[ccp4bb] Two Tenure-Track Assistant Prof. in Biochemistry Positions Open
The Department of Chemistry and Biochemistry at the University of Denver seeks applicants for up to two tenure-track Assistant Professor position beginning September 1, 2024, with research interests in the broad area of biochemistry, biophysical chemistry, bioanalytical chemistry, chemical biology, and related fields. The successful candidate will have a PhD and post-doctoral experience in a relevant field and demonstrated potential for leadership in their field including a record of high-impact research accomplishments. We are especially interested in applicants who have a demonstrated commitment to or experience incorporating inclusive teaching methods and/or pedagogies to effectively engage broadly diverse student populations. The candidate is expected to establish an extramurally-funded research program that augments the research directions of the department. Expectations include the teaching of undergraduate and graduate courses in chemistry and biochemistry. Departmental information is at https://science.du.edu/chemistry/. Depending on research interests, the successful applicant may be eligible to participate in the interdepartmental Molecular and Cellular Biophysics PhD program. https://science.du.edu/biophysics/. Best consideration date is October 22nd. For more details and to apply, please see the complete posting at https://jobs.du.edu/en-us/job/496811/chemistry-and-biochemistry-tenure-track-assistant-professor. Please let me know if you have questions! Best, Scott Scott Horowitz, Ph.D. Associate Professor Department of Chemistry & Biochemistry Knoebel Institute for Healthy Aging University of Denver ECS Building 2155 E. Wesley Ave Denver, CO 80208 Office: Room 561 Lab: Room 505 Phone: 303-871-4326 Fax: 303-871-7915 Email: scott.horow...@du.edu<mailto:scott.horow...@du.edu> Zoom Room: https://udenver.zoom.us/my/scotthorowitz Book an appointment: https://calendly.com/scott-horowitz 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/
[ccp4bb] biochem postdoc position in Denver
https://jobs.du.edu/cw/en-us/job/494678/postdoctoral-fellow-horowitz-lab The Horowitz lab is located in the Knoebel Institute for Healthy Aging as part of the Chemistry & Biochemistry Department at the University of Denver and boasts an interdisciplinary and inclusive environment. The University of Denver is situated in the Denver metro area, a vibrant and diverse urban center in the Rocky Mountain region that is home to nearly 2.6 million people. Our urban location supports faculty and student relationships with a number of local educational and cultural institutions. The University, ranked in the top 100 universities in the country and an R1 institution, comprises approximately 5600 undergraduates, 6200 graduate students, and nearly 700 full-time faculty. Position Summary: The Horowitz lab is seeking to hire a new postdoctoral fellow to work in one of two areas 1) investigating the activity of nucleic acids in affecting protein folding and aggregation, or 2) testing new structural biology tools in the citizen science video game Foldit via crystallography and/or cryo-EM. These research areas are supported by grants from the NIH, CDMRP, and NSF. Candidates are solicited with backgrounds in biochemistry, biophysics, molecular biology, structural biology, cell biology, microbiology, or related areas. Essential Functions: Performing lab-based biochemical research. Training students in biochemical research. Assisting with paper and grant writing. Fostering an inclusive laboratory environment. Knowledge, Skills, and Abilities: Knowledge of biochemistry, biophysics, molecular biology, structural biology, cell biology, microbiology, or related area. Commitment to diversity and inclusive excellence. Laboratory research experience. Required Qualifications: PhD degree in biochemistry, biophysics, molecular biology, structural biology, cell biology, microbiology, or related area. Record of research accomplishments. Preferred Qualifications: Experience: supervising students in a research lab. Thanks all, Scott Scott Horowitz, Ph.D. Assistant Professor Department of Chemistry & Biochemistry Knoebel Institute for Healthy Aging University of Denver ECS Building 2155 E. Wesley Ave Denver, CO 80208 Phone: 303-871-4326 Fax: 303-871-7915 Zoom Room: https://udenver.zoom.us/my/scotthorowitz Email: scott.horow...@du.edu Office: Room 561 Lab: Room 505 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] biomolecular NMR for IDPs
Hi Sorin, I hate to say it, but this is a really tough and expensive one. Solving a true conformational ensemble of one IDP of decent size (~>70 residues) at something like decent resolution is hard, and not that many labs actually do it (it's usually a different set of NMR techniques than solving folding proteins, and that knowledge is even somewhat specialized even within the NMR community). Solving a co-structural ensemble of two IDPs that bind is even harder, and I'm hard pressed to remember a single case right now where it's been done (probably has, but very rarely). Assuming they express really well and produce decent spectra, it is in theory doable, but I'd assume multiple years of work by a very good student or postdoc from a lab that specializes in this and many thousands of dollars (I'd very roughly assume ~$10k in materials costs alone) would be required for that co-structure. The SAXS route is certainly less expensive and faster if it works and gets you the info you need, but it certainly will be low-res. I'm not as familiar with it, but if you can differentially label the proteins, the neutron equivalent of SAXS might also help with the co-structural ensemble to differentiate which protein is where in the resulting blob. Scott Scott Horowitz, Ph.D. Assistant Professor Department of Chemistry & Biochemistry Knoebel Institute for Healthy Aging University of Denver ECS Building 2155 E. Wesley Ave Denver, CO 80208 Phone: 303-871-4326 Fax: 303-871-7915 Zoom Room: https://udenver.zoom.us/my/scotthorowitz Email: scott.horow...@du.edu Office: Room 561 Lab: Room 505 From: CCP4 bulletin board on behalf of Roopa Thapar <070a21fba45f-dmarc-requ...@jiscmail.ac.uk> Sent: Sunday, August 15, 2021 8:20 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [EXTERNAL] Re: [ccp4bb] biomolecular NMR for IDPs [External Email From]: owner-ccp...@jiscmail.ac.uk Hello Sorin, 1. The cost of getting NMR data on the IDPs you propose depends upon the expression levels of the protein/s as you will need to label with 15N and 13C - and depending upon your overall yields per liter of E.coli culture, this can add up. In addition you will need to run triple resonance experiments - so you should look into the hourly charge to access the NMR spectrometers where you are located. Moreover, you need to account for time required for optimization of solution conditions to collect the NMR data as the sample needs to be homogenous (as in no aggregation) at millimolar or hundreds of micromolar concentration. As Ethan Merritt suggested, it would be a good idea to use SAXS first as it requires very little sample, no isotope labeling, and you can try to narrow down the solution conditions that would be best suited for NMR. The Kratky plots, Rg values under different solution conditions can give very useful information about conformational states and ensembles populated by IDPs. However, although NMR tends to be more expensive than other techniques but is perfect for IDPs as you point out you can get residue specific information. A combined NMR/SAXS approach has proven to be very useful to validate computational models. 2. In general, CROs are much more expensive particularly for generating isotopically labeled samples - it is cost-prohibitive for academic labs. Genscript is one CRO that will express proteins, but I am not sure if they will make isotopically labeled proteins for NMR. 3. The amount of protein needed depends upon the size of the molecule. You will need at least 2-3 samples that are differentially labeled with 15N, 13C (also since you want data on the free and bound forms of the complex) at 0.5 - 1 mM depending upon the size of the molecule which relates to the complexity of the NMR spectrum due to number of resonances and the relaxation times. The total volume required for each sample is between 280 ul - 600 ul, depending upon which type of instrumentation and NMR probes you have access to. Hope this helps! Best regards, Roopa On Saturday, August 14, 2021, 04:12:58 PM CDT, Sorin Draga wrote: Hello everyone, I do realize that this is not a NMR focused group, but I do hope that there are a few spectroscopists lurking around that could possibly answer a few questions (I am more of a modeler/computationalist): The problem: I have two intrinsically disordered proteins that are known to interact (let's call them 1 and 2). I would like to get structural information (a conformational ensemble) for 1 and for the "complex" (1+2). Further down the line (depending on whether this is possible) I would also like to evaluate potential small molecule inhibitors for the said complex. Both 1 and 2 are <200 aminoacids long. The questions: 1. Could the cost of determining the "structure" for 1 and 1+2 be estimated? To be more precise, I am looking for a ball-park figure on how much a NMR measureme
[ccp4bb] looking for proteins with no homologues in pdb
For testing purposes, we want to solve structures of proteins that are not in the PDB and have no significant sequence homologues in the PDB (i.e. a blast of the pdb will get no significant hits). Does anyone happen know a good way to find such proteins efficiently? Having an interesting function isn't needed. Thanks, Scott Scott Horowitz, Ph.D. Assistant Professor Department of Chemistry & Biochemistry Knoebel Institute for Healthy Aging University of Denver ECS Building 2155 E. Wesley Ave Denver, CO 80208 Phone: 303-871-4326 Fax: 303-871-7915 Zoom Room: https://udenver.zoom.us/my/scotthorowitz Email: scott.horow...@du.edu Office: Room 561 Lab: Room 505 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/
[ccp4bb] Job posting: developer for cryo-EM and crystallography tools in Foldit
Hi all- a job posting below for a developer for Foldit to do crystallography and cryo-em tool development: Entry level developer position on the Foldit Team, focused on extending the Foldit framework to incorporate experimental data into the human modeling process. This position will focus on the creation of a multi-scale modeling toolbox, integrating new crystallography refinement capabilities within Foldit and adding new modes that allow much larger proteins to be handled in Foldit for cryo-EM. The ultimate goal of this work is to make Foldit a state-of-the-art structure solving suite for crystallography and cryo-EM. Salary commensurate with experience. *Location*: Remote (proximity to Seattle, Boston, or Denver encouraged) *Basic Qualifications:* - A bachelor's in Computer Science, Bioinformatics, Engineering or a related field. - Proficiency in C++. - Experience with large scale code-bases. - Works well in teams. - Able to work independently and remotely. - Self-motivated with great organization and communication skills. - Effective problem solving skills, able to think abstractly. - Adept at structuring code (design patterns, architecture, etc.) *Additional Skills/Preferences:* - Familiarity with Rosetta and python. - OpenGL or graphics optimization experience. - Proficiency with Coot. - Strong math skills. - X-ray crystallography/cryo-EM experience. - Cross platform development experience. - Ruby/Rails/CSS/HTML/javascript/Docker/SQL experience Thanks, Scott Scott Horowitz, Ph.D. Assistant Professor Department of Chemistry & Biochemistry Knoebel Institute for Healthy Aging University of Denver ECS Building 2155 E. Wesley Ave Denver, CO 80208 Phone: 303-871-4326 Fax: 303-871-6389 Zoom: MyZoomRoom <https://udenver.zoom.us/my/scotthorowitz> Office: Room 561 Lab: Room 505 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] how many crystallographers are there?
That gives me a place to start, thanks! On Wed, May 29, 2019 at 1:01 PM Diana Tomchick < diana.tomch...@utsouthwestern.edu> wrote: > Try asking the IUCr for information on crystallographers. > > Diana > > ** > Diana R. Tomchick > Professor > Departments of Biophysics and Biochemistry > UT Southwestern Medical Center > 5323 Harry Hines Blvd. > Rm. ND10.214A > Dallas, TX 75390-8816 > diana.tomch...@utsouthwestern.edu > (214) 645-6383 (phone) > (214) 645-6353 (fax) > > On May 29, 2019, at 1:54 PM, Scott Horowitz wrote: > > Hi all, I was recently asked how many biological > crystallographers plus cryo-EM users there are in the world (in relation to > how many people could therefore be theoretically impacted by Foldit > electron density tools, for the purposes of grant funding). I'm a bit at a > loss as to even what order of magnitude to provide. Any thoughts about how > to estimate a number? > > Thanks, > Scott > > Scott Horowitz, Ph.D. > Assistant Professor > Department of Chemistry & Biochemistry > Knoebel Institute for Healthy Aging > University of Denver > > > ECS Building > 2155 E. Wesley Ave > Denver, CO 80208 > Phone: 303-871-4326 > Fax: 303-871-7915 > Email: scott.horow...@du.edu > Office: Room 561 Lab: Room 505 > > > -- > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 > > > -- > > UT Southwestern > > Medical Center > > The future of medicine, today. > -- Scott Horowitz, Ph.D. Assistant Professor of Department of Chemistry & Biochemistry Knoebel Institute for Healthy Aging University of Denver ECS Building 2155 E. Wesley Ave Denver, CO 80208 Phone: 303-871-4326 Fax: 303-871-6389 Office: Room 561 Lab: Room 505 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] how many crystallographers are there?
Hi all, I was recently asked how many biological crystallographers plus cryo-EM users there are in the world (in relation to how many people could therefore be theoretically impacted by Foldit electron density tools, for the purposes of grant funding). I'm a bit at a loss as to even what order of magnitude to provide. Any thoughts about how to estimate a number? Thanks, Scott Scott Horowitz, Ph.D. Assistant Professor Department of Chemistry & Biochemistry Knoebel Institute for Healthy Aging University of Denver ECS Building 2155 E. Wesley Ave Denver, CO 80208 Phone: 303-871-4326 Fax: 303-871-7915 Email: scott.horow...@du.edu Office: Room 561 Lab: Room 505 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb]
mment line--- # cad HKLIN1 "C:/Users/scott.horowitz/Documents/Serenapdbprep/I19/I19_B5pt2_refine_5.mtz" HKLIN2 "C:/Users/scott.horowitz/Documents/Serenapdbprep/I19/nt14493v84_xdata2_free_I19_B5p2.mtz" HKLIN3 "C:/Users/scott.horowitz/Documents/Serenapdbprep/I19/I19_B_4p5_refine_2.mtz" HKLIN4 "C:/Users/scott.horowitz/Documents/Serenapdbprep/I19/AUTOMATIC_DEFAULT_free_I19_B_4p5.mtz" HKLIN5 "C:/Users/scott.horowitz/Documents/Serenapdbprep/I19/I19B_2p87_refine_2.mtz" HKLIN6 "C:/Users/scott.horowitz/Documents/Serenapdbprep/I19/nt14493v84_xdata2_free_I19B_2p87.mtz" HKLIN7 "C:/Users/scott.horowitz/Documents/Serenapdbprep/I19/I19_B_2p75_refine_2.mtz" HKLIN8 "C:/Users/scott.horowitz/Documents/Serenapdbprep/I19/nt14493v84_xdata3_free_I19_B_2p75.mtz" HKLIN9 "C:/Users/scott.horowitz/Documents/Serenapdbprep/I19/I19_B_5pt2m20_refine_2.mtz" HKLIN10 "C:/Users/scott.horowitz/Documents/Serenapdbprep/I19/nt14493v84_xdata2_free_I19_B5p2m20.mtz" HKLIN11 "C:/Users/scott.horowitz/Documents/Serenapdbprep/I19/I19_3_5p2_refine_3.mtz" HKLIN12 "C:/Users/scott.horowitz/Documents/Serenapdbprep/I19/nt14493v84_xdata2_free_I19_3_5p2.mtz" HKLIN13 "C:/Users/scott.horowitz/Documents/Serenapdbprep/I19/I19_3_5p2_m40_refine_3.mtz" HKLIN14 "C:/Users/scott.horowitz/Documents/Serenapdbprep/I19/nt14493v84_xdata1_free_I19_3_5p2_m40.mtz" HKLIN15 "C:/Users/scott.horowitz/Documents/Serenapdbprep/I19/I19_C_5p2_refine_2.mtz" HKLIN16 "C:/Users/scott.horowitz/Documents/Serenapdbprep/I19/nt14493v84_xdata2_free_I19_C_5p2.mtz" HKLOUT "C:/Users/scott.horowitz/Documents/Serenapdbprep/I19/I19comb.mtz" Comment line--- No CTYP lines input for file: 11 No CTYP lines input for file: 12 No CTYP lines input for file: 13 No CTYP lines input for file: 14 No CTYP lines input for file: 15 No CTYP lines input for file: 16 Indices output even if all data items flagged "missing" CAD: Error, NOT all LABIN data lines given Times: User: 0.0s System:0.0s Elapsed: 0:01 *** * Information from CCP4Interface script *** The program run with command: cad HKLIN1 "C:/Users/scott.horowitz/Documents/Serenapdbprep/I19/I19_B5pt2_refine_5.mtz" HKLIN2 "C:/Users/scott.horowitz/Documents/Serenapdbprep/I19/nt14493v84_xdata2_free_I19_B5p2.mtz" HKLIN3 "C:/Users/scott.horowitz/Documents/Serenapdbprep/I19/I19_B_4p5_refine_2.mtz" HKLIN4 "C:/Users/scott.horowitz/Documents/Serenapdbprep/I19/AUTOMATIC_DEFAULT_free_I19_B_4p5.mtz" HKLIN5 "C:/Users/scott.horowitz/Documents/Serenapdbprep/I19/I19B_2p87_refine_2.mtz" HKLIN6 "C:/Users/scott.horowitz/Documents/Serenapdbprep/I19/nt14493v84_xdata2_free_I19B_2p87.mtz" HKLIN7 "C:/Users/scott.horowitz/Documents/Serenapdbprep/I19/I19_B_2p75_refine_2.mtz" HKLIN8 "C:/Users/scott.horowitz/Documents/Serenapdbprep/I19/nt14493v84_xdata3_free_I19_B_2p75.mtz" HKLIN9 "C:/Users/scott.horowitz/Documents/Serenapdbprep/I19/I19_B_5pt2m20_refine_2.mtz" HKLIN10 "C:/Users/scott.horowitz/Documents/Serenapdbprep/I19/nt14493v84_xdata2_free_I19_B5p2m20.mtz" HKLIN11 "C:/Users/scott.horowitz/Documents/Serenapdbprep/I19/I19_3_5p2_refine_3.mtz" HKLIN12 "C:/Users/scott.horowitz/Documents/Serenapdbprep/I19/nt14493v84_xdata2_free_I19_3_5p2.mtz" HKLIN13 "C:/Users/scott.horowitz/Documents/Serenapdbprep/I19/I19_3_5p2_m40_refine_3.mtz" HKLIN14 "C:/Users/scott.horowitz/Documents/Serenapdbprep/I19/nt14493v84_xdata1_free_I19_3_5p2_m40.mtz" HKLIN15 "C:/Users/scott.horowitz/Documents/Serenapdbprep/I19/I19_C_5p2_refine_2.mtz" HKLIN16 "C:/Users/scott.horowitz/Documents/Serenapdbprep/I19/nt14493v84_xdata2_free_I19_C_5p2.mtz" HKLOUT "C:/Users/scott.horowitz/Documents/Serenapdbprep/I19/I19comb.mtz" has failed with error message CAD: Error, NOT all LABIN data lines given *** #CCP4I TERMINATION STATUS 0 " CAD: Error, NOT all LABIN data lines given" #CCP4I TERMINATION TIME 10 May 2019 14:54:41 #CCP4I MESSAGE Task failed -- Scott Horowitz, Ph.D. Assistant Professor of Department of Chemistry & Biochemistry Knoebel Institute for Healthy Aging University of Denver ECS Building 2155 E. Wesley Ave Denver, CO 80208 Phone: 303-871-4326 Fax: 303-871-6389 Office: Room 561 Lab: Room 505 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] ITC question
I recall a case of this a few years ago where it had to do with the relative concentration of the protein to the buffer/salt molecules (can't remember which anymore), which ended up being important in the binding that was observed. So it was entirely a concentration effect that caused the difference, where using the higher concentrations for ITC caused an increase in the observed Kd. Scott On Fri, Mar 17, 2017 at 1:47 PM, DUMAS Philippe (VIE) < p.du...@ibmc-cnrs.unistra.fr> wrote: > > Le Vendredi 17 Mars 2017 16:07 CET, Nicholas Larsen <nicholas_larsen@ > H3BIOMEDICINE.COM> a écrit: > > Do you mean that the affinity from ITC is 100-fold weaker ? Which would > mean that the Kd values from ITC are 100-fold larger (in the range 0.1-1 > µM) ? > If this is the case, it makes me think to a problem that we have observed > by comparing Kd values obtained by ITC and by Mass Spec. The Kd values by > mass spec were very well determined and smaller (higher affinity) than > those obtained by ITC after a classical processing. It turns out that > processing the ITC data with two competing modes of binding revealed the > correct higher affinity binding mode observed by Mass Spec (80 %) mixed > with the lower-affinity binding mode (20 %). The a priori very strange > thing, which we finally explained, is that the initial processing of the > ITC data with only one binding mode had mixed wrongly the Kd for the > low-affinity binding mode, but the DeltaH for the high-affinity binding > mode. > > I suggest that you have a look to our paper: Wolff et al., J Am Soc Mass > Spectrom. 2017; 28(2): 347–357 (Open access). > I hope it will help. > Philippe Dumas > > > Dear colleagues, > > We have a target where people have measured Kd's for ligands using > > radioligand binding assays. Several publications report Kd's of single > > digit nanomolar and we are able to reproduce that data using this assay > > format. When we try to do the same measurement using ITC, we generate > > beautiful data, but the Kd's from ITC are at least 100-fold weaker. Does > > anyone have a suggestion how to reconcile this huge difference? > > > > SPR studies show the ligands have a very long residence time, so one > thing > > I wondered is if ITC can underestimate a Kd if the off-rate is on the > order > > of minutes-hours. Is this a reasonable explanation? > > > > Please, any other ideas are welcome. > > Best, > > Nick > > > > -- > > [This e-mail message may contain privileged, confidential and/or > > proprietary information of H3 Biomedicine. If you believe that it has > been > > sent to you in error, please contact the sender immediately and delete > the > > message including any attachments, without copying, using, or > distributing > > any of the information contained therein. This e-mail message should not > be > > interpreted to include a digital or electronic signature that can be used > > to authenticate an agreement, contract or other legal document, nor to > > reflect an intention to be bound to any legally-binding agreement or > > contract.] > > > > > -- Scott Horowitz, Ph.D. Postdoctoral Fellow University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226
Re: [ccp4bb] Atom clashes in active site?
Hi Andrew, Here are those references: for CH...O hydrogen bonds I'd recommend our review: "Carbon-Oxygen Hydrogen Bonding in Biological Structure and Function" (2012) http://www.jbc.org/content/287/50/41576.full for chalcogen bonds, I don't know of a great recent review, but this recent article (2016) has a whole bunch of references (listed under 19 and 20) on it: https://www.ncbi.nlm.nih.gov/pubmed/27992115 Scott On Tue, Dec 20, 2016 at 8:45 PM, Andrew Marshall < andrew.c.marsh...@adelaide.edu.au> wrote: > Hi Scott, > > That would be great if you have some references handy? > Thanks very much, > > Andrew Marshall > PhD Candidate > Laboratory of Protein Crystallography > Dept. of Molecular and Cellular Biology > School of Biological Sciences > The University of Adelaide > > On Wed, Dec 21, 2016 at 1:48 AM, Scott Horowitz <horow...@umich.edu> > wrote: > >> Hi Andrew, >> >> Based on the atoms and distances you are mentioning, these don't sound >> like steric clashes, but like a chalcogen bond between the S and O atoms, >> and CH...O hydrogen bonds between the O and CH3. These are common and >> well-accepted interactions, but unfortunately aren't usually treated as >> such by refinement programs. Let me know if you want references for these >> interaction types. >> >> Scott >> >> On Mon, Dec 19, 2016 at 8:48 PM, Andrew Marshall < >> andrew.c.marsh...@adelaide.edu.au> wrote: >> >>> Hi all, >>> >>> Thank you for your suggestions. I tried the pdb file edit (making the >>> offending atoms of both the ligand and the protein 'B' altconf), but it >>> didn't seem to make any difference to their positions after a single round >>> of refinement..? >>> The atoms in the active site concern two acetyl groups - one from the >>> substrate, acetyl-CoA, and the other from an acetylated cysteine in the >>> protein - that I believe are poised ready for a condensation reaction. The >>> closest contacts are between S and O(carbonyl) atoms (2.9A) and O and CH3 >>> (3.1A), but going off the density, I think these should be closer (more >>> like 2.8 or 2.7A). It may be that I've trapped another reaction >>> intermediate (which would be cool), but I don't think that fits the density >>> quite as well. Any thoughts/ideas? >>> >>> Thanks, >>> >>> Andrew Marshall >>> PhD Candidate >>> Laboratory of Protein Crystallography >>> Dept. of Molecular and Cellular Biology >>> School of Biological Sciences >>> The University of Adelaide >>> >>> On Tue, Dec 20, 2016 at 12:09 AM, Scott Horowitz <horow...@umich.edu> >>> wrote: >>> >>>> Hi Andrew, >>>> >>>> I'm curious- what are the atoms that are clashing? I worked on this >>>> sort of thing back in my Ph.D., and so I might have some useful tidbits if, >>>> for example, the S is clashing with a carbon of some sort. >>>> >>>> Thanks, >>>> Scott >>>> >>>> On Mon, Dec 19, 2016 at 12:39 AM, Andrew Marshall < >>>> andrew.c.marsh...@adelaide.edu.au> wrote: >>>> >>>>> Hi all, >>>>> >>>>> I have a structure of a condensing enzyme with substrate bound. The >>>>> active site is very tight, requiring some of the substrate atoms to clash >>>>> with a catalytic cysteine. This means that although the substrate fits the >>>>> density nicely upon manual real-space refinement, phenix recognises the >>>>> clash, resulting in the displacement of substrate atoms so that they are >>>>> outside the density. I can mostly fix this by using distance restraints, >>>>> but I'd rather allow it to refine in a less biased manner, but ignore the >>>>> clash. Is this a acceptable way forward? If so, is there a parameter I can >>>>> edit to tell phenix to ignore clashes between these specific atoms? >>>>> >>>>> Thanks, >>>>> >>>>> Andrew Marshall >>>>> PhD Candidate >>>>> Laboratory of Protein Crystallography >>>>> Dept. of Molecular and Cellular Biology >>>>> School of Biological Sciences >>>>> The University of Adelaide >>>>> >>>>> >>>> >>>> >>>> -- >>>> Scott Horowitz, Ph.D. >>>> Postdoctoral Fellow >>>> >>>> University of Michigan >>>> Department of Molecular, Cellular, and Developmental Biology >>>> Bardwell lab >>>> 830 N. University Ave, Room 4007 >>>> Ann Arbor, MI 48109 >>>> phone: 734-647-6683 >>>> fax: 734-615-4226 >>>> >>> >>> >> >> >> -- >> Scott Horowitz, Ph.D. >> Postdoctoral Fellow >> >> University of Michigan >> Department of Molecular, Cellular, and Developmental Biology >> Bardwell lab >> 830 N. University Ave, Room 4007 >> Ann Arbor, MI 48109 >> phone: 734-647-6683 >> fax: 734-615-4226 >> > > -- Scott Horowitz, Ph.D. Postdoctoral Fellow University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226
Re: [ccp4bb] Atom clashes in active site?
Hi Andrew, Based on the atoms and distances you are mentioning, these don't sound like steric clashes, but like a chalcogen bond between the S and O atoms, and CH...O hydrogen bonds between the O and CH3. These are common and well-accepted interactions, but unfortunately aren't usually treated as such by refinement programs. Let me know if you want references for these interaction types. Scott On Mon, Dec 19, 2016 at 8:48 PM, Andrew Marshall < andrew.c.marsh...@adelaide.edu.au> wrote: > Hi all, > > Thank you for your suggestions. I tried the pdb file edit (making the > offending atoms of both the ligand and the protein 'B' altconf), but it > didn't seem to make any difference to their positions after a single round > of refinement..? > The atoms in the active site concern two acetyl groups - one from the > substrate, acetyl-CoA, and the other from an acetylated cysteine in the > protein - that I believe are poised ready for a condensation reaction. The > closest contacts are between S and O(carbonyl) atoms (2.9A) and O and CH3 > (3.1A), but going off the density, I think these should be closer (more > like 2.8 or 2.7A). It may be that I've trapped another reaction > intermediate (which would be cool), but I don't think that fits the density > quite as well. Any thoughts/ideas? > > Thanks, > > Andrew Marshall > PhD Candidate > Laboratory of Protein Crystallography > Dept. of Molecular and Cellular Biology > School of Biological Sciences > The University of Adelaide > > On Tue, Dec 20, 2016 at 12:09 AM, Scott Horowitz <horow...@umich.edu> > wrote: > >> Hi Andrew, >> >> I'm curious- what are the atoms that are clashing? I worked on this sort >> of thing back in my Ph.D., and so I might have some useful tidbits if, for >> example, the S is clashing with a carbon of some sort. >> >> Thanks, >> Scott >> >> On Mon, Dec 19, 2016 at 12:39 AM, Andrew Marshall < >> andrew.c.marsh...@adelaide.edu.au> wrote: >> >>> Hi all, >>> >>> I have a structure of a condensing enzyme with substrate bound. The >>> active site is very tight, requiring some of the substrate atoms to clash >>> with a catalytic cysteine. This means that although the substrate fits the >>> density nicely upon manual real-space refinement, phenix recognises the >>> clash, resulting in the displacement of substrate atoms so that they are >>> outside the density. I can mostly fix this by using distance restraints, >>> but I'd rather allow it to refine in a less biased manner, but ignore the >>> clash. Is this a acceptable way forward? If so, is there a parameter I can >>> edit to tell phenix to ignore clashes between these specific atoms? >>> >>> Thanks, >>> >>> Andrew Marshall >>> PhD Candidate >>> Laboratory of Protein Crystallography >>> Dept. of Molecular and Cellular Biology >>> School of Biological Sciences >>> The University of Adelaide >>> >>> >> >> >> -- >> Scott Horowitz, Ph.D. >> Postdoctoral Fellow >> >> University of Michigan >> Department of Molecular, Cellular, and Developmental Biology >> Bardwell lab >> 830 N. University Ave, Room 4007 >> Ann Arbor, MI 48109 >> phone: 734-647-6683 >> fax: 734-615-4226 >> > > -- Scott Horowitz, Ph.D. Postdoctoral Fellow University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226
[ccp4bb] Fwd: mapsig errors
Hi all, I tried using mapsig for the first time, and I got multiple errors (text pasted at bottom). This is on mac os x 10.8.5, and the CCP4 install is 6.4.0. I followed these instructions to be able to use CCP4 programs at the command line: http://plested.wordpress.com/2012/10/31/run-ccp4-programs-from-the-command-line-on-mac-osx/ http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=How_to_run_CCP4_programs_from_the_command_line I have also tried the csh version as well, with the same results. Any advice would be greatly appreciated. This is my first time attempting to use CCP4 without the GUI, so if there's additional setup necessary, that would be great info to know. Thanks, Scott mapsig MAPIN H96LA28I_6pt5superI.pdb MAPIN2 H96LQ17I10_6pt5superI.pdb TYPE RATIO MAPOUT test.map BFONT COLOR=#FF!--SUMMARY_BEGIN-- pre ### ### ### ### CCP4 6.4: MAPSIG version 6.4 : ## ### User: horowsah Run date: 20/10/2014 Run time: 09:06:01 Please reference: Collaborative Computational Project, Number 4. 1994. The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up. !--SUMMARY_END--/FONT/B # # TRANSLATION FUNCTION MAP SIGNAL ANALYSIS. # # BE WARNED THAT THIS PROGRAM ASSUMES PERIODIC MAP BOUNDARIES, (I.E. THE LEFT-HAND EDGE ABUTS ONTO THE RIGHT-HAND EDGE) AND THEREFORE MAY NOT LOCATE PEAKS AT THE EDGES OF THE MAP CORRECTLY IN OTHER CASES. IN SUCH CASES THE MAP SHOULD BE EXPANDED IN ONE OR MORE DIRECTIONS TO MAKE IT PERIODIC IN ALL DIRECTIONS. BFONT COLOR=#FF!--SUMMARY_BEGIN-- html !-- CCP4 HTML LOGFILE -- hr !--SUMMARY_END--/FONT/B CCP4 library signal ccp4_map:No associated header (Error) raised in ccp4_cmap_open CCP4 library signal ccp4_map:Cannot open file (Error) raised in MRDHDR mapsig: Error in opening input map file. mapsig: Error in opening input map file. Times: User: 0.0s System:0.0s Elapsed: 0:00 /pre /html !--SUMMARY_END--/FONT/B -- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226 -- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226
Re: [ccp4bb] mapsig errors
Please ignore my incredibly dumb last email… autocomplete had me putting in .pdb files, which obviously won't work. Scott On Mon, Oct 20, 2014 at 9:47 AM, Scott Horowitz horow...@umich.edu wrote: Hi all, I tried using mapsig for the first time, and I got multiple errors (text pasted at bottom). This is on mac os x 10.8.5, and the CCP4 install is 6.4.0. I followed these instructions to be able to use CCP4 programs at the command line: http://plested.wordpress.com/2012/10/31/run-ccp4-programs-from-the-command-line-on-mac-osx/ http://ccp4wiki.org/~ccp4wiki/wiki/index.php?title=How_to_run_CCP4_programs_from_the_command_line I have also tried the csh version as well, with the same results. Any advice would be greatly appreciated. This is my first time attempting to use CCP4 without the GUI, so if there's additional setup necessary, that would be great info to know. Thanks, Scott mapsig MAPIN H96LA28I_6pt5superI.pdb MAPIN2 H96LQ17I10_6pt5superI.pdb TYPE RATIO MAPOUT test.map BFONT COLOR=#FF!--SUMMARY_BEGIN-- pre ### ### ### ### CCP4 6.4: MAPSIG version 6.4 : ## ### User: horowsah Run date: 20/10/2014 Run time: 09:06:01 Please reference: Collaborative Computational Project, Number 4. 1994. The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up. !--SUMMARY_END--/FONT/B # # TRANSLATION FUNCTION MAP SIGNAL ANALYSIS. # # BE WARNED THAT THIS PROGRAM ASSUMES PERIODIC MAP BOUNDARIES, (I.E. THE LEFT-HAND EDGE ABUTS ONTO THE RIGHT-HAND EDGE) AND THEREFORE MAY NOT LOCATE PEAKS AT THE EDGES OF THE MAP CORRECTLY IN OTHER CASES. IN SUCH CASES THE MAP SHOULD BE EXPANDED IN ONE OR MORE DIRECTIONS TO MAKE IT PERIODIC IN ALL DIRECTIONS. BFONT COLOR=#FF!--SUMMARY_BEGIN-- html !-- CCP4 HTML LOGFILE -- hr !--SUMMARY_END--/FONT/B CCP4 library signal ccp4_map:No associated header (Error) raised in ccp4_cmap_open CCP4 library signal ccp4_map:Cannot open file (Error) raised in MRDHDR mapsig: Error in opening input map file. mapsig: Error in opening input map file. Times: User: 0.0s System:0.0s Elapsed: 0:00 /pre /html !--SUMMARY_END--/FONT/B -- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226 -- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226 -- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226
[ccp4bb] a more intelligent mapsig question
Hi all, Now that I have mapsig running, I am getting an error message that I am confused by. The maps I am using are anomalous maps generated by FFT. Originally, I had them covering just the asymmetric unit, but based on the error message below, I then redid it where I covered a user defined extent, where I went from 0 to the cell size for each axis, but the error message stayed the same, which means perhaps I'm misunderstanding what it means. Any help would be great, and the whole output is pasted below. Thanks, Scott bash-3.2$ mapsig mapin H96LY10I01_14combfull.map mapin2 H96LY10I01_6pt5combfull.map type ratio mapout test.map BFONT COLOR=#FF!--SUMMARY_BEGIN-- pre ### ### ### ### CCP4 6.4: MAPSIG version 6.4 : ## ### User: horowsah Run date: 20/10/2014 Run time: 10:20:01 Please reference: Collaborative Computational Project, Number 4. 1994. The CCP4 Suite: Programs for Protein Crystallography. Acta Cryst. D50, 760-763. as well as any specific reference in the program write-up. !--SUMMARY_END--/FONT/B # # TRANSLATION FUNCTION MAP SIGNAL ANALYSIS. # # BE WARNED THAT THIS PROGRAM ASSUMES PERIODIC MAP BOUNDARIES, (I.E. THE LEFT-HAND EDGE ABUTS ONTO THE RIGHT-HAND EDGE) AND THEREFORE MAY NOT LOCATE PEAKS AT THE EDGES OF THE MAP CORRECTLY IN OTHER CASES. IN SUCH CASES THE MAP SHOULD BE EXPANDED IN ONE OR MORE DIRECTIONS TO MAKE IT PERIODIC IN ALL DIRECTIONS. BFONT COLOR=#FF!--SUMMARY_BEGIN-- html !-- CCP4 HTML LOGFILE -- hr !--SUMMARY_END--/FONT/B Logical Name: MAPIN Filename: H96LY10I01_14combfull.map File name for input map file on unit 1 : H96LY10I01_14combfull.map file size 1917228 ; logical name MAPIN Number of columns, rows, sections ... 43 43 259 Map mode 2 Start and stop points on columns, rows, sections 0 420 420 258 Grid sampling on x, y, z 48 48 304 Cell dimensions . 42.7000 42.7000 258.299890.90.90. Fast, medium, slow axes .YXZ Minimum density .-0.04944 Maximum density . 0.19449 Mean density -0.0 Rms deviation from mean density . 0.01025 Space-group . 91 Number of titles 1 Labels: [No title given] Translation modulus = 43 43 259 *** ERROR - space group must be P1 if whole cell not given. -- Scott Horowitz, Ph.D. Research Associate Howard Hughes Medical Institute University of Michigan Department of Molecular, Cellular, and Developmental Biology Bardwell lab 830 N. University Ave, Room 4007 Ann Arbor, MI 48109 phone: 734-647-6683 fax: 734-615-4226
