: [ccp4bb] add ligand with AceDRG

On 25/04/2024 13:01, FREITAG-POHL, STEFANIE wrote: I have trouble adding a ligand with AceDRG in CCP4i2 into my refinement: I put in a smilesstring and the ligand is written ok, but since I can only chose already 'taken' 3-letter-codes the refinement always crashes as there is a clash with

Re: [ccp4bb] add ligand with AceDRG

Dear Stefanie, We routinely use DRG or LIG or numbers in running refmac and do not see the issue. Maybe check if .cif and .pdb file has the same code for the compound and also, if the issue is not coming from other molecule in the structure? Another option would to be try a different computer

Re: [ccp4bb] add ligand with AceDRG

Refmac by itself should not care about duplicated residue names in the monomer library. It takes the last monomer. There should be something on the interface preventing this. Longer than three letters should be available from the next release of ccp4. New acedrg and Refmacat should be able to

Re: [ccp4bb] add ligand with AceDRG

Dear all, thank you so much for all your suggestions. Unfortunately, nothing helped. Whatever 3-letter code I choose Refmac is complaining that there is a clash with an already existing ligand (even DRG, LIG, numbers) and AceDRG in CCP4i2 insists on 3 letters. I am not quite sure how to

[ccp4bb] Postdoctoral Position - Institut de Biologie Structurale (IBS/PATBAC) - Grenoble - France

Dear CCP4 community, a postdoctoral research position financed by the National Research Agency is on offer by the Bacterial Pathogenesis Group (DR Andréa DESSEN) at the IBS (Institut de Biologie Structurale) in Grenoble. Our group focuses on the study of the various mechanisms used by the