[ccp4bb] Offtopic: Is there a way to search protein-protein interface structural similarity in database ?

Hi All, I wonder if there is a way to search protein-protein interaction interface similarities in PDB database? For example, I have two proteins proA and proB, part of proA and part of proB contact with each other in a crystal structure, I want to search if there are similar interaction

[ccp4bb] Postdoctoral Position at the University of Chicago

Postdoctoral Position in Cellular Communication Applications are invited for an immediate opening at the Cellular Communication Group with Dr. Demet Araç, at the Department of Biochemistry and Molecular Biology, University of Chicago (http://arac.uchicago.edu). We

Re: [ccp4bb] VERY old mtz file..

In case one wants to play around with openVMS or just recover some now-unreadable old data, and doesn't have a vax farm or even a single vax computer,there are step-by-step instructions for setting up a vax system using the simh emulator:

[ccp4bb] Postdoc Position - Berkeley

Lawrence Berkeley Laboratory Postdoctoral Researcher Job ID: 85784 Division: Molecular Biophysics & Integrated Bioimaging (Joint BioEnergy Institute) Date Opened: 11/1/2018 Summary: A postdoctoral position is immediately available to study the structure and function of macromolecular complexes

[ccp4bb] Effect of ionic strength on temperature-dependence of solubility

Hi. I was wondering if anyone could explain or point me to a source that explains (I’ve been having trouble finding one) why proteins tend to be less soluble at higher temperatures at high salt but more soluble at higher temperatures at low salt?

Re: [ccp4bb] VERY old mtz file..

Congratulations, CCP4bb, you have just witnessed the longest thread on JISCMAIL.  38 messages (and counting, presumably). Now we know how to troll the BB:  not even that old evergreen of where to cut resolution generates a fraction of this traffic. phx On 14/11/2018 15:54, Robbie Joosten

[ccp4bb] Fwd: [ccp4bb] VERY old mtz file..

Begin forwarded message: From: "charles w carter, jr" mailto:cwcar...@ad.unc.edu>> Subject: Re: [ccp4bb] VERY old mtz file.. Date: November 14, 2018 at 10:16:23 AM EST To: Eleanor Dodson mailto:eleanor.dod...@york.ac.uk>> I’ve found this thread to be most interesting and out of near

Re: [ccp4bb] VERY old mtz file..

We'll, you never know when someone wants the data. I do know that I was incredibly impressed when you managed to conjure up the experimental data for 2ins (from 1982!) a few years ago. Cheers, Robbie P.S. this was a really fun thread to read :D On 14 Nov 2018 16:04, Eleanor Dodson

[ccp4bb] Computational Scientist Position at the UK site of Vertex Pharmaceuticals

I wanted to call attention to the following position for a Computational Scientist Position at the UK site of Vertex Pharmaceuticals. Also, please recognize that applications must go through the website below. Kind regards, Jay - Vertex Pharmaceuticals (Europe) Ltd has an immediate opening

[ccp4bb] Post-doctoral opportunity in membrane protein structural biology

Center for Biomolecular Therapeutics (CBT), University of Maryland School of Medicine, Baltimore MD The Hasan laboratory (https://www.ibbr.umd.edu/profiles/s-saif-hasan) is recruiting a post-doctoral fellow with an interest in utilizing high-resolution single particle cryo-electron

Re: [ccp4bb] VERY old mtz file..

You are all extremely informed and clever!! This file is part of an old archive of haemoglobin structures from the 1990s. I suspect they are all generated on a VAX from lcf files when I was "updating" the archive.. So now if I have the character I can update them all again, in the unlikely event

Re: [ccp4bb] VERY old mtz file..

Hi Nick, I think I've found the machine stamps in the ccp4 lib (Ian Tickle directed me to the C programs folder yesterday. Thanks Ian): ccp4_ssydep.h #define DFNTI_MBO 1 /**< Motorola byte order 2's compl */ #define DFNTI_IBO 4 /**< Intel byte order 2's compl */

Re: [ccp4bb] VERY old mtz file..

Hi Zhijie, Thanks for the answer. I'd read http://www.ccp4.ac.uk/html/mtzformat.html "The first 4 half-bytes represent the real, complex, integer and character formats, and the last two bytes are currently unused" - and assumed that a) formats meant size, given that it was (4,4,4,1) in files I'd

Re: [ccp4bb] VERY old mtz file..

Hi Nick, I guessed the machine stamp from MRC/CCP4 format description - half byte 01 means BE, half byte 04 means LE. Are these only applicable to intel machines? How are other machine architectures indicated? I do not know. We probably can find the authoritative answer from the CCP4 library,

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 Zhijie Li wrote: > The semiBE.mtz has the big endian stamp (0x11 11 00 00 at bytes 9-12 ) > put in the header of the original file; everything else is untouched > Is this correct? I thought machine stamp

Re: [ccp4bb] VERY old mtz file..

here is a minimal Fortran program that writes out the contents as H,K,L,FOBS,SDFOBS - could be fed into contemporary F2MTZ to produce a current MTZ file : REAL h,k,l,fobs,sfobs OPEN(1,file='hklin',convert='BIG_ENDIAN',ACCESS='STREAM') DO i=1,20 !skip first 20 4-byte units READ(1)h END

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..

yes - prob. converted from lcf to mtz at some point.. Maybe on a VAX / E On Wed, 14 Nov 2018 at 10:46, Harry Powell < 193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: > Hi > > Okay, I can read that (sort of) with errors using a copy of mtzdmp from > ccp4 v 5.0, dated 23/01/04; I can tell

Re: [ccp4bb] VERY old mtz file..

Hi Okay, I can read that (sort of) with errors using a copy of mtzdmp from ccp4 v 5.0, dated 23/01/04; I can tell that Ben Luisi's name is in there (hello Ben!) and that the file was "converted to MTZ file mark 1 on 15/ 5/92", inter alia. I can even tell that there are five columns and 17218

Re: [ccp4bb] VERY old mtz file..

Hi Weren't the CCP4 base-level routines re-written from FORTRAN to C sometime in the late 1990's? Very occasionally I used to find bugs that had been introduced in this process (or possibly not corrected...) so it's possible that Eleanor's file might be readable with a really old code base.

[ccp4bb] Ivana Bertini Award: call for nominations open

Dear All A biennial award has been set up in memory of Ivano Bertini, who pioneered innovative methodologies in the field of NMR and championed technology integration as a foundation for correlative structural biology. The award recognises

Re: [ccp4bb] VERY old mtz file..

The CCP4 routines for MTZ and map files are written in C and thus do not use a Fortran unformatted OPEN statement, they use C-style block read & write. Cheers -- Ian On Wed, 14 Nov 2018 at 08:59, Kay Diederichs wrote: > It is not necessary to do error-prone conversions manually: the ifort >

Re: [ccp4bb] VERY old mtz file..

The CCP4 library routines are supposed to read MTZ files in any recognised format, provided the correct machine stamp is present, so I’m puzzled that it doesn’t work in this case. In the days when multiple float formats were around, this certainly did work. The files were always written in the

Re: [ccp4bb] VERY old mtz file..

It is not necessary to do error-prone conversions manually: the ifort Compiler understands the convert='VAXD' Option in its OPEN statement - see https://software.intel.com/en-us/fortran-compiler-developer-guide-and-reference-open-convert-specifier Thus one could just write a tiny read-write