[ccp4bb] open Structural Biologist position at Rheos Medicines

. thank you and stay safe. Eric Larson eric.xt...@gmail.com 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 mem

[ccp4bb] Fwd: Crystallography job opportunities at HarkerBio in Buffalo, NY

skills – the ability to present complex ideas and results in an elegant, concise, and effective manner is a must. 6. Experience with the budgeting process, practical awareness and application of basic business accounting and cost control skills. -- _____ Eric Larson, PhD HarkerBIO

[ccp4bb] OFF TOPIC - zebra printer labels for SBS format plates

. thanks in advance for your suggestions/advice. sincerely, Eric Eric Larson Structural Research Boehringer Ingelheim Pharmaceuticals Ridgefield, CT USA

Re: [ccp4bb] Freezing crystal

Hi Theresa, A good place to start when searching for suitable cryo conditions are the tables in these references: Garman, et al. J. Appl. Cryst. (1996). 29, 584-587. McFerrin, et al. J. Appl. Cryst. (2002). 35, 538-545. hope they help and good luck. Eric __ Eric Larson

Re: [ccp4bb] pdb_extact and refmac5.6

Hi Jan, Have you tried using the x.refmac file that is created instead of the log file. It is in cif format and may be in the "DepositFiles" directory. Hope you are well and talk to you later, Eric Eric T. Larson, PhD Biomolecular Structure Center Departm

Re: [ccp4bb] Concentrating a protein solution - subbu

stallization is most affected by the pH, 2 - 10% glycerol or >temperature 4 - 25 degrees C. >Cheers >  >Ray Brown > >_________ >From: Eric Larson >To: CCP

Re: [ccp4bb] Concentrating a protein solution - subbu

Hi Subbu, You got crystals at 1mg/ml so you probably don't need to concentrate your protein any higher, especially since you suggest that concentrating beyond that is problematic. Instead, you may want to try to optimize the crystallization condition you have already identified. Some possibl

Re: [ccp4bb] Off Topic: How to delete loops from a protein

Hi Obayed, you could give in situ protolysis a try. This is where you add a bit of protease along with you target protein to the crystallization drop. It has been quite successful for the folks at the SGC. Here are the relevant references: Dong A, et al. In situ proteolysis for protein cry

Re: [ccp4bb] Off topic - transformation problems

oops - I just caught that the empty pET20 did transform well so the other suggestions about toxicity are probably more accurate. On Thu, 14 Jul 2011, Eric Larson wrote: On Thu, 14 Jul 2011, Wonjin Bae wrote: Hi, all Recently, some bactrial source enzyme(sialidase) was subcloned pET20b and

Re: [ccp4bb] Off topic - transformation problems

On Thu, 14 Jul 2011, Wonjin Bae wrote: Hi, all Recently, some bactrial source enzyme(sialidase) was subcloned pET20b and pGEX4T3 vector. Then, these two construct were transformed to BL21(DE3) expression host. DNA sequencing results were accurate. In case of pGEX, many colony was formed and s

Re: [ccp4bb] Convert .cif to mtz

Hi Madhu, You don't need to use scala, d*trek can do the job as well. The easiest thing to do is to continue with d*trek to scale and merge your data and then input this scaled and merged file into Dtrek2mtz. Eric Eric T. Larson, PhD Biomolecular Structure Ce

Re: [ccp4bb] Convert .cif to mtz

hu, 23 Jun 2011, Eric Larson wrote: Hi Madhu, D*trek is what you processed your data with. In the ccp4i gui, select the program "Dtrek2mtz" and then in the field that says "convert scaled data output from ... ", select "d*trek" from the pull down menu. Go to http:

Re: [ccp4bb] Convert .cif to mtz

Hi Madhu, D*trek is what you processed your data with. In the ccp4i gui, select the program "Dtrek2mtz" and then in the field that says "convert scaled data output from ... ", select "d*trek" from the pull down menu. Go to http://www.ccp4.ac.uk/html/dtrek2mtz.html for more information. good

Re: [ccp4bb] Change cell parameter

Hi Zhiyi, This is very easily done using Pointless. From the gui, click "Match index to reference", enter your two mtz files and run. ERic Eric T. Larson, PhD Biomolecular Structure Center Department of Biochemistry Box 357742 University of Washington Seattle,

Re: [ccp4bb] Low resolution refinement

Dear Joane, We have had very good luck refining low resolution structures with dramatic improvement using several newish options in refmac - particularly when NCS is present! Those options are jelly body restraints, automatic NCS restraints, and map sharpening. Here is a description cut-and-p

Re: [ccp4bb] Pymol questions

Hi Eric, On Wed, 4 May 2011, jlliu liu wrote: Hi All, I have two questions for Pymol. the pymol wiki is your friend (http://www.pymolwiki.org/index.php/Main_Page) as is the pymol users mailing list (http://sourceforge.net/mail/?group_id=4546). Follow the link to subscribe. 1. Can you w

Re: [ccp4bb] Met auxotroph and aa-mix

Hi Eric, If you are trying to express your Se-Met protein, it is typically done in a defined media starting with a minimal media base so a mixture of amino acids, particularly those that are essential, is needed. You likely will not get very high yields of SeMet-labeled protein if you simply

Re: [ccp4bb] Question about movie making

Hi Mark (and Matthias), I'm not sure if "Windows Movie Maker" is the same as (or maybe the predecessor to?) ""Windows Live Movie Maker" (http://explore.live.com/windows-live-movie-maker?os=other), but this is what I used recently to string together a series of png images from pymol to make a wm

Re: [ccp4bb] Is there any program for specifically calculating Rvalue in CCP4

Dear TingWei, Can you provide more details of what you are trying to do and why, and how you manipulated the model for which you want to determine the R-values? Is it data you collected and a model that you have been working on or is it a structure and its data from the PDB that you are worki

Re: [ccp4bb] off-topic: tag removal

Hi Phil, Must you tag your protein? Have you tried to express it without a tag? Perhaps you can purify the un-tagged protein with a series of chromatographic (or other) steps - particularly if it expresses well. Eric Eric T. Larson, PhD Biomolecular Structur

Re: [ccp4bb] How to align electron density maps?

Hello Hui, This is also done quite easily in coot. Go to Extensions --> maps --> Transform map by LSQ model fit... Eric Eric T. Larson, PhD Biomolecular Structure Center Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 email: l

Re: [ccp4bb] buffers for crystallization

Hi Chandan, What do you mean by problem in crystallization? Too much precipitate, too many clear drops, ...? If you state the specific problems you are experiencing it is easier to make specific suggestions. By 388 buffers, do you mean that you have only tried 388 crystallization conditions or ~

Re: [ccp4bb] So many clashes

Hi Careina, Are you using riding hydrogens during refinement? The default in Refmac is to use hydrogens only if present in the input file - change this setting under the "Refinement Parameters" to "generate all hydrogens". This significantly helps with clashes. Also, did you check the quality

Re: [ccp4bb] Saxs reviews or books

Hello Rojan, This paper from last year may be a good place to start. It provides a nice "road map" through the small angle scattering experiment that a non-expert can follow while also describing the scattering data so that a non-expert can more critically evaluate it. I found it very informa

Re: [ccp4bb] Structure based and motif based sequence alignment

you are looking for, Eric __ Eric Larson, PhD Biomolecular Structure Center Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 On Fri, 26 Nov 2010, Muhammed bashir Khan wrote: | Dear All; | | I have structures of two protein one full-length

Re: [ccp4bb] Problem with finding of spots

Eric __ Eric Larson, PhD Biomolecular Structure Center Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 On Tue, 23 Nov 2010, Petr Kolenko wrote: | Dear colleagues, | | I am working on one dataset that is hard to process. The data are about 3A of resol

Re: [ccp4bb] Off Topic - Nickel Column

troublemaker and your protein of interest may not be completely denatured in the process making refolding less of a proble! m. good luck, Eric __ Eric Larson, PhD Biomolecular Structure Center Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 On

Re: [ccp4bb] how to optimize small rod-shaped crystals

interested in testing to see if they are salt, you can gather up several of them in your loop and shoot the group - this won't be useful for data collection if it turns out to be protein but will be sufficient to tell you if your crystals are salt. good luck, Eric __ Eric L

Re: [ccp4bb] **Possible spam**cryoprotetant for 35% Dioxane

uck, Eric __ Eric Larson, PhD Biomolecular Structure Center Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 On Wed, 20 Oct 2010, Jerry McCully wrote: | Dear All; | |     We just got some crystals from 35% (v/v) Dioxane. We are going to co

Re: [ccp4bb] Deposition of riding H: R-factor is overrated

then submit this cif file to the pdb, all the information is retained. Eric __ Eric Larson, PhD Biomolecular Structure Center Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 On Thu, 16 Sep 2010, Dr. Mark Mayer wrote: Ethan wrote I

Re: [ccp4bb] how to optimize crystallization of a membrane proteinf

-Tips-for-Membrane-Protein-Crystallization http://mcl1.ncifcrf.gov/nihxray/Tips-and-Tricks_Crystallization_Membrane_Protein.pdf good luck, Eric __ Eric Larson, PhD Biomolecular Structure Center Department of Biochemistry Box 357742 University of Washington Seattle, WA

Re: [ccp4bb] process data in R32

change the space group name from R32 to H32 in the space group box in the "Extra Information for MTZ File" section of the scalepack2mtz gui and all should then be fine. good luck, Eric __ Eric Larson, PhD Biomolecular Structure Center Department of Biochemistry

Re: [ccp4bb] Off-topic: hollow protein crystals

nd authors list." ______ Eric Larson, PhD MSGPP Consortium Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 On Wed, 2 Jun 2010, Nat Echols wrote: On Wed, Jun 2, 2010 at 12:07 PM, Andre Ambrosio wrote: We have recently obtained crystals from a small protein, an

Re: [ccp4bb] How to align a sequence to a know profile

? __ Eric Larson, PhD MSGPP Consortium Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 On Tue, 1 Jun 2010, Thomas Juettemann wrote: Does chainsaw not the opposite? Pruning a coordinate file based on non-conserved residues identified in a MSA? Yuan has a MSA of

Re: [ccp4bb] protein monitoring

Hi Yogi, You can see your peptide on a gel so why can't you "monitor" it by SDS-PAGE? A little time consuming, yes, but then you have the extra benefit of also seeing if there are contaminating proteins in your sample. good luck, Eric ______ Eric La

Re: [ccp4bb] Question about modeling SAM into a protein structure

restraint file for SAM (which can be obtained by uploading the SAM coordinates into the PRODRG server) into coot for this though. Good luck, Eric PS - SSM will not work for ligands, as you saw. __ Eric Larson, PhD MSGPP Consortium Department of Biochemistry Box 357742

Re: [ccp4bb] Displaying electron density in PYMOL

FFT CCP4i gui) and use these maps in pymol. And don't forget to add the .ccp4 extension to the map files for reading into pymol. hope that solves your problem. Eric ______ Eric Larson, PhD MSGPP Consortium Department of Biochemistry Box 357742 University of Washi

Re: [ccp4bb] Slow COOT with Fedora 12

C2 02 Good luck, Eric __ Eric Larson, PhD MSGPP Consortium Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 On Thu, 4 Feb 2010, Mark A. White wrote: Hello, Does anyone know why COOT is suddenly as slow as molasses on my Fedora 12 desktop? 

Re: [ccp4bb] Methylation of macromolecular complexes

Hi Peter, How do you know you have crystallized the complex? Perhaps MR is not working because your crystals only contain the small protein. good luck, Eric  Hi all,   I have a small complex, one component is 13 kDa with structure available and the other is 7 kDa, which could not be able t

Re: [ccp4bb] cracking crystal

A is the limit even in the absence of freezing. Good luck, Eric __ Eric Larson, PhD MSGPP Consortium Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 On Tue, 1 Sep 2009, Fengxia Liu wrote: Dear All,   Could you please help me solve this

Re: [ccp4bb] elbow and compound library

Hi Eric, You can try the Dundee prodrg server: http://davapc1.bioch.dundee.ac.uk/prodrg/ Good luck, Eric __ Eric Larson, PhD MSGPP Consortium Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 On Tue, 3 Mar 2009, Eric Liu wrote: Hi All

Re: [ccp4bb] difficult MAD dataset

measured. Scalepack would not show "absences" for the third axis at the end of the logfile if none of the supposed-to-be absent reflections were measured so it could mislead you. good luck, Eric __ Eric Larson, PhD MSGPP Consortium Department of Biochemistry

Re: [ccp4bb] Quick-soak

anomalous signal of bromide generally requires a synchrotron source. Good luck, Eric __ Eric Larson, PhD MSGPP Consortium Department of Biochemistry Box 357742 University of Washington Seattle, WA 98195 On Thu, 25 Sep 2008, amit sharma wrote: Dear CCP4bbers, I have