Re: [ccp4bb] monovalent cation binding sites

Hi Ed, WASP analyse water molecules in high-resolution protein structure to check if some of those could be metal ions. WASP could be run as a part of STAN server. STAN - the STructure ANalysis server from USF ( http://xray.bmc.uu.se/cgi-bin/gerard/rama_server.pl ) One could also identity

Re: [ccp4bb] ccp4 v6.4.0 cannot extract mtz

Yes Uli. I have the same issue, but not solve it yet :-( Partha On Mon, Dec 16, 2013 at 10:52 AM, ulrich.goh...@mdc-berlin.de ulrich.goh...@mdc-berlin.de wrote: Dear colleagues, Trying to run the latest version of ccp4 (6.4.0), say Refmac, I get the following error when I fill in the

Re: [ccp4bb] ctruncate error

Yes.., I too had similar problem with Ctruncate, and used older truncate to overcome the issue. Best Wishes, Partha On Thu, Jun 19, 2014 at 2:38 PM, jie liu jl1...@njms.rutgers.edu wrote: Hi I also encountered the same problem after recent updates (not the most recent one, but a couple of

Re: [ccp4bb] software to generate protein topology diagram like those available at PDBsum webserver

Dear All, Thanks to Herb, John, Simanshu, and Anu for link: http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/Generate.html to generate PDBsum like topology diagrams. Partha On Sun, Apr 15, 2012 at 8:08 PM, Parthasarathy Sampathkumar spart...@gmail.com wrote: Dear All, I would like

Re: [ccp4bb] software to generate protein topology diagram like those available at PDBsum webserver

Dear All, Guillaume Ponchel referred me to ProOrigami (which can be installed locally) to generate protein topology diagrams: http://munk.csse.unimelb.edu.au/pro-origami/ Thanks again. Best wishes, Partha On Mon, Apr 16, 2012 at 12:12 AM, Parthasarathy Sampathkumar spart...@gmail.com wrote

Re: [ccp4bb] Strange density in solvent channel and high Rfree

Hi Andrey, I am taking a risky guess: From your slide #2, it looks like a termini (unless this correspond to the beginning or end of disordered a loop) of the protein chain(s) is (are) extending toward(s) the solvent channel. Are the density features shown in slides #3,4, and 5 extend from this

[ccp4bb] Blotting paper for plasmid DNA

Dear All, Apologies for non-CCP4 / non-Crystallography question. I planning to spot plasmid DNA on a blotting paper for transport. I do not have any idea what type of blotting paper is used for this purpose. 1. what type of blotting/filter paper should be used? will any type of Whatman paper is

[ccp4bb] Summary of answers to question on “Blotting paper for plasmid DNA”.

08 December 2010 Dear All, Below is a summary of answers I obtained for my questions on “Blotting paper for plasmid DNA”. Thank you all very much for your quick response and thanks to CCP4BB. -Partha __ Hideaki Moriyama: How about FTA filter papers (Whatman).

Re: [ccp4bb] (off-topic) Measurement of channel pore dimensions

Dear Bert, You could try the program Hole from http://www.ncbi.nlm.nih.gov/pubmed/9195488 J Mol Graph. http://www.ncbi.nlm.nih.gov/pubmed/9195488 1996 Dec;14(6):354-60, 376. HOLE: a program for the analysis of the pore dimensions of ion channel structural models. Smart

Re: [ccp4bb] LESS MR pleae.. 1.95A, different phase

Hi Mike, Often, I generate independent freeR set (especially in cases where soak dataset is of different resolution (usually worse) compared to the native dataset and do following two things to get rid-off the bias: 1. add a noise to the coordinates (this can be done using PDBSET). 2. set the

Re: [ccp4bb] Water

Dear Uma, The water pictured in W12-1.jpg: could this be a potential metal ion? If you flip the side chain on Asn at 3.08Angstrom, then this has 3 or 4 coordination with oxygen atoms. So, provided your crystallization condition or buffer contains metal ion(s), you could attempt to see if it fits

Re: [ccp4bb] contaminant when overexpressing a GST tagged protein

Hi Maria, As mentioned by Tony, it could be a chaperonin. Having little of ATP (0.5mM or less) and Mg2+ (1mM) in lysis buffer might help. Good Luck, Partha 2012/3/22 SANCHEZ BARRENA, MARIA JOSE xmj...@iqfr.csic.es Dear all, I am trying to express a eukatiotic protein (E. coli codon

Re: [ccp4bb] Active aggregates?

Hi Toyoyuki, If your protein bind to metal ions you could try low concentration of chelating agents in the purification and storage buffer. Take a look at the following reference: Chelating Agents Stabilize the Monomeric State of the Zinc Binding Human Papillomavirus 16 E6 Oncoprotein Degenkolbe

Re: [ccp4bb] To set a crystal tray with protein and Trypsin protease.

Hi Jing, Methods to perform In site proteolysis are available in the following publications: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0005094 http://www.nature.com/nmeth/journal/v4/n12/abs/nmeth1118.html Good Luck, -Partha On Sun, Oct 11, 2009 at 5:13 PM,

Re: [ccp4bb] To set a crystal tray with protein and Trypsin protease.

It should be In situ and not 'In site'. Sorry for the typo error. -Partha On Sun, Oct 11, 2009 at 9:59 PM, Parthasarathy Sampathkumar spart...@gmail.com wrote: Hi Jing, Methods to perform In site proteolysis are available in the following publications: http://www.plosone.org/article/info

Re: [ccp4bb] Colored proteins :)

ThyX (also known as Flavin Dependent Thymidyalte Synthase, FDTS) is yellow due to bound FAD. -Partha On Tue, Oct 20, 2009 at 5:25 PM, Artem Evdokimov ar...@xtals.org wrote: Hello CCP4 folks! I have a quick question - could you suggest a few naturally intensely colored proteins? Colors based

[ccp4bb] Unit of electrostatic potential in PyMol

Dear All, I used PyMol to generate a qualitative Vacum Electrostatic surface (without APBS calculations). Positve and negative potentials are displayed in the range 56.3 to -56.3. What is the units of these numbers? Thank you, -Partha

[ccp4bb] Fwd: Unit of electrostatic potential in PyMol

-- Forwarded message -- From: Parthasarathy Sampathkumar spart...@gmail.com Date: Mon, Nov 2, 2009 at 3:41 PM Subject: Unit of electrostatic potential in PyMol To: CCP4BB@jiscmail.ac.uk Dear All, I used PyMol to generate a qualitative Vacum Electrostatic surface (without APBS

Re: [ccp4bb] FW: [ccp4]: TDS upon flashcooling

Hi Rafael, If it has not been already suggested: try DMSO (20% to 40%). In my limited experience I found that often DMSO works well for crystallization conditions with high-salt or high buffer component (like 1M D,L,-Malic acid). HTH, -Partha On Thu, Dec 17, 2009 at 1:39 PM, Meitian Wang

Re: [ccp4bb] crystal contacts

Dear Amit, You might want to take a look at NOXclass webserver: http://noxclass.bioinf.mpi-inf.mpg.de/help.php Relevant paper is available at: http://www.biomedcentral.com/1471-2105/7/27 Goold Luck, Partha Sampathkumar NYSGXRC On Mon, Feb 22, 2010 at 6:49 AM, amit sharma 3112a...@gmail.com

Re: [ccp4bb] An alternative to glycerol in keeping protein soluble?

Dear Serah, It is likely that glycerol stabilized your protein via binding as it was available in plenty during purification. Therefore, you could attempt to purify the mutant enzymes in the presence of substrate or ligands. I am not sure if this will work, but worth a try since you have

Re: [ccp4bb] Cryo-EM

Hi Faisal, There are some good video introduction available too: https://www.youtube.com/watch?v=nkGRhYv01ag HTH, Partha On Tue, May 19, 2015 at 3:01 AM, Faisal Tarique faisaltari...@gmail.com wrote: Hi everyone A bit off topic..but..I request you to please suggest me some good readings

Re: [ccp4bb] Unknown electron density blob

Hi Uma, It is risky to guess based on one-view of of the density from 2-dimensional images. What is the contour-level of 2mFo-DFc (blue) map displayed here?!! If 2mFo-DFc density is continuous from Arg, say at 0.8 sigma, then could it be an alternate conformation of the Arg side-chain. One could

Re: [ccp4bb] Recommendations for Robotic Crystal Screening Services

Hi Elizabeth, HWI, University of Buffalo, NY offers high-throughout crystallization screen. See the link for more information: http://hwi.buffalo.edu/science/high-throughput-crystallization-center/ Good Luck Partha On Fri, Apr 14, 2017 at 9:06 AM Elizabeth Diaz wrote:

Re: [ccp4bb] Substrate density visible in relatively active mutant

Hi Seema, Couple scenarios plausible (i) mutant is "super slow" compared to WT that crystallization was setup prior to any significant reaction and / or (ii) components, as well the pH, of crystallization condition made the reaction even more slower. Of course, if the reaction has partially

Re: [ccp4bb] Difficult purification with imac columns

Hi Narayanan, This doesn't address your question; may be you could go-around this problem by using a different purification tag., say like GST?!! Good Luck, Partha On Fri, Sep 15, 2017 at 7:54 AM Narayanan Ramasubbu < ramas...@sdm.rutgers.edu> wrote: > Hi. We are working on a periplasmic

Re: [ccp4bb] His-6 versus His-10 tag

Hi Herman, I worked on a kinase, where moved from 6-His in the literature to 8-His, and it didn't impact crystallization or diffraction (which around 3Angs). Good Luck Partha On Tue, Sep 19, 2017 at 9:43 AM Oganesyan, Vaheh wrote: > Hi Herman, > > > > I haven’t done

Re: [ccp4bb] CC(1/2) reference

Hi Nicola, Here are references for CC1/2; https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3457925/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4684713/ Best Wishes Partha On Tue, Aug 29, 2017 at 10:06 AM Nicola Evans wrote: > Hello all, I have heard at several CCP4

Re: [ccp4bb] new ContaMiner features

Hi All, To add, on couple of occasions I re-determined the structure of so-called "contaminants". Once, the structure of Secreted Ferritin (PDB 1Z6O) from crystals that were supposedly that of TNF ligand:receptor complex (proteins expressed in Tni cells), and in the second instant re-determined

Re: [ccp4bb] Non crystallography question

Hi Vandna, A typical approach would be to generate different models (experimental or otherwise, if X-ray structure it could be "completed" further by modeling missing loops / side-chains) of your sequence to calculate a SAXS profile, and then compare / fit those to experimental SAXS profile. Some

Re: [ccp4bb] Unknown electron density

Hi Vijay, Why there is no 2mFo-DFc (blue) feature on this mFo-DFc (green) map?!! Is the contour level for blue map set high?!! If there is no 2mFo-DFc density, should this be consider as noise?!! Hope this helps, Best Wishes, Partha On Thu, Oct 26, 2017 at 10:23 AM, Vijaykumar Pillalamarri <

[ccp4bb] Suggestions for deglycosylaiton enzymes

Dear All, I am in a situation, almost for the first time within my limited experience, that deglycosylation might be necessary to obtain crystal. So, I thought of tapping to vast experience of CCP4BBers, while I am searching literature. I have protein that has been expressed in HEK293 cells,

Re: [ccp4bb] Suggestions for deglycosylaiton enzymes

*Savvas Savvides* > >> VIB Center for Inflammation Research > >> Dept. Biochemistry & Microbiology, Ghent University > >> Technologiepark 927, B-9052 Ghent (Zwijnaarde), Belgium > >> +32 (0)472 928 519 (mobile) ; +32 9 331 36 60 (office) ; Skype: > savvas.sa

Re: [ccp4bb] Suggestions for deglycosylaiton enzymes

y > EndoH). Caveat emptor. > > Artem > > - Cosmic Cats approve of this message > > On Mon, Jul 16, 2018 at 2:53 PM, Parthasarathy Sampathkumar < > spart...@gmail.com> wrote: > >> Dear All, >> >> I am in a situation, almost for the first time within

Re: [ccp4bb] Suggestions for deglycosylaiton enzymes

gt; *Savvas Savvides* > VIB Center for Inflammation Research > Dept. Biochemistry & Microbiology, Ghent University > Technologiepark 927, B-9052 Ghent (Zwijnaarde), Belgium > +32 (0)472 928 519 (mobile) ; +32 9 331 36 60 (office) ; Skype: > savvas.savvides_skype > http://www

[ccp4bb] Job Posting: RA / SRA - Biophysics / Biochemistry Position at Surrozen

link. Thanks, Best Wishes, Partha __ Parthasarathy Sampathkumar PhD Senior Scientist, Surrozen Inc., 171 Oyster Point Blvd., Suite 400 South San Francisco, CA 94080 Email: par...@surrozen.com

Re: [ccp4bb] Help for Twin Refinement in Refmac5 / CCP4i2

Amplitudes in a single MTZ file :-) Thanks, Partha On Mon, Jan 25, 2021 at 9:47 PM Parthasarathy Sampathkumar < spart...@gmail.com> wrote: > Dear All, > > I have not had much experience in refining structure using data from > twinned crystals and has started using CCP4i2

[ccp4bb] Help for Twin Refinement in Refmac5 / CCP4i2

Dear All, I have not had much experience in refining structure using data from twinned crystals and has started using CCP4i2 very recently only. Here is a background: antigen-Fab crystal structure determined by MR first in P4(3)2(1)2 space group with 1-complex molecule in the asymmetric unit

[ccp4bb] Job Opportunity at Surrozen (SFO Bay Area): Research Associate/Senior Research Associate, Biochemistry and Biophysics

Dear All, I would like to bring to the attention of suitable candidates the following exciting job opportunities at Surrozen Inc, located in South San Francisco. Surrozen is a biotechnology company focused on discovering and developing novel regenerative medicines with a focus on unlocking the

Re: [ccp4bb] extra Fo-Fc density in two Cysteines

Hi Liliana, May be it would be good to know if this adduct was formed during crystallization or protein was modified prior to crystallization. One could consider performing a protease digestion, followed by LC-MS/MS to determine the molecular weight of the adduct and then work backwards to

Re: [ccp4bb] OT: design of a stable alpha-helical peptide

Hi Erik, A couple of things to consider: 1. Begin the N-terminus from helix "initiating" residues (i.e. one residue overhang might not be sufficient) 2. If not done already, add the 6-carboxy-fluorescein moiety at C-terminus of the peptide Good Luck, Partha On Wed, Mar 20, 2024 at 6:03 AM Erik