Dear Colleagues,
This exchange is a wonderful illustration of the simple fact that
different scientists
work differently, favoring different approach and different tools. For
some, the latest
and greatest formats and support systems are what they need to be
productive. For
a surprising large n
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
On Mon, Aug 5, 2013 at 12:37 PM, Boaz Shaanan wrote:
> There seems to be some kind of a gap between users and developers as far
> the eagerness to abandon PDB in favour of mmCIF. I myself fully agree with
> Jeffrey about the ease of manipulating PDB's during work, particularly when
> encounterin
There seems to be some kind of a gap between users and developers as far the eagerness to abandon PDB in favour of mmCIF. I myself fully agree with Jeffrey about the ease of manipulating
PDB's during work, particularly when encountering unusual circumstances (and there are many of those, as we
On Mon, Aug 5, 2013 at 11:11 AM, Phil Jeffrey wrote:
> While alternative programs exist to do almost everything I prefer
> something that works well, works quickly, and provides instant visual
> feedback. CCP4 and Phenix are stuck in a batch processing paradigm that I
> don't find useful for thes
Questionable practice is writing an interpretation program for
operations that can be handled simply at the command line. Programs
that use the API that Eugene implicitly refers to are no panacea, e.g.
Coot has strange restrictions on things like changing the chain label
that can be fixed in a
I always assumed there was a broad consensus that the PDB format was
ancient and by now profoundly rubbish.
Ho hum, live and learn.
On 05/08/2013 14:53, Pavel Afonine wrote:
Tim,
PDB file format is good because of its simplicity and that's perhaps
it. However, it cannot accommodate wealth o
Tim,
PDB file format is good because of its simplicity and that's perhaps it.
However, it cannot accommodate wealth of information that is available at
the end of refinement. Of course one can keep creating remarks for PDB file
etc but I guess mmCIF is just a better way of doing it rather than ugl
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Hi Ian,
yes, also as Andrew pointed at, I meant to refer to the ration of xml
vs. cif rather than cif vs. PDB.
My worry was that future versions of programs like refmac, phenix, or
buster-TNT would only write large files (in xml-format) and no more
P
On 05/08/13 09:03, Tim Gruene wrote:
having read Gerard Kleywegt's latest announcement on the wwPDB Workshop
(1st August) made me wonder whether it is planned to introduce mmCIF as
working format to users in addition to using it at e.g. the PDB, because
I think that would make life unnecessarily
We used expression of full length beta-galatosidase in yeast for a lab
class. Simple to purify, simple to assay.
On Mon, Aug 5, 2013 at 6:55 AM, Alan F Scott wrote:
> Dear All,
>
> Sorry for the off-topic post. I am looking to overproduce a protein for
> crystallography purposes in *Saccharom
Dear All,
Sorry for the off-topic post. I am looking to overproduce a protein
for crystallography purposes in /Saccharomyces cerevisiae/. Nobody in my
lab has ever overproduced a protein in yeast before so I need to try
producing a control protein first. Does anybody know an /E. coli /or
yea
Hi Tim,
I just downloaded GroEL entry 4KI8 in pdb format and cid format from
RSCB. The PDB format was 4.7Mb and the CIF format was 5.9Mb, doesn't seem such
a big difference to me ? Which example were you looking at ?
Andrew
On 5 Aug 2013, at 09:03, Tim Gruene wrote:
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I just hope that one day we all will be discussing a sort of universal API to
read/write structural information instead of referencing to raw formats, and
routines to query MX data, which would be more appropriate than grep (would
many SB students/postdocs use grep these days? but many if them w
Tim,
Having not read Gerard Kleywegt's announcement, and not considering myself a
programmer, I have to disagree with the majority of your statement. Yes, using
grep on mmcif files is "awk"ward (but petfectly possible); awk on the other
hand works much better. It's actually more of a pain to u
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Dear all,
having read Gerard Kleywegt's latest announcement on the wwPDB Workshop
(1st August) made me wonder whether it is planned to introduce mmCIF as
working format to users in addition to using it at e.g. the PDB, because
I think that would make
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