[ccp4bb] TCA or acetone precipitation of proteins

in the gel. Unfortunately, I already added protein dye with SDS and all. Cheers and thanks. Raji -- -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University

[ccp4bb] Crack-resistant tubes for centrifugation

without problems and I want to be able to spin down bacterial lysates without a mess. Any suggestions for tubes that have worked well in your experience? Thanks, Raji -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Vis

Re: [ccp4bb] Crack-resistant tubes for centrifugation

oes your 9000 rpm translate ? Perhaps that's the problem ? > 10 minutes @ 5000xg for pelleting cells is more than enough in my opinion. > > Jürgen > > On Jan 31, 2012, at 11:59 AM, Raji Edayathumangalam wrote: > > Hi Folks, > > Are you any favorite brands

[ccp4bb] THANK YOU: Crack-resistant tubes for centrifugation

stion and a bunch of folks suggested that breakage may have AS MUCH to do with centrifuge and shape-complementarity (understandably) as much as with the centrifuge tubes. Many thanks for your time and help. Go CCP4BB! Raji -- Forwarded message -- From: Raji Edayathumangalam Date

Re: [ccp4bb] [OFF-TOPIC] Site-Directed Mutagenesis [OFF-TOPIC]

7;s temperature > annealing (best is 62 oC) and I've increased the extension time up to 9 > min. Is there anything else I can try? > Any help is appreciated! > Regards. > Fred > > P.S.: Agilent's e-mail support is not working. > P.P.S.: this might not be of other

[ccp4bb] Fwd: HR3699, Research Works Act

ose-hr3699-research-works-act/vKMhCX9k -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University

[ccp4bb] Aggregated protein for crystallization

and set up some crystal trays (after perhaps testing by CD). So I'd like to hear from folks who have been successful in solving structures from aggregates when many many known and tested optimization methods still leave one with aggregated protein. Thanks. Raji -- Raji Edayathumangalam Instr

[ccp4bb] Human multi-pass integral membrane protein crystal structures

atisfy all following criteria: "human + multi-pass + alpha-helical + integral membrane protein." If anyone can provide the answer, that would be very helpful. I need this information for a fellowship application. Thanks much. Raji -- Raji Edayathumangalam Instructor in Neurology, Ha

Re: [ccp4bb] weird--No protein expression using pET30a

; the soluble fraction or as inclusion bodies. > > Could anyone give some instruction? > >Thanks a lot and have a nice weekend, > > Jerry > -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University

Re: [ccp4bb] how to Collecting Data from Long Unit Cell Axes ?

index .we think it is because that > there > > is a long unit cell axes. so is there any method to solve this problem? > > > > best wishes. > > > > 2011-04-05 > > ____ > > dengzq1987 > > > > -- > *

Re: [ccp4bb] immobilized DNA resin

ve a tag in this case... > > Thanks a lot, > Alex > -- --- Raji Edayathumangalam Research Fellow in Neurology, Harvard Medical School Postdoctoral Fellow, Center for Neurologic Diseases, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University

[ccp4bb] Potential Space Group Issue

tors can relate a p212121 cell to a p21 cell with almost identical unit cell parameters as that of the p212121 cell and leave all systematic absences intact? Thanks much. Raji --- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and W

Re: [ccp4bb] Potential Space Group Issue

Oops sorry for the slippery fingers. I meant h00, 0k0 and 00l in my original email and NOT "00h, 00k, 00l". Note the correction especially if you are a first-year graduate student trying to learn stuff from these emails :) Raji On Thu, Jul 7, 2011 at 11:30 PM, Raji Edayathumang

Re: [ccp4bb] Pymol question

ellow, (HISA and elem S) > set stick_radius=0.20, HISA > #hide everything, HISA > > > -- > Dr. Christopher Browning > Post-Doctor to Prof. Petr Leiman > EPFL > BSP-416 > 1015 Lausanne > Switzerland > Tel: 0041 (0) 02 16 93 04 40 > -- -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University

[ccp4bb] Coot "File Save Coordinates"

at just happened now! Haven't upgraded Coot or anything. Am using Coot 0.6.2-pre-1 (revision 3468) [with guile 1.8.7 embedded] [with python 2.7.1 embedded]. Help? Thanks. Raji -- ------ Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Bri

Re: [ccp4bb] Coot "File Save Coordinates"

:) Raji On Mon, Aug 15, 2011 at 3:56 PM, Bosch, Juergen wrote: > Have you moved your primary window away ? I mean just in case the pop up > window opened behind the actual scene window. > > Jürgen > > On Aug 15, 2011, at 3:54 PM, Raji Edayathumangalam wrote: > > Hi Fo

Re: [ccp4bb] Coot "File Save Coordinates"

from my iPhone > > On 15 Aug 2011, at 21:25, "Raji Edayathumangalam" > wrote: > > Thanks Mischa and Juergen. That was probably my most ridiculous post to > the CCP4BB!! I found the pop-up dialog box hiding behind all my zillion > windows. Now why the pop-up window would n

Re: [ccp4bb] Expression of large proteins in E. coli

. Try Studier's autoinduction protocol 5. Try expression with chaperone kit, trigger factor (Takara) 6. You don't mention whether the protein is human etc., but you may have to move to yeast or insect cells, in the worst case. DISCLAIMER: I am not paid by Takara to mention their kit. Good luc

Re: [ccp4bb] Reg Protein purification

(21):4624-8 It is a great method when many others fail to efficiently remove DNA. Hope that helps. Raji --- Raji Edayathumangalam Joint Research Fellow Harvard Medical School/ Brigham and Women's Hospital Brandeis University On Mar 6, 2010, at 7:23 AM, Sivaraman Padavattan

[ccp4bb] Symposium & Celebration of Greg Petsko and Dagmar Ringe

-Ringe Lab --- Raji Edayathumangalam Joint Research Fellow Harvard Medical School/ Brigham and Women's Hospital Brandeis University

[ccp4bb] Petsko-Ringe Symposium on June 18-19, 2010

posium2010/ Please post your congratulatory messages for Greg Petsko and Dagmar Ringe on our online Message Board at: http://prsymposium2010.blogspot.com/2010/05/celebration-of-dynamic-duo.html With Warm Regards, Members of the Petsko-Ringe Lab --- Raji Edayathumangalam Joint Resea

Re: [ccp4bb] Elspeth Garman's husband

My deepest and heartfelt condolences to Elspeth and her family at this very difficult time. May his soul rest in peace. Raji --- Raji Edayathumangalam Joint Research Fellow Harvard Medical School/ Brigham and Women's Hospital Brandeis University On Jul 3, 2010, at 6:28 AM,

[ccp4bb] Protein melting temperatures

. Please could you share some examples. Many thanks. Raji --- Raji Edayathumangalam Joint Research Fellow Harvard Medical School/ Brigham and Women's Hospital Brandeis University

Re: Writing out common waters from multiple files

[mailto:[EMAIL PROTECTED] On Behalf Of Raji Edayathumangalam Sent: Friday, January 19, 2007 11:17 AM To: [EMAIL PROTECTED] Subject: Writing out common waters from multiple files Hi Everyone, I think there might be a very simple way to do this but I don't know the easy way out. I

Writing out common waters from multiple files

y to write out the common waters? Thanks for your suggestion. Raji -- Raji Edayathumangalam Postdoctoral Fellow The Rockefeller University Box 224. 1230 York Avenue New York, NY 10021

Re: [ccp4bb] mtz to hkl conversion

Hi Vineet, Try using TEXTAL for model building at your resolution. I heard that this is optimized for 2.8Ang or so resolution. For MTZ to HKL with HL's intact, read the Tutorial section on the CNS webpage with example scripts. Go to section 'Data Conversion' and look at 'Converting a CCP4 MTZ ref

Re: [ccp4bb] protease cleavage sites

PreScission protease worked great for all proteins and constructs I tested and purified. The cleavage is very specific and works in a decent range of salt conditions as well. Sometimes, you may have to optimize digestion time and enzyme/protein ratio to get 100% or maximum-possible cleavage. R

Re: [ccp4bb] Multiple nucleation

I've found that crystallization in sitting drops under oil dramatically reduces the no. of nucleation events and increases the overall crystal size. Now, if the increased crystal size helps improve diffraction is something to be tested. Among the many other suggestions... Raji -Includ

[ccp4bb] Ecoli protein staining with AntiHis?

Hi Everyone, I see a band that lights up in my anti-His Western blots. While I investigate what else the band might be (truncated protein etc.), does anyone know whether there is an E. coli protein that migrates ~ 30-40kDa (SDS-PAGE), which binds to anti-His antibodies? Thanks. Raji

Re: [ccp4bb] parameter and topology files in CNS

Hi Jae, Try resetting the MAXJNT parameter (increase the set value). I had problems with MAXA and other parameters and I suspect your problem has the same solution. You might need root access for the same. Also, make sure that you are specifically asking to read the topology and parameter file

Re: [ccp4bb] heavyatom soaking problem

In one case, co-crystallization with heavy atom (Au) was one of the few approaches that worked. Not sure if you've also tried short soaks with Hg, Pt, Au. Helped for one of my former colleagues while long soaks messed things up. You have not mentioned if Selenomethionine derivatization has bee

Re: [ccp4bb] How to remove nucleic acid contamination for crystallizing zinc finger protein

Yes, I have seen colleagues get rid of tons of DNA contamination in bacterial RNA polymerase preps by PolyminP (PEI) precipitation. Seemed like it was the only method that worked (among several tried) to remove all the non-specific DNA. Worked very well. As painful as it appeared, PEI precipit

Re: [ccp4bb] Help with reducing crystal mosaicity

Hi Mary, What final percent MPD do you have prior to flashcooling? Karolin Luger (and perhaps others) found that the final percent MPD had a significant effect on crystal mosaicity and final diffraction limit for nucleosome crystals. For example, if the crystals are left in mother liquor con

Re: [ccp4bb] Help with reducing crystal mosaicity

You can also try to use the micromount loops (look like ink-pen nibs) sold by Mitegen. They are a much easier alternative to capillary mounts; they are easy to handle and work well for room temperature data collection. Good luck. Raji -Included Message-- >At the risk of sound

Re: [ccp4bb] Program to 'visualize' the reciprocal space ?

I am often receiving only responses to the original queries posted on CCP4BB but not the original query itself. They are not going to my spam box either. Has anyone else noticed the same? Thanks. Raji -Included Message-- >Many thanks to good people who have responded >to my mes

Re: [ccp4bb] Protein-DNA complex for crystallization

Hi Kumar, 1) While you contemplate other ideas, have you tried the following already? - microseeding or macroseeding with the tiny crystals you have? - crystallization using sitting drop vapour diffusion under oil? Often, one gets a burst of nucleation with several tiny crystals. Not sure if thi

Re: [ccp4bb] questions about CNS

Well, I guess you can mess with the "overall B-factor correction" in the anneal.inp and rigid.inp files and say, turn them off. NOT a good way to proceed. That is just to let you know where to find it. If you haven't already done so, do the following after the simulated annealing step. After

Re: [ccp4bb] High Wilson B

Hi Mike, To my limited understanding, it is hard to get an accurate Wilson estimate for data below 3Ang (am I right??!). To me, the B-factor you list doesn't sound bad although some folks might holler 'Bloody Murder' when I say so. I have a structure to 3.7Ang (I'd have liked higher resolution

Re: [ccp4bb] Crystallography short courses?

The Rapidata course held at Brookhaven every year is a five-day course precisely for what you are talking about. I benefited much from attending the course. Check the link: http://www.px.nsls.bnl.gov/courses/rr_course_2007/ Hope that helps. Raji -Included Message-- >I am lookin

Re: [ccp4bb] Strange diffraction images

Very dumb question perhaps: If there were two interpenetrating lattices of slightly different cell dimensions, would we not expect that the indexing program would leave out a lot of the spots as "unpredicted" or "uncovered"? Could someone clarify with respect to the diffraction pattern that has

Re: [ccp4bb] The importance of USING our validation tools

I would like to mention some other issues now that Ajees et al. has stirred all sorts of discussions. I hope I haven't opened Pandora's box. >From what I have learned around here, very often, there seems to be little >time allowed or allocated to actually learn--a bit beyond the surface--some of

Re: [ccp4bb] Molecular replacement

The answer to your question is called Phaser. Using Phaser, you can input multiple search models in one search routine to look for solutions. You should read the online manual and tutorials, if you are not already familiar with Phaser. You can also 'modify' or appropriately 'trim' your search

Re: [ccp4bb] alternate confirmations of residues

Hi Vineet, I am not sure that you are defining things as expected in the CNS documentation. If you haven't already, please read the CNS FAQ page with description of how to define and include alternate side-chains for refinement. In any case, I summarise the steps for you- 1. Run generate.inp wi

Re: [ccp4bb] Ni-NTA purifications contaminated with E coli Glucosamine-fructose-6-phosphate aminotransferase

How about trying two opposite ion-exchange columns??!! Namely, monitoring co-elution behaviour on anion exchange and cation exchange. For example, we have a case where the contaminant and protein of interest will both bind and co-elute from monoQ but only protein of interest or contaminant (can'

Re: [ccp4bb] problem with 'generate' (cns_solve)

Hi Mareike, Did you also use Coot to fit the small molecule into the structure? If so, there might be some glitch at the stage of writing out the remodeled ligand... Do the coordinates for the small molecule look different within the input and output pdb files for the ligand when you look at

Re: [ccp4bb] protein expression problem

I wholly agree with the below. I am not sure how well E.coli can correctly fold snaky misfolded/unfolded protein that are chaperoned by folded tags! Not to rule out that tags do it sometimes... "Folded by association" for insoluble proteins has often not worked well for me. Sometimes, when it '

Re: [ccp4bb] Web site GOOD, Attachment BAD (was: salt sensitive complex)

Can the CCP4BB provide something like a website to upload pictures and then have the BB-ers just post the link in their email. Please! These attachments are clogging my inbox... Thanks much. Raji -Included Message-- >Date: 31-jan-2008 03:58:44 -0500 >From: "Frank von Delft" <[

[ccp4bb] Solved: PDB file column-cut-paste issues

Thanks everyone for all your suggestions. What's the issue? Each residue has one CSV value (per residue value) and the PDB line contains many lines of B-values per residue. This would leave us with no easy one-to-one line correlation between the B-value column and the CSV column. From what I u

[ccp4bb] PDB file column-cut-paste issues

Hi People, I post this on behalf of my colleague. My colleague has a file containing chemical-shift values for the 150 aa in his structure. He also has the PDB file for the crystal structure. Now, he would like to replace the B-factor column with the CS values to make some figures. It would be

Re: [ccp4bb] Solved: PDB file column-cut-paste issues

Ooh..la la! Where were you 12 hrs ago when we were suffering brain damage! Cheers! Raji PS: Thanks! >Oh dear - too late :-(. You can do it in Coot too! (The solution is on >the Coot Wiki now) > >http://xanana.ucsc.edu/~wgscott/xtal/wiki/index.php/Coot#Example_Scheme_Script_7:_Applying_arbitrar

Re: [ccp4bb] secondary structure restraints

Hi Sean, Not an answer to your question but have you looked into model building with TEXTAL? I am not sure about 3.6Ang resolution data but it might be worth looking into. Raji -Included Message-- >Date: 13-feb-2008 16:54:33 -0500 >From: "Sean Johnson" <[EMAIL PROTECTED]> >T

Re: [ccp4bb] Tough Low-Res MR

Absolutely try Phaser! See Phaser documents for all the nifty combinations. Multiple molecules in MR model; break down molecule by domains etc etc. You can trim down side chains, make hybrid models and what not. All easy to get up and going through the GUI. Once the GUI drove me insane because

Re: [ccp4bb] Co-expression plasmids

I do use the Duet vectors extensively and they work just fine. I have trouble with my protein complex, but that is solely related to my proteins. My lab mate has used these vectors very successfully. I have been using pRSF-Duet and pETDuet1 more than pCDFDuet1 or pACYCDuet1 for no specific rea

Re: [ccp4bb] Co-expression plasmids

I thought only I was having trouble with cloning into pETDuet1. But just to add to what someone just said Yes, I had hell with trying to get one of my ~2kb fragments into pETDuet1 (5.4kb). Could be a combination of vector size and insert size.. Who knows! Sometimes, I do what Tasos says: Tra

[ccp4bb] Bacterial induction at 18C

Hi Folks, I am working with E. coli cells co-transformed with two plasmids and I find that my cells lyse following overnight inductions at 18C. I suspect (among many things) that Ampicillin+ Chloramphenicol+ Kanamycin in the medium may be the source of my woes. My colleagues have suggested grow

Re: [ccp4bb] Bacterial induction at 18C

Thanks to everyone for all your suggestions. I am growing the cultures as we speak and have increased the temp to 22C and plan to harvest in about 6-8 hrs. Thanks for the Q7 rule. I read it before but I couldn't remember exactly and a quick-and-dirty Google and Pubmed search did not bring it up

Re: [ccp4bb] sa_omit_map

To me, it seems that your syntax for chain and residue definitions is incorrect. See the 'Tutorial' section on the CNS website, which gives some very nice examples. For example, if you want to select chain K and residues 2 and 15, chain L and residues 1, 2, and 14, and so on, here's pne possib

Re: [ccp4bb] Two off-topic questions

hloy cow! taht msut be vrey crortcet idened ! rjai -Included Message-- >Date: 12-may-2008 14:15:03 -0400 >From: "Scapin, Giovanna" <[EMAIL PROTECTED]> >To: >Subject: Re: [ccp4bb] Two off-topic questions > >Hello there, I don't usually do this, but the missing letter reminded me

Re: [ccp4bb] DLS and SEC-LS facility

The facility at Yale University is very good. http://keck.med.yale.edu/biophysics/ Don't know about current wait times. I got excellent service. Good luck! Raji -Included Message-- >Date: 1-jun-2008 22:48:00 -0400 >From: "Michael Colaneri" <[EMAIL PROTECTED]> >To: >Subject:

Re: [ccp4bb] Anion binding sites in proteins

Hi Albert, Please refer to the following paper (and references therein) for a description of the four chloride located in the nucleosome structure.. 1: Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ. Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a

Re: [ccp4bb] regarding cloning

Hi Vijay, I have heard of TOPO-TA cloning. Not sure what T/A cloning is. I have a couple to check based on your description: 1) Do you CIP-treat your vector? If not, that might be a step to add. Also, you could include a 'vector only' transformation control to determine how many colonies are ob

Re: [ccp4bb] Troubleshooting protein purification cation IEX

Hi, Many things can lead to your observation. Please outline all steps of your purification procedure as it is not clear what is done before and after the Ion Exchange steps. I am not sure if IEF in your emails refers to Isoelectric focusing, as the acronym is usually used?? Couple of s

[ccp4bb] Phylogenetic analysis??

Hi Everyone, Could someone please tell me how to display the evolutionary/ phylogenetic tree of the homologs of my protein of interest. When I perform a PSI-BLAST search for my protein, I receive about 130 top hits for homologs. The NCBI or EBI tools that I've laid my hands on seem to only

[ccp4bb] Thanks: Phylogenetic analysis??

Thanks to all who responded. I was able to somewhat generate the info I needed. Raji

[ccp4bb] Summary: Phylogenetic analysis??

Hi Everyone, Since some folks have been asking me, below is my original question and here's a summary of the responses. I had already googled a bunch of these links before posting to ccp4bb but still lots of useful info in responses, as always! Raji DNAStar will do t

[ccp4bb] Pymol: Zoom without Mouse

How does one zoom into the molecule in Pymol without a mouse and with just the Mac trackpad and keyboard? Have tried to look it up in the manual and on the web. No success finding it yet; I did figure it out once before but can't redo it now for the life of me. Need to know how to do it wit

[ccp4bb] Thanks: Pymol: Zoom without Mouse

lickpad. 3. With the clickpad depressed, remove ring finger from pad and move your middle finger. You should be zooming. 4. Practice steps 1-3 over and over. 5. Buy a mouse. From: Raji Edayathumangalam <[EMAIL PROTECTED]> Reply-To: Raji Edayathumangalam <[EMAIL PROTECTED]>

[ccp4bb] Quikchange cloning: Insert length

Hi Folks, Sorry for the non-xtallo posting. I am curious to hear what is the longest insert anyone has cloned using a modification of the Quikchange cloning strategy. Basically, ligation-independent cloning by strapping on homologous regions of the vector onto the primers which also genera

Re: [ccp4bb] Off topic: Mammalian gene expression in E. coli

Did you not know that the CCP4BB-- even when all else appears to be melting down-- is Nature's sustained gift to humankind? Did you also not know that astronauts, astronomers, astrologers, artists, musicians, sportsmen, scientists, politicians, writers and everyone else subscribes to the bo

Re: [ccp4bb] Off topic: Mammalian gene expression in E. coli

Some thoughts about SUMO tags and fusion tags in general. Fusion tags also follow the "Garbage In, Garbage Out" philosophy. Yes, if for many of the reasons already hashed out extensively on CCP4BB, one is dealing with lack of expression or miniscule expression, often tagging the protein wit

Re: [ccp4bb] how to show double conformation in PyMol

Although there are more elegant ways to do the same, an easy way is to simply write out either just the loop region or the entire molecule containing the second conformation into a second PDB file and to simply read in the two PDB files as two separate molecules in PyMol. Raji On Feb 26

[ccp4bb] Eukaryotic Membrane Proteins

Hello Folks, My enquiry pertains to membrane proteins. If you have been able to successfully express a eukaryotic integral MEMBRANE protein in E. coli or know of such a case, would you please provide some details. Thanks. Raji

Re: [ccp4bb] Lowest resolution you can do MR with

If you look at the molecular replacement search parameters, you will find that the rotational and translational searches can be done at 4 Angstrom or lower values assigned to the 'high resolution' values. So the real worry in your case, in all likelihood, is not whether MR will work for 3.

[ccp4bb] Link two proteins into one polypeptide

Hi People, Could anyone point me to successful examples for two unrelated proteins that have been stitched together into one single polypeptide chain with flexible amino acids to create a functional chimera that was subsequently crystallized. I've looked up a few. I am particularly intere

[ccp4bb] SUMMARY (Link two proteins into one polypeptide)

Hi Folks, First of all, thanks to all the people that responded. Many of you asked me for a summary of responses. So, below is a concise summary containing mainly the references that people pointed me to: Cheers, Raji --- ORIGINAL POST: Hi People, Could any

Re: [ccp4bb] problem in transformation of pqe 30 clone

One thing to check is whether there is too much DNA in the transformation reaction. This is sometimes a reason for failed transformations, be it DNA from regular minipreps, PCR DNA or ligation reactions etc. Raji On May 4, 2009, at 3:57 PM, b...@freesurf.fr wrote: This story is rather puz

Re: [ccp4bb] desktop models

I've seen some very pretty 3D models in optical crystal glass made and sold by http://www.luminorum.com/ Cheers, Raji Disclaimer: I have nothing to do with this company. On May 5, 2009, at 2:41 PM, Christopher Rife wrote: Hi, I am looking to have a model produced from a PDB, i.e. somethin

Re: [ccp4bb] How to express a >95KD FAD protein

Hi Wei Yong, Sounds like a tricky situation. A couple of things come to mind: 1) Have you tried expression from a synthetic gene? Sometimes the mRNA is unstable and improving mRNA stability through optimization (synthetic gene) helps. 2) Are you able to look at either human isoforms or ortho

Re: [ccp4bb] problems of co-crystallization of protein-DNA complex

that helps. Raji --- Raji Edayathumangalam Joint Research Fellow Brigham and Women's Hospital/ Harvard Medical School Brandeis University On Aug 13, 2009, at 12:56 AM, ruheng wrote: Dear CCP4bbers, I am now working on a DNA binding protein and the purity of the protein is quite

Re: [ccp4bb] Weird expression behavior

Hi Ezra and others, Just thought I'd let you know that I have noticed that one or two of those E. coli proteins that love to bind Ni-affinity resin do not bind to Cobalt resin. Of course, there is always a price to pay (for the Co resin, in this case) :)! Cheers, Raji ---

Re: [ccp4bb] Nobel prize for chemistry 2009

This makes for a great week for crystallography along with the 2009 Nobel Prize in Physics awarded "for the invention of an imaging semiconductor circuit – the CCD sensor"!! Raji --- Raji Edayathumangalam Joint Research Fellow Brigham and Women's Hospital/ Harvard

Re: [ccp4bb] align DNA structures

Hi Mike, By 'align', if you mean superimposition, lsqman will do the job. Raji --- Raji Edayathumangalam Joint Research Fellow Brigham and Women's Hospital/ Harvard Medical School Brandeis University On Oct 21, 2009, at 11:06 AM, Mike England wrote: Hi all,

Re: [ccp4bb] off topic

oes anybody know if ethidium bromide binds to > poly(dI-dC)? > Careina > -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University

[ccp4bb] Detergent solubilization step (membrane proteins)

lubilize may be misfolded, just cut my losses and grow tons more bacterial cultures. Many thanks for sharing your successes and heartaches on this matter! Raji -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visit

Re: [ccp4bb] Detergent solubilization step (membrane proteins)

mount of total detergent and will definitely try that. Jim, thanks for suggesting Elugent. Never heard about it before so great to know. Many thanks and cheers, Raji On Wed, Jul 10, 2013 at 5:23 PM, Raji Edayathumangalam wrote: > Dear BBers, > > Sorry for the non-ccp4 post. > &

[ccp4bb] Concentrating purified membrane protein

ow to concentrate my low MW protein without concentrating the DDM? Many thanks. Raji -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University

Re: [ccp4bb] Concentrating purified membrane protein

otein. Just occurred to me that I could simply dialyze out the imidazole after the affinity step. Thanks again! Raji On Sat, Jul 13, 2013 at 8:47 PM, Raji Edayathumangalam wrote: > Hi Folks, > > Sorry for the non-ccp4 post. > > I have purified an 18kDa membrane protein and wan

[ccp4bb] Off-topic post: Inverted DNA repeats vs direct repeats

thus far haven't yielded much more than what I've shared above. Many thanks! Raji -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University

Re: [ccp4bb] Off topic: Gel filtration of membrane protein

cult. the > > Has anyone faced a similar proble? Or is there a way that buffers with > detergents are supposed to be made? Or are there any particular coloumns > meant for such runs. > > Thanks > > -- > Nazia Nasir > PhD Scholar > Protein Crystallography Lab > Natio

Re: [ccp4bb] Xtal formed during purification

d not diffract at all but after he optimized his buffer conditions to prevent those non-diffracting crystals and screened for optimal crystallization conditions, he got hits from the screens that diffracted to 1.8 Ang. Cheers and good luck! Raji -- Raji Edayathumangalam Instructor in Neurology, Ha

[ccp4bb] What kind of reflection data to deposit to PDB

ght be the best approach. Many thanks and cheers, Raji -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University

Re: [ccp4bb] About molecular replacement

y molecular replacement failed thought > over-all fold is same?. > > > -- > *Dhanasekaran Varudharasu* > Post-Doctoral Fellow > Department of Oral Biology > Rutgers school of Dental Medicine > Rutgers Biomedical and Health Sciences > Newark, NJ 07103 > USA > >

Re: [ccp4bb] PDB structure validation

*** > > ** ** > > -- > > Randy J. Read > > Department of Haematology, University of Cambridge > > Cambridge Institute for Medical Research Tel: + 44 1223 336500 > > Wellcome Trust/MRC Building Fax: + 44 1223 336827 &

Re: [ccp4bb] Membrane fractionation

ultracentrifugation for one of my membrane proteins because the pellet from the second round is invisible and the protein is pure and functional after purification. Good luck! Raji -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women

Re: [ccp4bb] A question on protein-DNA complex crystallization

rett wrote: > Dear All, > > I am now working on the crystallization of a complex of protein-16 bp DNA > by co-crystallization. In the screening very small needle-like crystal > occurs. If not salt crystal, is there a method to know it is not the > crystal of the DN

[ccp4bb] Determining concentration of membrane protein

would like to know what other folks working on membrane proteins are doing. Thanks very much. Raji -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University

Re: [ccp4bb] Sister CCPs

ntific impact that a global and diverse group of researchers from various interrelated disciplines can have on one other. Many thanks to the amazing members of the ccp4bb! Raji -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's H

Re: [ccp4bb] Determining concentration of membrane protein

nably pure. > > Cheers, > > ___ > Roger S. Rowlett > Gordon & Dorothy Kline Professor > Department of Chemistry > Colgate University > 13 Oak Drive > Hamilton, NY 13346 > > tel: (315)-228-7245 > ofc: (315)-228-7395 &g

Re: [ccp4bb] Determining concentration of membrane protein

t;> Cheers, >> >> ___ >> Roger S. Rowlett >> Gordon & Dorothy Kline Professor >> Department of Chemistry >> Colgate University >> 13 Oak Drive >> Hamilton, NY 13346 >> >> tel: (315)-228-7245 >> of

[ccp4bb] Trouble cleaving SUMO tag off of membrane protein

membrane protein without a SUMO tag and the expression is abysmal. Thanks very much for your time and suggestions! Raji -- Raji Edayathumangalam Instructor in Neurology, Harvard Medical School Research Associate, Brigham and Women's Hospital Visiting Research Scholar, Brandeis University

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