[ccp4bb] Registration open for the SSRL/LCLS User Meeting

Registration is open for the SSRL/LCLS User's Meeting, which will be September 24-29, 2023 (https://events.bizzabo.com/SLAC-2023/home). It will be in person for the first time since 2019. This meeting attracts the lightsource community to a single scientific event that is inclusive of many

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] ILLUSTRATE in PYMOL

e CCSB Illustrate site uses slightly different colors for different parts of the molecule (phosphate, sugar, base), which is a nice effect. Hope that helps. Cheers, Jared On Tue, Aug 15, 2023 at 10:40 PM Mooers, Blaine H.M. (HSC) mailto:blaine-moo...@ouhsc.edu>> wrote: Hi Faisal, I m

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] ILLUSTRATE in PYMOL

Hi Faisal, I made a number of such figures several years ago. I finally found the code. Load the molecule of interest into PyMOL and paste the following code onto the command line just below the command history window. I was using our school colors: crimson and cream. Ligands are colored

[ccp4bb] Staff scientist position for an experienced biomolecular crystallographer

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

[ccp4bb] reminder: tomorrow is last day to register for the virtual and free SSRL/LCLS Users Meeting

Tomorrow is the last day to register for the virtual and free SSRL/LCLS Users Meeting https://events.bizzabo.com/SLAC-UsersMeeting-2022/home There are 30 half-day workshops. Of particular interest to this mailing list are the following - Fundamentals at SSRL and LCLS - Part I and II -

[ccp4bb] Poster deadline approaching for SSRL/LCLS User's Meeting

This is a reminder of the fast approaching deadline of September 9th for poster abstract submissions for the SSRL/LCLS User's Meeting, September 26-30, 2022. The meeting will be virtual again due to COVID, but the of the sessions will be recorded live. Registration is free and open to all.

[ccp4bb] SSRL/LCLS User's Meeting registration is open

The SSRL/LCLS User's Meeting will be September 26-30, 2022. It will be virtual again due to COVID, but the of the sessions will be recorded live. Registration is free and open to all. We had about 1600 registrants last year. We will have

Re: [ccp4bb] [EXTERNAL] [ccp4bb] Issue with Phenix/Coot/PyMol after installing ccp4 v8

Hi Dale, Which version of PyMOL are you using? (PyMOL questions should really be directed to the PyMOL mailing list). Ancient versions of PyMOL may not accept cif files via fetch unless you include the type=cif​ keyword. To get the pdb file downloaded, try fetch 6wrh type=pdb​. I can download

Re: [ccp4bb] Phasing a difficult RNA heteroduplex structure

Hi Charles, Congratulations on getting an RNA heteroduplex to crystallize! Most do not crystallize. You should make and look at a native Patterson map to find the off-origin peak(s) that give the report of tNCS. The direction and distance of this peak from the origin can be enlightening. For

[ccp4bb] Opportunity for experienced crystallographer

Associate Director of the Laboratory of Biomolecular Structure and Function 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

[ccp4bb] last day to register for the SSRL/LCLS User Meeting

Dear CCP4BB, Today is the last day to register for the SSRL/LCLS User Meeting that starts on Monday. It is free. https://events.bizzabo.com/SLAC-UsersMeeting-2021/home. The poster session runs 12 - 1 PM Pacific Time M-Th. You use the gathertown software to attend it. Navigation of the poster

[ccp4bb] Experienced crystallographer needed

Dear all, Please share this job announcement with potential candidates. Associate Director of the Laboratory of Biomolecular Structure and Function The Laboratory of Biomolecular Structure and Function (LBSF) at the University of Oklahoma Health Sciences Center (OUHSC) seeks an experienced

Re: [ccp4bb] writing coordinates of full biomol into one (PDB) file

If you have PyMOL installed, you can paste the bash function below into your .bashrc file, enter 'source .bashrc', and then enter 'bu PDB-ID'. All that you have to remember a month from now is 'bu'. Otherwise, you can replace the pymol command with one of the other commands that have been

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] phenix.refine with ligand with ambiguous electron density

Dear Nika, The question is about a Fo-Fc map and the replies have been focused on such maps. However, I question why you are bothering with Fo-Fc maps. The ligand was soaked into the crystal. There is probably an isomorphous apo data set available. A [Fo(ligand complex) -

Re: [ccp4bb] [EXTERNAL] [ccp4bb] Contouring Patterson map?

Hi Gloria, The lack of repsonse to your question sadly suggests that not many people have made a Harker section recently. You could probably make a fancier plot with matplotlib in Pytbon or Gnuplot, but I use Map Slicer under the Visuallization pulldown in the ccp4i gui to make old-fashion

Re: [ccp4bb] Displaying solvent channels in protein crystal

Hi Steve, Take a look at MAP_CHANNELS: a computation tool to aid in the visualization and characterization of solvent channels in macromolecular crystals by Douglas H. Juersa and Jon Ruffin doi: 10.1107/S160057671402281X. Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor

Re: [ccp4bb] [EXTERNAL] [ccp4bb] Macports and Fink - failed building open source pymol on MacOS Catalina

Hi Javier, Because this is an issue about open-source pymol, open an issue on the open-source GitHub site and report the problem https://github.com/schrodinger/pymol-open-source/issues Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular

Re: [ccp4bb] Generating rotation/translation matrices for biological assemblies

Hi Eric, You can lookup the symmetry operator in the International Tables (http://img.chem.ucl.ac.uk/sgp/LARGE/sgp.htm). Alternatively, you can use coot to find the crystallographic symmetry operator that generates the second half of your tetramer. Draw/Cell & Symmetry and then generate the

Re: [ccp4bb] [EXTERNAL] [ccp4bb] cryo suggestions for lithium sulphate xt condition containing 1.8 - 2 M Li2SO4

Hi Almu, In my hands, 2M LiSO4 is not enough. If your crystals cannot survive transfer to higher concentrations, transfer them to 1.8 M NaMalonate at the same pH and then transfer or add aliquots of Na Malonate stock at higher concentration until the drop has about 3.5 - 3.8 M Na Malonate.

Re: [ccp4bb] [EXTERNAL] [ccp4bb] suggestions for cryoprotectant

Hi Firdous, What Diana suggested may work if done carefully; however, I failed to transfer crystals from 1.5 LiSO4 salts to higher concentrations of LiSO4 in many attempts. I did have success in transferring said crystals to 1.5 M sodium malonate then to incrementally to 2.8 or 3.2 M sodium

Re: [ccp4bb] [EXTERNAL] [ccp4bb] Python3 and MTZ

Hi Kay, clipper_tools is python3 compliant. https://github.com/clipper-python Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology, College of Medicine University of Oklahoma Health Sciences Center 975 NE 10th Street, BRC 466 Oklahoma

Re: [ccp4bb] SUMMARY: Equation Editor woes with Office 2011 for Mac

I have had good experiences with MathJak for html. It too gives beautiful renderings on webpages of equations encoded in LaTeX. It is very easy to use. It grew out of jsMath. http://www.mathjax.org/ Best regards, Blaine Mooers From: CCP4 bulletin

Re: [ccp4bb] Equation Editor woes with Office 2011 for Mac

Hi Randy, You could use a LyX--LaTeXiT--MS Word workflow to solve the equation editing issue without anyone learning LaTeX syntax. The LyX document with equations can be exported to a LaTeX *.tex file, and you can open this tex file in any text editor to copy the equations encoded in LaTeX

Re: [ccp4bb] Equation Editor woes with Office 2011 for Mac

Hi Randy, I too suggest LaTeXiT. To add to what has already been suggested, LaTeXiT allows the assembly of a custom library of equations. You can send your collaborators this library as a file, and they could make minor edits to the equations in LaTexit gui editor without having to learn the

Re: [ccp4bb] Graphic for rotation about axis

Hi Nick, These symmetry element fonts at the IUCr website might be useful or at least inspirational: http://www.iucr.org/resources/symmetry-font Best regards, Blaine Blaine Mooers, Ph.D. Assistant Professor Director of the Laboratory of Biomolecular Structure and Function Department of

Re: [ccp4bb] [ot]: nedit on Mac 10.10 yosemite

nedit is available in macports. sudo port install nedit Best regards, Blaine Blaine Mooers, Ph.D. Assistant Professor Department of Biochemistry and Molecular Biology University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center Rm. 466 Shipping address: 975 NE 10th

Re: [ccp4bb] Calculating over all bend in a DNA

Hi Sasha, You can also use Richard Lavery's webservice for Curves+ ( http://gbio-pbil.ibcp.fr/cgi/Curves_plus/ ) and visualize the curve of the helical axis in 3D in a molecular graphics program. In addition, you can do a normal vector analysis similar to the one suggested by Tim Gruene by

Re: [ccp4bb] High Salt Cryo

For crystals grown out of a 2 uL drop of 1.2-1.8 M LiSO4 or 1.6-2.4 M AmmSO4, we do in situ cryoprotection with sodium malonate. We add 2-4 uL of 1.9 M Na malonate to the crystallization drop, wait 10 seconds and add 2-4 uL of 2.4 M sodium malonate, repeat with 2.8 M and then 3.4 M. We do not

[ccp4bb] create a lower resolution data set by truncating a high resolution data

For some simulated phasing experiments, I want to create a lower resolution diffraction data set by truncating a high resolution data set. I would like to avoid Fourier ripples due to the truncation of the high resolution data by downscaling the data such that I/sigma=2.0 in the highest

Re: [ccp4bb] anomalous scattering server down?

Bernhard Rupp has a calculator of Bijvoet ratios: http://www.ruppweb.org/new_comp/anomalous_scattering.htm Blaine Mooers Assistant Professor Director Macromolecular Crystallography Lab Member Stephenson Cancer Center Department of Biochemistry and Molecular Biology University of Oklahoma

Re: [ccp4bb] cc1/2

In the output file from xscale XSCALE.LP Look in the middle of the file for the table STATISTICS OF SCALED OUTPUT DATA SET : Blaine Mooers Assistant Professor Department of Biochemistry and Molecular Biology University of Oklahoma Health Sciences Center S.L. Young Biomedical Research Center

Re: [ccp4bb] usefulness of cacodylate?

Hi Frank, In our hands, some RNAs only crystallize out of cacodylate buffers. We would otherwise stop using it out of health and safety concerns. Blaine Blaine Mooers Assistant Professor Department of Biochemistry and Molecular Biology University of Oklahoma Health Sciences Center S.L. Young

[ccp4bb] Postdoctoral Fellow in Mooers Laboratory

Postdoctoral Fellow in Mooers Laboratory Dept. of Biochemistry Molecular Biology College of Medicine University of Oklahoma Health Sciences Center (OUHSC) Oklahoma City, OK, USA A post-doctoral fellow position is available in structural (X-ray diffraction and SAXS) and biophysical studies of

[ccp4bb] FACULTY POSITION IN STRUCTURAL BIOLOGY

FACULTY POSITION IN STRUCTURAL BIOLOGY 08-24-2009 Department of Biochemistry Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City The Department of Biochemistry Molecular Biology in the College of Medicine at the University of Oklahoma Health Sciences Center

[ccp4bb] off topic: plasmid for high fidelity DNA polymerase

This is off topic but probably of great interest to others. Where can I find an over-expression plasmid for a high fidelity thermostable DNA polymerase? I want to make DNA polymerase to use in a large number of PCR reactions. Many thanks in advance, Blaine Mooers