Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB -- N-glycans are now separate chains if more than one residue

; >>> In generally I like the treatment of carbohydrates now as branched >>> polymers. I didn't realise there was an exception. It makes sense for >>> unlinked carbohydrate ligands, but not for N- or O-glycosylation sites as >>> these might change during mode

Re: [ccp4bb] Coming July 29: Improved Carbohydrate Data at the PDB -- N-glycans are now separate chains if more than one residue

Hi all, I was confused when I saw mysterious new glycan chains emerging during PDB deposition and spent quite some time trying to find out what was wrong with my coordinates. Then it occurred to me that a lot of recent structures also had tens of N-glycan chains. Finally I realized that this

Re: [ccp4bb] protein expression in human cells

Hi all, If anybody is interested in non-viral stable expression, we have a piggybac-based, doxycycline-inducible system. It is the reference 40 in the lentiviral paper that Tomas directed to. We’d be happy to distribute the plasmids. Zhijie > On Jan 25, 2020, at 3:26 AM, Tomas Malinauskas

Re: [ccp4bb] Generating symmetry mates using python

Hi Orly, REMARK 290 should be the easiest way for generating symmetry mates. Other routes are just going to give you the same results. As Jonathan already pointed out, the symm ops do not garantee that the symm copies are close to each other. The most simple-minded solution to this problem

Re: [ccp4bb] microscope camera

There are CCD modules (often come with lenses, which can be taken off) sold on Amazon, eBay or aliexpress (or even better, Taobao) costing USD 20-40. These modules should be capable of taking full HD movies (MPEG or YUV2 compressed) at 30fps these days. Some may allow 120fps@640x480 or promise

Re: [ccp4bb] More LCF archaeology (unit cell parameters this time).

Hi Jonathan, We discussed about VAX floats last November: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1811=CCP4BB=D=63307 https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1811=CCP4BB=D=65015 https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1811=CCP4BB=D=65531 In short, the factor of 4

Re: [ccp4bb] beryllium chloride

Sometime ago when I was watching a Youtube video on magnetron I learnt that at least at at certain point of time the antenna port of the magnetron was sealed using beryllium oxide ceramic(probably for its high thermal conductivity). The video maker warned that this ceramic was extremely

Re: [ccp4bb] map rotation

Hi Jan, As Paul pointed out, you can use COOT to accomplish what you want. Particularly you can take a look at the following functions in section 6 of the COOT manual (these are in scheme): (set-map-mask-atom-radius radius) (mask-map-by-molecule imol-map imol-model invert-mask?)

Re: [ccp4bb] map rotation

Hi Jan, Sorry I didn't read your script earlier. If you change your mapmask command to output a map instead of a mask it may work for you: mapmask \ mapin 2mol_2mFo-DFc.map \ xyzin 2mol_B.pdb \ MAPOUT B.map \ << eof border 2 eof then you should get a map that covers the whole molecule

Re: [ccp4bb] map rotation

Hi Jan, I guess you might be seeing a flat cut surface on the maps? It might be that the map’s extent is not covering the protein molecule, which is usually the case. When you rotate crystallographic maps it is usually no longer possible to take adjacent unit cells to continue the density on

Re: [ccp4bb] TEV Protease in low reducing agent?

Hi Nicola, 0.1-1mM Cysteine, GSH or BME will work fine. You can also try using very fresh TEV without reducing reagent (or store it with BME and remove the reducing reagent by some column just before use). Depending on how concentrated the stock is, diluting it 3-5x could also sufficiently

Re: [ccp4bb] AW: [EXTERNAL] [ccp4bb] Is there any alternative to siliconized glass coverslips for crystallization?

Hi, I believe that one can put a 50-100uL drop of fresh SigmaCote (in a tube cap) with the glass pieces (surface well exposed), sealed in a dedicated (because the container will be coated too) container (air-tight lunch boxes). After a while the SigmaCote vapor should react with the glass

Re: [ccp4bb] Off topic question

PCA? On Jan 3, 2019, at 3:41 PM, Reza Khayat mailto:rkha...@ccny.cuny.edu>> wrote: ​Hi, Happy new year to all! A bit of an off topic question. Does anyone know of a method/program to extract the most distinct "n" (n>2) sequences from a sequence alignment? Thanks. Best wishes, Reza

Re: [ccp4bb] Non-specific disulfides in a secreted protein

Yes, we have also seen some indication that overdriving the expression can cause problems. In our cases this may range from bad aggregations or loss of expression. Since we use induced stable cells we simply reduced the doxycyline levels. Zhijie > On Dec 14, 2018, at 1:13 PM,

Re: [ccp4bb] Non-specific disulfides in a secreted protein

Hi Tomas, Some thoughts: a) I guess the thermodynamic drive for all part of this small ectodomain to fold into a single lowest energy conformation is not very strong. The cells can’t know that the little artificial domain is supposed to be a monomer when the oligomers are also sufficiently

Re: [ccp4bb] VERY old mtz file..

ible for MTZ files (not maps because we can put anything into MRC/ccp4 map). Yes, the idea is to try all possibilities until we can recover miller indices that look normal. Zhijie From: Nicholas Devenish Sent: Wednesday, November 14, 2018 9:29 AM To: Zh

Re: [ccp4bb] VERY old mtz file..

it as half bytes! Zhijie From: Nicholas Devenish Sent: Wednesday, November 14, 2018 8:54 AM To: Zhijie Li Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] VERY old mtz file.. Hi Zhijie, Looks like we both had the same thoughts! On Wed, Nov 14, 2018 at 1:19 PM

Re: [ccp4bb] VERY old mtz file..

Hi Nick, Our LE outputs are exactly the same. Rmerge=100.0%! Zhijie From: CCP4 bulletin board on behalf of Nicholas Devenish Sent: Wednesday, November 14, 2018 7:15 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] VERY old mtz file.. Hi

Re: [ccp4bb] VERY old mtz file..

It's also said here, at the end of file : https://www.cs.auckland.ac.nz/~patrice/210LN/DR4.pdf "add 1 to the left, with the binary point" 0.1. From: CCP4 bulletin board on behalf of Zhijie Li Sent: Tuesday, November 13, 2018 7:43 PM

Re: [ccp4bb] VERY old mtz file..

To: Zhijie Li Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] VERY old mtz file.. Hi Zhijie It's definitely a factor 4. The code is in subroutine QTIEEE in the Fortran source I mentioned previously at this line: See line: A(I)=((A(I)+SIGN(2,A(I)))/4.AND..NOT.MNAN).OR.MDN2 If you prefer it in C

Re: [ccp4bb] VERY old mtz file..

Hi Ethan, Thanks for the information. My guess is that in MTZ only F-float is expected, because it is the only 32bit form? Zhijie > On Nov 13, 2018, at 3:44 PM, Ethan A Merritt wrote: > >> On Tuesday, November 13, 2018 11:51:55 AM PST Zhijie Li wrote: >> If somebod

Re: [ccp4bb] VERY old mtz file..

with Convex, Cray, Fujitsu, or VAX reals/strings? > I’d be interested to see what those files actually look(ed) like. > > // Best wishes; Johan > >> On Nov 9, 2018, at 18:38, Zhijie Li wrote: >> >> Hi all, >> >> On linux there are a few good GUI HE

Re: [ccp4bb] VERY old mtz file..

Hi all, On linux there are a few good GUI HEX editors. Here I’d like to recommend BLESS, which conveniently displays all possible numerical interpretations of the four bytes under cursor. It also allows the user to switch between big endian or little endian through a checkbox. Unfortunately

Re: [ccp4bb] [Offtopic] Protein stain in Coomassie Blue dyes

Hi, At high concentration (1-2%) the published saturating SDS:protein binding ratio is about 1.4:1 by weight, that is roughly one SDS molecule per two aa on average. It is dense but not that dense to prevent any further interaction. More importantly, as a quite hydrophilic small molecule SDS

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Electron density maps for Cryo-EM structures.

Hi Kevin, a) If your goal is merely to display EM maps, then UCSF Chimera, COOT, pymol, etc. should all do. The EM maps are saved in the MRC format (.mrc or .mrcs). Despite a different extension and some minor differences in the headers, the MRC format is essentially the same format as our

Re: [ccp4bb] Off topic: denaturing urea gels

Smith: One should expect to see ladders each separated by 1 nt in such cases. Mohammed: My suggestions: 1) running at 70V seems low. I do not see a reason for not using higher voltages. 200Vx45min should be OK. IT is better to not let the BPB front run out of the gel - so that you know whether

Re: [ccp4bb] Best method for carbohydrate refinement

Hi Gustavo, If I understand you correctly, you are concerned about N-glycans (N-glycosylation) on your proteins. According to your description, you have 2 protein molecules in each ASU, each bearing one potential N-glycan site. Then there are only two N-glycan sites you need to build for

Re: [ccp4bb] NCS axis detrmination

Hi Vandna, Assuming you have two copies, chain A and B. In UCSF chimera: 1) open two copies of the pdb (model #0 and #1) 2) in command line, type: match #1:.B@CA #0:.A@CA showMatrix true Besides moving model #1 chain B to model #0 chain A, the match command also outputs the

Re: [ccp4bb] off topic: high resolution animation in chimera

Update: to get transparent background in GIF: Chimera command file (now saves PNG with transparent background by adding "set bgTransparency"): close all;open #0 ABCD.pdb; set bgTransparency; ~disp;ribbon :.a; movie record directory "D:\mov_temp\" format png pattern frame_*; turn y 1

Re: [ccp4bb] off topic: high resolution animation in chimera

Hi Shanti, To get more control, you can use Chimera to generate the frames, save each of them as PNG, then process and re-assemble the frames in photoshop to make GIFs. The command line toolbox Imagemagick is also a great way for making GIFs (shown below). Step1 generating the frames

Re: [ccp4bb] Glycoprotein expression question

Hi Bernhard, I guess you knew all these and is really asking for people's experience, but please excuse me to start from the theory: N-glycans in eukaryotes are known to be involved in glycoprotein folding in the ER. They allow the nascent protein to get into the calnexin/calreticulin cycle

Re: [ccp4bb] Coot and Pymol through SSH by Xming/PUTTY on a windows client?

Hi Chen, I followed instructions on this page and it seems to be working: http://www.geo.mtu.edu/geoschem/docs/putty_install.html One thing I think is worth mentioning is that in Putty-connection-SSH-X11, I put localhost:0.0 instead of 10.0, as for putty itself, it is requesting from Xming

Re: [ccp4bb] Hi

Hi Vijay, I am not sure if I understand you correctly. If you want to align by the two nucleotide in two GTPase structures, you can simply do it in COOT using the “LSQ superpose” function. You need to fill in the chain id and residue number only for the nucleotide and choose “all atoms”.

Re: [ccp4bb] Superdex vs Sephadex

Hi Ivan, In simple words: superdex is a few generations newer than sephadex. Main difference: superdex is a physically and chemically, tougher medium. Among all GE healthcare beads (or the ones I know of), superdex offers the best resolution and mechanical strength (thus higher flow rate, very

Re: [ccp4bb] 3BDN, 16.5% Ramachandran Outliers!!!!!

The methods part of the 2008 nature paper also mentioned the two earlier, high-res structures 1F39 (1.9 A) and 1LMB (1.8 A), which together cover almost the whole strucutre except the linker regions. I wonder, in such situations, is it a good practise to use the high res structures, either as

Re: [ccp4bb] how to recover my data

Smith, As Ian said, mtzdump can give you some clues, but will not solve your problem. The file that mtzdump could not read apparently has changed length due to some sort of insertion. The other file that mtzdump could process has the correct length and the stats look reasonable, so it might

Re: [ccp4bb] how to recover my data

Hi Ian, Unix/Linux uses a single byte 0A (the linefeed character) as the line end marker for text, while DOS/Win use two bytes 0D 0A (carriage return + line feed). Old Mac systems use 0D. (what a mess!) So a simple UNIX to DOS operation should expand every 0A in a file to 0D 0A: perl -pe

Re: [ccp4bb] how to recover my data

, the cursor should land on the M of “VERS MTZ”. You can find descriptions of the MTZ format here: http://www.ccp4.ac.uk/html/mtzformat.html Zhijie From: Smith Lee Sent: Thursday, March 05, 2015 3:46 AM To: Zhijie Li Subject: Re: [ccp4bb] how to recover my data Zhijie, Is any mtz editor? I

Re: [ccp4bb] Superposition of select residues

(25,35,B,25,35,D,2) apply_lsq_matches(0,1)#assuming imol 1 is the moving one and imol 0 is the reference Zhijie -Original Message- From: yanfeng zhou Sent: Thursday, February 12, 2015 9:03 AM To: Zhijie Li Subject: Re: [ccp4bb] Superposition of select

Re: [ccp4bb] Superposition of select residues

Hi Oarabile, Coot allows you to align structures by selected atoms: https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/docs/coot-faq.html#How-do-I-do-a-superposition-on-just-a-part-of-my-structure_003f I guess what you are trying to do can be accomplished by the “multi-range LSQ superposition”

Re: [ccp4bb] chloride or water

Hi Jacob, I would agree with Nat. I think with the 3A data and the local environment, putting a Cl there is only justified by the need of supressing a peak in the difference map. Yes the peak can really be a Cl or a water or a mixture of the two (I would like to do an experiment with my Cl

Re: [ccp4bb] chloride or water

: Zhijie Li Sent: Wednesday, January 21, 2015 2:12 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] chloride or water Hi Jacob, I would agree with Nat. I think with the 3A data and the local environment, putting a Cl there is only justified by the need of supressing a peak in the difference map

Re: [ccp4bb] A basic question about Fourier Transform

Hi Chen, Here is what I think: Assuming a crystal is perfect and is being shot at 0 K, then the maximum resolution one experiment can achieve is limited by the wavelength of the X-ray. It can’t be better than the half-wavelength under the normal experimental setting (minimum

Re: [ccp4bb] chloride or water

Hi Rohit, If it is of some significance you may consider replacing NaCl with KI or NaI in your crystallization condition and collect a dataset at 1.5-2 Angstrom. The Iodide anomalous signal might be of some help for identifying Chloride binding sites. Without further evidence for a Cl ion,

Re: [ccp4bb] Adding a residue with an insertion code

: Sampson, Jared Sent: Wednesday, January 14, 2015 3:48 PM To: Zhijie Li Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Adding a residue with an insertion code Thanks to Paul and Zhijie for the suggestions. In the past, I’ve also renumbered everything from 1 (using pdbset) for the duration

Re: [ccp4bb] Coot: How to connect N-terminal to neighbouring C-terminal

Have you done it? 1) Click “add residue...” 2) Click that “real space refine zone” button. You will see what will happen. From: Dialing Pretty Sent: Wednesday, January 14, 2015 9:24 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Coot: How to connect N-terminal to neighbouring C-terminal Dear

Re: [ccp4bb] Adding a residue with an insertion code

wrote: If the residues are consecutively numbered (Calculate Renumber residues), and are assigned the same chain ID (Calculate Change Chain ID), Coot might surprise you and link them on its own. On Wed, Jan 14, 2015 at 9:39 AM, Zhijie Li zhijie...@utoronto.ca wrote: Have you done

Re: [ccp4bb] off-topic;Crystal cannot dissolved in buffer

Hi Xiao, I would poke the crystal with a piece of glass fiber or an oocyte needle to make sure it is not salt. Some protein crystals can be a little tough (rubber-like), but they react to poking very differently from rocks (salts) and will eventually shatter. So far I have found this test to

Re: [ccp4bb] [phenixbb] local BLAST server

Hi Rob, The BLAST nr database (fasta format) can be downloaded from the NCBI ftp: ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/ As I remember it is the nr.gz file. When unzipped the file is called nr. According to BLAST the nr database does contain PDB entries.

Re: [ccp4bb] [phenixbb] local BLAST server

Hello, My apologies for sending the previous post to the wrong BB. Zhijie -Original Message- From: Zhijie Li Sent: Friday, August 08, 2014 11:10 AM To: R.D. Oeffner ; CCP4BB@JISCMAIL.AC.UK Subject: Re: [phenixbb] local BLAST server Hi Rob, The BLAST nr database (fasta format) can

Re: [ccp4bb] protocol for seleno-methionine incorporation...

Hi Mintu, I suggest using purified whole protein for ESI-MS. You will get a series of protein peaks (if the substitution is not 100%, which is often the case), each differ for 47 Dalton. You can determine how many Se each peak corresponds to if you know the molecular weight of your protein.

Re: [ccp4bb] HisTrap Trap

Hi Bernhard, I too suspect that it is some kind of metal chelating reagent causing the problem (possibly used in medium for carrying Fe2+, as the free Fe2+ is toxic to cells). One simple test would be to load a liter of the unused medium to the Ni2+ column and see what happens. Do you

Re: [ccp4bb] Stereo monitors for use with Pymol and Coot

I beg to differ on this: Also, passive screens have a pol-filter in place, the fine lines of which you will observe on a white background, the more disturbing the closer the viewing distance to the screen is. So, for general office applications (writing text), the screens are less useful. Our

Re: [ccp4bb] Aggregation assay

Hi, Two things i would like to add: 1) Due to the dependence of A280 on amino acid composition, a simple two-wavelength 280 and 340 or 320 comparison is not very ideal for determining the scatter component of the UV absorption of protein/protein aggregate particles (the usefulness of this

Re: [ccp4bb] Recovering crystals from dry drops

Hi Debasish, I would first use some of those crystals to make seeds and grow some new crystals so that I would not lose the crystal. Dehydration, even done systematically (eg, http://www.mitegen.com/mic_catalog.php?c=jenCrystaloptdehydrate), may or may not improve the diffraction. Like most

Re: [ccp4bb] Can not see density map when I turn off normalization in PYMOL

note: the same applies to UCSF Chimera, where the volume data (maps) control also requires you to specify the cut off or gradient in real map values instead of RMSD. Zhijie From: hongshi WANG Sent: Wednesday, February 19, 2014 3:47 PM To: Zhijie Li Subject: Re: [ccp4bb] Can not see density

Re: [ccp4bb] identifying protein crystals via visible light only?

Hi Richard, I am not sure if this is what you are looking for: second order nonlinear optical imaging of chiral crystals (SONICC). It is not based on a computational algorithm but the nonlinear optical property of chiral crystals to double the wavelength when illuminated by intense light.

Re: [ccp4bb] 3D stereo notebook

Hi Zhongzhou, For laptops, the passive stereo (Zalman mode) would be the easiest way to go. All you need to do is to plug that monitor to the VGA port of you laptop. The halving of the vertical resolution under stereo mode only affects reading the characters, which can be solved by setting the

Re: [ccp4bb] AW: [ccp4bb] Dealnig with O-linked mannose

Hi Dimetry, The difference between LINK and LINKR can't be explained better: http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg11865.html Older versions of COOT used to not display the LINKR record, but now the newer versions display both LINK and LINKR records as dotted bonds. I assume that

Re: [ccp4bb] Dealnig with O-linked mannose

Hi Dmitry, COOT does have the MAN-SER linkage record in its monomer lib, but it won't detect the bond for you. It also haven't provided an interface for the user to specify the bond type yet. The COOT procedure you described is perfectly fine for generating a generic covalent bond record for

Re: [ccp4bb] Dealnig with O-linked mannose

It seem the LINK line I provided eariler was chopped by the email system. Here it is again: LINKRC1**MAN*C***1*OG**SER*B*912MAN-SER Simply replace each * with a space and change the residue IDs. Also to clarify the procedure of using refmac to generate

Re: [ccp4bb] Dealnig with O-linked mannose

Hi Dmitry, I think the best way is not to make a new monomer. MAN-SER and MAN-THR linkages do exist in the ccp4 monomer lib. If you simply build a mannose with its O1 removed and put the C1 ~1.4 Angstrom to the OG of the serine I think refmac should be able to detect the linkage. When this

Re: [ccp4bb] Staining Crystals with comassie

Hi Danilo and all, A little trick for the glutaraldehyde staining: you can hang a 1-2uL drop of 25% glutaraldehyde (or the most concentrated stock solution you can find) besides your crystal drop in the vapour diffusion chamber. The glutaraldehyde will get into the crystal drop via vapour

Re: [ccp4bb] Staining Crystals with comassie

Izit is an aqueous solution of methylene blue, which you can prepare simply and cheaply. Look here: http://www.ysbl.york.ac.uk/ccp4bb/2000/msg00387.html One word of warning: not every crystal stains. I found poking crystal with hair or glass fibre to see if it cracks or breaks is more

Re: [ccp4bb] shape complimentarity for small molecule

Hi Tom, Yes, SC can be used for calculating protein-small molecule ligand SC. Simply put the ligand and protein on two separate chains. You probably need to edit the $CLIBD/sc_radii.lib file to add some atom radii for your ligand. For example: ABC N* 1.65 ABC C* 1.90 Zhijie

Re: [ccp4bb] off topic: good peak on gel filtration

Hi Ed, I guess by 24mL SD200 Peter meant the Superdex 200 10/300 column, which most of us should be quite familiar with. According to GE healthcare, a new Superdex 200 10/300 GL column should have TP 25000/m. For comparison, a new Superdex200 16/600 PG, which uses bigger beads, has TP

Re: [ccp4bb] Negative FoFc around ligand

Hi Kavya, If I understand you correctly (from title and text), you meant your negative FoFc was around your ligand, is that right? I wonder if this is a case in which the ligand has an occupancy below 1, but was modeled as 1, so the refinement program had to give it a high B factor to

Re: [ccp4bb] Off-topic (SPR)

Hi Jahan, Maybe you are using a new model of BiaCore. Our old BiaCore X never cares to tell us how to do our experiment. However if your RU did go below that of the empty chip, then maybe you really didn't get anything conjugated. The pH 3.8 condition is not good for the amine coupling

Re: [ccp4bb] off topic, BN PAGE

the gel and spend the 1-5 hrs there, your initial conditions are lost anyways. Zhijie From: Careina Edgooms Sent: Thursday, March 28, 2013 3:03 AM To: Zhijie Li Subject: Re: [ccp4bb] off topic, BN PAGE Hi Zhijie Thanks for the helpful reply. The attractive thing about BN PAGE (if it works

Re: [ccp4bb] ./configure problem

Hi Alex, The CCP4 package you downloaded seems to be a prebuilt binary package for the X86_64 architecture. You do not need to compile yourself - and you can't without the source code. Running ./configure is for configuring the compilation environment before running make to compile source

[ccp4bb] COOT running slow after upgrading to CENTOS 6.4 from 6.3

Hello, We have a curious situation here: after upgrading CentOS 6.3 to 6.4, COOT runs slowly every time after the go to atom command is executed - every rotation of the molecules takes nearly 1 second to finish. But if the go to atom command is never sent then the speed is normal. A COOT

Re: [ccp4bb] column tube

Hi George, What is the plastic tube? Is it part of the end adaptors or it is part of the tubing? What type of plastic it is? If you can provide a photograph of the broken part maybe someone can give you more useful suggestions. Zhijie From: George Kontopidis Sent: Wednesday, March 20, 2013

Re: [ccp4bb] column tube

To: 'Zhijie Li' Subject: RE: [ccp4bb] column tube Dear Zhijie, I am looking for the external clear plastic tube of Bio-rad UNO Q1 Column 720-0001 Column information: http://www.bio-rad.com/prd/en/GR/LSR/PDP/d825a6ab-49cf-4140-91c3-ea131c886b74/UNO-Monolith-Anion-Exchange-Columns

Re: [ccp4bb] off topic question BIAcore problem

Hi Xianchi, First of all: a very slow dissociation rate can also be an artifact: the analyte can be simply precipitating on the surface. You do need to rule this out by proper controls. But there is no rule saying that 10e-6 s-1 off rate is not realistic. Even with protein-small molecule

Re: [ccp4bb] off topic question BIAcore problem

Hi Xianchi, How did you treat the control flow cell? And what is the composition of the control buffer that you use to disrupt binding? Is it denaturing or a mild condition? If the Rmax=150 and Koff=1e-6, then at 7200 s (2 hr), the signal will only drop 1RU from 150RU (assuming you can reach

Re: [ccp4bb] Sighting of Protein Crystals in Vivo?!

Hi Jacob, Interesting topic. This reminds me the posters I saw on ACA 2010, on the femto-second infrared laser based instrument . That instrument utilizes the nonlinear optical properties of crystals of chiral molecules to detect very small crystalline materials from amorphous background:

Re: [ccp4bb] GeForce Graphics cards

Hi, Since it is mentioned, I would like to take this chance to clarify: We have used the Zalman and LG 2342P under Linux, Windows(XP and 7) and a VM Windows within a Linux system, on either desktop (with a minimal on-board graphic chip) or laptops. The monitor is quite plug-and-play in all

Re: [ccp4bb] GeForce Graphics cards

Hi Alex, The graphical computational power of even the lowest-end graphic chips these days will suffice the displaying of our models. To give you some idea: we are still using a Quadro FX 1000 card and an old CRT on one of our stereo systems; my 6-year old laptop has an ATI Radeon X1300,

Re: [ccp4bb] GeForce Graphics cards

Sent: Wednesday, February 13, 2013 6:51 PM To: Zhijie Li Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] GeForce Graphics cards Hi Zhijie, thanks for the link. I was actually referring to that post. Can you please tell me what graphics card you are using? Alex On Wed, Feb 13, 2013 at 6:16

Re: [ccp4bb] 3D Monitors

Hi Sabine, We are absolutely happy with our LG D2342P. The major advantages include the simplicity in setting up and the light weight of the glasses. For more information, please read this thread: http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg27816.html Zhijie

Re: [ccp4bb] Boveral in SFCheck

Hi, Seems not officially retracted from Nature either. On the paper's web page, there was only a line in small font read like this: There is a Brief Communications Arising (9 August 2007) associated with this document. It took me more than half an hour to find this line. I normally won't

Re: [ccp4bb] CCP4superpose_only superpose interesting residues

Hi Wenhe, Superpose allows you to specify residue (as well as Ca/main chain/side chain) ranges. Also in COOT you can select the range of residues used in the LSQ superpose calculation. For superposing parts of the proteins only, a little trick is to cut the interested fragments from the

Re: [ccp4bb] PNAS on fraud

-cnrs.unistra.fr Sent: Friday, October 19, 2012 6:15 AM To: Zhijie Li zhijie...@utoronto.ca Subject: Re: [ccp4bb] PNAS on fraud Le Jeudi 18 Octobre 2012 22:52 CEST, Zhijie Li zhijie...@utoronto.ca a écrit: Thank you for this funny (and yet significant) comment. But I do not see clearly whether

Re: [ccp4bb] PNAS on fraud

On curve fitting: http://twitpic.com/8jd081 -- From: DUMAS Philippe (UDS) p.du...@ibmc-cnrs.unistra.fr Sent: Thursday, October 18, 2012 1:52 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] PNAS on fraud Le Jeudi 18 Octobre 2012 19:16 CEST,

Re: [ccp4bb] sarkosyl

Hi, We used it in some lysis/refolding buffers. Sigma marked this biodegradable detergent as Highly toxic by inhalation - when it's used in toothpastes and shampoos if I am not mistaken. when I called, Sigma said that since someone published a paper saying that when they sprayed it into a

Re: [ccp4bb] sarkosyl

established for the specific proteins. I suppose that supports the idea that it at the minimum does not always cause problems. Zhijie From: Rashmi Panigrahi Sent: Thursday, September 20, 2012 8:29 AM To: Zhijie Li Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] sarkosyl Thanks Zhijie, So do

Re: [ccp4bb] off topic: pdf to word conversion

If you have acrobat (instead of acrobat reader), then you can save PDF to RTF file which is fully supported by word. This is probably the easiest way to get the maximum out of a PDF file. If this doesn't work to your satisfaction, then you can try saving the PDF to TIFF images, then OCR.

Re: [ccp4bb] off topic: pdf to word conversion

P.S. If the images are important and you want to extract them as independent image files, then you can try saving the PDF as html. Acrobat will generate an image directory that contains the image files. I am using acrobat 8 and there are two options, saving as html 3.2 and saving as html 4 with

Re: [ccp4bb] Question on stereo monitor: LG D2342P-PN

Professor University of Maryland IBBR/CBMG Rm 3127E CARB-2 9600 Gudelsky Drive Rockville, MD 20850 email: swals...@umd.edu phone: (240) 314-6478 fax: (240) 314-6255 On Aug 9, 2012, at 2:26 PM, Zhijie Li wrote: Hello, We have received our LG D2342P-PN monitor yesterday and did a little test

[ccp4bb] Question on stereo monitor: LG D2342P-PN

Dear CCP4BBers: Sorry to bring up this highly repeated topic again. After some internet research, we are about to make the commitment to buy an LG D2342P-PN for setting up a stereo system. I would like to have a final confirmation from someone with real life experience that this model does

Re: [ccp4bb] harvesting in cold room

RE: [ccp4bb] harvesting in cold roomDensity of LN2=807g/L, that's roughly 807/28*22.4=645.6L gas at RT, 1 atm. At 4C the volume will be less: 645.6/298*277=600L. An empty 2x2x2m cold room=8000L, containing 8000x21%=1680L oxygen. We normally won't let the whole liter of LN2 to evaporate when

Re: [ccp4bb] offtopic: packing gel filtration columns

Hi, Yes, it can be done by yourself. I repacked our 26/60 column a few years ago with homemade apparatus. The column has been working for us since then. Basically the loading apparatus was a tubing connecting the top of the column and bottom of a reservoir (a flask with an opening near the

Re: [ccp4bb] Where to get a thermo-cycling controlled chamber

Hi Jun, In this following article an metallic adapter was used to mount a 192 well sitting drop plate on a conventional thermocycler. http://journals.iucr.org/d/issues/2006/05/00/av5047/av5047bdy.html. However I guess there would be significant evaporation and condensation if you use vapor

Re: [ccp4bb] protein precipitate in all PEG kit

Hi, The idea used by the Qiagen pre-screen might be relevant to your case: http://www.qiagen.com/products/protein/crystallization/screeningproteincrystallizationconditions/prescreenassay.aspx http://www.qiagen.com/literature/handbooks/literature.aspx?id=239 Zhijie From: fengjuanlv12

Re: [ccp4bb] protein precipitate in all PEG kit

Hi Fengjuan, It has been proposed that for a specific protein there are hard precipitants and soft precipitants. Hard ones precipitates the the protein effectively, while soft ones may help stabilizing the protein. By playing with the two types of precipitants, one may get better

Re: [ccp4bb] Death of Rmerge

I am little curious about the anisotropically truncated data for 3RKO: Percent Possible(All)96.0 Mean I Over Sigma(Observed) 0.8 In the supplementary table of the nature paper it was made clear that this 3.16-3.0A, I/sigmaI=0.8 and Rmerge=1.216 shell was the outer shell of the

Re: [ccp4bb] SUMO(ULP-1) protease

Hi Gloria, I asked for a little baker's yeast from a lab in our department and PCRed both the SMT3 domain and the SUMOase gene from its genomic DNA, then cloned them to E coli vectors. The good thing about yeast is that most of its genes are single exon so one do not really need to find cDNA

Re: [ccp4bb] how to ignore spot overlap in imosflm?

Hi Xinghua, The total intensity of each reflection needs to be accurately quantitated in order to calculate the structure factors. Not only the dots need to be well separated in the 3D reciprocal space, but also a small area around the dots are often needed to calculate the background for

Re: [ccp4bb] Anisotropic diffraction

-- From: chen c chenc...@gmail.com Sent: Sunday, April 29, 2012 6:09 PM To: Zhijie Li zhijie...@utoronto.ca Subject: Re: [ccp4bb] Anisotropic diffraction I accept your advice. In fact, this is the first time I am involved in anisotropic issue. And I learned a lot from all

Re: [ccp4bb] Anisotropic diffraction

Hi, My first thought was same with David: the truncation won't change the crystal's space group. The symmetry of the crystal is reflected by the symmetry of the amplitudes of many many reflections across all resolutions. Ellipsoidal truncation itself only removes some very weak reflections

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