Re: [ccp4bb] Off-topic-Cleavage with TEV protease

Also keep in mind that many of the purchased TEVs are formulated with some reducing agent (e.g. AcTEV comes in a buffer with 5mM DTT, if I recall correctly). So unless the enzyme is buffer exchanged beforehand, there will be some reducing agent introduced alongside it, depending on the dilution.

Re: [ccp4bb] Molprobity Clashscore

On Thu, Jan 12, 2012 at 8:11 AM, Pavel Afonine wrote: > >>  Who needs hydrogens? > > > may be you need to read this (for example): > > http://www.phenix-online.org/papers/dz5209_reprint.pdf > While this reference is useful, it neglects the role of prior chemical forces (vdW and electrostatics, fo

Re: [ccp4bb] Babinet solvent correction [WAS: R-free flag problem]

the polynomial/Gaussian model in the paper). The protein structure factors (Fc) are not used in the bulk solvent correction - nor, in my opinion, should they be (as I attempted to point out in my previous email). Regards, Tim -- - Tim

Re: [ccp4bb] Babinet solvent correction [WAS: R-free flag problem]

to try out the differentiable models we describe. The Babinet trick was a convenient way to make coding easier. Anyway, I hope this helps explain it a bit more, and again: sorry for the long-windedness. Regards, Tim -- - Tim Fen

Re: [ccp4bb] Babinet solvent correction [WAS: R-free flag problem]

way from describing the solvent region as > "flat". But the paper does not include a Babinet model in the tables > of comparative results. > > Do you know of any published or unpublished results that compare > the R factors achieved by Babinet treatment with those obtained f

Re: [ccp4bb] Off-topic: Univ California boycott of Nature publishing group

ublishing" on his webapge: http://www-cs-faculty.stanford.edu/~uno/news03.html with a link to an excellent letter he sent to Journal of Algorithms a few years ago: http://www-cs-faculty.stanford.edu/~uno/joalet.pdf -Tim -- ----- Tim F

Re: [ccp4bb] best linux for laptops?

ck to set up. ubuntu and fedora are pretty much identical otherwise. -Tim -- ----- Tim Fenn f...@stanford.edu Stanford University, School of Medicine James H. Clark Center 318 Campus Drive, Room E300

Re: [ccp4bb] LINKR in refmac

.peptide cis-peptide-link PCIS ..peptide PRO .. cis-peptide-link_pro NMCIS..peptide PRO .. cis-peptide-link_cn so you probably want TRANS. HTH, Tim -- --------- Tim Fe

Re: [ccp4bb] From oscillation photographs to seeing specific sections of reciprocal lattice.

/libc/manual/html_node/Opening-Streams.html#index-fopen64-931 on 64 bit machines, the file size limit is 2^63 bytes (this also depends on the file system type, just to make things even more complicated). Here's another easy way to test it: dd if=/dev/zero of=bigfile bs=1024 count=3145728 Hope this helps! -Tim -- - Tim Fenn f...@stanford.edu Stanford University, School of Medicine James H. Clark Center 318 Campus Drive, Room E300 Stanford, CA 94305-5432 Phone: (650) 736-1714 FAX: (650) 736-1961 -

Re: [ccp4bb] ANISOU

On Mon, 16 Mar 2009 11:01:34 +0800 Sheng Li wrote: > > Please read the coordinate file with alwyn's O, and then save it to > another file. The ANISOU lines will be removed. > only if you use s_a_i - pdb_read will preserve ANISOU. It might be easier to just grep them out: grep -v "^ANISOU" fo

Re: [ccp4bb] COOT Problem

On Sat, 13 Dec 2008 09:33:11 + Paul Emsley wrote: > Ethan Lai wrote: > > Dear all, > > > > I have recently installed Coot version 0.5 on Fedora 9. However, > > when I tried to open a mtz file, the following error occurs. > > > >>> CCP4 library signal library_file:Bad mode (Error) > >

Re: [ccp4bb] Crystallographic computing platform recommendations?

leases are only > supported for 18 months. > The comparable distribution to LTS is centos or the official rhel releases, which are on a 7 year support cycle. The standard ubuntu releases follow almost the same 18 month cycle as fedora. -Tim -- ------

Re: [ccp4bb] Crystallographic computing platform recommendations?

m4 macros coot uses (mmdb/ssm/guile-gtk) are broken such that 32 and 64 bit libraries can get mixed up, so you may not be using a 64 bit binary. HTH, Tim -- --------- Tim Fenn [EMAIL PROTECTED] Stanford University, School o

Re: [ccp4bb] off-topic: Enzymology textbook recommendations?

quot;Enzymatic Reaction Mechanisms" Christopher Walsh -- ----- Tim Fenn [EMAIL PROTECTED] Stanford University, School of Medicine James H. Clark Center 318 Campus Drive, Room E300 Stanford, CA 94305-5432 Phone: (650) 736-1714 FAX: (650) 736-1961 -

Re: [ccp4bb] Hardware problem: "nVidia NV41 [Quadro FX 3450/4000 SDI]" on Redhat EL 5 (needed for stereo viewing)

;s repositories, which include fedora/rhel rpms for nvidia drivers: http://atrpms.net -- ----- Tim Fenn [EMAIL PROTECTED] Stanford University, School of Medicine James H. Clark Center 318 Campu

Re: [ccp4bb] diffraction images images/jpeg2000

ts *designed* for this kind of thing, is an open standard and comes with many ready-to-go command line utilities and visualization programs. -Tim -- --------- Tim Fenn [EMAIL PROTECTED] Stanford University, School of Medici

Re: [ccp4bb] possibility of other fabricated structures

the same group, if they weren't > published in Nature." > > So, are there OTHER SUSPECT STRUCTURES from the same group or same authors > published elsewhere??? > Yes. I expect a similar letter, albeit to a different journal, soon. Regards, Tim -- ------

Re: [ccp4bb] The CCP4 license is ambiguous

On Wed, 4 Jul 2007 23:21:33 -0700 Tim Fenn <[EMAIL PROTECTED]> wrote: > > I think the reason most folks have problems with the licensing on the > ccp4 *libraries* is that the ccp4 format for maps and reflection files > should be an *open* format - the way it stands now, with

Re: [ccp4bb] The CCP4 license is ambiguous

y. So yes, I strongly disagree with the SHELX license, but since its so frequently done amongst the crystallographic community, I've almost come to expect it. Regards, Tim -- ----- Tim Fenn [EMAIL PROTECTED] Stanford Un

Re: [ccp4bb] The CCP4 license is ambiguous

rious > deficiencies of the older libraries. > Are the libraries with the patches available publicly? Regards, Tim -- --------- Tim Fenn [EMAIL PROTECTED] Stanford University, School of Medicine James H. Cl

Re: [ccp4bb] compiler question

rs? How can I install it? > I am using the Fedora5 system. Thanks! > as root: yum install libstdc++ -- ----- Tim Fenn [EMAIL PROTECTED] Stanford University, School of Medicine James H. Clark Center

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 on new site

ces are this can be set depending on the admin's preferences. -Tim -- ----- Tim Fenn [EMAIL PROTECTED] Stanford University, School of Medicine James H. Clark Center 318 Campus Drive, Room E300 Stanford, CA 94305-5432 Phone: (650) 736-1714 FAX: (650) 736-1961 -

Re: ccp4bb on new site

arker be put back in, once the wrinkles of the software have been explored. > The "standard" method of filtering out list mails is to use one of Return-Path, List-Id, X-loop, X-BeenThere... headers. jiscmail seems to at least set the Return-Path. -Tim --