[ccp4bb] DLS

Hi there Sorry for the off ccp4 topics. I am planning to get a DLS to set up my crystallography lab. I got a tight budget. Around USD 8 perhaps. I'm quite new to this field. Thanks in advance for your suggestions Regards Shukuri

Re: [ccp4bb] resolution limit stuck in Refmac5

On Fri, Oct 29, 2010 at 5:46 PM, Tom Huxford wrote: > I'm working with good quality relatively complete x-ray diffraction data > collected to a resolution limit 2.6 Å from a crystal of a protein with a > small molecule ligand bound. I ran MR from 10-4 Å and then did maximum > likelihood rigid bod

[ccp4bb] resolution limit stuck in Refmac5

Hi all, I'm working with good quality relatively complete x-ray diffraction data collected to a resolution limit 2.6 Å from a crystal of a protein with a small molecule ligand bound.  I ran MR from 10-4 Å and then did maximum likelihood rigid body refinement in Refmac5 against data from 50-3.

Re: [ccp4bb] Strange spots

They remind me of the fiber bundle on optic taper between the phosphor and the CCD. That's from things I saw years ago (BC - before crystallography) and I don't know the system in use here. I suspect it's instrumental and any diffraction in that area of the detector should show similar effects

Re: [ccp4bb] Strange spots

The shape reminds me of the focused beam spot profile from slightly misaligned capillary optics. I don't have too much experience with these, but the incident beam profile does tend to "propagate" through to the spots on the detector. I wonder, could what you are seeing be a "halo" of minor incid

Re: [ccp4bb] Strange spots

Kris, the link works for me and obviously for other people. I don't know why you don't have access to it... Anyway, thank you Konstantin for providing the pdf! Julian On 10/29/10 4:17 PM, Konstantin v. Korotkov wrote: The link worked for me, pages 320-322 attached. -Konstantin On Fri, 29 O

Re: [ccp4bb] Strange spots

Are these very strong reflections? Do they appear on more than one image? Are they an artefact of the detector or the image display program?

Re: [ccp4bb] Strange spots

Hi Dave, The circles are quite prominent in the "inner circle (lune)" that you highlight but not in the next one. The full image is too small to see details but I don't see any clear circular halos for any of the other lunes. If you start with the lune going through the origin and number it z

Re: [ccp4bb] Strange spots

Dear Liz, You will be disappointed. I went immediately to that link, but page 321 is not available as part of the Googlebook sample, which jumps directly from page 320 to page 325. With best wishes, Gerard. -- On Fri, Oct 29, 2010 at 09:13:27PM +0100, elizabeth.d...@d

Re: [ccp4bb] Strange spots

On Fri, Oct 29, 2010 at 4:25 PM, Ethan Merritt wrote: > You may laugh, but the Google finds hits on the topic here: > >   http://atlas-conferences.com/cgi-bin/abstract/cauu-47 anyone who made complete sense of that abstract is invited to go here : http://snarxiv.org/vs-arxiv/ and if you do, ple

Re: [ccp4bb] Strange spots

Autoindexing in the truest sense of the word? ;-) On 10/29/10 12:08 PM, "David Goldstone" wrote: Dear All, Does anyone have any insight into what the circles around the spots might be? cheers Dave -- David Goldstone, PhD National Institute for Medical Research Molecular Structure The Ridgewa

Re: [ccp4bb] Strange spots

On Friday, October 29, 2010 12:59:40 pm Jacob Keller wrote: > > Yes, but the question is what in real space gives rise to reciprocal-space > frog spawn? (Frogs, I guess?) You may laugh, but the Google finds hits on the topic here: http://www.ph.surrey.ac.uk/newsite/ugrad_uploads/Lisowski2004

Re: [ccp4bb] Strange spots

There is always hope!!! Seriously though, I have never seen anything like this before! I am watching this thread with interest to see what others suggest. THanks Also thanks should go specifically to Julian Nomme who took the trouble to send us all the Helliwell book link. Liz __

Re: [ccp4bb] Strange spots

I think this is a poly-crystalline incommensurately modulated crystal, i.e. incommensurately modulated crystal, which fractured upon freezing, resulting in averaging of satellite spots. Fig. 3b from here: http://www.princeton.edu/~actin/documents/Proteincrystalscanbeincommensurate lymodulated.pdf

Re: [ccp4bb] Strange spots

Only when you do refinement(explains other thread about the unexplained R-gap) JPK - Original Message - From: Sanishvili, Ruslan To: Jacob Keller ; CCP4BB@JISCMAIL.AC.UK Sent: Friday, October 29, 2010 3:08 PM Subject: RE: [ccp4bb] Strange spots C'mon now! Everybody k

Re: [ccp4bb] Strange spots

C'mon now! Everybody knows that frogs in real space become handsome princes in the reciprocal one... N. Ruslan Sanishvili (Nukri), Ph.D. GM/CA-CAT Biosciences Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667 rsanishv...@anl.gov ___

Re: [ccp4bb] Strange spots

Yes, but the question is what in real space gives rise to reciprocal-space frog spawn? (Frogs, I guess?) - Original Message - From: Marcus Winter To: CCP4BB@JISCMAIL.AC.UK Sent: Friday, October 29, 2010 2:56 PM Subject: Re: [ccp4bb] Strange spots Dear Davi

Re: [ccp4bb] Strange spots

Dear David, Further to the previous learned responses, surely, this is just frog spawn ? My apologies: it is a Friday evening, after all... Marcus Winter. -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of David Goldstone Sen

[ccp4bb] Which version CCP4 output DFc colume in SIGMAA?

Hi, I remember the SIGMAA utility in some version of CCP4 can output DFC colume in the mtz file. If somebody see this colume in you SIGMAA mtz file, could you let me know which version CCP4 you are using? THanks! Best Regards, Hailiang

Re: [ccp4bb] Strange spots

Gerard, I happen to have inherited a copy of Sir John's book from Joe Becker some years ago. Don't get your hopes up as the effect is apparently unexplained: "No satisfactory explanation for these features has yet been found, but they are probably related to defects in the crystal lattice." Per

Re: [ccp4bb] Strange spots

Google books: http://books.google.com/books?id=RqNb241Q484C&printsec=frontcover&dq=Macromolecular+Crystallography+with+Synchrotron+Radiation&hl=en&ei=JA3LTMe2NMSnnQfAjN3mDw&sa=X&oi=book_result&ct=result&resnum=1&ved=0CC8Q6AEwAA#v=onepage&q&f=false

Re: [ccp4bb] Help with model bias in merihedral twin + Refmac5

Dear Colin, Thank you for the email. To be honest, I don't know exactly which map they are. From my understanding (and according to http://www.ccp4.ac.uk/schools/India-2010/tutorials/refmac/Murshudov30th.pdf), Refmac5 outputs 'normal map' 2mF(obs)-DF(calc) and 'difference map' 2mF(obs)-DF(cal

Re: [ccp4bb] Strange spots

Dear Gerard I will do a scan of fig 8.1b asap, probably Monday. Greetings, John Sent from my iPad On 29 Oct 2010, at 18:44, Gerard Bricogne wrote: > Dear John, > > Would it be possible to know more about what you are referring to > without having to buy (or steal) your book :-)) ? > >

Re: [ccp4bb] Strange spots

Dear John, Would it be possible to know more about what you are referring to without having to buy (or steal) your book :-)) ? Thank you in advance! With best wishes, Gerard. -- On Fri, Oct 29, 2010 at 06:41:51PM +0100, John R Helliwell wrote: > Dear Da

Re: [ccp4bb] Strange spots

Dear Dave, You have a collector's item there! The closest I have seen is illustrated in my book 'Macromolecular Crystallography with Synchrotron Radiation' page 321, which is a small molecule example. Best wishes, John Prof John R Helliwell DSc On Fri, Oct 29, 2010 at 5:08 PM, David Goldstone wr

Re: [ccp4bb] Bug in c_truncate?

Dear All, Thank you kindly for the replies and concerns over the problem I've experienced. I really appreciate them. I do not know how often the I -> F conversion is done in CCP4i's F2MTZ GUI, especially with the FreeR flags preserved. Nevertheless, as mentioned, the problem seems to arise be

Re: [ccp4bb] Real space refinement [was: Against Method (R)]

Hi Dirk, yes, the apparently larger radius of convergence in real space refinement > impresses me, too. Therefore, I usually do local real space refinement after > manually correcting errors, either with Moloc at lower resolution or with > Coot at higher resolution, prior to reciprocal space refi

Re: [ccp4bb] Against Method (R)

On 10-10-29 12:03 AM, Robbie Joosten wrote: Hi Bart, I agree with the building strategy you propose, but at some point it stops helping and a bit more attention to detail is needed. Reciprocal space refinement doesn't seem to do the fine details. It always surprises me how much atoms st

Re: [ccp4bb] Bug in c_truncate?

Dear Phil, I think ctruncate is used as a general tool to convert I's to F's, so it would be good to have an option to propagate FreeRflags. The workaround, of course, is to use cad for this. I have the feeling (did not check) that the problem of Peter arose because to ccp4i F2MTZ-SHELX gui was no

Re: [ccp4bb] Against Method (R)

Dear George, thanks a lot! I see the point, that in reciprocal space refinement one could refine directly against the observed intensities and sigmas. But in principle, one could do iterative real space refinement, structure factor and intensity calculation for refinement statistics and weight

Re: [ccp4bb] Bug in c_truncate?

Hi Phil, I do, but the freeR flag problem is easily circumvented. One can just use cad with the output mtz from ctruncate and the input mtz: cad \ HKLIN2 $WORKDIR/raw.mtz \ HKLIN1 $WORKDIR/ctruncate.mtz \ HKLOUT $WORKDIR/ctruncate_withRfree.mtz \ <>$WORKDIR/mtz_creation.log   LABIN FILE 2  E

Re: [ccp4bb] Bug in c_truncate?

The normal use of [c]truncate is to take intensities from Scala, so it wouldn't expect FreeR flags in the file. I suppose this should be added for other uses of the program Is this something that is often used? Do people import intensities into CCP4 to convert them to Fs? Phil On 29 Oct 2010

Re: [ccp4bb] Bug in c_truncate?

Dear Peter, Since I did not hear that your problem is solved here my two cents. I did some tests using the ccp4i option "Convert Intensities to SFs" and found that here ctruncate completely ignored the FreeRflags. So my conclusion is that ctruncate does not need FreeRflags and you can use the foll

Re: [ccp4bb] Bug in c_truncate?

Tim, Although I always like to advocate XPREP, that would not work because the .sca format - most unfortunately - does not know about free R flags. George Prof. George M. Sheldrick FRS Dept. Structural Chemistry, University of Goettingen, Tammannstr. 4, D37077 Goettingen, Germany Tel. +49-551-3

[ccp4bb] Position as Postdoctoral Research Fellow - in membrane proteins structural biology , Oslo Norway

Dear CCP4 I have an open postion for biochemist/structural biologist with interest in membrane proteins. I would be most grateful if you could forward this email to any suitable candidates you may know of Best regards, Preben Postdoctoral Research Fellow - (Membrane Proteins Structural

Re: [ccp4bb] Bug in c_truncate?

Hello Peter, the easiest way to overcome the problem might be to use xprep to export to sca-format and use scalepack2mtz for the conversion. That seems to be the least hasslesome way, although I am not totally sure that this procedure preserves the R-free flags set by xprep. Tim On Thu, Oct 28,

Re: [ccp4bb] Against Method (R)

Dear Dirk, There are good reasons why real space refinement has never become popular. With reciprocal space refinement, you refine directly against what you measured, taking the standard uncertainly of each individual intensity into account. In this context I was pleased to read in CCP4bb that

Re: [ccp4bb] Against Method (R)

Hi Robbie, yes, the apparently larger radius of convergence in real space refinement impresses me, too. Therefore, I usually do local real space refinement after manually correcting errors, either with Moloc at lower resolution or with Coot at higher resolution, prior to reciprocal space refi