Re: ccp4bb on new site

Andy Purkiss-Trew wrote: Dear Charles (and the rest of the bulletin board) I have a question regarding the new version of the software. Can the [ccp4bb] be put in front of the message subjects again? I use this in my e-mail filtering, to get the ccp4 stuff out from under the groaning weight of

Re: [ccp4bb] Fancy crystal, poor diffraction

Hi Tiancen, nobody so far has suggested to mount the smallest crystals, 0.4x0.4x0.3 seems to be pretty large, this also means that the freezing procedure is longer. Then the other question is do you freeze in the Cryostream or by plunging into LN2, I'd prefer the latter technique. Good luck, Jue

Re: [ccp4bb] Cannot running NTA to purify the protein having His-tag?

Ngo Duc Tri wrote: Dear CCP4 users, I'm purifying a kind of protease having His-tag. The protein is expressed in insect cells and broken by sonication. I used NTA resin to purify this protein. Buffer A is 50mM phosphate buffer pH 7.5 and 300mM NaCl. Buffer B is 50mM phosphate buffer pH 7.5,

Re: [ccp4bb] change the B-factor for a residue

Lucas Bleicher wrote: Is there a program in CCP4 with a command to change the B-factor of a single residue? I checked the documentation for pdbset and it seems to assign B-factors only for the whole molecule. What I'd like to do is plot a given residue property in a graphic software using the "

Re: [ccp4bb] (bigger) fragment identification of limited proteolysis w/ mass-spec

You should be able to solve your problem with the following link: http://us.expasy.org/tools/findpept.html Jürgen Yong Tang wrote: Dear all, just a super dummy question: I treated a protein with trypsin, found the protein being degraded into two well-define fragments, ran a sizing column to f

Re: [ccp4bb] salt or protein?

Hi Sreeram, assuming you have plenty of those crystals, why don't you loop a few pass them through a drop of your reservoir for washing and load them on a SDS gel ? Juergen Sreeram Mahesh wrote: Hi All! I have been trying to screen for my protein crystals, from the crystals grown

Re: [ccp4bb] search-and-replace

[EMAIL PROTECTED] wrote: Hello everyone, I have two pdb files for molecule A (A.pdb and A_polyala.pdb) from which I would like to make a hybrid file A_semi.pdb. A_semi.pdb will have some residues with full sidechains (so derived from A.pdb) and some residues with only a C-beta atom for a

Re: [ccp4bb] extra high B factor

Hi Jiamu, is the high B-value of your protein due to motions, which are not modeled appropiately ? Which program by the way are you using for refinement ? Then the TLSMD server might help you here. Monomer or multimer in the asu ? NCS used, if so checked that they actually follow NCS and you'

Re: [ccp4bb] Ligand insertion and orientation...

Hi James, start Coot, and read in your cif file plus a coordinate file containing your ligand. Read in your structure and read in your mtz file as Auto, then you end up with two maps FWTxPHWT and DELFWTxPHDELWT. Next go to Calculate / Other Modelling Tools and select Fit Ligand. Since you shou

Re: [ccp4bb] Program to find the center of mass

Nian Huang wrote: Dear all, I was trying to do a NCS averaging of the map using Resolve. I had a partial model, which generated a rotation and translation matrix by program lsqkab. Resolve also requires a center of mass input. Do you know any program can estimate it either by map or pdb file? T

Re: [ccp4bb] CCP4 GUI

Hi Martyn, how about option c: in each gui window at the lower left corner have a button called "Display script", or call it "Expert Mode" if people feel better as "Experts" :-) , before running of course. Then people who would like to edit their stuff could do so before running the script. I

Re: [ccp4bb] CCP4 GUI

tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: [EMAIL PROTECTED] -Original Message- From: CCP4 bulletin board [mailto:[EMAIL PROTECTED] On Behalf Of Juergen Bosch Sent: Thursday, May 10, 2007 10:40 AM To: CCP4BB@JISCMAIL.AC.UK Su

Re: [ccp4bb] Low resolution model building

Hi Kolstoe, Kolstoe S.E. wrote: Dear ccp4bb, I am about to start model building a fairly low resolution structure (3A) with ten identical monomers in the asu, solved using MR. What I am thinking of doing is to build one monomer using some form of averaged NCS map, replicate and translate my

Re: [ccp4bb] Superdex 200 PC columns

Hi all, Isn't the flow cell volume the limiting factor for your detection limit ? I believe for the "old" Aktas (~5-8 years old) there were two cell sizes a laerger one and a smaller one, and I don't think it is the same size as in the SMART system. But I might be wrong. Jürgen [EMAIL PROTE

Re: [ccp4bb] Movie for Powerpoint in windows

Ask somebody with a Mac to convert your .mov into avi would be an option. But perhaps you can find something useful under the following link: www.versiontracker.com select Windows and search for something like movie generator, merge images etc. On Mac you can used e.g. Framed if you are not wil

Re: [ccp4bb] crystal shipping at room temperature

Hi Junhua, you should contact TSA in Houston, speak to them prior to your flight arrange a contact person who will be there when you are traveling. Send them a Fax explaining what and why you are carrying your crystals with you and how e.g. small cooler with pads etc. I carried some RT 96 well

Re: [ccp4bb] mac pro configuration for crystallographic computing

Gretchen Meinke wrote: Hi-- I last saw some entries on the Mac Pro Xeon dated ~ April 2007. Were they purchased? Are you happy with them? Does ccp4, mosflm, hkl2000, coot run seamlessly on them? If so, what was the final cost and configuration (we would like stereo). How much memory should

Re: [ccp4bb] Help with reducing crystal mosaicity

Hi Mary, not sure if you received this suggestion already. Despite the low resolution diffraction 4-5 A as you report, try mounting smaller crystals and see how well they perform. Very often our crystals had a better freezing experience when they were small, even if sufficient cryo protectant

Re: [ccp4bb] Structure help

Hi Yanming, when you use your two correctly placed molecules have you tried to calculate a composite omit map using CNS. I assume your crystal lattice does not look very well packed when you only have two molecules per asu ? That would be a good indication that your third molecule is truly th

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

I think the average structure is much less than 20 GB since most data seems to be collected as SAD. I quickly looked at my data ~20 structures 3 MAD, 9 SAD, 3 MIR, 4 MR, number of amino acids per asu 150 - 9600, the average was closer to 3 GB (compressed). The largest dataset 24 GB (compressed

Re: [ccp4bb] High Rfac/Rfree for a 1.6A reso structure

Santarsiero, Bernard D. wrote: On Fri, August 17, 2007 10:56 am, Eleanor Dodson wrote: There are obvious ones like - incomplete structure etc, but have you tried TLS? Sometimes this can dramaticaly improve the R factors. When people run TLS, are they trying to improve the R-factor

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

Hi Mischa, I think you are right with ligand structures and it would be very difficult if not impossible to distinguish between real measured data and faked data. You just need to run a docking program dock the ligand calculate new structure factors add some noise and combine that with your r

Re: [ccp4bb] "Quick soak" method

There's a nice databank out there in the world wild web: http://www.sbg.bio.ic.ac.uk/had/ Juergen Derek Logan wrote: Hi Uwe, Just what I wanted to hear, and with a limited set of compounds too! Follow-up question: what are these 4-6 most successful compounds? Thanks also for the tips on

Re: [ccp4bb] XDS.INP for BNL X29A

Agnes Rinaldo-Matthis wrote: Dear all, I wonder if anyone has a XDS.INP file for the beamline X29A at Brookhaven National Lab? I collected the data March 2007, ADSC Quantum 315 detector, and cannot process the data with other programs. I asked the beamline scientists and they don´t appear to

Re: [ccp4bb] protein/dna complex crystal

W.M. B. wrote: Dear All: My protein/DNA complex crystal diffracts to 3.2 A ( in-house source). It crystalized in 20% PEG 8K, NaCaCo 6.5. I tried to add ATP, CaCl2 and spermidine. The diffaction doesn't improve. Would you please give me some advice? Thanks a lot, Steve How does

Re: [ccp4bb] problems with map quality, refinement and R/Rfree

Hi Joe, have you tried to process the data in different programs ? This can sometimes make a dramatic difference, being completely unbiased I would recommend XDS over Mosflm or HKL2000. Was your data carefully collected ? How many rejections, overlaps do you have ? Juergen -- Jürgen Bosch U

Re: [ccp4bb] MR with 40% identical model failed

1) How can I make a mask as mentioned above? Am I doing it the wrong way? You can run NCSMASK with your first placed domain and generate a suitable mask file for DM. 2) Is there any other method to improve the density of the missing structure? I tried several MR probes of the sec

[ccp4bb] X-tallography on OS X aka 10.5 Leopard

Hi all, just a quick draft report on 10.5 and our beloved programs. Upgraded an existing 10.4.10 ( by the way you will need ~5 GB to upgrade your existing system), no clean install. Coot 0.31 does not work (need to upgrade anyway, more sometime this weekend, seems to have troubles with libti

Re: [ccp4bb] protein degradation?

Another possibility, since you say MS looks identical and you are unable to separate those two bands by other chromatografic means, is simple a metal binding site in your protein. If the charge is changed in your protein due to metal binding then the apparent molecular weight will differ - that

Re: [ccp4bb] Problematic P2 dataset with pseudotranslation

Hi Julian, I didn't see in Elenor's reply the "calculate a native Patterson map" option and verify that you actually have translational symmetry. You should have an off origin peak which will then give you the translation vector. When running Molrep look at the logfile it should automatically

Re: [ccp4bb] To bathe or not to bathe.

One additional point to add not raised by Bob is that crystals are different. So you can shoot at one end of the crystal and say have a mosaicity of 0.2 degrees but somewhere else it might be 1.4 or even worse. In such cases e.g. rod like needles it pays off to have a smaller than crystal beam

Re: [ccp4bb] To bathe or not to bathe.

Richard Gillilan wrote: I am currently working on guidelines for when helium and microbeam are necessary (based on both simulations and explicit measurements). At the present time, my feeling is that crystals below 50 micron can certainly make the extra hassle worthwhile. It really depen

Re: [ccp4bb] Unidentified ligand (electron density) found at active site

Did you had an inhibitor present in your purification ? Complete tablets ? Can you derive from the chemical environment perhaps if some of the atoms are nitrogens or oxygens ? Then you could sketch your putative molecule and search in the NCI database for homologous structures to your sketch.

Re: [ccp4bb] I have my bound ligand (I think), now what?

Hi Brenda, you'll need a cif description file for your ligand which you will read in either Coot or Refmac so that it will also refine correctly. I usually get my cif's from the Dundee PRODRG server, you can either paste your current coordinates as ATOMS in the provided field or sketch your m

Re: [ccp4bb] SUMMARY: PEG MW vs. cryoprotectivity

Something else I thought to include in my earlier email, not sure if you guys are aware of this nice database. Search for your main precipitant and see what others did to protect their poor crystals. http://idb.exst.jaxa.jp/db_data/protein/search-e.php Juergen -- Jürgen Bosch University of Wa

Re: [ccp4bb] Pseudo Merohedral twining in C2 space group?

Hi Hiaolei, I believe you have C2 with pseudo translation and that screws up the merohedral twinning test. As you also write you know the translation vector already. Most likely your crystal truly is in a higher symmetry, but for example during freezing (and the high solvent content) your mul

Re: [ccp4bb] artificial dimerization modules

Search for e.g. Leucine zippers and you should find some references. or e.g. Yamada et al. Protein Science 16(7) 1389-1397 Juergen Arnon Lavie wrote: This is not strictly a crystallography question, but I imagine (and hope) that some of you would be able to advise me. In short, I would like

Re: [ccp4bb] Coot 0.4 on Mac OS X 10.4

Wrong board, here's what Bill posted to the cootbb yesterday: Hope that solves your problem, Juergen forwarded email: Hi Folks: In response to the numerous death threats, I've tried to make a stand- alone coot for OS X 10.5 intel. http://tinyurl.com/24mchk It might work on 10.4 intel as

[ccp4bb] Webcast of the CCP4 study weekend ?

Hi CCP4 study weekend organisers, will there be a live webcast of the event, or alternatively can one view on demand certain lectures ? Thank you very much in advance for any useful links ! Juergen -- Jürgen Bosch University of Washington Dept. of Biochemistry, K-426 1705 NE Pacific Street S

Re: [ccp4bb] Ramachandran statistics

Molprobity -- Jürgen Bosch University of Washington Dept. of Biochemistry, K-426 1705 NE Pacific Street Seattle, WA 98195 Box 357742 Phone: +1-206-616-4510 FAX: +1-206-685-7002 Web: http://faculty.washington.edu/jbosch

Re: [ccp4bb] Webcast of the CCP4 study weekend ?

Rajesh Ponnusamy wrote: Do the webcast is working in this link ? http://extrplay.dl.ac.uk/ Thank you Rajesh Ponnusamy Except of the archived lectures nothing works for me, (OS X Safari, Firefox, Linux, Mozilla) I was ready to watch Piet at 6 am PST, but then decided to have another cup

Re: [ccp4bb] Webcast of the CCP4 study weekend ?

D] On Behalf Of Juergen Bosch Sent: Friday, January 04, 2008 9:35 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Webcast of the CCP4 study weekend ? Rajesh Ponnusamy wrote: Do the webcast is working in this link ? http://extrplay.dl.ac.uk/ Thank you Rajesh Ponnusamy Except of the arc

Re: [ccp4bb] How to refine large moleculars?

How does the Molprobity report look like ? How many Rama outlieres, bad Cbeta, rotamers ? What's your percentile ? Look at the multicriterion chart to fix your problems :-) http://molprobity.biochem.duke.edu/ Juergen Yongchao Li wrote: Dear all, Thanks for all replies. After water addition,

Re: [ccp4bb] microsoft 3-button wheel mouse with OS X 10.5

Hi David, since you said you bought a few iMacs, try the mouse first without any drivers on a virgin iMac, if that works, then reinstall those which you had exposed to the drivers for that mouse. All procedures you describe seem to me pretty standard out of the box and work on my mighty mouse

Re: [ccp4bb] protein expression problem

Another point not yet brought up is how do you express ? things to check: - different media (LB. TB, auto) - when do you induce (mid log phase, or end log phase) - how long do you induce (before reaching stationary phase, going over night into starvation phase) - how much IPTG do you add - MBP

Re: [ccp4bb] crashing-out protein eluted from Nickel column

Not sure if somebody mentioned it already, but have you played with other buffers than the recommended sodium phosphate from the manual ? Most lazy people use Tris because there's a 1 M stock solution - but you can try also other buffers as long as you stay in a pH range >pH6 Of course you sti

Re: [ccp4bb] Check the conformation of one important amino acid

Chavas Leo wrote: Dear Sun -- I want to check the conformation of one important amino acid in the structure by looking the difference density map. Should I just omit that amino acid in the refinement or should I also omit its flanking amino acids? Which one is better? The real expert will

Re: [ccp4bb] Vista

Hi all, sorry I couldn't help it :-) flames on http://movies.apple.com/movies/us/apple/getamac/apple-getamac-chooseavista_480x376.mov flames off Juergen James Stroud wrote: For those who risk becoming blinded and/or deafened by the vista bells and whistles: http://pcworld.co.nz/pcworld/p

Re: [ccp4bb] Off topic: ask about cryoprotectant selection using lithium sulfate as precipitant for crystal growth

Have you tried the various oils ? As a last resort Greek olive oil if paratone and others fail. How about sugars ? Stay away from propanol, your crystals will start floating through your wells with very rapid movements. I once had a 30% 2-propanol crystal condition and mounting crystals only wo

Re: [ccp4bb] multiple sequence alignment from multiple pairwise structural alignments

Not so long ago someone posted this link in this bord: http://www.charite.de/bioinf/strap/ It convinced me. Maybe that should also be included in the CCP4wiki a collection of what program do I use when I want to make X Y or Z Juergen Ashley Buckle wrote: I can recommend MUSTANG: http://p2

Re: [ccp4bb] finicky protein

Something else you could try is adding know ligands to your purification step - depending on your proteein (or even during expression, e.g. metals come to mind). Juergen [EMAIL PROTECTED] wrote: Just beware that changing how you break the cells open can change the average size of chromosome

Re: [ccp4bb] Low resolution data with substrate

yang li wrote: Hi All, We have several substrate-soaked data with resoltuion from 3.1~3.6A, after refinement with the native structure, the rfree are in the range of 0.29~0.34. We found in the expected active site there do have extra densities, but not very clear. In some chains the densi

Re: [ccp4bb] Kay Diederichs and Novel_R source?

David J. Schuller wrote: I would like to get a hold of the program Novel_R, the source code for which is supposed to be available on Kay Diederichs' web site. However, the links I have seem to be outdated. Does Diederichs have a new web site, and is the Novel_R source still available? The outda

Re: [ccp4bb] discontinuous data wedges in XDS

You can integrate them as separate wedges (in different directories), then later merge them (XDS_ASCII.HKL) in Xscale. Make sure though you have the orientation right and starting angles etc. You'll have to first refine one wedge, then once you are happy with it copy the GXPARM.XDS into the othe

Re: [ccp4bb] Bacterial induction at 18C

Hi Raji, you can't compare cultures with only one protein expressed by amount of cell yield or OD at the end. It's not really fun for the poor E.coli's to produce our favourite proteins (even if they're not toxic to E.coli). We keep thinking you just induce and harvest later E.coli takes care

Re: [ccp4bb] question on how crystals form

Hi Mike, how does your protein look on a sizing column ? Perhaps a dimer ? That would then explain the tendency to form dimers in different crystal forms, as it is a biological relevant dimer. for the eventuality that you have no clue how the sizing looks like, run one and find out. Juergen

Re: [ccp4bb] Mosflm : data process of crystal with huge unit cell

Hi Francisco, you could try using these keywords in Mosflm: POSTREF WIDTH 3 #since you have 0.1 degree oscillation and Mosflm can only handle 30 images at once, the default I believe is 5 images if I'm not mistaken SEPARATION CLOSE PROFILE RMSBG 25 POSTREF USEBEAM Then I would start indexing

Re: [ccp4bb] Finding NCS operator from one heavy atom site?

Hi Partha, you could add "artificial" sites close to the Se sites in regions of density which look similar to you, you will need at least three sites then let resolve figure out the NCS operators. You can also scratch your head and look at the selfrotation function of your dataset. You might

Re: [ccp4bb] crystallisation

Hi Sajid, congratulations to your nice looking crystals. I'm not sure if someone already sugested to mount smaller crystals ? You write they need 4-5 days, I assume you can already see them earlier before they reach that size. Am I roughly right in the assumption that these crystals are about

Re: [ccp4bb] crystallisation and mosaicity

Hi Charlie, yes you are right, but I assumed if people see a cloud of condensed fog over their LN2 bath they should remove that by a) filling up the bowl completely e.g. some LN2 drips out of the bowl b) blow the fog away before you dip c) ask someone for advice In general I have observed much

Re: [ccp4bb] 3D model building without CRT monitor

Dima Klenchin wrote: Vangelis Christodoulou wrote: Philips is offering an interesting solution: http://www.business-sites.philips.com/3dsolutions/products/3dscreens/index.html Interesting! Their PDF says it

Re: [ccp4bb] cryo-cooling, was: Re: [ccp4bb] crystallisation and mosaicity

But for some crystals flash-cooling is better at temperatures higher than in the 77 K to 100 K regime for unknown reasons. This can be one reason why flash-cooling in the gas stream occassionally is better. It is also why liquid propane worked for Raji E. and Karolin L.: they were using a

Re: [ccp4bb] Activity of a mutant enzyme compared to wild type - puzzle

Narayanan Ramasubbu wrote: Dear all: I have a single residue mutant whose enzyme activity is about 50% of the wild type. Interestingly, the mutation is in a region that involves a secondary site but not the active site. The two structures with or without ligands fit well (0.18 A) and the metal

Re: [ccp4bb] Off topic: insect cell expression

Hi, can you perform a thermal shift assay ? Google or it or find some references in a posting not too long ago perhaps 6 months or less. If so you can check your protein with various "additives" and see which ones stabilize your protein. What happens if you dialyse your sample instead of concen

Re: [ccp4bb] Coiled Coils

How about Coils ? http://www.ch.embnet.org/software/COILS_form.html jürgen On 15 Jul 2008, at 14:38, Neeraj wrote: Hi all, I was wondering if anyone knows a good website/software for prediction of coiled coil regions within proteins based on the amino acid sequence. Also does anyone kn

Re: [ccp4bb] SUMMARY: synchrotron remote data collection

Hi all, now that we know who does remote data collection, how many different systems are our there which are incompatible with each other in terms of sending crystals in pucks or SSRl types of cassettes for robot remote data collection ? - Jürgen Bosch University of Washington Dept. of Bi

Re: [ccp4bb] SUMMARY: synchrotron remote data collection

A start is made, if somebody would like to comment / add information to the open "?" that would be great. http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Synchrotrons Jürgen - Jürgen Bosch University of Washington Dept. of Biochemistry, K-426 1705 NE Pacific Street Seattle, WA 981

Re: [ccp4bb] question about getting rid of model bias in refinement

Hi Sun, you could address this problem by using CNS omit maps during your refinement. Resolve and Phenix offer same/similar options, the poor man's omit option would be delete a stretch of residues manually and re-refine. Omitting single residues is not enough, as a rule of thumb you shou

Re: [ccp4bb] Pymol movie ration along any axis

You should also have a look at emovie http://www.weizmann.ac.il/ISPC/eMovie_download.html That gives you more flexibility, but if you really want to control things, then write a script which saves frames step by step as you turn your molecule in any direction you want. Jürgen On 1 Aug 2008,

Re: [ccp4bb] protein crystal decay problem

I'd rather go for a complete low resolution dataset. Is this a native crystal ? HA derivative ? Even with a 4Å data set you can do something it's painful but not impossible e.g. molecular replacement if possible. Then at least you would know your spacegroup & perhaps gain some insights from

Re: [ccp4bb] Change reflection file names

Is your "problem" Mosflm related ? Then you could have used the command Template XXX_.img Jürgen On 7 Aug 2008, at 01:40, yanming Zhang wrote: All UNIX gurus, I need to change 300 image file names sequentially, such as: XXX_10001.img to XXX_101.img XXX_10002.img to XXX_102.img ...

Re: [ccp4bb] Ammonium citrate tribasic buffer

Just on a side note, can someone clarify why Hasselbach is not Hasselbalch or vice versa ? Or is that the same guy just somewhere sometime misspelled and for ever in the records ? See here: http://www.britannica.com/EBchecked/topic/261188/Henderson-Hasselbach-equation Jürgen On 7 Aug 2008,

Re: [ccp4bb] Progresss with Stereo 3D under Mac OS X Leopard

Very well phrased Steve, and I do agree - however stereo is helpful e.g. looking at binding pockets etc. I think it depends very much on your workflow what you are actually doing if you really need lots of stereo. In my case I run everything on my MacbookPro but I occasionally walk over to ou

[ccp4bb] Facebook for Neerds

Hi all, this is another generation question :-) Some of you are familiar with the social networking webpage Facebook, now there's something similar for Academics http://www.academia.edu/ And here's a link for some background: http://arstechnica.com/news.ars/post/20080918-academia-edu-traces-a

Re: [ccp4bb] Helix builder

Not quite sure if I understand your question correctly. But how about Moleman from the USF suite ? Use the command HELIx_generate, then later mutate that helix into your sequence. Jürgen On 19 Sep 2008, at 11:19, john peter wrote: Hi CCP4ers, Apologies for this off-topic question, but I

Re: [ccp4bb] Troubleshooting protein purification cation IEX

Another suggestion that comes to mind is crosslinking via Cys, are you purifying under reducing conditions ? Or since you have inclusion bodies they're in general not correctly folded hence expose hydrophobic regions and can interact with other proteins, to avoid unspecific interaction add

Re: [ccp4bb] Off-topic: coomassie linearity?

On 25 Sep 2008, at 14:35, Jacob Keller wrote: Dear Crystallographers, I remember having seen on this listserve that coomassie stain is horribly non-linear in intensity per protein concentration, which leads me to two questions: 1. Does anybody have a reference for quantitation of coomassi

Re: [ccp4bb] Off-topic: coomassie linearity? SUMMARY

On 26 Sep 2008, at 08:20, Jacob Keller wrote: Hi All, thanks for the responses. It seems that coomassie linearity is not so bad after all, especially when measured by IR fluorescence (reference from Steve Darnell). Others mentioned silver stain, but it seems that silver has a narrower dyn

Re: [ccp4bb] resuspending precipitated protein

6M Guanidiniumhydrochloride works pretty good, the question is only will you be able to refold it correctly ? I believe a better approach is to avoid precipitation in the first place and optimize your purification procedure in such a way that it works. When do you observe precipitate ? Dial

Re: [ccp4bb] SOme wquestions about refining.......

Hi AA, On 1 Oct 2008, at 20:34, AA wrote: Hello everyone, Please forgive my ignorance about the field of crystallography. I have recently started to process the diffraction data of a protein with a ligand attached to it. we have the structure of this protein already known and also known w

Re: [ccp4bb] non ccp4 question

Hi Jonathan, try using the PRODRG Server with your coordinates, or alternatively run Refmac reading in the cif file for your ligand. Jürgen On 3 Oct 2008, at 14:25, Jonathan Marvin Caruthers wrote: Sorry, but I've nowhere else to turn, I hope nobody minds. In trying to model a nonyl gluc

Re: [ccp4bb] refmac and average B factors

Hi Engin, you are correct, you have to run TLSANL and report the corrected B- factor in your table 1. Jürgen On 4 Oct 2008, at 18:32, Engin Ozkan wrote: Hi everyone, I was in the middle of creating a "Table 1" for a finished structure and was puzzled by one number. It is the average B f

Re: [ccp4bb] foam dewar usage ?

Hi Carsten, since you don't use them anymore I would volunteer to have them shipped to me for free :-) I might cough up the shipping fee. We have both in the lab, for certain purposes I prefer the stainless steel over the foam dewars e.g. freezing protein as 20 µl drops then picking them

Re: [ccp4bb] Crystal growing in one direction...need suggestions

You could also try seeding, crush up your needles seed a new plate and re-screen. With re-screen I mean not your original conditions but e.g. Hampton 1&2 or orthers and see if you get a different condition with other crystals. You might also see into your current condition. I assume you have

Re: [ccp4bb] buster-tnt on OSX ?

@all, we've been comparing various programs during our SGPP times (that was about 2 years ago) Sharp, Shelx, bp3, mlphare, SnB (BnP). If I remember it correctly at that time Sharp was the winner, although the site finding was the major bottleneck/problem. What we ended doing was finding s

Re: [ccp4bb] crystallization of proteins with His-tag and/or c-myc tags

I seem to recall a paper by the SGC group showing their flowscheme, all proteins are first crystallized with the His-tagged variant, only if no crystals are obtained or they diffract poorly a TEV cleaved version is purified. I think the success rate of solved structures between His-tagged a

Re: [ccp4bb] X-Ray versus NMR Structure

I think we should slowly arrive in the 21st century and realize that methods are complementary to each other. I've never done NMR by myself only some xray stuff and attempts to merge EM data with xray almost 10 years ago to arrive at ab initio phases. Sure one can argue what information can y

Re: [ccp4bb] SUMMARY - crystallization of proteins with His-tag and/or c-myc tags

Here's another paper you might want to have a look at: Carson et al. His-tag impact on structure. Acta Crystallogr D Biol Crystallogr (2007) vol. 63 (Pt 3) pp. 295-301 and here's the Structural Genomics paper (or one of them, I believe there was another one which I originally thought of): Li

Re: [ccp4bb] Crystallographic computing platform recommendations?

Anyone out there using a current 8 core MacPro with 32GB and OSX running the usual x-tallographic programs ? Send me an email off the list if you should be such a person. Thanks, Jürgen On 18 Nov 2008, at 07:26, William G. Scott wrote: On Nov 18, 2008, at 7:01 AM, Mischa Machius wrote: F

Re: [ccp4bb] looking for a program

Hi Lucas, you can send your PDB file to this server and get the information you want in one of their analysis. http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/upload.html Jürgen On 22 Nov 2008, at 14:45, Lucas Bleicher wrote: By the way, is there a program (perhaps one of those cited on

Re: [ccp4bb] NCS and manual building

Use Coot option 1) rebuild your chain A and superimpose manually with Coot A to the other chains, then write out a new merged PDB file option 2) use the Coot command which allows you to copy whatever you have modeled in one chain to the other chains. for more info check out the link: http://

Re: [ccp4bb] co-crystallization

The Km changes with your reservoir, so predictions are limited. In general if you have a low Km this is favourable but not a given that your ligand will be found in the electron density map. As a starting point try a molar ratio of >3 of the ligand to your protein and you can go as high as

Re: [ccp4bb] site mutation evaluation

Pymol the question is, into how much trouble do you want to get ? MD simulations ? Energy minimisation ? Then you will need to do more than just mutate on the sreen one residue with Pymol. Jürgen On 2 Dec 2008, at 17:29, Hongmin Zhang wrote: Dear All, I am trying to mutate a single amino

Re: [ccp4bb] site mutation evaluation

tated residue would disturb ligand binding because of the side chain flexibility. Best! Hongmin On Wed, Dec 3, 2008 at 12:50 PM, Juergen Bosch <[EMAIL PROTECTED] > wrote: Pymol the question is, into how much trouble do you want to get ? MD simulations ? Energy minimisation ? Then you will

Re: [ccp4bb] site mutation evaluation

ing or not. Best! Hongmin On Wed, Dec 3, 2008 at 2:15 PM, Juergen Bosch <[EMAIL PROTECTED]> wrote: In that case you might want to use CNS with model_anneal.inp or model_minimize.inp, or the equivalents in phenix Jürgen On 2 Dec 2008, at 21:29, Hongmin Zhang wrote: Yes, it is bett

Re: [ccp4bb] Fwd: [ccp4bb] site mutation evaluation

d need some docking softwares or the structures of the complex. ta liu Hongmin Zhang wrote: Thanks! I think we still can't tell if the mutant would disturb ligand binding or not. Best! Hongmin On Wed, Dec 3, 2008 at 2:15 PM, Juergen Bosch <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTE

Re: [ccp4bb] AW: [ccp4bb] suggestions for UV spectrometer

Hi, really strange, I always dilute my protein when taking an absorption spectra. I try to adjust my expected concentration to a readout of ~ 0.2-0.3 OD280. And the Bradford is just as well as 'picking house numbers', depending on your protein, you can underestimate your protein concentra

[ccp4bb] PW XrayDB

Hi Tracy, I think I know the PW for XrayDB. Let's talk tomorrow. Jürgen - Jürgen Bosch University of Washington Dept. of Biochemistry, K-426 1705 NE Pacific Street Seattle, WA 98195 Box 357742 Phone: +1-206-616-4510 FAX: +1-206-685-7002 Web: http://faculty.washington.edu/jbosch

Re: [ccp4bb] updated XDS binaries available

But it keeps you busy and you have the feeling you are running the latest version. Jürgen On 13 Dec 2008, at 11:35, George M. Sheldrick wrote: Is it really essential to force users to update XDS every four months, especially when "No other changes were made to the binaries"? George Prof. Geo