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] eLBOW aromatic restraints

Dear Henry, First of all, directly asking for help about eLBOW on the ccp4bb is a little bit impolite. It is a bit like asking a Nottingham Forest* fan about how Derby City* played on the weekend. Anyway this is my suggestion (as kind of a Leicester City* supporter). Directly asking any

Re: [ccp4bb] isopeptide bond and shelx topology file

Hi Amit, If you are interested in generating restraints for SHELX then Grade2 supports this (apply the cosine rule like Jon suggests) and producing ‘dfix’ files for SHELXL (is this what you mean by a “shelxl” topology file)? The Grade Web Server: https://grade.globalphasing.org can be used

[ccp4bb] Grade Web Server 11th Anniversary and a major upgrade

for their continued support of the service. With best wishes, The Global Phasing developers: Gerard Bricogne, Claus Flensburg, Peter Keller, Wlodek Paciorek, Andrew Sharff, Oliver Smart, Clemens Vonrhein, and Thomas Womack. P.S. There is now a wide range of excellent restraint generation

Re: [ccp4bb] ChEBI and SMILES

Please see https://gitlab.com/-/snippets/2468156 an extension that downloads SDF files > On 7 Oct 2022, at 10:12, Harry Powell > <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > > Hi > > Probably a silly question, but I was wondering how to

Re: [ccp4bb] ligands found in ChEBI...

Hi Harry, The SDF found at ChEBI is a 2D SDF with the coordinates used for the diagram. I do not think that ChEBI has 3D coordinates. Why not use PubChem instead as this does provide 3D sdf files? For your caffeine example: https://pubchem.ncbi.nlm.nih.gov/compound/64119

Re: [ccp4bb] Question about CCP4 monomer dictionaries

Hi everyone, Prompted by this discussion I ran a series of CSD conquest searches for peroxide in various environments. CSD conquest makes it easy to perform fairly complex searches (and was used for the Engh & Huber amino acid restraint library for amino acids still extensively used today).

Re: [ccp4bb] ChEBI and SMILES

On 7 Oct 2022, at 10:12, Harry Powell <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:HiProbably a silly question, but I was wondering how to search for a ligand in ChEBI with a SMILES string? It’s not immediately obvious to my Friday-morning mind

Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed

age) I hope that the restraint dictionary works for you. All the best, Oliver Smart, Andrew Sharff for BUSTER Developers. > On 7 Jun 2022, at 08:35, Rafal Dolot wrote: > > Dear all, > > Thank you very much for all your messages. Unfortunately, I'm still on the > same plac

Re: [ccp4bb] on space group P 3 2 1

Dear Lee, I would recommend that you visit: https://www.ebi.ac.uk/pdbe/entry/pdb/1g4a/analysis there you can download the assembly indicated by the REMARK 350 Octadecamer that describes the "AUTHOR DETERMINED BIOLOGICAL UNIT". The download will be in mmcif format that many programs can

Re: [ccp4bb] Cation-channel pore representation for solvent accessible area

want any further assistance on HOLE. Best regards, Oliver Oliver Smart, Anglia Ruskin University oliver.smart AT anglia.ac.uk To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi

Re: [ccp4bb] Blob Game

on 23/2/15 6:57 PM, jens Preben Morth j.p.mo...@ncmm.uio.no wrote: a horrible water molecule would fit in there :-) On 23/02/15 19:42, Keller, Jacob wrote: A little more info: -Resolution is 1.75 Ang at edge of detector, but I/sig was still ~3; pushing integration to corners gives 1.66

[ccp4bb] future of MolProbity?

. Many people use MolProbity from their own sites, or using 3rd party software tools (such as buster-report or the wwPDB validation server) so they would not have seen the message. Oliver -- Dr Oliver Smart Director SmartSci Limited http://www.smartsci.uk/ Consultant Global Phasing

Re: [ccp4bb] molprobity clashscore, symmetry-related molecules?

(but reduce does a great job otherwise). But this might have been improved. Oliver - Dr Oliver Smart Director SmartSci Limited http://www.smartsci.uk/ Consultant Global Phasing Ltd http://www.globalphasing.com/

Re: [ccp4bb] Refinement of Iron-sulphur clusters

chiral volume terms then I would ask the question why? But this is just my personal take. If CCP4 would like to redistribute/work the dictionaries sent then we would be happy (please email off-list). Dr Oliver Smart Director SmartSci Limited http://www.smartsci.uk/ Consultant Global Phasing Ltd http

Re: [ccp4bb] Refinement of Iron-sulphur clusters

mining restraints for Fe2S2 and Fe4S4 from CSD structures (this has to be done manually). Please find attached the resulting FES.cif and SF4.cif restraint dictionaries (distributed with BUSTER). Good luck, Oliver --- Dr Oliver Smart Director SmartSci Limited http://www.smartsci.uk

Re: [ccp4bb] how to measure the angle between two aromatic ring plane in PYMOL?

Oliver Smart | | Global Phasing Ltd., Cambridge UK | | http://www.globalphasing.com/people/osmart/ |

[ccp4bb] HOLE program availability

by 1st September. Regards, Oliver Smart

[ccp4bb] Grade other ligand tools was Re: ccp4 ligand tools..

://www.globalphasing.com/buster/wiki/index.cgi?AutobusterLigandQM If you have concerns about Grade or other dictionaries then using MMFF94 instead provides a really good 2nd opinion. Hope that ccp4bb will forgive this bit of promotion but Grade can be used with CCP4 (and SHELX). Regards, Oliver | Dr Oliver

[ccp4bb] Vitamin B12 (cobalamin) geometry issues

. The problem also effects the PDB chemical components definition of B12. Please see https://www.globalphasing.com/buster/wiki/index.cgi?B12Dictionary This page provides a dictionary for B12 with the problem fixed. Hope this proves useful. Regards, Oliver | Dr Oliver Smart

Re: [ccp4bb] mtz2cif capable of handling map coefficients

On Thu, 5 Apr 2012, Ethan Merritt wrote: On Thursday, April 05, 2012 09:30:25 am Phil Jeffrey wrote: Fc doesn't contain the weighting scheme used in the creation of the map coefficients, so Fc would require some sort of program to be run to recreate those for both 2Fo-Fc and Fo-Fc maps. The

[ccp4bb] Announcement of a working group for PDBx/mmCIF format adoption

Womack, Global Phasing (BUSTER) Oliver Smart, Global Phasing (BUSTER) - Working Group Chair Please contact me for any further details. Regards, Oliver | Dr Oliver Smart | | Global Phasing Ltd., Cambridge UK | | http://www.globalphasing.com/people/osmart/ |

Re: [ccp4bb] Announcing a Web Server for the Grade ligand restraints generator.

find grade restraint dictionary useful. Many thanks Oliver | Dr Oliver Smart | | Global Phasing Ltd., Cambridge UK | | http://www.globalphasing.com/people/osmart/ |

Re: [ccp4bb] unusual bond lengths in PRODRG cif file (Grade Web Server)

that are (partly) based on CSD small molecule structures try using: http://grade.globalphasing.org Regards, Oliver | Dr Oliver Smart | | Global Phasing Ltd., Cambridge UK | | http://www.globalphasing.com/people/osmart/ |

Re: [ccp4bb] unusual bond lengths in PRODRG cif file

for the positive comments about grade. We have just launched the Grade Web Server so it should be now be much easier for academic and occasional users to generate ligand restraints with it. http://grade.globalphasing.org Regards, Oliver | Dr Oliver Smart | | Global

Re: [ccp4bb] unusual bond lengths in PRODRG cif file (Another possibility - direct use of QM)

then the actual method itself is used. Regards, Oliver | Dr Oliver Smart | | Global Phasing Ltd., Cambridge UK | | http://www.globalphasing.com/people/osmart/ |

Re: [ccp4bb] reliable/unreliable maps? (Deposition of map coefficients)

://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ccp4bb;325e1870.1112 Cheers, Oliver | Dr Oliver Smart | | Global Phasing Ltd., Cambridge UK | | http://www.globalphasing.com/people/osmart/ | On Tue, 10 Jan 2012, Robbie Joosten wrote: Hi Frank, EDS already does

[ccp4bb] How to patch CCP4 cif2mtz so it can handle PDB entries with Map Coefficients

/index.cgi?CCP4cif2mtzPatchToHandleMapCoefficients Regards, Oliver | Dr Oliver Smart | | Global Phasing Ltd., Cambridge UK | | http://www.globalphasing.com/people/osmart/ |