Dear David and Kaiser:
While the PDB format is (thankfully--to those used to it) around, it seems to
me it is certainly a rather poor deterrent to the enjoyment of AWK:
For fixed-field format input, the designers of AWK suggested a useful solution:
the function substr(s,p,n), i.e., return
Dear CCP4bb,
I would like to calculate the shape complementarity of several
protein-ligand complexes (crystal structures with ligand available). This
involves a set of different proteins and also different ligands. The
ligands are similar in size, but not in chemical composition.
I have looked
VROCS, www.eyesopen.comhttp://www.eyesopen.com
Jürgen
On Aug 7, 2013, at 9:03 AM, Tobias Beck wrote:
Dear CCP4bb,
I would like to calculate the shape complementarity of several protein-ligand
complexes (crystal structures with ligand available). This involves a set of
different proteins and
Dear CCP4bb,
I have a few questions concerning SANS data recently collected that I'm having
trouble analyzing. The data was collected at 2 different detector distances
(4m, 2.5m) to achieve higher q-range, but I worry that the curves don't overlap
enough at intermediate q, which might indicate
This question may be better suited for more small-angle-oriented forum,
e.g.
http://www.saxier.org/forum/
On 08/07/2013 11:22 AM, Remec, Mark wrote:
Dear CCP4bb,
I have a few questions concerning SANS data recently collected that
I'm having trouble analyzing. The data was collected at 2
Dear All,
In light of the recent studies emphasizing the need for careful analysis
and validation of
protein-ligand complex structures, Ruben Abagyan from UCSD and myself are
conducting an intense 2-day workshop on drug target/ligand structure
determination
and the use of such X-ray models in
Are all the APIs open source ? I was under the impression that CCP4 had moved
away from that, which might justifiably reduce interest in any
limited-availability API.
Phil Jeffrey
Princeton
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of
This is to confirm very publicly that CCP4 libraries (of which APIs is one
example) are open source and free to use. There are no plans to change this
and, on contrary, there is a common consensus that it should stay as is.
Eugene
On 7 Aug 2013, at 19:16, Jeffrey, Philip D. wrote:
Are all
On 08/07/2013 01:51 PM, James Stroud wrote:
In the long term, the MM structure community should perhaps get its inspiration
from SQL
For this to work, a particular interface must monopolize access to
structural data. Then maintainers of that victorious interface could
change the underlying
On Aug 7, 2013, at 1:06 PM, Ed Pozharski wrote:
On 08/07/2013 01:51 PM, James Stroud wrote:
In the long term, the MM structure community should perhaps get its
inspiration from SQL
For this to work, a particular interface must monopolize access to structural
data.
Not necessarily, although
On Wed, Aug 7, 2013 at 12:54 PM, James Stroud xtald...@gmail.com wrote:
All that needs to happen is that the community agree on
1. What is the finite set of essential/useful attributes of macromolecular
structural data.
2. What is the syntax of (a) accessing and (b) modifying those
Nobody has addressed the fact that mmCIF is a format
that allows for many ways of presenting the same data. The
recent discussions seem to be based on the assumption that
all mmCIF files will look like those currently prepared by
the PDB.
Any code that reads an mmCIF file should be
The flexibility of CIF is indeed infinite. Even the names of the
unit-cell dimsnsions are different in mmCIF and (small molecule) core CIF.
One of the main reasons why I had to bring out a new version of SHELXL
recently (SHELXL-2013 to replace SHELXL-97) was that in the
meantime COMCIFS
On 08/07/2013 03:54 PM, James Stroud wrote:
On Aug 7, 2013, at 1:06 PM, Ed Pozharski wrote:
On 08/07/2013 01:51 PM, James Stroud wrote:
In the long term, the MM structure community should perhaps get its inspiration
from SQL
For this to work, a particular interface must monopolize access to
Ed Pozharski wrote:
[snip]
If I understand your proposal and reference to SQL correctly, you want
some scripting language that sounds like simple English. Is the
advantage over existing APIs here that one does not need to learn
Python, C++, (or, heaven forbid, FORTRAN)? I.e. programs would
On Aug 7, 2013, at 2:35 PM, Ed Pozharski wrote:
If I understand your proposal and reference to SQL correctly, you want some
scripting language that sounds like simple English.
I didn't say anything about being English-like. English and other natural
languages are ill-adapted to describing the
On Wed, Aug 7, 2013 at 2:36 PM, James Stroud xtald...@gmail.com wrote:
Although it is likely the best library for working with structural data,
CCTBX requires a loop just to change a specific chain ID (to the best of my
knowledge):
...
I don't intend to pick on CCTBX specifically (because
The cctbx provides comprehensive tools for handling mmcif files (and indeed all
types of cif files - it is not fussy), freely available under the BSD-style
cctbx licence.
Cheers,
Richard
On 7 Aug 2013, at 19:16, Jeffrey, Philip D. pjeff...@princeton.edu wrote:
Are all the APIs open source ?
James,
On 08/07/2013 05:36 PM, James Stroud wrote:
Anyone can learn Python in an hour and a half.
Isn't this a bit of an exaggeration? Python is designed to be easy to
learn, but we probably talking about different definitions of learning
and anyone.
I.e. programs would look like this
On 08/07/2013 05:54 PM, Nat Echols wrote:
Personally, if I need to change a chain ID, I can use Coot or pdbset
or many other tools. Writing code for this should only be necessary
if you're processing large numbers of models, or have a spectacularly
misformatted PDB file. Again, I'll repeat
On Wednesday, August 07, 2013 04:00:16 pm Ed Pozharski wrote:
On 08/07/2013 05:54 PM, Nat Echols wrote:
Personally, if I need to change a chain ID, I can use Coot or pdbset
or many other tools. Writing code for this should only be necessary
if you're processing large numbers of models,
I.e. programs would look like this
---
GRAB protein FROM FILE best_model_ever.cif;
SELECT CHAIN A FROM protein AS chA;
SET chA BFACTORS TO 30.0;
GRAB data FROM FILE best_data_ever.cif;
BIND protein TO data;
REFINE protein USING BUSTER WITH TLS+ANISO;
DROP protein INTO FILE
Nat Echols wrote:
Personally, if I need to change a chain ID, I can use Coot or pdbset or many
other tools. Writing code for
this should only be necessary if you're processing large numbers of models,
or have a spectacularly
misformatted PDB file.
Problem. Coot is bad at the chain label
Quoting Jeffrey, Philip D. pjeff...@princeton.edu:
Nat Echols wrote:
Personally, if I need to change a chain ID, I can use Coot or
pdbset or many other tools. Writing code for
this should only be necessary if you're processing large numbers of
models, or have a spectacularly
misformatted
On Wednesday, August 07, 2013 04:54:39 pm Jeffrey, Philip D. wrote:
Nat Echols wrote:
Personally, if I need to change a chain ID, I can use Coot or pdbset or
many other tools. Writing code for
this should only be necessary if you're processing large numbers of models,
or have a
25 matches
Mail list logo
