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
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.
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 Do you know of any published or unpublished results that compare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
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
--
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Tim Fen
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
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
--
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Tim F
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
--
ces
are this can be set depending on the admin's preferences.
-Tim
--
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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
-
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
rs? How can I install it?
> I am using the Fedora5 system. Thanks!
>
as root:
yum install libstdc++
--
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Tim Fenn
[EMAIL PROTECTED]
Stanford University, School of Medicine
James H. Clark Center
rious
> deficiencies of the older libraries.
>
Are the libraries with the patches available publicly?
Regards,
Tim
--
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Tim Fenn
[EMAIL PROTECTED]
Stanford University, School of Medicine
James H. Cl
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
--
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Tim Fenn
[EMAIL PROTECTED]
Stanford Un
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
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
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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
--
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Tim Fenn
[EMAIL PROTECTED]
Stanford University, School of Medici
;s repositories, which include fedora/rhel
rpms for nvidia drivers:
http://atrpms.net
--
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Tim Fenn
[EMAIL PROTECTED]
Stanford University, School of Medicine
James H. Clark Center
318 Campu
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
-
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
--
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Tim Fenn
[EMAIL PROTECTED]
Stanford University, School o
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
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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)
> >
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
/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
-
.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
ck to set up. ubuntu
and fedora are pretty much identical otherwise.
-Tim
--
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Tim Fenn
f...@stanford.edu
Stanford University, School of Medicine
James H. Clark Center
318 Campus Drive, Room E300
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