Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed
Dear Rafal, Acedrg could not handle with ligands containing metal elements at the moment. When your input file was a mol file, acedrg gave that information. For other kind of input format, acedrg should give the same information. We are checking why it produced those confusing info. The developments are under way to make acedrg capable of handling with ligands containing atoms of metal elements. Sorry about your situations. Best wishes, Fei Dear all, Thank you very much for all your messages. Unfortunately, I'm still on the same place, as yesterday... First of all, I prepared a pdb/cif file of the ligand based on CCDC entry 1176355 containing FESAN molecule. Also, I prepared SMILES file based on SMILES of CB5 ligand (COSAN) available on PDB, where I simply switched Co into Fe atom. -> When I tried use acedrg with SMILES, I received an error info: Input file: FSM.smi Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_27.cif Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_27.pdb workMode : 12 Can not generate a molecule from the input SMILES string! Check your SMILES or report the bug Can not get the element symbols of atoms. Check input file format Error : The job stops because of errors -> When I tried use acedrg with *pdb/*cif files I received no output files: Input file: fsm.cif Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_21.cif Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_21.pdb workMode : 11 Number of atoms in the cif file 0 -> When I tried use acedrg with *.mol file I received no output files: Input file: fsm.mol Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_28.cif Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_28.pdb workMode : 13 The system contains atoms of the following elements C B Fe H The input ligands/molecules contains metal or other heavier atoms Acedrg currently deals with ligands/molecules with following elements only C, N, O, S, P, B, F, Cl, Br, I, H The job finishes succesfully -> When I tried use prodrg, the program has been crashed: The program run with command: cprodrg XYZIN "C:/data_cryst/hsa_fesan_04/fsm.pdb" LIBOUT "C:/data_cryst/hsa_fesan_04/fsm_prodrg1.cif" XYZOUT "C:/data_cryst/hsa_fesan_04/fsm_prodrg1.pdb" MOLOUT "C:/data_cryst/hsa_fesan_04/fsm_prodrg1.mol" has failed with error message forrtl: severe (157): Program Exception - access violation Image PCRoutineLine Source cprodrg.exe7FF623CB058F Unknown Unknown Unknown cprodrg.exe7FF623CB05E0 Unknown Unknown Unknown cprodrg.exe7FF623CAFB4F Unknown Unknown Unknown cprodrg.exe7FF623CB008E Unknown Unknown Unknown cprodrg.exe7FF623C5BDA8 Unknown Unknown Unknown cprodrg.exe7FF623C3204E Unknown Unknown Unknown cprodrg.exe7FF623CAA81E Unknown Unknown Unknown cprodrg.exe7FF623CB3144 Unknown Unknown Unknown KERNEL32.DLL 7FFEB3447034 Unknown Unknown Unknown ntdll.dll 7FFEB4A22651 Unknown Unknown Unknown *** -> I am still waiting for tokens from the prodrg web page ;) To be sure, I used two emails, but with no response... -> Ok, then I back to way I used years ago... JLigand was a good solution, but... actually it is not working at all. I'm working under Windows 10 / CCP4i, and I remember, there was the same issue in previous version of CCP4. -> Ok, then I back to the oldest solution -> using Sketcher. The program is reading my PDB/CIF, but gave a warning when preparing a library, and of course, no output _mon_lib.cif: WARNING : monomer:FSM - has a minimal description. WARNING: there is no metal chirality for:Fe1 WARNING: coords are not good enough to create Chirality WARNING : /subroutine CALC_VOBSN/ I attached the PDB file containing the ligand of interest. From my knowledge, it looks correct, but maybe I'm wrong. Have you any idea, where is a problem? Best, Rafal --- |--| |Rafal Dolot, Ph.D.| | | |Polish Academy of Sciences| |Centre of Molecular and Macromolecular Studies| |Division of Bioorganic Chemistry | |Macromolecular Crystallography Laboratory | |Sienkiewicza 112 | |90-363 Lodz, Poland | |Phone: +48(42)6803325 | |Cell: +48 502897781 | |--| W dniu 2022-06-06 14:52, Paul Emsley napisał(a): > Although it may not be apparent, there has been a lot of work going on > in
[ccp4bb] Postdoctoral position at the University of the Free State, South Africa
Good morning everyone, The *Biocatalysis and Structural Biology* group within the *Department of Microbiology and Biochemistry (University of the Free State, South Africa)* is looking for a post-doctoral candidate interested in biocatalysis and structural biology. We are interested in understanding the structure-function relationship of various biocatalysts in oxyfunctionalization reactions. We are looking for highly motivated and enthusiastic candidates with a background in biochemistry, enzymology, biotechnology, or related fields and with an interest in biocatalysis and structural biology. Previous experience in molecular biology, protein purification and enzyme characterization is desired. Knowledge and experience in X-ray crystallography will be advantageous. We offer close supervision in a stimulating and interdisciplinary atmosphere. Applicants should hold a PhD degree conferred no more than 3 years ago. Applications should include a cover letter with a statement of your research interests, a CV and the names and contact details of two references. Successful candidates will be required to start as soon as possible. *Please apply via e-mail to * *Prof. Dirk Opperman at oppe...@ufs.ac.za .* Best wishes, Carmien Tolmie To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed
Dear all, Thank you very much for all your messages. Unfortunately, I'm still on the same place, as yesterday... First of all, I prepared a pdb/cif file of the ligand based on CCDC entry 1176355 containing FESAN molecule. Also, I prepared SMILES file based on SMILES of CB5 ligand (COSAN) available on PDB, where I simply switched Co into Fe atom. -> When I tried use acedrg with SMILES, I received an error info: Input file: FSM.smi Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_27.cif Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_27.pdb workMode : 12 Can not generate a molecule from the input SMILES string! Check your SMILES or report the bug Can not get the element symbols of atoms. Check input file format Error : The job stops because of errors -> When I tried use acedrg with *pdb/*cif files I received no output files: Input file: fsm.cif Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_21.cif Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_21.pdb workMode : 11 Number of atoms in the cif file 0 -> When I tried use acedrg with *.mol file I received no output files: Input file: fsm.mol Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_28.cif Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_28.pdb workMode : 13 The system contains atoms of the following elements C B Fe H The input ligands/molecules contains metal or other heavier atoms Acedrg currently deals with ligands/molecules with following elements only C, N, O, S, P, B, F, Cl, Br, I, H The job finishes succesfully -> When I tried use prodrg, the program has been crashed: The program run with command: cprodrg XYZIN "C:/data_cryst/hsa_fesan_04/fsm.pdb" LIBOUT "C:/data_cryst/hsa_fesan_04/fsm_prodrg1.cif" XYZOUT "C:/data_cryst/hsa_fesan_04/fsm_prodrg1.pdb" MOLOUT "C:/data_cryst/hsa_fesan_04/fsm_prodrg1.mol" has failed with error message forrtl: severe (157): Program Exception - access violation Image PCRoutineLine Source cprodrg.exe7FF623CB058F Unknown Unknown Unknown cprodrg.exe7FF623CB05E0 Unknown Unknown Unknown cprodrg.exe7FF623CAFB4F Unknown Unknown Unknown cprodrg.exe7FF623CB008E Unknown Unknown Unknown cprodrg.exe7FF623C5BDA8 Unknown Unknown Unknown cprodrg.exe7FF623C3204E Unknown Unknown Unknown cprodrg.exe7FF623CAA81E Unknown Unknown Unknown cprodrg.exe7FF623CB3144 Unknown Unknown Unknown KERNEL32.DLL 7FFEB3447034 Unknown Unknown Unknown ntdll.dll 7FFEB4A22651 Unknown Unknown Unknown *** -> I am still waiting for tokens from the prodrg web page ;) To be sure, I used two emails, but with no response... -> Ok, then I back to way I used years ago... JLigand was a good solution, but... actually it is not working at all. I'm working under Windows 10 / CCP4i, and I remember, there was the same issue in previous version of CCP4. -> Ok, then I back to the oldest solution -> using Sketcher. The program is reading my PDB/CIF, but gave a warning when preparing a library, and of course, no output _mon_lib.cif: WARNING : monomer:FSM - has a minimal description. WARNING: there is no metal chirality for:Fe1 WARNING: coords are not good enough to create Chirality WARNING : /subroutine CALC_VOBSN/ I attached the PDB file containing the ligand of interest. From my knowledge, it looks correct, but maybe I'm wrong. Have you any idea, where is a problem? Best, Rafal --- |--| |Rafal Dolot, Ph.D.| | | |Polish Academy of Sciences| |Centre of Molecular and Macromolecular Studies| |Division of Bioorganic Chemistry | |Macromolecular Crystallography Laboratory | |Sienkiewicza 112 | |90-363 Lodz, Poland | |Phone: +48(42)6803325 | |Cell: +48 502897781 | |--| W dniu 2022-06-06 14:52, Paul Emsley napisał(a): Although it may not be apparent, there has been a lot of work going on in Acedrg development regarding Boron. One cannot say the same for Coot though and I can reproduce the behaviour reported by Rafa Dolot. If/when I can fix it, it will be available in 0.9.8.4. Paul. On 06/06/2022 13:24, Boaz Shaanan wrote: Hi, In case you don't have a cif file for the ligand, I would load the SMILES expression into acedrg (or use any other input option) to create a cif file which
