From pozharskibb at gmail.com Mon Oct 3 08:30:41 2022 From: pozharskibb at gmail.com (Edwin Pozharski) Date: Mon, 3 Oct 2022 11:30:41 -0400 Subject: [phenixbb] Phenix secondary structure restraints bug Message-ID: When using phenix.secondary_structure_restraints (from command line, not sure if it's different in GUI) ss_by_chain flag is ignored when using default method (ksdssp, even if explicitly selected). Works fine when mmtbx_dssp is used though. Details: > phenix.secondary_structure_restraints model.pdb format=pdb ss_by_chain=False only produces intrachain beta sheets. > phenix.secondary_structure_restraints model.pdb format=pdb ss_by_chain=False search_method=mmtbx_dssp produces both intrachain and interchain beta-sheets. I am fairly certain this is not KSDSSP bug per se, since output of $PHENIX/build/ksdssp/exe/ksdssp model.pdb contains interchain beta-sheets. This is with 1.20.1-4487. -------------- next part -------------- An HTML attachment was scrubbed... URL: From osobolev at lbl.gov Mon Oct 3 15:26:02 2022 From: osobolev at lbl.gov (Oleg Sobolev) Date: Mon, 3 Oct 2022 15:26:02 -0700 Subject: [phenixbb] Phenix secondary structure restraints bug In-Reply-To: References: Message-ID: Dear Edwin, Thank you for reporting this issue. I'm afraid there is a slight misunderstanding of the parameter because of lack of description in our documentation. The ss_by_chain flag only affects "from_ca" search_method. It has no effect when you choose any other methods. For the sake of completeness, from_ca_conservative, max_rmsd, use_representative_chains and max_representative_chains also only affect "from_ca" method. I'll adjust the description of parameters that can be seen at the bottom of this page: https://phenix-online.org/documentation/reference/secondary_structure.html It would be helpful if you could share (off-list) the model.pdb you were experimenting with, so I can look deeper into why output of > > phenix.secondary_structure_restraints model.pdb format=pdb > ss_by_chain=False > $PHENIX/build/ksdssp/exe/ksdssp model.pdb is different. They should be the same from the first look. Best regards, Oleg Sobolev. On Mon, Oct 3, 2022 at 8:34 AM Edwin Pozharski wrote: > When using phenix.secondary_structure_restraints (from command line, not > sure if it's different in GUI) ss_by_chain flag is ignored when using > default method (ksdssp, even if explicitly selected). Works fine when > mmtbx_dssp is used though. Details: > > > phenix.secondary_structure_restraints model.pdb format=pdb > ss_by_chain=False > > only produces intrachain beta sheets. > > > phenix.secondary_structure_restraints model.pdb format=pdb > ss_by_chain=False search_method=mmtbx_dssp > > produces both intrachain and interchain beta-sheets. > > I am fairly certain this is not KSDSSP bug per se, since output of > > $PHENIX/build/ksdssp/exe/ksdssp model.pdb > > contains interchain beta-sheets. > > This is with 1.20.1-4487. > _______________________________________________ > phenixbb mailing list > phenixbb at phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave at phenix-online.org -------------- next part -------------- An HTML attachment was scrubbed... URL: From joel.harp at vanderbilt.edu Thu Oct 6 10:24:39 2022 From: joel.harp at vanderbilt.edu (Harp, Joel M) Date: Thu, 6 Oct 2022 17:24:39 +0000 Subject: [phenixbb] Drug Discovery Scientist opening Vanderbilt University In-Reply-To: References:

Message-ID: Drug Discovery Scientist Position An opening is available in the drug discovery laboratory of Dr. Stephen Fesik for a candidate with experience in the field of protein x-ray crystallography or NMR. Responsibilities will include protein production, fragment screening by NMR, and all aspects of x-ray crystallography including preparation of protein-ligand complexes, crystallization, home/synchrotron data collection, and structure determination. Additional experience in molecular biology including construct design, cloning, site-directed mutagenesis and modeling is a plus but not required. The ideal candidate should be self-motivated and be able to communicate efficiently in a highly collaborative environment. Please send cv to jason.phan at Vanderbilt.Edu The Vanderbilt campus is located in Nashville Tennessee. Also known as Music City, Nashville is a fast growing and dynamic environment with plenty of cultural attractions and opportunities for outdoor recreation. -------------- next part -------------- An HTML attachment was scrubbed... URL: From joel.harp at vanderbilt.edu Thu Oct 6 10:42:28 2022 From: joel.harp at vanderbilt.edu (Harp, Joel M) Date: Thu, 6 Oct 2022 17:42:28 +0000 Subject: [phenixbb] Postdoctoral position in drug discovery Message-ID: Postdoctoral position in drug discovery An opening is available in the drug discovery laboratory of Dr. Stephen Fesik for a post-doc in the field of protein x-ray crystallography. Responsibilities will include protein production, fragment screening by NMR, and all aspects of x-ray crystallography including preparation of protein-ligand complexes, crystallization, home/synchrotron data collection, and structure determination. Additional experience in molecular biology including construct design, cloning, site-directed mutagenesis and modeling is a plus. The ideal candidate should be self-motivated and be able to communicate efficiently in a highly collaborative environment. Please send cv to jason.phan at Vanderbilt.Edu The Vanderbilt campus is located in Nashville Tennessee. Also known as Music City, Nashville is a fast growing and dynamic environment with plenty of cultural attractions and opportunities for outdoor recreation. -------------- next part -------------- An HTML attachment was scrubbed... URL: From Brent.Nannenga at asu.edu Fri Oct 7 08:50:51 2022 From: Brent.Nannenga at asu.edu (Brent Nannenga) Date: Fri, 7 Oct 2022 15:50:51 +0000 Subject: [phenixbb] 2022 MicroED Workshop In-Reply-To: References: Message-ID: Hi everyone, This is just a reminder of the 2022 MicroED workshop held UCLA Dec. 11th to the 14th. The due date for applying to the workshop is October 11 For more information please see https://cryoem.ucla.edu/course-2022 Thanks, Brent Nannenga From: phenixbb-bounces at phenix-online.org on behalf of Brent Nannenga Date: Tuesday, September 13, 2022 at 11:35 AM To: phenixbb at phenix-online.org Subject: [phenixbb] 2022 MicroED Workshop Dear all, We are pleased to announce the 7th MicroED workshop to be held the evening of December 11th to the 14th, 2022, and will be open to both academia and industry. This workshop will be held at the MicroED Imaging Center at UCLA and will contain both lectures and hands on demonstrations and training. For more information, tentative schedule, and to apply please see the following website: https://cryoem.ucla.edu/course-2022 Space is limited and historically, the workshop is typically oversubscribed, therefore we encourage applications to be sent in early. Topics covered will include all aspects of microcrystal electron diffraction (MicroED) of diverse samples such as soluble proteins, membrane proteins, small molecules, natural products, and other materials. We will cover * Sample preparation methodologies for proteins and small molecules * MicroED data collection * Camera performance * Cryo-FIB-milling procedures for MicroED * Data analysis software, structure solution, and refinement The schedule is available on the registration page. // Sincerely; on behalf of the organizing committee (Tamir Gonen, Brent Nannenga) -------------- next part -------------- An HTML attachment was scrubbed... URL: From Gabor.Bunkoczi at astx.com Sun Oct 9 10:31:09 2022 From: Gabor.Bunkoczi at astx.com (Gabor Bunkoczi) Date: Sun, 9 Oct 2022 17:31:09 +0000 Subject: [phenixbb] X-ray crystallography software developer position at Astex Message-ID: Dear All, We have an opening for a skilled software developer with crystallographic computing background at our Cambridge (UK) site. For more information about the position, please see the full advert: https://www.cloudonlinerecruitment.co.uk/Astex/VacancyDetails.aspx?FromSearch=True&MenuID=&VacancyID=30 To apply, please follow the link in the advert. For informal enquiries, please feel free to contact me. Best wishes, Gabor Bunkoczi Astex Therapeutics Ltd 436 Cambridge Science Park Cambridge CB4 0QA, UK This email and any attachments thereto may contain private, confidential, and privileged material for the sole use of the intended recipient. Any review, copying or distribution of this email (or any attachments thereto) by others is strictly prohibited. If you are not the intended recipient, please delete the original and any copies of this email and any attachments thereto and notify the sender immediately. -------------- next part -------------- An HTML attachment was scrubbed... URL: From adrian.gonzalez.lopez at icm.uu.se Fri Oct 14 01:30:20 2022 From: adrian.gonzalez.lopez at icm.uu.se (=?iso-8859-1?Q?Adri=E1n_Gonz=E1lez_L=F3pez?=) Date: Fri, 14 Oct 2022 08:30:20 +0000 Subject: [phenixbb] Bond angle outliers missing from the list Message-ID: <024CADA0-BA3A-41A3-8C25-FF3ECB8D2825@icm.uu.se> Hi! I performed a real space refinement on my EM map and my validation summary indicates that I have 17 bond angle outliers. However, when I check on the MolProbity tab, Geometry Restraints, it only shows me one of them (and it still says there are 17). Is this a bug or something else? You can see it on the screenshot below: [cid:BADACC33-3B23-4F5B-8847-E5C39FCB01F3] Thanks! /Adrian N?r du har kontakt med oss p? Uppsala universitet med e-post s? inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om hur vi g?r det kan du l?sa h?r: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2022-10-14 at 10.28.53.png Type: image/png Size: 36028 bytes Desc: Screen Shot 2022-10-14 at 10.28.53.png URL: From anshahar at bgu.ac.il Fri Oct 14 04:14:30 2022 From: anshahar at bgu.ac.il (Anat Shahar) Date: Fri, 14 Oct 2022 11:14:30 +0000 Subject: [phenixbb] 3rd CCP4/BGU Workshop on Data Collection and Structure Determination Message-ID: Dear all, We are very pleased to announce the 3rd CCP4/BGU Workshop on Data Collection and Structure Determination, which will take place at Ben-Gurion University of the Negev (BGU) in Beer-Sheva, Israel, between 26th February to 1st March, 2023. The workshop is limited to 25 participants, and everybody who is interested is welcome to apply. The workshop program will be suitable for last-year PhD students, as well as postdoctoral researchers and young scientists in their first years of research. The workshop will concentrate on practical aspects of data collection, structure solution, model building, refinement and validation. Modern methods, benefiting from structure prediction with AlphaFold-2, as well as more traditional approaches to Molecular Replacement and Experimental Phasing will be considered in detail. In addition, all participants will have an opportunity to carry out remote data collection at Diamond Light Source on their own samples. A team of leading structural biology software developers from around the world will present lectures and tutorials and will also be available to help participants with their own projects, such as processing own data and solving structures during hands-on sessions of the workshop. More information, including ?how to apply?, registration form and tentative program, can be found at: https://lifeserv.bgu.ac.il/wp/ccp4workshop/ The closing date for application is 20.12.2023. Best wishes, Anat Shahar & Eugene Krissinel -------------- next part -------------- An HTML attachment was scrubbed... URL: From anshahar at bgu.ac.il Fri Oct 14 05:03:47 2022 From: anshahar at bgu.ac.il (Anat Shahar) Date: Fri, 14 Oct 2022 12:03:47 +0000 Subject: [phenixbb] 3rd CCP4/BGU Workshop on Data Collection and Structure Determination Message-ID: Dear all, We are very pleased to announce the 3rd CCP4/BGU Workshop on Data Collection and Structure Determination, which will take place at Ben-Gurion University of the Negev (BGU) in Beer-Sheva, Israel, between 26th February to 1st March, 2023. The workshop is limited to 25 participants, and everybody who is interested is welcome to apply. The workshop program will be suitable for last-year PhD students, as well as postdoctoral researchers and young scientists in their first years of research. The workshop will concentrate on practical aspects of data collection, structure solution, model building, refinement and validation. Modern methods, benefiting from structure prediction with AlphaFold-2, as well as more traditional approaches to Molecular Replacement and Experimental Phasing will be considered in detail. In addition, all participants will have an opportunity to carry out remote data collection at Diamond Light Source on their own samples. A team of leading structural biology software developers from around the world will present lectures and tutorials and will also be available to help participants with their own projects, such as processing own data and solving structures during hands-on sessions of the workshop. More information, including ?how to apply?, registration form and tentative program, can be found at: https://lifewp.bgu.ac.il/wp/ccp4workshop/ The closing date for application is 20.12.2022. Best wishes, Anat Shahar & Eugene Krissinel -------------- next part -------------- An HTML attachment was scrubbed... URL: From anshahar at bgu.ac.il Fri Oct 14 05:07:10 2022 From: anshahar at bgu.ac.il (Anat Shahar) Date: Fri, 14 Oct 2022 12:07:10 +0000 Subject: [phenixbb] 3rd CCP4/BGU Workshop on Data Collection and Structure Determination Message-ID: Dear all, We are very pleased to announce the 3rd CCP4/BGU Workshop on Data Collection and Structure Determination, which will take place at Ben-Gurion University of the Negev (BGU) in Beer-Sheva, Israel, between 26th February to 1st March, 2023. The workshop is limited to 25 participants, and everybody who is interested is welcome to apply. The workshop program will be suitable for last-year PhD students, as well as postdoctoral researchers and young scientists in their first years of research. The workshop will concentrate on practical aspects of data collection, structure solution, model building, refinement and validation. Modern methods, benefiting from structure prediction with AlphaFold-2, as well as more traditional approaches to Molecular Replacement and Experimental Phasing will be considered in detail. In addition, all participants will have an opportunity to carry out remote data collection at Diamond Light Source on their own samples. A team of leading structural biology software developers from around the world will present lectures and tutorials and will also be available to help participants with their own projects, such as processing own data and solving structures during hands-on sessions of the workshop. More information, including ?how to apply?, registration form and tentative program, can be found at: https://lifewp.bgu.ac.il/wp/ccp4workshop/ The closing date for application is 20.12.2022. Best wishes, Anat Shahar & Eugene Krissinel -------------- next part -------------- An HTML attachment was scrubbed... URL: From pafonine at lbl.gov Sat Oct 15 17:48:45 2022 From: pafonine at lbl.gov (Pavel Afonine) Date: Sat, 15 Oct 2022 17:48:45 -0700 Subject: [phenixbb] Bond angle outliers missing from the list In-Reply-To: <024CADA0-BA3A-41A3-8C25-FF3ECB8D2825@icm.uu.se> References: <024CADA0-BA3A-41A3-8C25-FF3ECB8D2825@icm.uu.se> Message-ID: <8f637f8a-82b0-082f-5f24-c9227d4ee40e@lbl.gov> Hi Adrian, could you please send me the PDB file (off mailing list, to me directly) for investigation? Thanks! Pavel On 10/14/22 01:30, Adri?n Gonz?lez L?pez wrote: > Hi! > > I performed a real space refinement on my EM map and my validation > summary indicates that I have 17 bond angle outliers. However, when I > check on the MolProbity tab, Geometry Restraints, it only shows me one > of them (and it still says there are 17). Is this a bug or something else? > You can see it on the screenshot below: > > Thanks! > > /Adrian > Page Title -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2022-10-14 at 10.28.53.png Type: image/png Size: 36028 bytes Desc: not available URL: From csmith at slac.stanford.edu Wed Oct 19 09:34:15 2022 From: csmith at slac.stanford.edu (Smith, Clyde) Date: Wed, 19 Oct 2022 16:34:15 +0000 Subject: [phenixbb] RapiData at SSRL 2022 - application deadline extended by two weeks! In-Reply-To: References: Message-ID: Dear all, Applications are now open for the 2023 edition of RapiData at SSRL. RapiData is a practical course in macromolecular X-ray diffraction data collection, data processing and structure solution. The aim of the RapiData course is to educate and train young scientists in data collection and processing methods at synchrotron beamlines, using state-of-the-art software and instrumentation. The course will be held virtually at the Stanford Synchrotron Radiation Lightsource (SSRL) located on the SLAC National Accelerator Laboratory campus in Menlo Park, CA, from March 22 - April 1, 2023. The course will comprise hands-on experiments at the SSRL beamlines, software tutorials, and lectures on the following topics: Specimen preparation, Data collection strategies, X-ray light sources, X-ray detectors, Data reduction, Structure solution by MAD, SAD and Molecular Replacement, Complementary methods (spectroscopy and small angle scattering) Please visit https://www-ssrl.slac.stanford.edu/rapidata/rapidata-2023/ and use the link on the "Application/Registration" page to apply for the course. The application deadline is January 13, 2023. Successful applicants will be notified early in late January 2023 and invited to register Please direct questions to Silvia Russi (srussi at slac.stanford.edu) or Clyde Smith (csmith at slac.stanford.edu). Clyde and Silvia From cpmasmit at gmail.com Wed Oct 19 19:04:09 2022 From: cpmasmit at gmail.com (CPMAS Chen) Date: Wed, 19 Oct 2022 22:04:09 -0400 Subject: [phenixbb] geometry minimization with ligand present In-Reply-To: References: Message-ID: Hi, All, I have a structure calculated with NMR restraints but it has quite some geometry violation, such as torsion angles, clashes etc. The structure has a small molecule ligand bound. Is it possible to add an CIF file for the ligand and use phenix.geometry_minimization to idealize/optimize the protein structure? I have tried the following and phenix reported an error for missing CIF file. phenix.geometry_minimization model.pdb pdb_intepretation.apply_cif_restraints.restraints_file_name=ligand.cif what would be the correct syntax to add ligand cif for this geometry_minimization? Or what would be the proper way to idealize/optimize a protein structure with ligands present? The structure optimization during NMR calculation is not good enough in my case. Thanks! Charles *************************************************** Charles Chen Research Instructor University of Pittsburgh School of Medicine Department of Anesthesiology ****************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From pafonine at lbl.gov Thu Oct 20 16:26:13 2022 From: pafonine at lbl.gov (Pavel Afonine) Date: Thu, 20 Oct 2022 16:26:13 -0700 Subject: [phenixbb] geometry minimization with ligand present In-Reply-To: References: Message-ID: Hi Charles, it should be as simple as phenix.geometry_minimization model.pdb ligand.cif However, note that geometry restraints used in this case are very simplistic, for example, there are no attraction term. This means helices may unfold unless you do a good thorough job defining secondary structure restraints (and generally restrain all known hydrogen bonds). You can do this by making a hydrogen bond restraint file: phenix.hbond model.pdb (model.pdb needs to have explicit H added) and then supply that file to the above minimization command: phenix.geometry_minimization model.pdb ligand.cif hbond.eff It may be a good idea to verify hbond.eff to make sure it is as complete and accurate as possible. This is because H-bond definitions in this file are made based on input model and if input model geometry isn't great, the H-bond annotations (and corresponding restraints) may not be accurate either. In summary, here are the steps: 1) Add H to the model: phenix.ready_set model.pdb 2) Make H-bond restraints definitions: phenix.hbond model_with_H.pdb This command will create hbonds_pymol.pml file that you can load into PyMol and see all H bonds as dashed line. This lets you verify all H bonds that the program found (or missed). Edit hbond.eff if needed. 3) Finally, run geometry regularization: phenix.geometry_minimization model.pdb ligand.cif hbond.eff Let me know if you have any questions! Good luck, Pavel On 10/19/22 19:04, CPMAS Chen wrote: > Hi, All, > > I have a structure calculated with NMR restraints but it has quite > some geometry violation, such as torsion angles, clashes etc. > The structure has a small molecule ligand bound. > > Is it possible to add an CIF file for the ligand and use > phenix.geometry_minimization to idealize/optimize the protein structure? > > I have tried the following and phenix reported an error for missing > CIF file. > > phenix.geometry_minimization model.pdb > pdb_intepretation.apply_cif_restraints.restraints_file_name=ligand.cif > > what would be the correct syntax to add ligand cif for this > geometry_minimization? > > Or what would be the proper way to idealize/optimize a protein > structure with ligands present? > > The structure optimization during NMR calculation is not good enough > in my case. > > Thanks! > > Charles From cpmasmit at gmail.com Fri Oct 21 06:41:03 2022 From: cpmasmit at gmail.com (CPMAS Chen) Date: Fri, 21 Oct 2022 09:41:03 -0400 Subject: [phenixbb] geometry minimization with ligand present In-Reply-To: References:

Message-ID: This is great, thank you so much! Since my structure is from NMR, it contains all protons. Thanks! Charles On Thu, Oct 20, 2022 at 7:26 PM Pavel Afonine wrote: > Hi Charles, > > it should be as simple as > > phenix.geometry_minimization model.pdb ligand.cif > > However, note that geometry restraints used in this case are very > simplistic, for example, there are no attraction term. This means > helices may unfold unless you do a good thorough job defining secondary > structure restraints (and generally restrain all known hydrogen bonds). > You can do this by making a hydrogen bond restraint file: > > phenix.hbond model.pdb > > (model.pdb needs to have explicit H added) > > and then supply that file to the above minimization command: > > phenix.geometry_minimization model.pdb ligand.cif hbond.eff > > It may be a good idea to verify hbond.eff to make sure it is as complete > and accurate as possible. This is because H-bond definitions in this > file are made based on input model and if input model geometry isn't > great, the H-bond annotations (and corresponding restraints) may not be > accurate either. > > In summary, here are the steps: > > 1) Add H to the model: > > phenix.ready_set model.pdb > > 2) Make H-bond restraints definitions: > > phenix.hbond model_with_H.pdb > > This command will create hbonds_pymol.pml file that you can load into > PyMol and see all H bonds as dashed line. This lets you verify all H > bonds that the program found (or missed). Edit hbond.eff if needed. > > 3) Finally, run geometry regularization: > > phenix.geometry_minimization model.pdb ligand.cif hbond.eff > > Let me know if you have any questions! Good luck, > > Pavel > > On 10/19/22 19:04, CPMAS Chen wrote: > > Hi, All, > > > > I have a structure calculated with NMR restraints but it has quite > > some geometry violation, such as torsion angles, clashes etc. > > The structure has a small molecule ligand bound. > > > > Is it possible to add an CIF file for the ligand and use > > phenix.geometry_minimization to idealize/optimize the protein structure? > > > > I have tried the following and phenix reported an error for missing > > CIF file. > > > > phenix.geometry_minimization model.pdb > > pdb_intepretation.apply_cif_restraints.restraints_file_name=ligand.cif > > > > what would be the correct syntax to add ligand cif for this > > geometry_minimization? > > > > Or what would be the proper way to idealize/optimize a protein > > structure with ligands present? > > > > The structure optimization during NMR calculation is not good enough > > in my case. > > > > Thanks! > > > > Charles > -- *************************************************** Charles Chen Research Instructor University of Pittsburgh School of Medicine Department of Anesthesiology ****************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From cpmasmit at gmail.com Fri Oct 21 07:06:10 2022 From: cpmasmit at gmail.com (CPMAS Chen) Date: Fri, 21 Oct 2022 10:06:10 -0400 Subject: [phenixbb] geometry minimization with ligand present In-Reply-To: References:

Message-ID: Hi, Pavle When I use phenix.hbond to generate hbond.eff, it reports an error as the cif file for the ligand is missing. When I use the following commands, it says cif file is not used. phenix.hbond model.pdb ligand.cif or phenix.hbond model.pdb files=ligand.cif What will be the right syntax to include cif for phenix.hbond? Thanks! Charles On Thu, Oct 20, 2022 at 7:26 PM Pavel Afonine wrote: > Hi Charles, > > it should be as simple as > > phenix.geometry_minimization model.pdb ligand.cif > > However, note that geometry restraints used in this case are very > simplistic, for example, there are no attraction term. This means > helices may unfold unless you do a good thorough job defining secondary > structure restraints (and generally restrain all known hydrogen bonds). > You can do this by making a hydrogen bond restraint file: > > phenix.hbond model.pdb > > (model.pdb needs to have explicit H added) > > and then supply that file to the above minimization command: > > phenix.geometry_minimization model.pdb ligand.cif hbond.eff > > It may be a good idea to verify hbond.eff to make sure it is as complete > and accurate as possible. This is because H-bond definitions in this > file are made based on input model and if input model geometry isn't > great, the H-bond annotations (and corresponding restraints) may not be > accurate either. > > In summary, here are the steps: > > 1) Add H to the model: > > phenix.ready_set model.pdb > > 2) Make H-bond restraints definitions: > > phenix.hbond model_with_H.pdb > > This command will create hbonds_pymol.pml file that you can load into > PyMol and see all H bonds as dashed line. This lets you verify all H > bonds that the program found (or missed). Edit hbond.eff if needed. > > 3) Finally, run geometry regularization: > > phenix.geometry_minimization model.pdb ligand.cif hbond.eff > > Let me know if you have any questions! Good luck, > > Pavel > > On 10/19/22 19:04, CPMAS Chen wrote: > > Hi, All, > > > > I have a structure calculated with NMR restraints but it has quite > > some geometry violation, such as torsion angles, clashes etc. > > The structure has a small molecule ligand bound. > > > > Is it possible to add an CIF file for the ligand and use > > phenix.geometry_minimization to idealize/optimize the protein structure? > > > > I have tried the following and phenix reported an error for missing > > CIF file. > > > > phenix.geometry_minimization model.pdb > > pdb_intepretation.apply_cif_restraints.restraints_file_name=ligand.cif > > > > what would be the correct syntax to add ligand cif for this > > geometry_minimization? > > > > Or what would be the proper way to idealize/optimize a protein > > structure with ligands present? > > > > The structure optimization during NMR calculation is not good enough > > in my case. > > > > Thanks! > > > > Charles > -- *************************************************** Charles Chen Research Instructor University of Pittsburgh School of Medicine Department of Anesthesiology ****************************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: From andrew.alexander2010 at gmail.com Sat Oct 22 23:54:49 2022 From: andrew.alexander2010 at gmail.com (Andrew Alexander) Date: Sun, 23 Oct 2022 08:54:49 +0200 Subject: [phenixbb] Bond angle outliers missing from the list In-Reply-To: <8f637f8a-82b0-082f-5f24-c9227d4ee40e@lbl.gov> References: <024CADA0-BA3A-41A3-8C25-FF3ECB8D2825@icm.uu.se> <8f637f8a-82b0-082f-5f24-c9227d4ee40e@lbl.gov> Message-ID: Dear All, Was the cause and solution of this problem identified? I have also seen this problem with both Phenix v1.20.1-4487 and dev-4742. Many thanks, Andrew ? On Sun, 16 Oct 2022 at 02:49, Pavel Afonine wrote: > Hi Adrian, > > could you please send me the PDB file (off mailing list, to me directly) > for investigation? > > Thanks! > Pavel > On 10/14/22 01:30, Adri?n Gonz?lez L?pez wrote: > > Hi! > > I performed a real space refinement on my EM map and my validation summary > indicates that I have 17 bond angle outliers. However, when I check on the > MolProbity tab, Geometry Restraints, it only shows me one of them (and it > still says there are 17). Is this a bug or something else? > You can see it on the screenshot below: > > Thanks! > > /Adrian > > > _______________________________________________ > phenixbb mailing list > phenixbb at phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave at phenix-online.org -------------- next part -------------- An HTML attachment was scrubbed... URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2022-10-14 at 10.28.53.png Type: image/png Size: 36028 bytes Desc: not available URL: From Blaine-Mooers at ouhsc.edu Fri Oct 28 14:52:28 2022 From: Blaine-Mooers at ouhsc.edu (Mooers, Blaine H.M. (HSC)) Date: Fri, 28 Oct 2022 21:52:28 +0000 Subject: [phenixbb] staff scientist position for an experienced protein crystallographer Message-ID: The Laboratory of Biomolecular Structure and Function (LBSF) at the University of Oklahoma Health Sciences Center (OUHSC) seeks an experienced crystallographer to run the daily operations of the LBSF. The position is at the Staff Scientist level. The candidate will be responsible for working with PIs to advance their structural biology projects. These efforts will include routine technical operations, developing new protocols to overcome challenging problems, and training the staff of user labs in protein purification, crystallization, data collection, and structure determination. The ideal candidate for this position will have a PhD and ten years of experience in macromolecular crystallography, a strong work ethic, and the ability to independently carry out each step of the standard crystallographic study workflow: this a service position, not a training position. The candidate will not be expected to write grant applications to support their position. Pluses in a candidate's background include experience with instrument repair, eukaryotic protein expression, membrane protein purification and LCP crystallization, Cyro-EM, microED, SAXS, SANS, XAFS, NMR, or XFELS. The LBSF is part of a suite of core labs supported in part by the OUHSC Vice President of Research. The LBSF is also part of the Biomolecular Structure Core (BSC) for the Oklahoma Center of Biomedical Research Excellence in Structural Biology (OCSB), which is based on the main campus in Norman. The OCSB was awarded five more years of NIH funding in May 2022. The BSC has contributed to the awarding of 26 million dollars in grant funding and 36 publications in the past ten years. The OCSB has been the focal point of Oklahoma's structural biology community for nine years. The community includes 50 labs at three major research institutions. The BSC is a vital part of a new Center for Therapeutic Science. The center coordinates and fosters the drug development pipeline with the BSC playing a central role in structure-based drug design. The LBSF is working closely with Dr. Matt Hart (https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/hart-matthew-phd-1), Director of the newly established Center for High Throughput Screening. Most of the 12 major users of the LBSF have cancer-related projects. One project led to the 2021 publication of crystal structures of RET Kinase bound to two drug molecules recently approved by the FDA for the treatment of non-small cell lung cancer (https://pubmed.ncbi.nlm.nih.gov/33161056/). Most of the major users are members of the Stephenson Cancer Center, a National Cancer Institute-designated cancer center. The compensation level for this full-time position includes a generous benefits package. The position is based in Oklahoma City -- an affordable place to raise a family. To apply, please submit a cover letter, CV and contact information (name and email) for three references to Blaine Mooers, Director of the Laboratory of Biomolecular Structure and Function at OUHSC, at blaine-mooers at ouhsc.edu. Also apply for Job # 223015 ? Staff Scientist Structural Biology at jobs.ou.edu. The position will remain open until filled. Application review will begin immediately. OUHSC is an equal opportunity employer and is committed to creating a diverse and inclusive environment for all employees. Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology, College of Medicine Director of the Laboratory of Biomolecular Structure and Function Academic Director, Biomolecular Structure Core, COBRE in Structural Biology Full Member, Cancer Biology Program, Stephenson Cancer Center University of Oklahoma Health Sciences Center Mailing Address: 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Office: 405-271-8300 Lab: 405-271-8312 Websites: Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Structure-and-Function COBRE in Structural Biology: https://www.ou.edu/structuralbiology -------------- next part -------------- An HTML attachment was scrubbed... URL: From misba.ahmad at gmail.com Mon Oct 31 07:15:05 2022 From: misba.ahmad at gmail.com (Misba Ahmad) Date: Mon, 31 Oct 2022 15:15:05 +0100 Subject: [phenixbb] Scientist in Protein Crystallography -- ZoBio Leiden Message-ID: ZoBio (www.zobio.com) was founded in 2004 and is located in Leiden, Netherlands. We offer innovative research services in the field of small-molecule drug discovery to the pharmaceutical and biotech industries. Our international team of 40 people covers five fields of expertise: Protein Sciences, Assay Development and Screening, Structural Biology, Medicinal Chemistry, and Data and Information Sciences. We are looking to strengthen our Structural Biology team with an enthusiastic scientist with a track record in protein X-ray crystallography. The structural biology team plays a critical role in supporting our clients? drug discovery programs by providing structural insights into protein-ligand complexes by both NMR spectroscopy and X-ray crystallography. Our crystallization laboratory is equipped with state-of-the-art liquid handlers and automated imagers, and we have regular access to the main European synchrotrons. The team is involved in many projects with challenging targets and engaged in exploring innovative workflows. It is fully expected that the successful candidate will become a permanent and integral member of the ZoBio team after an initial 12-month contract. A tailored remuneration package will be proposed in line with individual qualifications and experience. The position is immediately available; the evaluation and assessment of candidates will run until the position is filled. *TASKS & RESPONSIBILITIES* As a member of the Structural Biology group, you will work on site in the laboratory primarily to support crystallization and structure determination of protein-ligand complexes. You will work with minimal supervision but in a highly collaborative environment within the Structural Biology group and will effectively cooperate on a per-project basis with other research groups at ZoBio. Your role will require working simultaneously on multiple projects in a rapidly evolving environment. You will: Provide input to research projects: - Design and implement (co-) crystallization and soaking strategies utilizing automation and robotics - High-throughput and -quality structure elucidation and interpretation of biological macromolecules in complexes with small molecules of interest - Troubleshoot proactively various challenges relating to protein crystallization - Perform experiments with deadlines - Report project results in an accurate and concise manner, both verbally and written - Keep up to date with relevant literatures and developments in the field of protein crystallography Organize logistics, planning and quality control for research projects: - Contribute to the overall quality control process of data that is generated by the group members - Control the integrity of data imported in project databases - Develop innovative approaches to protein crystallization and/or structure determination, including evaluation of new technologies that support and improve the workflow - Share knowledge, observations, and insights within the group and ZoBio to improve quality and efficiency of project proceedings - Collaborate with clients, external CROs and suppliers *PROFILE & COMPETENCIES* The ideal candidate has a strong background in biochemistry, biophysics or structural biology and at least 4 years of hands-on experience in protein crystallization and structure determination using standard crystallization software (e.g., CCP4, Phenix). Hands-on experience with crystallization robots and understanding of molecular interactions in the context of ligand modelling is desirable; a willingness to learn is required. The multitude of ongoing projects in a rapidly changing environment demands a flexible, creative, and highly organized person with hands-on mentality and excellent communication skills. Required competencies include: - Problem analysis: ability to identify problems, recognize important information, make connections between data, and trace possible causes of problems - Creativity: ability to come up with original solutions, and think ?out-of-the-box? to design novel strategies - Work standards: setting high quality standards with respect to performance of experiments and data analysis, and act accordingly - Oral and written communication: ability to communicate in a clear, persuasive, and effective way to colleagues and clients about ideas, and to report project progress in an accurate and reproducible manner - Adaptability: ability to adjust one?s behavior, planning, and organization in response to frequent changes, delays, and unexpected events - Teamwork: ability to contribute actively to a joint result or solution, even when such teamwork concerns a matter which is not of immediate personal interest - Tenacity: ability to stay with a plan of action or point of view until the desired goal has been attained or is no longer reasonably attainable - Planning and organization: ability to plan and organize tasks and projects to meet the defined goals Please send your CV, motivation letter and names of potential referees to < hrm at zobio.com*>* with the subject: ?Scientist in Protein Crystallography?. -------------- next part -------------- An HTML attachment was scrubbed... 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