Re: [ccp4bb] Problem with understanding mtz and hkl files of S SAD data
Dear Saha, If you are not used to use ccp4 with the command line, you first need to tell your computer where to find the ccp4 programs by using the command "source". For example, I am working on a Mac, where ccp4 is installed in the Applications folder, so in a terminal I just have to run "source /Applications/ccp4-8.0/bin/ccp4.setup-sh" and then I can run the ccp4 command line toold such as mtzdmp. If you are using another operating system or if you have installed ccp4 elsewhere then the path to the setup script will be different. Also upon installing ccp4, you might also have the program "viewhk" which can open an mtz file and show its information. Good luck, Elke De: "Pedro Matias" À: CCP4BB@JISCMAIL.AC.UK Envoyé: Mardi 10 Mai 2022 15:08:34 Objet: Re: [ccp4bb] Problem with understanding mtz and hkl files of S SAD data Shelxc/d/e require text files (either SHELX hkl or SCALEPACK sca format), not binary files like mtz. You can convert directly the XDS_ASCII.HKL from XDS to SHELX hkl with XDSCONV, which you can then input to shelxc to begin the pipeline. You still need to supply cell parameters and space group info, though. I recommend using the hkl instead of the sca file because you can create an unmerged file with all the measured observations and then you get a graphical analysis of the anomalous self-correlation. Ideally it should be very high (>80-90%) at low resolution and should not fall below 30% below about 2 A resolution. If you don't see this type of curve then it is highly unlikely that you will be able to solve your structure using S-SAD. Unless you used a very long wavelength to collect your data (~ 2A) the anomalous differences arising from the sulfur atoms are very small and you need a dataset with very high multiplicity to succeed. As an alternative, and if your crystals are good enough you can try soaks with 1M KI before cryocooling your crystal. The iodide ions have a much higher anomalous signal, even at the Cu K-alpha wavelength, and even though nearly all sites will be only partially occupied, the multiplicity requirements are less stringent and it might be enough to solve your structure. Em 10/05/2022 13:51, Rituparna Saha escreveu: Thank you for the suggestions. I had searched the mtzdump in CCP4i, but didn't find any, I only found the mtz2various program. I am using the Shelxc/d/e suite. I had converted the ASCII.HKL file (the one that I had mentioned before) to mtz using Pointless. Then, when I used this file to run Shelxc/d/e, the job failed and I encountered errors each time. For this reason, I wanted to view and analyze the mtz file and HKL file. I donot know how to solve this problem as well. Kindly guide me if I went wrong anywhere here. On Tue, May 10, 2022 at 5:49 PM Pedro Matias < [ mailto:mat...@itqb.unl.pt | mat...@itqb.unl.pt ] > wrote: BQ_BEGIN Hi there, I assume you processed the data with XDS. If so, you can use xdsconv to convert the file other formats, including mtz To analyze (view?) an mtz file you can use mtzdump. MTZ2Various is a format conversion program, just like xdsconv. You can convert directly to SCALEPACK format without a USER FORMAT option, and the output from a .sca file created from an mtz file with MTZ2various looks like this: BQ_BEGIN 1 -987 105.794 62.940 110.050 90.000 105.008 90.000 c 1 2 1 <-- cell parameters and SG info -73 1 3 5.1 5.1 7.5 4.5 <--- h,k,l, I+, sigI+, I-, sigI- (bijvoet mates) -73 1 4 -1.4 6.8 3.4 5.3 What is the software you are using to solve the structure via S-SAD? I recomment the shelxc/d/e suite that can be easily run via the hkl2map GUI. Best, Pedro Em 10/05/2022 12:51, Rituparna Saha escreveu: BQ_BEGIN Dear all, I am trying to solve a protein structure via S SAD phasing. I have the ASCII.HKL file, but whenever I opened the text file I couldn't understand which one is the F+ and F- values. Also, how can I read and analyze an mtz file? I tried using the MTZ2VARIOUS program in CCP4, where I changed it into USER FORMAT, it generated a .sca file, and the text file so generated did not have any labels (headers) inside it. It just gave me a list of values. Kindly guide me through this since I am really a novice in this field. -- -- - Regards, Rituparna Saha Research Scholar Bioseparation and Structural Biochemistry Lab Department of Biotechnology, IIT Kharagpur To unsubscribe from the CCP4BB list, click the following link: [ https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 | https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ] BQ_END -- Industry and Medicine Applied Crystallography Macromolecular Crystallography Unit ___ Phones : (351-21) 446-9100 Ext. 1669 (351-21) 446-9669 (direct) Fax : (351-21) 441-1277 or 443-3644 email : [ mailto:mat...@itqb.unl.pt | mat...@itqb.unl.pt ] [ http://www.itqb.unl.pt/
Re: [ccp4bb] Refinement of ligand with alternate chemical structure
Dear Stuart, I had some issues with different entities with the same residue number. To solve this, I used different numbers for the two entries and different altlocs (e.g. LIG-A gets number 401 and altloc A, LIG-B gets number 402 and altloc B). In your case you might want to call LIG-A and altloc A, LIG-A and altloc B, LIG-B and altloc C. Then you can restrain the occupancies to a sum of 1.0 in phenix.refine as described in the article shared by Pavel. This works for me with Phenix 1.19 and Coot 0.8.9 on Mac. Elke De: "Eleanor Dodson" <176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> À: "CCP4BB" Envoyé: Jeudi 16 Février 2023 18:40:31 Objet: Re: [ccp4bb] Refinement of ligand with alternate chemical structure Well - I made a copy of a ligand A 2001 and called it B 2001; gave each of the "Ligands" occupancy 0.5, mangled the B molecule a bit and ran REFMAC . It notes these atoms are too close but carries on refinement happily enough.. But when I read the structure into COOT and try to refine the A copy say it has a hissy fit and blows both copies out of the density... This is Coot version 0.9.8.7 >From REFMAC log Link info given in this sectoion is for information only If you want to use this links then either add them into the pdb/mmcif file or use make link yes option Status Link Mon1 At1 alt1 ch1 res1 Mon2 At2 alt2 Ch2 Res2 distM distI Unused :. LIG C01 . A 2001 LIG C01 . B 2001 0.599 1.524 Unused :. LIG C01 . A 2001 LIG N02 . B 2001 1.266 1.414 Unused :. LIG C01 . A 2001 LIG C11 . B 2001 1.863 1.507 Unused :. LIG N02 . A 2001 LIG C01 . B 2001 1.799 1.414 Unused :. LIG N02 . A 2001 LIG N02 . B 2001 0.398 1.304 Unused :. LIG N02 . A 2001 LIG C11 . B 2001 0.702 1.397 Unused :. LIG C03 . A 2001 LIG N02 . B 2001 1.287 1.397 Unused :. LIG C03 . A 2001 LIG C03 . B 2001 0.699 1.490 Unused :. LIG C03 . A 2001 LIG C04 . B 2001 1.313 1.490 On Thu, 16 Feb 2023 at 17:25, Nigel Moriarty < [ mailto:nwmoria...@lbl.gov | nwmoria...@lbl.gov ] > wrote: Stuart The sum of occ in these three is 1.3 and it looks like you put the occ in the B-factor column. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : nwmoria...@lbl.gov Web : [ http://cci.lbl.gov/ | CCI.LBL.gov ] ORCID : [ https://orcid.org/-0001-8857-9464 | orcid.org/-0001-8857-9464 ] On Thu, Feb 16, 2023 at 9:10 AM Stuart McQuarrie < [ mailto:974c6ca32bc4-dmarc-requ...@jiscmail.ac.uk | 974c6ca32bc4-dmarc-requ...@jiscmail.ac.uk ] > wrote: BQ_BEGIN Dear everyone that replied, thanks so much for the help thus far. Just for info I’m using Coot for Windows version 0.9.6 EL and phenix.refine version 1.20rc4-4416-000 RE Eleanor: It appears my version of coot/refmac do not support separate ligands in the same space at <0.5 occupancy. As an experiment, I tried adding ATP and ADP at 0.45 occupancy to a different structure of mine. I’m able to real space refine in coot (so both .cifs loaded successfully) until I edit->merge the 2nd ligand and then the bonds look wrong and when I try RSR it wants to force the ligand out and explodes the molecule. Original message: I thought that REFMAC tolerated dual occupancies if the sum of the two conformers was <= 1.0? Eleanor Will test.. RE Pavel: I tried following that as a guide, however I’m running into an issue with restraints: I have made some progress troubleshooting the big cyclic molecule (ca6) and products (pA3). I re-editted the pdb; gave them the altlocs ABC; made sure they were same chain ID and residue number. However, when I try to real space refine with coot I get the error: “No restraints found! Non-existent or minimal description of restrained residues. Are you sure that you read a non-minimal mmCIF dictionary for this monomer? Are you sure the PDB residue name matches the dictionary residue name? If not, try File -> Import CIF dictionary. Alternatively, did you check that the atom names of the PDB file match those of the restraints? The residues in the chain are out of order. This can cause problems with residues selection. Suggest you re-order residues in increasing order. I definitely loaded the cifs. But it only allows me to rsr the ligand with altloc A. If cA6 is A then I can only rsr cA6. If pA3 is A then I can only refine pA3. When I delete->residue/monomer the cA6 with altloc A I can suddenly rsr the pA3, so both libraries must have been loaded successfully prior. I have included the snippet with the ligands just incase anyone wants to see. Funnily enough
[ccp4bb] Two-year postdoctoral position in time-resolved crystallography at IBS in Grenoble
Dear all, We have an immediate opening for a two-year postdoctoral researcher in SNaX team of the DYNAMOP group at the Institute for Structural Biology in Grenoble (France). The successful candidate will work on the development and optimization of bio-scavengers towards toxic organophosphorus compounds. To attain this goal, the researcher will use time-resolved crystallography and in silico protein design methods. The position is funded by the French National Research Agency via the University Grenoble Alpes, and is open for a young researcher. Applicants must have obtained a Ph.D. in structural biology, biochemistry, biophysics, physics, chemistry, or a related field, no more than two years before the start of the project. The candidate must show a track-record of publications in peer-reviewed journals, and is expected to be proficient in English and highly motivated to learn new skills. The candidate will work in the multidisciplinary DYNAMOP group and thus needs to be a good team player as well as being capable of working independently. While the research will be carried out in English, non-French-speaking candidates are expected to learn the basics of French in order to facilitate communication and integration into the laboratory. Experience with one or more of the following skills would be highly evaluated: protein design or the usage of artificial intelligence for structural biology, protein expression and purification, protein crystallization and macromolecular crystallography, serial crystallography, programming or scripting. Interested candidates can apply via [ https://emploi.univ-grenoble-alpes.fr/offres/doctorants/postdoctoral-researcher-in-time-resolved-crystallography-1357683.kjsp?RH=1135797159702996 | https://emploi.univ-grenoble-alpes.fr/offres/doctorants/postdoctoral-researcher-in-time-resolved-crystallography-1357683.kjsp?RH=1135797159702996 ] . We advice to contact Elke De Zitter (elke.de-zit...@ibs.fr) to obtain more information about the postdoctoral position and application procedure. All the best, Elke Elke De Zitter Institut de Biologie Structurale - IBS group DYNAMOP 71 avenue des Martyrs 38044 Grenoble Cedex 9, France +33 4 57 42 86 56 elke.de-zit...@ibs.fr To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/
[ccp4bb] Two-year postdoctoral position in time-resolved crystallography at IBS in Grenoble
Dear all, We have an immediate opening for a two-year postdoctoral researcher in SNaX team of the DYNAMOP group at the Institute for Structural Biology in Grenoble (France). The project focuses on the development and optimization of bio-scavengers targeting toxic organophosphorus compounds. The successful candidate will employ time-resolved crystallography and in silico protein design methodologies. The 2-year postdoctoral position is funded by the French National Research Agency via the University Grenoble Alpes, and is open for a young researcher. Applicants must have obtained a Ph.D. in structural biology, biochemistry, biophysics, physics, chemistry, or a related field, no more than three years before the start of the project. The candidate must show a track-record of publications in peer-reviewed journals, and is expected to be proficient in English and highly motivated to learn new skills. The candidate needs to be a good team player as well as being capable of working independently. Experience with one or more of the following skills would be highly evaluated: protein design or the usage of artificial intelligence for structural biology, protein expression and purification, protein crystallization and macromolecular crystallography, serial crystallography, programming or scripting. Interested candidates should apply through the University Grenoble Alpes job portal at https://emploi.univ-grenoble-alpes.fr/job-offers/postdoctoral-researcher-in-time-resolved-crystallography-1400617.kjsp?RH=1681202200872 (application deadline: 02/04/2024). For inquiries regarding the position and application process, please contact Elke De Zitter at elke.de-zit...@ibs.fr. All the best, Elke Elke De Zitter Institut de Biologie Structurale - IBS group DYNAMOP 71 avenue des Martyrs 38044 Grenoble Cedex 9, France +33 4 57 42 86 56 elke.de-zit...@ibs.fr To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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] Parameters for phenix.refine in phenix 1.21
Hi, If you indeed run phenix.refine --show-defaults=3 you will see that many parameter names have been changed as compared to 1.20, e.g. refinement.input.xray_data.r_free_flags.generate has been replaced by data_manager.fmodel.xray_data.r_free_flags.generate I haven't checked all of your parameters, but I think you will be able to find the corresponding new names in a similar way. I went over the unrecognized parameters for my scripts, adapted them accordingly and it worked. All the best, Elke From: "Dennis Brookner" To: "CCP4BB" Sent: Friday, April 12, 2024 4:49:39 PM Subject: [ccp4bb] Parameters for phenix.refine in phenix 1.21 Hey all, I’m wondering if anyone has an example .eff script that works with phenix.refine 1.21. My software package writes a parameters.eff file to be run through phenix.refine, and it works fine with phenix 1.20, but throws the error seen below with phenix 1.21 due to missing parameters. Based on the information here: [ https://phenix-online.org/documentation/reference/refinement.html#list-of-all-available-keywords | https://phenix-online.org/documentation/reference/refinement.html#list-of-all-available-keywords ] I have gathered that the parameters listed below are in fact not recognized by phenix 1.21’s phenix.refine. However, I’m unable to locate the new versions of these parameters! Does anyone know what is going on here? Best, Dennis Here’s the error message thrown by phenix.refine: Unrecognized PHIL parameters: - refinement.input.pdb.file_name (file "params.eff", line 9) refinement.input.xray_data.file_name (file "params.eff", line 12) refinement.input.xray_data.labels (file "params.eff", line 13) refinement.input.xray_data.r_free_flags.generate (file "params.eff", line 15) refinement.input.xray_data.force_anomalous_flag_to_be_equal_to (file "params.eff", line 17) refinement.output.prefix (file "params.eff", line 24) refinement.output.serial (file "params.eff", line 25) refinement.output.serial_format (file "params.eff", line 26) Sorry: Some PHIL parameters are not recognized by phenix.refine. Please run this program with the --show-defaults option to see what parameters are available. To unsubscribe from the CCP4BB list, click the following link: [ https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 | https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ] To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/
[ccp4bb] Multiple postdoctoral and Ph.D. positions at IBS (Grenoble)
Dear all, We have four immediate openings for postdoctoral researchers and one opening for a Ph.D. student in the DYNAMOP group at the Institute for Structural Biology in Grenoble (France). The first postdoctoral project focuses on the development and optimization of bio-scavengers targeting toxic compounds. The researcher with use time-resolved crystallography and in silico design methodologies. Interested candidates can find more information at [ https://www.ibs.fr/en/careers/job-offers/two-year-postdoctoral-position-for-the-dynamop-group-time-resolved | https://www.ibs.fr/en/careers/job-offers/two-year-postdoctoral-position-for-the-dynamop-group-time-resolved ] (application deadline: 12/07/2024 ). In the second postdoctoral project, the researcher will study the binding of toxic compounds to their physiological target and subsequent chemical reactivation via time-resolved crystallography. The third postdoctoral project is focused on the development of an experimental approach for the determination of the photoinduced structural dynamics of photosensitive biomolecules both in vitro and in cell using time-resolved X-ray scattering techniques. More information and the application procedure can be found on [ https://emploi.cnrs.fr/Offres/CDD/UMR5075-VALLAN-024/Default.aspx?lang=EN | https://www.ibs.fr/en/careers/job-offers/two-year-postdoctoral-position-for-the-dynamop-group-time-resolved ] (application deadline 30/06/2024). In the fourth postdoctoral project, the researcher will apply serial diffraction techniques (SSX, SFX, SED) to structurally study natural and recombinant protein nanocrystals Last, a 3-year funded PhD fellowship is available to explore the structural dynamics of the orange carotenoid protein by means of time-resolved serial crystallography. Applicants for the postdoctoral positions must have obtained a Ph.D. in structural biology, biophysics, biochemistry, physics, chemistry, or a related field. The candidates must show a track-record of publications in peer-reviewed journals. Applicants for the Ph.D. position are expected to have a master's degree in one of the above mentioned fields. All candidates are expected to be proficient in English and highly motivated to learn new skills. The candidates need to be a good team player as well as being capable of working independently. For inquiries regarding the positions and application processes, please contact Elke De Zitter ( [ mailto:elke.de-zit...@ibs.fr | elke.de-zit...@ibs.fr ] ), Martin Weik ( [ mailto:martin.w...@ibs.fr | martin.w...@ibs.fr ] ), Giorgio Schiro ( [ mailto:giorgio.sch...@ibs.fr | giorgio.sch...@ibs.fr ] ) or Jacques-Philippe Colletier ( [ mailto:jacques-philippe.collet...@ibs.fr | jacques-philippe.collet...@ibs.fr ] ) Best regards, Martin, Giorgio, Jacques-Philippe and Elke Elke De Zitter Institut de Biologie Structurale - IBS group DYNAMOP 71 avenue des Martyrs 38044 Grenoble Cedex 9, France +33 4 57 42 86 56 elke.de-zit...@ibs.fr To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=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/
