Re: [ccp4bb] weighting term in refmac

Hi, Check out this post by Tassos regarding the MATRIX weight http://www.dl.ac.uk/list-archive-public/ccp4bb/2005-10/msg00592.html Good luck, Hidong Leo Chavas <[EMAIL PROTECTED]> Sent by: CCP4 bulletin board 03/05/2007 06:27 PM Please respond to Leo Chavas <[EMAIL PROTECTED]>

Re: [ccp4bb] weighting term in refmac

Dear Li, There is a value of weighting term with default 0.3 in refmac5, what is the exact meaning of it? You might want to have a look at: http://www.ccp4.ac.uk/html/refmac5/keywords/xray-principal.html#weig What is the best value of it for different resolution data? I don't know exa

Re: [ccp4bb] practical limits of MR?

Feed it common substructures and see what happens... On Mon, 5 Mar 2007, Nat Echols wrote: > I'm not sure what "in desperation" means. You're trying to solve a > structure, so all options are open, right? They don't have to be elegant, > it just has to work. :) Yes, but

Re: [ccp4bb] practical limits of MR?

I'm not sure what "in desperation" means. You're trying to solve a structure, so all options are open, right? They don't have to be elegant, it just has to work. :) Yes, but it's not worth wasting time and resources on something that is guaranteed to fail. In this case, it's a 50kD protein tha

Re: [ccp4bb] practical limits of MR?

We just solved a 142 nucleotide asymmetric unit of a novel ribozyme structure using only A-form RNA helical fragments and phaser. I'm trying to find some time to write the paper but the basic idea is sketched out in the supplementary material to the paper that comes out March 16th in Science. I

Re: [ccp4bb] Problems in MR

Dear Lei, just in case: would that be possible that you are encountering a swapping, ie 3D domain swapping, behavior? To check this, have a look at the electron density around the "crash". If it is continuous, you might consider this possibility. Regards. Leo On Mar 3, 2007, at 12:10 AM

Re: [ccp4bb] SUMMARY: Cannot run NTA to purify the protein having Histag?

Hi, to add to your list: You could also try Ni-IDA (e.g. from Pharmacia, I hope I remember the name correctly) instead of Ni-NTA. If I remember correctly, IDA chelates the metal ion only two-fld instead of three-fold as the NTA does. During my PhD th protein would not bind at all to NTA but i

Re: [ccp4bb] practical limits of MR?

Nat Echols wrote: I had a debate with a coworker about using MR in desperation and I'm curious what the most extreme case is where a very different model was used to solve a structure. This could be highest RMSD, lowest % identity, or most incomplete model. I'm also curious whether homology

Re: [ccp4bb] practical limits of MR?

On Mon, March 5, 2007 2:16 pm, Nat Echols wrote: > I had a debate with a coworker about using MR in desperation and I'm > curious what the most extreme case is where a very different model was > used to solve a structure. This could be highest RMSD, lowest % identity, > or most incomplete model.

[ccp4bb] practical limits of MR?

I had a debate with a coworker about using MR in desperation and I'm curious what the most extreme case is where a very different model was used to solve a structure. This could be highest RMSD, lowest % identity, or most incomplete model. I'm also curious whether homology modelling has ever

Re: [ccp4bb] MTZ to Shel-X?

On Mon, Mar 05, 2007 at 10:53:55AM +, Kevin Cowtan wrote: > You are absolutely right! The difficulty in getting from MTZ to any > other format or back is unacceptable. Expecting working > crystallographers to write Fortran format statements is ridiculous. I've > been trying to address this b

Re: [ccp4bb] MTZ format conversion

Hello all and Hello Kevin, I just have by now a probleme concerning this point and especially concerning a CNS reflection file with PHASES. The main point is that CNS consider Bijvooet as separate reflections (and far away from each other in the file) whereas CCP4 uses 1 line for Bijvooet pair

[ccp4bb] Ordered His-tags

I remember reading once or twice people requiring examples of PDBs which contained ordered His-tags. Someone did a survey on this, which is on the latest Acta Cristallographica D: http://journals.iucr.org/d/issues/2007/03/00/en5203/index.html Lucas ___

Re: [ccp4bb] MTZ to Shel-X?

Martyn Winn wrote: Yes, there is: C input FP(+) IF(LOOKUP(23).GT.0 .AND. IFSQ.NE.0) + SCCHK = 9.00/(RANGES(2,LOOKUP(23))* RANGES(2,LOOKUP(23))) C IF (SCAL.GE.SCCHK .AND.IFSQ.NE.0) SCAL = SCCHK IF(IFSQ.NE.0) WRITE(6,'(/,a,/,a,F8.4,/)') + ' *** You are inpu

Re: [ccp4bb] protease cleavage sites

TeV is great but it isn't always a magic bullet for producing native N-termini: we've experimentally determined the obvious, that if you bury part of its recognition site in secondary structure, it cleaves very very slowly. We tried this on a protein where M1 is cleaved in vivo and aa#2 is th

[ccp4bb] AW: [ccp4bb] MTZ format conversion

I have a program what just does that. It keeps reading CNS records until it encounters the next 'INDE' item. Herman -Ursprüngliche Nachricht- Von: CCP4 bulletin board [mailto:[EMAIL PROTECTED] Im Auftrag von Eleanor Dodson Gesendet: Montag, 5. März 2007 17:06 An: CCP4BB@JISCMAIL.AC.UK

[ccp4bb] AW: [ccp4bb] MTZ format conversion

Dear Kevin and others, Most important in my eyes is to have f2mtz 1) read hkl files in free format. There is no reason nowadays to have users specify a format statement which dates back to the time of the punch-cards. 2) parse CNS reflection files. The CNS labels could then be used as column la

Re: [ccp4bb] MTZ to Shel-X?

Yes, there is: C input FP(+) IF(LOOKUP(23).GT.0 .AND. IFSQ.NE.0) + SCCHK = 9.00/(RANGES(2,LOOKUP(23))* RANGES(2,LOOKUP(23))) C IF (SCAL.GE.SCCHK .AND.IFSQ.NE.0) SCAL = SCCHK IF(IFSQ.NE.0) WRITE(6,'(/,a,/,a,F8.4,/)') + ' *** You are inputting Fs and re

Re: [ccp4bb] MTZ format conversion

<[EMAIL PROTECTED]> <[EMAIL PROTECTED]> <[EMAIL PROTECTED]> <[EMAIL PROTECTED]> <[EMAIL PROTECTED]> From: "Ian Tickle" <[EMAIL PROTECTED]> To: <[EMAIL PROTECTED]> Cc: Return-Path: [EMAIL PROTECTED] X-OriginalArrivalTime: 05 Mar 2007 16:21:56.0880 (UTC) FILETIME=[64E8B1

Re: [ccp4bb] How to get rid of Membrane formed on hanging droplets?

A less viscous oil used in small molecule low-temp work is PerFluoroPolyEther. Its general use is as an ultra-high vacuum pump oil, so it has an extremely low volatility. Additionally, PFPE has a very low fracture temperature and is non-reactive. I have used it in both small molecule and macromo

[ccp4bb] SCSB Structural Biology Symposium, May 18-19th, Galveston Texas

Dear Colleague: You and your colleagues are cordially invited to join us for the 12th Annual Structural Biology Symposium to be held at the University of Texas Medical Branch at Galveston on May 18th and 19th, 2007. The meeting is organized by the Sealy Center for Structural Biology & Molecular

Re: [ccp4bb] MTZ format conversion

All formats I know except CNS have single records per reflection. In CNS a reflection record can go over several lines - I know no way of avoiding requiring a format tt to read such a record.. A clever programmer could parse a few lines and work one out, but in fact the format is not nec. co

Re: [ccp4bb] MTZ to Shel-X?

That is done I believe in mtz2various.. Eleanor George M. Sheldrick wrote: I would like to second Ian's bug report, and suggest one minor improvement. Rather than multiplying I and sigI by 10, one could find the largest intensity value I(max) and multiply all the I and sigI values by (say) 99

[ccp4bb] How to get rid of Membrane formed on hanging droplets?

Hi, What you describe is "skin" - rumoured to be denatured protein. http://xray.bmc.uu.se/~terese/crystallization/pics/SKIN2.JPE And it's a pain, especially when your crystals stick to it. Best suggestions are: 1) Try screening ad

Re: [ccp4bb] protease cleavage sites

Since people asked: http://www.usbweb.com/category.asp?cat=118&id=22293 is my preferred source. Please note that I don't have any relation to USB whatsoever (but large amounts of money sent to my unnamed Swiss bank account are always appreciated. The password for the account is BACON). Artem >

[ccp4bb] How to get rid of Membrane formed on hanging droplets?

Dear everyone, I am working on crystallization of a protein/RNA complex recently. The crystals were initially grown from BICINE(9.0) 0.1M, 1,4-Dioxane 2%(v/v) , PEG 20,000 10%(w/v), at 10mg/ml. I noticed that there was a membrane formed on the surface of the hanging droplets. This membrane seem

[ccp4bb] MTZ format conversion

On a more general note, having looked at mtz2various it looks a lot better than last time I used it, and the problem of keeping I's is a separate issue. But we still get fairly regular format conversion questions on both this and the coot list. From memory, the most common questions concern c

Re: [ccp4bb] protease cleavage sites

The important bit about Thrombin is to find the right source of it. Some suppliers are *much* better than others. I've had no problems with this protease in the recent year, but had trouble earlier. Note that Thrombin leaves 2 amino acids whereas TVMV, TEV, and 3C leave one amino acid (or even non

Re: [ccp4bb] protease cleavage sites

I'd like to third TeV & second 3C ("PreScission"). Both have high specificity, good processivity and I have had a lot of success with 3C. I have _never_ got Thrombin to cut cleanly - but I guess I could have been unlucky... Dave On 05/03/07, Cynthia Kinsland <[EMAIL PROTECTED]> wrote: Hi, I'

Re: [ccp4bb] : MTZ to SHELX question

Eleanor is correct, if the intensities are (still) in the mtz file, they should be good. The problems arises when you use TRUNCATE to turn them into F and then the current MTZ2VARIOUS with the FSQUARED keyword to square them again, this degrades sigI. If you use XPREP to transfer the free R fl

Re: [ccp4bb] protease cleavage sites

Hi, I'll second the TEV protease suggestion. We use it routinely because it is highly specific and easy to make ourselves (and, therefore, cheap). We have never seen it cut non-specifically and, since it is cheap, we just chuck in a bunch and let it go. The Prescission protease is also

Re: [ccp4bb] protease cleavage sites

Rene, There are many proteases that are suitable for digestion of an N-terminal tag. Interestingly, there are NOT many (any?) proteases suitable for digestion of thr C-terminal tag (except for the dual-enzyme His-tag digest system that sometimes work and sometimes does not). I personally like TVM

Re: [ccp4bb] : MTZ to SHELX question

Truncate does not change intensities, only amplitudes. (Why should it? ) Eleanor The mtzvarious output will have what you want.. h k l I+ -h -k -l I- Nat Echols wrote: *** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk

Re: [ccp4bb] MTZ to Shel-X?

I would like to second Ian's bug report, and suggest one minor improvement. Rather than multiplying I and sigI by 10, one could find the largest intensity value I(max) and multiply all the I and sigI values by (say) .99/I(max) to avoid any possibility of overflowing the format. An additiona

[ccp4bb] problems with polarrfn - CCP4 6.0.2

Dear CCP4ers, I am trying to compute a self rotation function with polarrfn (ccp4 ver 6.0.2), and it keeps failing with this error message: END PLOT: Picture number91 *** * Information from CCP4Interface script ***

Re: [ccp4bb] : MTZ to SHELX question

Assign LABI I(+)= etc I(-) etc OUTP SHELX and I think you get what you want.. Eleanor Nat Echols wrote: *** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** A coworker recently solved a structure at high resolution

Re: [ccp4bb] CNS v1.2 and unwanted introduction of OXT

Check also these two fields in generate.inp: {* convert chainid to segid if chainid is non-blank *} {+ choice: true false +} {===>} prot_convert_1=false; {* separate chains by segid - a new segid starts a new chain *} {+ choice: true false +} {===>} prot_separate_1=false; And check carefully th

Re: [ccp4bb] CNS v1.2 and unwanted introduction of OXT

On Mon, 5 Mar 2007, Fred. Vellieux wrote: > Hi James, > > I tried to increase the parameter value to 3.0 A. The resulting file gives > the same behaviour (and the newly introduced OXTs are within 0.05 A of the > N atom of the following residue) so I think the distances are reasonable. > > So unf

Re: [ccp4bb] Problems in MR

You dont say the spacegroup. Different MR solutions can exist relative to any of the acceptable alternate origins. Eg If it were P21 say the two solutions could lie anywhere along the b axis. Try running superpose (coordinate utility ) matching sequences. If the rotation looks like a symmetry o

Re: [ccp4bb] CNS v1.2 and unwanted introduction of OXT

On Mon, 5 Mar 2007, James Irving wrote: > Hi Fred, > > From memory, this can occur due to long bond lengths in the model being > interpreted as chain breaks, try editing the generate.inp or > generate_easy.inp script and increase the value for "break_cutoff": > > {* cutoff distance in Angstro

Re: [ccp4bb] CNS v1.2 and unwanted introduction of OXT

Hi Fred, From memory, this can occur due to long bond lengths in the model being interpreted as chain breaks, try editing the generate.inp or generate_easy.inp script and increase the value for "break_cutoff": {* cutoff distance in Angstroms for identification of breaks *} {* the default of 2

Re: [ccp4bb] MTZ to Shel-X?

<[EMAIL PROTECTED]> <[EMAIL PROTECTED]> <[EMAIL PROTECTED]> <[EMAIL PROTECTED]> <[EMAIL PROTECTED]> <[EMAIL PROTECTED]> <[EMAIL PROTECTED]> From: "Ian Tickle" <[EMAIL PROTECTED]> To: <[EMAIL PROTECTED]>, <[EMAIL PROTECTED]> Cc: Return-Path: [EMAIL PROTECTED]

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

[ccp4bb] CNS v1.2 and unwanted introduction of OXT

Dear CCP4BB, Sorry about the non-ccp4 question, it has to do with CNS v1.2 and (perhaps) Coot. Also, can you avoid "hilarious" replies such as "go build a better model" or "provide us with the data and current model, we will build and refine and publish it for you" (no harm meant there, this is n

Re: [ccp4bb] MTZ to Shel-X?

A glance through the CVS history of mtz2various and f2mtz shows that there has been a lot of work keeping these up-to-date for various formats, work that is largely unrewarded and unacknowledged. But they are indeed still deficient in places. The required code writing is relatively trivial. The ha

Re: [ccp4bb] protease cleavage sites

Hi Rene We use Tobacco Etch Virus (TeV) protease - its pretty active and very specific - As long as you are not using it for commercial purposes (i.e. selling it), it is possible to source the clone for it and readily express buckets of it (or alternatively just get the gene synthesised and ban

Re: [ccp4bb] MTZ to Shel-X?

You are absolutely right! The difficulty in getting from MTZ to any other format or back is unacceptable. Expecting working crystallographers to write Fortran format statements is ridiculous. I've been trying to address this by adding support for other formats to clipper, but my pace has been g

Re: [ccp4bb] Solubility of ligands - Summary

Hi everybody, Two days ago I posted the question given below regarding the solubility of ligands for crystallization and activity assays. Thanks to everybody who replied to my question. I'm giving the summary of the answers below: I like the Anthony's approach, I think I'll follow i

[ccp4bb] DCO-X error with setup

I am trying to run DCO-X to make composite omit maps. I'm starting by using the test set provided with the package and following the steps outlined in the tutorial, but when I click "Setup", I get the following error: Error with Setup Setup did not complete properly. Please make certain that you

Re: [ccp4bb] MTZ to Shel-X?

<[EMAIL PROTECTED]> <[EMAIL PROTECTED]> <[EMAIL PROTECTED]> From: "Ian Tickle" <[EMAIL PROTECTED]> To: <[EMAIL PROTECTED]> Cc: Return-Path: [EMAIL PROTECTED] X-OriginalArrivalTime: 02 Mar 2007 11:50:40.0074 (UTC) FILETIME=[FFEFF2A0:01C75CC0] Thanks Eleanor, sorry I wasn't trying

Re: [ccp4bb] Very weird

It seems very odd..in fact almost impossible. You still have 3 correct molecules I wonder if there is some error in the coordinate file? Errors I make are: leaving and end record, between 2 parts. - many programs stop reading coordinates at the first END leaving CRYST1 and SCALE cards in t

[ccp4bb] protease cleavage sites

Hi, A non-ccp4 Q. Sorry. I would like to use a cleavable purification tag at the N-terminus/ extracellular end of my membrane protein for purification. Before I start, I wonder if someone could recommend a particular protease site that I can engineer between the tag and my protein? How abo

Re: [ccp4bb] MTZ to Shel-X?

Dear Ian, It is all part of a diabolical CCP4 plot to make it as inconvenient as possible to move from a REFMAC refinement to SHELXL! I hope that i do not get excommunicated like DVD for this comment. To summarize your and Martin's suggestions, I know of only two ways to move from mtz to hkl

[ccp4bb] weighting term in refmac

Hi, There is a value of weighting term with default 0.3 in refmac5, what is the exact meaning of it? What is the best value of it for different resolution data? Does it affect the result R value much? Li Yang

[ccp4bb] question about a script

Hi All, If I have two scripts named 1.inp, 2.inp, I can run them with command like ./1.inp, now I should modify some parameter in 2.inp according to the result of ./1.inp before run it. How can I write a program to run then together? For example, I get two numbers a and b from 1.inp, and

[ccp4bb] SUMMARY: Cannot run NTA to purify the protein having Histag?

Dear CCP4 users, Thank you all of your advices which help me to solve this problem. I believe that all of your advices will help me and others having the same problem. This is the summary of experienced advices about how you will do if the protein having His-tag don't bind to NTA resin. 1. The pr

[ccp4bb] Problems in MR

Hi all. I am trying to solve a structure with one molecules in the asu through MR. Using a not good data set at 3.0A and a structure with sequence similarity of 37%, Phaser gave a result of z score 14.7 and LL-gain 220, probably a right solution. But when I slightly modified the model I got from P

[ccp4bb] SUMMARY: Main topic of the day: Protein crystallization

Dear CCP4bb users, I would like to thank everyone who answered my question and apologize for my delay in posting the summary. Here is the question and the answers I got. What was the minimun protein concentration reported with success in crystallization trials? We've done crystallization at 1.2

Re: [ccp4bb] luzzati numbers in ccp4/refmac

I guess John was referring to PDB requirements. CNS reports "sigmaa coordinate error", "cross-validated luzzati coordinate error" and "cross-validated sigmaa coordinate error" - I always thought this is what PDB means. If I refined structure with refmac, I just leave these blank. Ethan Merr

Re: [ccp4bb] MTZ to Shel-X?

On Mar 1, 2007, at 10:17 PM, Artem Lyubimov wrote: mtz2various to convert the data to MTZ format whilst taking care to keep the original R-free flags. Just to clarify; here you probably mean f2mtz and not mtz2various? But yes that is a good idea if you want to do most of your refinement i

Re: [ccp4bb] Fwd: [ccp4bb] Swiss humour - no laughing matter? (Re: [ccp4bb] process SeMet labelled data)

Hello Klaus, I think you should give Gerard some "Hofnarrenfreiheit". (That's a fine German word for you to figure out, Gerard.) He is certainly not an evil racist at heart. Andreas Klaus Piontek wrote: Greetings (or in "correct" Swiss German "Grüezi wohl", with Umlaut=vowel mutation) t

[ccp4bb] RE : [ccp4bb] MTZ to Shel-X? + Process Se-labeled datas

Dears, I discovered HKL2MAP during a workshop in Grenoble which is maybe interesting for you http://schneider.group.ifom-ieo-campus.it/hkl2map/index.html#Reference It works very straightforward (at least for me). In another hand, have a look at the mtz2sca program. I benefit from this opportu

Re: [ccp4bb] MTZ to Shel-X?

Of course, if the refinement is not too far along, you could start over and first import the scaled data into SHELX, generate the R-free flags using SHELXPro, and THEN use mtz2various to convert the data to MTZ format whilst taking care to keep the original R-free flags. Worked very well f