[ccp4bb] {Spam?} Re: [ccp4bb] OT: "Who's Afraid of Peer Review?"

[Miguel Ortiz Lombardia]

Hi Marco,

Impact factor is the last refuge of the publishing system as it is.
Precisely because in this ocean of untrusted publications we tend to
believe that high impact factor journals deserve our respect. This is
more or less all right: among those who have investigated the issue some
are more pessimistic than others about the quality of papers published
in those journals. Yet, it is hard to believe that their papers are
generally worse than those of not-so-high impact factor journals. But
from a scientific point of view, taking into account the evolution of
research and publishing, the trust that we give to high impact journals
is, in my opinion, wishful thinking.

Concerning peer-reviewing, I don't think that adding more opacity will
help. On the contrary. What I believe, but I don't have any proof of it,
is that peer-reviewing is useful only if it is more transparent, engages
in a real scientific discussion (understood as a conversation, not as an
exchange of messages separated by weeks) and is open to (many) more
reviewers. But that alone will not help if the way research is done does
not evolve at the same time.

Miguel Ortiz Lombardía

Architecture et Fonction des Macromolécules Biologiques (UMR7257)
CNRS, Aix-Marseille Université
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 86 44
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

El 10/10/13 03:56, Marco Lolicato escribió:
> Hi scientists,
> this interesting topic brought back to my mind a similar discussion I had 
> with a colleague of mine and now I want to share it with you guys.
> As Vale already pointed out, the peer-review process seems to be far from an 
> ideal system: there are many papers in which one of the author is himself the 
> editor of the journal in which the paper is published; the impact factor of a 
> journal is becoming the "only" way to judge the quality of a paper (and of 
> the authors) [example:  one of the European Commission grants has as 
> mandatory eligibility criterium that the applicant should have at least one 
> paper published in a "high IF journal"...I'm asking...Why?].
> I have also the suspect (from my insignificant experience) that some papers 
> are accepted in really high IF journals without a clear peer-review process, 
> but basing the decision mostly on the authors listed in that paper.
> Anyway, for those reasons and more, I was wondering if maybe is nowadays 
> needed to revisit the peer-review process. One thing that immediately came 
> out was: the authors of a papers should be hidden to both the reviewers and 
> the editors, so that paper will be judged only on the intrinsic quality and 
> not from the names on it or from the country.
> 
> I'm looking forward to see your opinion. 
> 
> 
> Marco
> 
> 
> 
> 
> Il giorno 09/ott/2013, alle ore 15.00, Miguel Ortiz Lombardia ha scritto:
> 
>> Hi denizens,
>>
>> Now that Biology has gone missing, at least in the programs of the
>> funding agencies in this part of the world, the reflections that I'm
>> going to expose concern at best that even smaller field of natural
>> philosophy that we euphemistically call, not without a twist of candour,
>> "biomedicine". At worst, they only concern the world whose limits are
>> the limits of my language.
>>
>> As I understand it, the main purpose of really existing peer-reviewing
>> is to act as a filter. By selecting those papers deemed publishable it
>> spares us the herculean task of reading every possible piece emanating
>> from our overheated brains. This actually reveals a big problem of
>> really existing research (with the caveat expressed in the first
>> paragraph). But I'm not going to venture into that problem: more clever
>> minds have drowned in its muddy waters. Back to the point, if the need
>> of publishing were not such a strong source of inspiration and we
>> researchers would feel the compelling necessity of publishing only when
>> we could write well-structured and thoughtful papers, full of useful
>> data and rich in new ideas and hypotheses, we could then read a
>> reasonable percentage of the papers concerning our fields of interest.
>> In that utopia, peer-reviewing could be a continuous, transparent and
>> open process that would involve a relevant part of the community. Not
>> likely to happen and probably for good: knowledge seems to progress by a
>> combination of slow accretion of small steps and sudden
>> (re)interpretations of those steps.
>>
>> But what is interesting to see in that utopian/dystopian possibility is
>> that really existing peer-reviewing suff

Re: [ccp4bb] OT: "Who's Afraid of Peer Review?"

[Miguel Ortiz Lombardia]

Hi denizens,

Now that Biology has gone missing, at least in the programs of the
funding agencies in this part of the world, the reflections that I'm
going to expose concern at best that even smaller field of natural
philosophy that we euphemistically call, not without a twist of candour,
"biomedicine". At worst, they only concern the world whose limits are
the limits of my language.

As I understand it, the main purpose of really existing peer-reviewing
is to act as a filter. By selecting those papers deemed publishable it
spares us the herculean task of reading every possible piece emanating
from our overheated brains. This actually reveals a big problem of
really existing research (with the caveat expressed in the first
paragraph). But I'm not going to venture into that problem: more clever
minds have drowned in its muddy waters. Back to the point, if the need
of publishing were not such a strong source of inspiration and we
researchers would feel the compelling necessity of publishing only when
we could write well-structured and thoughtful papers, full of useful
data and rich in new ideas and hypotheses, we could then read a
reasonable percentage of the papers concerning our fields of interest.
In that utopia, peer-reviewing could be a continuous, transparent and
open process that would involve a relevant part of the community. Not
likely to happen and probably for good: knowledge seems to progress by a
combination of slow accretion of small steps and sudden
(re)interpretations of those steps.

But what is interesting to see in that utopian/dystopian possibility is
that really existing peer-reviewing suffers from a fundamental problem:
statistical significance. Because, what significance is to be deposited
in the opinions, whether reasonably argued or not (another thorny
Pandora box I won't dare to open), of two, three or at best four people
acting as editors or reviewers? Anonymous people in the latter case, to
complete the scene.

In the tension between these requirements trust is suppose to build up
and give us a reasonable path to pursue our noble endeavours. In my
insignificant opinion, in the current state of matters, trust is
seriously broken. Too much pressure to publish, too many journals, too
much money to make from publishing, too restricted and opaque a
peer-reviewing system... As a corollary, my impression is that while
many of us suspect we live in a bubble, we all seem to tacitly expect
that we will not see it explode. A good friend of mine once offered me a
book about the Spanish Armada; no joke. Its title was "The confident
hope of a miracle".

To rebuild trust we need, among other things, to rebuild our tools. And
we better do it before the next big bang. Research is not the only human
activity involving knowledge and its transmission, we could use some
curiosity beyond our noses.

Vale.

Miguel Ortiz Lombardía

Architecture et Fonction des Macromolécules Biologiques (UMR7257)
CNRS, Aix-Marseille Université
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 86 44
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

El 09/10/13 20:04, Navdeep Sidhu escribió:
> John Bohannon wrote about his experience writing "a computer program to 
> generate hundreds of unique papers." Thought some of you might find it of 
> interest:
> 
> John Bohannon. Who's Afraid of Peer Review? Science 342 (Oct. 4, 2013) 60-65.
> DOI: 10.1126/science.342.6154.60
> http://www.sciencemag.org/content/342/6154/60.full
> 
> Best regards,
> Navdeep
> 
> ---
> Navdeep Sidhu
> University of Goettingen
> ---
> 

Re: [ccp4bb] announcement: (another) GUI for XDS

[Miguel Ortiz Lombardia]

Yep, sorry that is the link I actually made, I wrote it too hastily, my bad.

Miguel Ortiz Lombardía

Architecture et Fonction des Macromolécules Biologiques (UMR7257)
CNRS, Aix-Marseille Université
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

El 26/06/13 19:46, Kay Diederichs escribió:
> Hi Sebastiano,
> 
> ok, I think I have the solution, and, hoping it's correct, have put it into
> http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDSgui#Installation
> 
> 
> What you need is the symlink
> ln -s /Applications/XDS-Viewer.app/Contents/MacOS/xds-viewer-bin
> /usr/local/bin/xds-viewer
> 
> In the above please note the "xds-viewer-bin" - I guess you have it
> differently.
> 
> HTH,
> 
> Kay
> 
> 
> Am 26.06.13 19:23, schrieb Sebastiano Pasqualato:
>>
>> Hi Kay,
>> xds nicely outputs the FRAME_##.cbf image in the temp directory.
>> The problem is that the command
>>
>> xds-viewer FRAME_10.cbf
>>
>> does not open the frame, but only the viewer, without loading the frame.
>> If I then open the frame from the FIle --> Load image menu commands, I
>> have it.
>> Of course that's ok, but a little more tedious.
>>
>> Miguel, the xds-viewer command is nicely added to the path, I guess, by
>> exporting the directory in the .bashrc
>>
>> export XDSVIEWERPATH=/Applications/XDS-Viewer.app/Contents/MacOS/
>>
>> I have tried setting the link as you suggested, but that does not make
>> the command above open the image directly.
>>
>> Still puzzled,
>> Sebastiano
>>
>> On Jun 26, 2013, at 5:04 PM, Kay Diederichs
>> mailto:kay.diederi...@uni-konstanz.de>>
>> wrote:
>>
>>> Hi Sebastiano,
>>>
>>> sorry, I don't see immediately what's wrong. The console seems to show
>>> the XDS output of an INTEGRATE job that only looked at a single
>>> (judging from the small number of reflections ...) frame (number 10,
>>> I'd guess; you could check this if you scroll up a bit). Could you
>>> please check the contents of the "temp" directory? It should have a
>>> file FRAME_10.cbf . If you use the console window, "cd" to that
>>> directory and run
>>> xds-viewer FRAME_10.cbf
>>> then you should be able to see what you want to see. If that works,
>>> then I do not understand why the script fails. If the file is _not_
>>> there or "xds-viewer FRAME_10.cbf" does _not_ show it, then we'll have
>>> to sort this out. I suggest to move the debugging to private email,
>>> though, and to only post the solution. But maybe someone else has the
>>> solution already?
>>> By the way, a newer version of xdsGUI is available for download, and
>>> there's also versions that run on older Linux systems.
>>>
>>> best,
>>>
>>> Kay
>>>
>>>
>>>
>>>
>>
>> -- 
>> *Sebastiano Pasqualato, PhD*
>> Crystallography Unit
>> Department of Experimental Oncology
>> European Institute of Oncology
>> IFOM-IEO Campus
>> via Adamello, 16
>> 20139 - Milano
>> Italy
>>
>> tel +39 02 9437 5167
>> fax +39 02 9437 5990
>>
>>
>>
>>
>>
>>
> 

Re: [ccp4bb] off topic:how to prevent DNA tetraplexe forming?

[Miguel Ortiz Lombardia]

El 21/12/12 05:16, dengzq1987 escribió:
> Hi all,
> recently, i perform an EMSA experiment.when i prepared the DNA with a 5'
> poly(G)-tailed ,i find that it formed guanine tetraplexes .how can i
> prevent this happen,or has any method to disrupt the
> guanine tetraplexes  structure? any suggestion is appreciation.
>  
>  
> dengzq
>  

Hi,

How you know the tail forms tetraplexes? Couldn't be other type of
structure? Tetraplexes are stabilized by potassium and, to a lesser
extent by sodium cations. Try to avoid them in your buffer or to keep
them to a minimum. Or you can use lithium as counterion, it is too small
to stabilize the tetraplexes. Another option is to add a complementary
poly(C) oligo before running your EMSA.

Cheers,

-- 
Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR7257)
CNRS, Aix-Marseille Université
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

Re: [ccp4bb] Help with curves+

[Miguel Ortiz Lombardia]

El 02/07/12 21:16, James Stroud escribió:
> The star is usually for sugar atoms, not for the bases. I don't remember what 
> curves wants.
> 
> Does your PDB have apostrophes instead of stars? If so you should just do a 
> global search and replace.
> 
> If you still have a problem, you should copy-paste the error message.
> 
> James
> 
> 
> On Jul 2, 2012, at 12:44 PM, Nikolai Suslov wrote:
> 
>> Hello,
>>
>> I am trying to analyze an RNA helix with curves+. I keep receiving an
>> error message that base atom C1*  is missing from the pdb. C1 atoms
>> are certainly all there.
>>
>> Any advice on how to troubleshoot this will be much appreciated.
>>
>> Sincerely,
>> Nikolai Suslov
> 

C1* ( or C1') is certainly a sugar atom.
As far as I remember, curves+ wants stars for desoxy-riboses. I presume
it is the same for RNA riboses.

-- 
Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR7257)
CNRS, Aix-Marseille Université
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

Re: [ccp4bb] how to install coot on ubuntu 11.10

[Miguel Ortiz Lombardia]

El 25/04/12 17:54, Michael Murphy escribió:
> I am trying to install Coot on a laptop that runs Ubuntu. Following the
> instructions on the CCp4wiki
> http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Coot#Packages_for_Ubuntu
>  
> 
>  sudo apt-key adv --keyserver keyserver.ubuntu.com 
> <http://keyserver.ubuntu.com> --recv-keys 1DC81A57
>  sudo add-apt-repository ppa:mok0/ppa
> apt-get update && apt-get install coot <- I had to add "sudo" to the 
> beginning of this command and after the &&
> 
> 
> and I received this fail message
> 
> "Package coot is not available, but is referred to by another package.
> This may mean that the package is missing, has been obsoleted, or
> is only available from another source
> 
> E: Package 'coot' has no installation candidate"
> 
> 
> is there some other name/link for the package other than the word "coot"
> or do I need to install it by some other method other than what I have
> been doing?
> 
> 

Hi Michael,

Just this weekend I installed coot on a similar computer. It's an Ubuntu
11.10 (oneiric ocelot) at 64bit. I had no much problem installing it
using Paul's autobuild script
(http://www.biop.ox.ac.uk/coot/software/build-script/build-install-coot-from-scratch)
after a couple of tweaks of that script and of the one that this script
downloads (so you may download both manually, apply de patches and
comment the if/fi lines in the first script). The tweaks are included as
diff files in the attached file.

The only other thing I had to do was to install guile-1.8 and
guile-1.8-dev from the Ubuntu repositories. Anything else compiled just
fine with Paul's script.

Good luck,


-- 
Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr
http://w2.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia


cootbuilddiffs.tgz
Description: application/compressed-tar

Re: [ccp4bb] Off-topic: Supplying PDB file to reviewers

[Miguel Ortiz Lombardia]

y and not just of a few
big-brains would be clear for everyone to see... Keeping the rules as
they are reminds me of those astronomers complicating the Ptolemaic
system to "save the appearances". And this is what we, you can include
myself, are doing. Until the bubble collapses?


-- 
Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr
http://w2.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

Re: [ccp4bb] DNA in coot

[Miguel Ortiz Lombardia]

El 16/02/12 05:06, Xun Lu escribió:
> Hi Lisa,
> 
> Please go check your PDB file.  Are those bases written out like "DT" or
> "THY" or "Td". Coot recognizes certain format for DNA bases but I forgot
> which one coot likes.  I don't have my laptop with me right now. My
> guess would be "Td".  :)
> 
> Best,
> 
> Xun
> 
> 

Hi,

And that is compounded with the fact that depending on your
installation, Coot may be using its own libraries or the CCP4 ones. And
they may differ, especially if you're using the "new dictionnaries" for
refmac5. Plus the fact that depending on your preferences Coot converts
atoms to PDB v.2.x so they may not come back as you gave them to it. A
mess...

Paul, at the very least, it would be helpful if like in Lisa's case, an
ideal DNA/RNA is created consistent with whatever libraries Coot is
going to use for real space refining it.


Best regards,

-- Miguel

> On Wednesday, February 15, 2012, LISA  <mailto:science...@gmail.com>> wrote:
>> Hi all,
>>
>> I am refining a structue  of protein-DNA complex with coot. I add DNA
> by "adding ideal DNA/RNA" in the other model. But I cannot edit chi
> angle of these nucletide, neither the mutate.  When I press the mutate 
> and my DNA, coot give amino acid not nucletide. Why?
>>
>> Thanks
>>
>> Lisa
>>
> 
> -- 
> Department of Molecular and Structural Biochemistry
> North Carolina State University


-- 
Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

Re: [ccp4bb] Autoreply: [ccp4bb] A story of acetoacetate decarboxylase

[Miguel Ortiz Lombardia]

El 25/01/12 01:19, Kevin Jin escribió:
> Dear All,
> 
> I got this email. Is my account blocked?
> 
> Thanks,
> 
> Kevin
> 
> 2012/1/24  :
>> Esta cuenta de correo electrónico dejara de existir dentro de 6 meses 
>> (25/05/2012).
>>
>> Si desea ponerse en contacto con el titular de este correo hágalo a través 
>> del siguiente e-mail: annie_sch...@yahoo.de
>>
>> Todo el correo recibido está siendo redirigido a la cuenta indicada 
>> anteriormente.
>>
>> Si desea contactar con el Centro de Investigación Príncipe Felipe puede 
>> hacerlo por teléfono llamando al 963.289.680.
>>
>> Muchas gracias y disculpen las molestias.
>>
>>
>>
> 

I get this e-mail as well when I post to the list. In fact, it says that
Annie Schott's e-mail account at the CIPF, a Spanish research centre,
will disappear on May 25.

Perhaps unrelated to this case, but what is happening at the CIPF centre
is just one of many exemples of how this "crisis" ( I would better call
it a *fraud* ) is breaking many socially important assets, including
research, not serving well the interests of the capital. I don't know in
detail this particular story; if you are interested you can read
something about it in Nature:

Spanish institute faces cash crisis -
http://www.nature.com/news/2011/01/full/news.2011.623.html


-- 
Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

Re: [ccp4bb] Problem with getting Rfree and Rf down

[Miguel Ortiz Lombardia]

El 24/01/12 18:56, Greg Costakes escribió:
> Whoops, I misspoke... I meant Rsym and Rmerge increase with higher
> redundancies. 
> 

But then suppose that one merges data from a crystal that is degrading
while exposed, sp the data gets degraded. This is not at all unusual. In
the absence of a deep understanding of refinement, intuition suggests
that degraded data should produce degraded models. If Rwork and Rfree
are measuring anything useful they should go up redundancy in those
not-so-unusual cases. Or intuition is misguiding me again.


-- Miguel

> ---
> Greg Costakes
> PhD Candidate
> Department of Structural Biology
> Purdue University
> Hockmeyer Hall, Room 320
> 240 S. Martin Jischke Drive, West Lafayette, IN 47907
> 
> 
> ** Hard work often pays of in time, but Procrastination always pays off
> now **
> 
> 
> *From: *"Dale Tronrud" 
> *To: *"Greg Costakes" 
> *Cc: *CCP4BB@JISCMAIL.AC.UK
> *Sent: *Tuesday, January 24, 2012 12:43:43 PM
> *Subject: *Re: [ccp4bb] Problem with getting Rfree and Rf down
> 
> 
>Is this observation about redundancies a general rule that I missed?
> It seems rather surprising to me.  What have results have others seen?
> 
> Dale Tronrud
> 
> On 01/24/12 07:23, Greg Costakes wrote:
>> snip...
> 
>> Higher redundancies (>7 or so) do tend to increase overall R/Rfree.
> 
>> snip...
>>
> ---
>> Greg Costakes
>> PhD Candidate
>> Department of Structural Biology
>> Purdue University
>> Hockmeyer Hall, Room 320
>> 240 S. Martin Jischke Drive, West Lafayette, IN 47907
>>
>>
> 
>> ** Hard work often pays of in time, but Procrastination always pays off
>> now **
>>
>> 
>> *From: *"Sam Arnosti" 
>> *To: *CCP4BB@JISCMAIL.AC.UK
>> *Sent: *Monday, January 23, 2012 4:48:50 PM
>> *Subject: *[ccp4bb] Problem with getting Rfree and Rf down
>>
>> Hi every one
>>
>> I have some crystals in the space group P3121. I collect 180 frames of
> data.
>>
>> My crystals do not diffract better than at most 2.0 angstrom, but the Rf
>> barely goes below 23%,
>>
>> and Rfree also remains somewhere between 28-33%. I have tried to refine
>> my data as much as I can.
>>
>> I do not know whether the problem is because of the bad diffraction or
>> collecting extra frames.
>>
>> The structure factors are also high but they get better as the crystals
>> diffract better.
>>
>> Thanks
>>
>> Sam


-- 
Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

Re: [ccp4bb] Open position at Bristol-Myers Squibb (Princeton, NJ, USA) Third time is the charm?

[Miguel Ortiz Lombardia]

 reproduction, distribution or other use
> of this message or any attachments by an individual or entity other
> than the intended recipient is prohibited.
> 


-- 
Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

Re: [ccp4bb] image compression

[Miguel Ortiz Lombardia]

Le 08/11/2011 20:46, mjvdwo...@netscape.net a écrit :
> Hmmm, so you would, when collecting large data images, say 4 images,
> 100MB in size, per second, in the middle of the night, from home, reject
> seeing compressed images on your data collection software, while the
> "real thing" is lingering behind somewhere, to be downloaded and stored
> later? As opposed to not seeing the images (because your home internet
> access cannot keep up) and only inspecting 1 in a 100 images to see
> progress?
> 

1. I don't need to *see* all images to verify whether the collection is
going all right. If I collect remotely, I process remotely, no need to
transfer images. Data is collected so fast today that you may, even
while collecting at the synchrotron, finish the collection without a)
seeing actually all the images (cf. Pilatus detectors) b) keeping in
pace at all your data processing. The crystal died or was not collected
properly? You try to understand why, you recollect it if possible or you
try a new crystal. It's been always like this, it's call trial and error.

2. The ESRF in Grenoble produces thumbnails of the images. If all you
want to see is whether there is diffraction, they are good enough and
they are useful. They are extremely lossy and useless for anything else.

3. Please, compare contemporary facts. Today's bandwidth is what it is,
today's images are *not* 100 Mb (yet). When they get there, let us know
what is the bandwidth.

> I think there are instances where compressed (lossy or not) images will
> be invaluable. I know the above situation was not the context, but
> (y'all may gasp about this) I still have some friends (in the US) who
> live so far out in the wilderness that only dial-up internet is
> available. That while synchrotrons and the detectors used get better all
> the time, which means more MB/s produced.

I would understand a situation like the one you describe for a poor, or
an embargoed country where unfortunately there is no other way to
connect to a synchrotron. Still, that should be solved by the community
in a different way: by gracious cooperation with our colleagues in those
countries. Your example is actually quite upsetting, given the current
state of affairs in the world.

> 
> James has already said (and I agree) that the original images (with all
> information) should not necessarily be thrown away. Perhaps a better
> question would be "which would you use for what purpose", since I am
> convinced that compressed images are useful.
> 

I think I was clear: as long as we have access to the original data, I
don't care. I would only use the original data.

> I would want to process the "real thing", unless I have been shown by
> scientific evidence that the compressed thing works equally well. It
> seems reasonable to assume that such evidence can be acquired and/or
> that we can be shown by evidence what we gain and lose by
> lossy-compressed images. Key might be to be able to choose the best
> thing for your particular application/case/location etc.
> 

This still assumes that future software will not be able to detect the
differences that you cannot see today. This may or may not be true, the
consequences may or may not be important. But there is, I think,
reasonable doubt on both questions.

> So yes, James, of course this is useful and not a waste of time.
> 

I have said to James, off the list, that he should go on if he's
convinced about the usefulness of his approach. For a very scientific
reason: I could be wrong. Yet, if need be to go into the compression
path, I think we should prefer lossless options.

Best regards,


-- 
Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
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Re: [ccp4bb] image compression

[Miguel Ortiz Lombardia]

Le 08/11/2011 19:19, James Holton a écrit :
> At the risk of putting this thread back on-topic, my original question
> was not "should I just lossfully compress my images and throw away the
> originals".  My question was:
> 
>  "would you download the compressed images first?"
> 
> So far, noone has really answered it.
> 
> I think it is obvious that of course we would RATHER have the original
> data, but if access to the original data is "slow" (by a factor of 30 at
> best) then can the "mp3 version" of diffraction data play a useful role
> in YOUR work?
> 
> Taking Graeme's request from a different thread as an example, he would
> like to see stuff in P21 with a 90 degree beta angle.  There are
> currently ~609 examples of this in the PDB.  So, I ask again: "which one
> would you download first?".  1aip? (It is first alphabetically).  Then
> again, if you just email the corresponding authors of all 609 papers,
> the response rate alone might whittle the number of datasets to deal
> with down to less than 10.  Perhaps even less than 1.
> 
> -James Holton
> MAD Scientist
> 

Hmm, I thought I had been clear. I will try to be more direct:

Given the option, I would *only* download the original,
non-lossy-compressed data. At the expense of time, yes. I don't think
Graeme's example is very representative of our work, sorry.

As long as the option between the two is warranted, I don't care. I just
don't see the point for the very same reasons Kay has very clearly exposed.

Best regards,

-- 
Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

Re: [ccp4bb] image compression

[Miguel Ortiz Lombardia]

ould be fine in most instances.  However, when what is being
>>>>   done hinges on the really fine details -- looking for lost faint
>>>>   spots just peeking out from the background, looking at detailed
>>>>   peak profiles -- then the lossless compression version is the
>>>>   better choice.  The annotation for both sets should be the same.
>>>>   The difference is in storage and network bandwidth.
>>>>
>>>>   Hopefully the fraud issue will never again rear its ugly head,
>>>>   but if it should, then having saved the losslessly compressed
>>>>   images might prove to have been a good idea.
>>>>
>>>>   To facilitate experimentation with the idea, if there is agreement
>>>>   on the particular lossy compression to be used, I would be happy
>>>>   to add it as an option in CBFlib.  Right now all the compressions
>>>   >  we have are lossless.
>>>>   Regards,
>>>>Herbert
>>>>
>>>>
>>>>   =
>>>>Herbert J. Bernstein, Professor of Computer Science
>>>> Dowling College, Kramer Science Center, KSC 121
>>>>  Idle Hour Blvd, Oakdale, NY, 11769
>>>>
>>>>   +1-631-244-3035
>>>>   y...@dowling.edu
>>>>   =
>>>>
>>>>   On Mon, 7 Nov 2011, James Holton wrote:
>>>>
>>>>>   At the risk of sounding like another "poll", I have a pragmatic
>>>>> question
>>>>>   for the methods development community:
>>>>>
>>>>>   Hypothetically, assume that there was a website where you could
>>>>> download
>>>>>   the original diffraction images corresponding to any given PDB file,
>>>>>   including "early" datasets that were from the same project, but
>>>>> because of
>>>>>   smeary spots or whatever, couldn't be solved.  There might even
>>>>> be datasets
>>>>>   with "unknown" PDB IDs because that particular project never did
>>>>> work out,
>>>>>   or because the relevant protein sequence has been lost. 
>>>>> Remember, few of
>>>>>   these datasets will be less than 5 years old if we try to allow
>>>>> enough time
>>>>>   for the original data collector to either solve it or graduate
>>>>> (and then
>>>>>   cease to care).  Even for the "final" dataset, there will be a
>>>>> delay, since
>>>>>   the half-life between data collection and coordinate deposition
>>>>> in the PDB
>>>>>   is still ~20 months. Plenty of time to forget.  So, although the
>>>>> images were
>>>>>   archived (probably named "test" and in a directory called "john")
>>>>> it may be
>>>>>   that the only way to figure out which PDB ID is the "right
>>>>> answer" is by
>>>>>   processing them and comparing to all deposited Fs.  Assume this
>>>>> was done.
>>>>>But there will always be some datasets that don't match any PDB.
>>>>> Are those
>>>>>   interesting?  What about ones that can't be processed?  What
>>>>> about ones that
>>>>>   can't even be indexed?  There may be a lot of those! 
>>>>> (hypothetically, of
>>>>>   course).
>>>>>
>>>>>   Anyway, assume that someone did go through all the trouble to
>>>>> make these
>>>>>   datasets "available" for download, just in case they are
>>>>> interesting, and
>>>>>   annotated them as much as possible.  There will be about 20
>>>>> datasets for any
>>>>>   given PDB ID.
>>>>>
>>>>>   Now assume that for each of these datasets this hypothetical
>>>>> website has
>>>>>   two links, one for the "raw data", which will average ~2 GB per
>>>>> wedge (after
>>>>>   gzip compression, taking at least ~45 min to download), and a
>>>>> second link
>>>>>   for a "lossy compressed" version, which is only ~100 MB/wedge (2 min
>>>>>   download). When decompressed, the images will visually look
>>>>> pretty much like
>>>>>   the originals, and generally give you very similar Rmerge,
>>>>> Rcryst, Rfree,
>>>>>   I/sigma, anomalous differences, and all other statistics when
>>>>> processed with
>>>>>   contemporary software.  Perhaps a bit worse.  Essentially, lossy
>>>>> compression
>>>>>   is equivalent to adding noise to the images.
>>>>>
>>>>>   Which one would you try first?  Does lossy compression make it
>>>>> easier to
>>>>>   hunt for "interesting" datasets?  Or is it just too repugnant to
>>>>> have
>>>>>   "modified" the data in any way shape or form ... after the detector
>>>>>   manufacturer's software has "corrected" it?  Would it suffice to
>>>>> simply
>>>>>   supply a couple of "example" images for download instead?
>>>>>
>>>>>   -James Holton
>>>>>   MAD Scientist
>>>>>
>>
> 


-- 
Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

Re: [ccp4bb] Linux vs MacOS for crystallographic software

[Miguel Ortiz Lombardia]

Le 29/09/2011 11:43, Johan Turkenburg a écrit :
> This discussion will rage forever, it seems, but that won't stop us
> all chipping in. My experience is the opposite: all crystallographic
> software I use is available as binaries for the major linux distros,
> and installs without problems. Ubuntu is easy to maintain on desktops
> (your mileage on laptops may vary). I constantly hear people complain
> about Office being a pain when exchanging documents between PC and
> Mac. So it is a personal preference, based on what you have experience
> with etc., there is no a clear-cut answer.
> 
> And by the way, if it all works so well on Macs, why is the BB awash
> with people asking about installation problems on Macs? If the answer
> is that this is due to inexperience, then the same applies to problems
> with Linux boxes ;-)
> 
> Dr. Johan P. Turkenburg X-ray facilities manager
> York Structural Biology Laboratory
> University of York   Phone (+) 44 1904 328251
> York YO10 5DD   UK  Fax   (+) 44 1904 328266
> 
> 
> 
> On 29 September 2011 09:54, Simon Kolstoe  wrote:
>> I am routinely having the Mac vs Linux conversation with crystallographers 
>> and new students, especially given the price of Macs.
>>
>> Generally I think that the extra money spent on a Mac pays for less time 
>> spent messing around installing software, sorting out dependencies, swearing 
>> at the less than effective office software etc. that plagues Linux which is 
>> more of a "computer experts" platform. I'd say if your interest is in 
>> solving structures with the least hassle get a Mac, but if you want to 
>> develop software get Linux. Meanwhile I think windows is slowly improving as 
>> a crystallography platform - and Microsoft is perhaps no longer hated in 
>> principle - however the one student in our lab who opted to go the windows 
>> route seems very limited in the software he can run.
>>
>> Of course getting the highest spec machine one can afford at the time 
>> applies to all platforms. Mind you I've been using mid range MacBook Pro's 
>> for the last few years which work fine, with the added bonus that you can 
>> keep your coffee warm by placing it near the processor during MR!
>>
>> Simon
>>
>>
>> On 29 Sep 2011, at 01:26, Jacqueline Vitali wrote:
>>
>>> Dear colleagues,
>>>
>>> I need some advice for a new computer.
>>>
>>> (1) I have the option of an HP Z210  8 GB with a low end Quadro Nvidia 400 
>>> 512 MB.
>>>
>>> --How does Coot run with this card?
>>>
>>> --I am happy with any Linux.  However, the system needs updates for 
>>> security purposes (the University requires it).  Do I have to remake the 
>>> NVidia driver every time there is a kernel update or is there a way around 
>>> it for this NVidia card?  Do you suggest another NVidia card (inexpensive) 
>>> that is good for coot and automatically updates when the kernel is updated?
>>>
>>> (2) Second option is an IMAC 4 GB 2.5 GHz with AMD Radeon HD 6750M 512 MB 
>>> GDDRS.
>>>
>>> --How does Coot work with this graphics card?
>>>
>>> --Should I get more memory for Lion?
>>>
>>> --Is this platform advisable for crystallographic software for the next 
>>> four years?
>>>
>>> Thank you in advance for any advice.
>>>
>>> Jackie Vitali
>>> Cleveland State University
>>>
>>>
>>>
>>>
>>
> 

I totally agree with Johan. I have experience now with both linux and
apple osx and I cannot say that things are easier in osx. It's rather
the opposite when it comes to the management of the OS in itself. Add to
this that when you have more or less learnt how to deal with a
particularity of the apple OS, they may change it in the next "upgrade".
Example: NFS. Non-unix idioms are becoming so frequent in osx that one
would say that it will soon depart completely from the BSD origins. But
this is a quite subjective view, of course.

However, if you compare the price/performance ratio, at least in Europe,
you will come easily with an answer.

-- 
Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

Re: [ccp4bb] refmac and DNA

[Miguel Ortiz Lombardia]

Le 11/09/2011 00:23, Ed Pozharski a écrit :
> On Sat, 2011-09-10 at 08:21 +0200, Miguel Ortiz Lombardía wrote:
>> A, C and G are RNA nucleotides. T is (mostly) not, its RNA-equivalent
>> is
>> uridine phosphate, U.
>>
>>
> 
> Right, that was my suspicion.  But I thought that RNA bases would be Xr,
> not Xd.  Plus, refmac does not complain about missing oxygens.  

My understanding is that the Xr/Xd scheme has been dropped from the
latest refmac5/coot to comply with the X/DX (and OP1, OP2, prime signs
instead of asterisks...) standard from the PDB/NDB.

Cheers,


-- 
Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

Re: [ccp4bb] E. coli mutant strains

[Miguel Ortiz Lombardia]

Le 26/02/2011 03:51, Dima Klenchin a écrit :
> It surely is not. An N-end rule has to do with ubiquitination, and it is
> absent in E.coli.

Not true. There is indeed and N-end rule in prokaryotes, including E.
coli. Mediated by the ClpP protease-based system. See:

http://www.cell.com/molecular-cell/abstract/S1097-2765%2808%2900692-8

-- 
Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
mailto:miguel.ortiz-lombar...@afmb.univ-mrs.fr
http://www.afmb.univ-mrs.fr/Miguel-Ortiz-Lombardia

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Re: [ccp4bb] Calculation of the net charge of an electrostatic surface for secondary structural elements

[Miguel Ortiz Lombardia]

Le 25 mars 2010 à 16:43, Tim Gruene a écrit :

> Hello Rebecca,
> 
> this is merely a guess, but I think, it should work.
> 
> As you calculate the electrostatic surface potential in pymol, it uses apbs.
> apbs, if I remember correctly creates an intermediate PDB-file where the
> B-factor column is replaced with the partial charge of that atom.
> 
> So if you can get hold of that file you can use a text editor to cut out the
> helices of interest into separate files and use shell commands to sum up the
> B-factor columns.
> 
> The following (all in one line, in case any mail program splits the line) adds
> up the B-values in the PDB-file:
> 
> grep "^ATOM" helix.pdb|cut -c61-66|awk '{pcharge += $1}END{print pcharge}'
> 
> Having said that I would be curious to hear what the community has to say 
> about
> how trustful and meaningful such calculations actually are, because I have
> always wondered about this since I looked at my first GRASP surface.
> 
> Tim

It depends on what you want to do with the information. If you want something 
qualitative, like to decide whether a helix is more or less negative than 
another, it may be enough. But that's about all you can get from this approach. 
The coordinate file that you mention (in pqr format in fact) it's not unique 
and is not produced by APBS, but by other tools, such as pdb2pqr. That file 
will include charges and atom radii as derived from a particular force field. 
For surface representations, the PARSE force-field is a simple and perhaps good 
representation. In this force field the charges and atom radii are not the same 
than in other force fields, like CHARMM or AMBER. From this pqr file, APBS 
solves the Poisson-Boltzmann equation under certain conditions. Those include, 
for example, the presence of counter-ions in the implicit solvent. So, the 
results depend on the way you pose the problem, something that standard plugin 
users perhaps/probably don't do.

In any case, I must confess that I don't understand what a "net charge of an 
electrostatic surface" means. In my mind, a net charge is a property of a 
molecule not of a surface. Actually, I would say that "electrostatic surface" 
is a shorcut for something like a "surface-mapped electrostatic potential". The 
electrostatic potential is not restricted to the molecular surface and its 
representation as an isosurface is often more informative than its mapping to a 
particular surface.

These calculations can be very useful, for example to study binding properties, 
provided they are carried out carefully.

Best,


-- Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr
Web: http://www.pangea.org/mol/spip.php?rubrique2







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Re: [ccp4bb] ARP_wARP 7.1 release

[Miguel Ortiz Lombardia]

Hi Mark,

Yes, it must be as you say.
But I don't want to maintain two fink installations side-by-side, I'll better 
wait for a proper fix and use the scripts in the mean time.

Cheerio,


Miguel

Le 26 déc. 2009 à 16:57, Mark Del Campo a écrit :

> Miguel,
> 
> I'm pretty sure you need a 32-bit fink installation for this workaround to 
> work. You have to source /sw/bin/init.sh.
> 
> Best,
> 
> Mark
> 
> On 12/26/09 6:51 AM, Miguel Ortiz Lombardia wrote:
>> Le 26 déc. 2009 à 09:51, Anastassis Perrakis a écrit :
>> 
>>   
>>> Dear all,
>>> 
>>> A couple of people have pointed out problems when installing the ARP/wARP 
>>> CCP4i GUI over 64-bit fink installations
>>> of CCP4, in Mac OSX 10.6 Snow Leopard. Although I am not confident we 
>>> understand the problem 100%, it appears
>>> to be genuine, and most likely related to 64-bit versions of bltwish.
>>> 
>>> With the kind help of Felix Frollow and - you would not have guessed - Bill 
>>> Scott, it appears that the following workaround is valid:
>>> 
>>> sudo /bin/bash  {or /bin/tcsh, or /bin/zsh, should not matter}
>>> source /sw/bin/init.csh {or .sh. that the fink setup, you need to do that 
>>> steo}
>>> ccp4i
>>> {use the gui to uninstall previous versions and install the new one}
>>> 
>>> Then you can exit, and from a new terminal you can go on using your 
>>> installation as a normal user.
>>> 
>>> Note, that this installation problem only affects the GUI, and you can 
>>> anyway use the scripts
>>> (e.g. auto_tracing.sh) and use for e.g. ligand fitting the functionality of 
>>> arpnavigator, or use a 32-bit installation.
>>> 
>>> Best wishes to all -
>>> 
>>> Tassos
>>> 
>>> On Dec 24, 2009, at 20:29, Victor Lamzin wrote:
>>> 
>>> 
>>>> Dear All,
>>>> 
>>>> We are happy to announce the release of ARP/wARP version 7.1.
>>>> 
>>>> Please visit http://www.arp-warp.org for details and software download.
>>>> 
>>>> The major implementations and improvements are:
>>>> 
>>>> • A prototype of the molecular graphics ARP/wARP front-end, allowing the
>>>> display of molecules and electron densities.
>>>> • A prototype version of the new module for building poly-nucleotides
>>>> (DNA or RNA).
>>>> • Improved and faster protein chain tracing with higher performance at
>>>> lower resolution.
>>>> • The loop building as well as helix/strand building are now also
>>>> inherent parts of protein model building, resulting in enhanced model
>>>> completeness.
>>>> • Refinement procedures during automated model building have been
>>>> enhanced in the new versions of our preferred refinement engine, REFMAC,
>>>> notably including the implementation of 'conditional restraints'.
>>>> • Direct use of experimental single-wavelength anomalous diffraction
>>>> data (SAD) during model building is now also possible.
>>>> • Improved performance of automated ligand building.
>>>> • Supported computer platforms are Mac powerpc, Mac Intel and Linux
>>>> (including 32 and 64-bit versions and itanium).
>>>> 
>>>> Merry Xmas and Happy New Year!
>>>> 
>>>> Victor and Tassos on behalf of the ARP/wARP developers' team.
>>>>   
>> Dear Tassos,
>> 
>> Unfortunately, it does not seem to be a general cure. I get the same error 
>> as before:
>> 
>> [...@pmacmol2~]
>> (A)>  sudo /bin/bash
>> [r...@pmacmol2~]
>> (A)>  source /sw64/bin/init.sh
>> [r...@pmacmol2~]
>> (A)>  ccp4i
>> Top level CCP4 directory is /sw64/share/xtal/ccp4-6.1.2
>> Using CCP4 programs from /sw64/share/xtal/ccp4-6.1.2/bin
>> UnpackTaskArchive: uncompress failed to create 
>> "/tmp/mol/install_ARP_wARP_CCP4I6/ARP_wARP_CCP4I6.tar"
>> ExamineTaskArchive: failed to unpack temporary copy of 
>> /usr/local/arp_warp_7.0.1/ARP_wARP_CCP4I6.tar.gz
>> UnpackTaskArchive: uncompress failed to create 
>> "/tmp/mol/install_ARP_wARP_CCP4I6/ARP_wARP_CCP4I6.tar"
>> ExamineTaskArchive: failed to unpack temporary copy of 
>> /usr/local/arp_warp_7.0.1/ARP_wARP_CCP4I6.tar.gz
>> 
>> And the task is not installed.
>> 
>> So, it seems that for the time being we will be using the scripts...
>> 
>> Thank you for trying!
>> 
>> Best regards,
>> 
>> 
>> -- Miguel
>> 
>> Architecture et Fonction des Macromolécules Biologiques (UMR6098)
>> CNRS, Universités d'Aix-Marseille I&  II
>> Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
>> Tel: +33(0) 491 82 55 93
>> Fax: +33(0) 491 26 67 20
>> e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr
>> Web: http://www.pangea.org/mol/spip.php?rubrique2
>> 
>> 
>> 
>> 
>> 
>>   
> 
> -- 
> This message has been scanned for viruses and
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> 

-- Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr
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Re: [ccp4bb] ARP_wARP 7.1 release

[Miguel Ortiz Lombardia]

Just realized that I had tried before installing ARP/wARP 7.1 (it was 7.0.1)

Unfortunately, also to confirm that the same error appears after installing 7.1

As others observed, the installation of 7.1 reports that the GUI has been 
succesfully installed. But nothing has changed in $CCP4I_TOP/tasks and the task 
is not there.

Best regards,


Miguel

Le 26 déc. 2009 à 13:51, Miguel Ortiz Lombardia a écrit :

> Le 26 déc. 2009 à 09:51, Anastassis Perrakis a écrit :
> 
>> Dear all,
>> 
>> A couple of people have pointed out problems when installing the ARP/wARP 
>> CCP4i GUI over 64-bit fink installations
>> of CCP4, in Mac OSX 10.6 Snow Leopard. Although I am not confident we 
>> understand the problem 100%, it appears
>> to be genuine, and most likely related to 64-bit versions of bltwish.
>> 
>> With the kind help of Felix Frollow and - you would not have guessed - Bill 
>> Scott, it appears that the following workaround is valid:
>> 
>> sudo /bin/bash  {or /bin/tcsh, or /bin/zsh, should not matter}
>> source /sw/bin/init.csh {or .sh. that the fink setup, you need to do that 
>> steo}
>> ccp4i
>> {use the gui to uninstall previous versions and install the new one}
>> 
>> Then you can exit, and from a new terminal you can go on using your 
>> installation as a normal user.
>> 
>> Note, that this installation problem only affects the GUI, and you can 
>> anyway use the scripts
>> (e.g. auto_tracing.sh) and use for e.g. ligand fitting the functionality of 
>> arpnavigator, or use a 32-bit installation.
>> 
>> Best wishes to all -
>> 
>> Tassos
>> 
>> On Dec 24, 2009, at 20:29, Victor Lamzin wrote:
>> 
>>> Dear All,
>>> 
>>> We are happy to announce the release of ARP/wARP version 7.1.
>>> 
>>> Please visit http://www.arp-warp.org for details and software download.
>>> 
>>> The major implementations and improvements are:
>>> 
>>> • A prototype of the molecular graphics ARP/wARP front-end, allowing the 
>>> display of molecules and electron densities.
>>> • A prototype version of the new module for building poly-nucleotides 
>>> (DNA or RNA).
>>> • Improved and faster protein chain tracing with higher performance at 
>>> lower resolution.
>>> • The loop building as well as helix/strand building are now also 
>>> inherent parts of protein model building, resulting in enhanced model 
>>> completeness.
>>> • Refinement procedures during automated model building have been 
>>> enhanced in the new versions of our preferred refinement engine, REFMAC, 
>>> notably including the implementation of 'conditional restraints'.
>>> • Direct use of experimental single-wavelength anomalous diffraction 
>>> data (SAD) during model building is now also possible.
>>> • Improved performance of automated ligand building.
>>> • Supported computer platforms are Mac powerpc, Mac Intel and Linux 
>>> (including 32 and 64-bit versions and itanium).
>>> 
>>> Merry Xmas and Happy New Year!
>>> 
>>> Victor and Tassos on behalf of the ARP/wARP developers' team.
> 
> Dear Tassos,
> 
> Unfortunately, it does not seem to be a general cure. I get the same error as 
> before:
> 
> [...@pmacmol2~]
> (A)> sudo /bin/bash
> [r...@pmacmol2~]
> (A)> source /sw64/bin/init.sh 
> [r...@pmacmol2~]
> (A)> ccp4i
> Top level CCP4 directory is /sw64/share/xtal/ccp4-6.1.2
> Using CCP4 programs from /sw64/share/xtal/ccp4-6.1.2/bin
> UnpackTaskArchive: uncompress failed to create 
> "/tmp/mol/install_ARP_wARP_CCP4I6/ARP_wARP_CCP4I6.tar"
> ExamineTaskArchive: failed to unpack temporary copy of 
> /usr/local/arp_warp_7.0.1/ARP_wARP_CCP4I6.tar.gz
> UnpackTaskArchive: uncompress failed to create 
> "/tmp/mol/install_ARP_wARP_CCP4I6/ARP_wARP_CCP4I6.tar"
> ExamineTaskArchive: failed to unpack temporary copy of 
> /usr/local/arp_warp_7.0.1/ARP_wARP_CCP4I6.tar.gz
> 
> And the task is not installed.
> 
> So, it seems that for the time being we will be using the scripts...
> 
> Thank you for trying!
> 
> Best regards,
> 
> 
> -- Miguel
> 
> Architecture et Fonction des Macromolécules Biologiques (UMR6098)
> CNRS, Universités d'Aix-Marseille I & II
> Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
> Tel: +33(0) 491 82 55 93
> Fax: +33(0) 491 26 67 20
> e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr
> Web: http://www.pangea.org/mol/spip.php?rubrique2
> 
> 
> 
> 
> 

-- Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr
Web: http://www.pangea.org/mol/spip.php?rubrique2







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Re: [ccp4bb] ARP_wARP 7.1 release

[Miguel Ortiz Lombardia]

Le 26 déc. 2009 à 09:51, Anastassis Perrakis a écrit :

> Dear all,
> 
> A couple of people have pointed out problems when installing the ARP/wARP 
> CCP4i GUI over 64-bit fink installations
> of CCP4, in Mac OSX 10.6 Snow Leopard. Although I am not confident we 
> understand the problem 100%, it appears
> to be genuine, and most likely related to 64-bit versions of bltwish.
> 
> With the kind help of Felix Frollow and - you would not have guessed - Bill 
> Scott, it appears that the following workaround is valid:
> 
> sudo /bin/bash  {or /bin/tcsh, or /bin/zsh, should not matter}
> source /sw/bin/init.csh {or .sh. that the fink setup, you need to do that 
> steo}
> ccp4i
> {use the gui to uninstall previous versions and install the new one}
> 
> Then you can exit, and from a new terminal you can go on using your 
> installation as a normal user.
> 
> Note, that this installation problem only affects the GUI, and you can anyway 
> use the scripts
> (e.g. auto_tracing.sh) and use for e.g. ligand fitting the functionality of 
> arpnavigator, or use a 32-bit installation.
> 
> Best wishes to all -
> 
> Tassos
> 
> On Dec 24, 2009, at 20:29, Victor Lamzin wrote:
> 
>> Dear All,
>> 
>> We are happy to announce the release of ARP/wARP version 7.1.
>> 
>> Please visit http://www.arp-warp.org for details and software download.
>> 
>> The major implementations and improvements are:
>> 
>> • A prototype of the molecular graphics ARP/wARP front-end, allowing the 
>> display of molecules and electron densities.
>> • A prototype version of the new module for building poly-nucleotides 
>> (DNA or RNA).
>> • Improved and faster protein chain tracing with higher performance at 
>> lower resolution.
>> • The loop building as well as helix/strand building are now also 
>> inherent parts of protein model building, resulting in enhanced model 
>> completeness.
>> • Refinement procedures during automated model building have been 
>> enhanced in the new versions of our preferred refinement engine, REFMAC, 
>> notably including the implementation of 'conditional restraints'.
>> • Direct use of experimental single-wavelength anomalous diffraction 
>> data (SAD) during model building is now also possible.
>> • Improved performance of automated ligand building.
>> • Supported computer platforms are Mac powerpc, Mac Intel and Linux 
>> (including 32 and 64-bit versions and itanium).
>> 
>> Merry Xmas and Happy New Year!
>> 
>> Victor and Tassos on behalf of the ARP/wARP developers' team.

Dear Tassos,

Unfortunately, it does not seem to be a general cure. I get the same error as 
before:

[...@pmacmol2~]
(A)> sudo /bin/bash
[r...@pmacmol2~]
(A)> source /sw64/bin/init.sh 
[r...@pmacmol2~]
(A)> ccp4i
Top level CCP4 directory is /sw64/share/xtal/ccp4-6.1.2
Using CCP4 programs from /sw64/share/xtal/ccp4-6.1.2/bin
UnpackTaskArchive: uncompress failed to create 
"/tmp/mol/install_ARP_wARP_CCP4I6/ARP_wARP_CCP4I6.tar"
ExamineTaskArchive: failed to unpack temporary copy of 
/usr/local/arp_warp_7.0.1/ARP_wARP_CCP4I6.tar.gz
UnpackTaskArchive: uncompress failed to create 
"/tmp/mol/install_ARP_wARP_CCP4I6/ARP_wARP_CCP4I6.tar"
ExamineTaskArchive: failed to unpack temporary copy of 
/usr/local/arp_warp_7.0.1/ARP_wARP_CCP4I6.tar.gz

And the task is not installed.

So, it seems that for the time being we will be using the scripts...

Thank you for trying!

Best regards,


-- Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr
Web: http://www.pangea.org/mol/spip.php?rubrique2







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Re: [ccp4bb] to model or not to model, that's not the question

[Miguel Ortiz Lombardia]

Le 17 nov. 09 à 12:40, Morten Kjeldgaard a écrit :


Tim Gruene wrote:

Yes, but models that can be validated against experimental data.  
The

defining characteristics of computational models is that they (A)
are 100% dependent on the algortihm, (B) can't be validated at  
all.


Cheers,
Morten

Sorry, they can be validated to some extend using biochemical data!


You are joking, right?



I would say that any prediction that can be derived from a model and
confirmed is a validation of the model and the model remains valid  
until
replaced by a better one. The sun was orbiting the earth until  
evidence

became too contradictorily for this model. Until then it was a good
model - better than no model at all, be it wrong or not.


Whoa there. Let's move back a few steps. This discussion started  
because
someone said that there are "rumblings" that modelbuilding would  
soon be a

competitive technique to xray-crystallography.



That was perhaps a joke. In any case, it can't be seriously  
considered. I think the potentially useful discussion is about what  
information can we gain from each other.


I objected with the fact that computational models cannot be  
validated, a
claim which was countered with "they can be validated using  
biochemical data".


I think that is really funny. So, you want to compute a model of a
macromolecule from first principles, and then spend the next 10  
years in the
biochemistry lab validating it? Because that is what it will take  
until you
can convince anyone that the positions of your loops, your rotamers,  
your

co-factors and your metal-binding sites are correct.



You don't need 10 years to test a clear prediction. From whatever kind  
of model. If you need 10 years the prediction is probably useless in  
its present form. I presume that is precisely your point. My point is  
that such models may produce clear, testable predictions.


From the way we are discussing it would seem that this is a matter of  
opinion. The fact is that some models are validated, even  
structurally, see:


Qian, B., Raman, S., Das, R., Bradley, P., McCoy, A. J., Read, R. J.,  
and Baker, D. (2007) High-resolution structure prediction and the  
crystallographic phase problem. Nature, 450: 259–264.



I thought this list was for crystallographers, but apparently people  
no

longer understand what "validation" means in structural science.



I agree with this, but not in the way you think. Crystallographers may  
be/need to be inerested by other fields related to structural biology.  
Even if they don't agree with the way other fields research is carried  
out.



 (...) OTOH, a poor molecular model may cause
unlimited waste of time and money by other scientists.



That's what happened for example with the crystal structures of the  
Emr multidrug transporters. Biochemists found a hard time to get  
funding for research that was in contradiction with those, later  
retracted crystallographic models. I hope that they don't conclude  
from that episode that trusting crystallographic models is useless or  
even dangerous to them.


Best,


-- Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr
Web: http://www.pangea.org/mol/spip.php?rubrique2







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Re: [ccp4bb] video that explains, very simply, what Structural Molecular Biology is about

[Miguel Ortiz Lombardia]

Le 15 nov. 09 à 12:54, Kjeldgaard Morten a écrit :


On 14/11/2009, at 20.17, Miguel Ortiz Lombardia wrote:


Le 14 nov. 09 à 19:15, Kjeldgaard Morten a écrit :


On 14/11/2009, at 18.55, Ronald E Stenkamp wrote:

The rumblings here at the Univ. of Washington among the  
computational modelers is that some of their current models might  
be more representative of protein structures in solution than are  
the crystal structure models.  It may take less than a "couple of  
decades" for a reduced emphasis on crystallographic studies.


Molecular models are the result of numbers emerging from computer  
programs. The results of such computations do not reflect anything  
in nature. There's no experimental evidence whatsoever, making  
modelling a very theoretical -- in my eyes uninteresting --  
exercise.


For what it's worth, protein molecules in crystal structures, with  
typically > 50% solvent, are already "in solution" to the extent  
that protein molecules are ever "in solution" in their natural  
environment.



Hi,

I think that strong statements and future foretelling are probably  
not very useful to a discussion that is indeed interesting and that  
will be put forward more and more often. Crystal structures are  
actually models themselves.


Yes, but models that can be validated against experimental data. The  
defining characteristics of computational models is that they (A)  
are 100% dependent on the algortihm, (B) can't be validated at all.



I don't agree (a) they depend not only on the algorithm(s) but also on  
the setting of the problem, which is kind of an experiment, call it  
thought experiment if you want, and (b) they can indeed be validated  
if they make predictions that can be tested experimentally. Just like  
our own models. True, we can validate our models against our own data,  
which makes life easier for us, but our data may prove artifactual to  
some extent: proteins are most often crystallised very far from  
physiological conditions, crystal contacts may be misinterpreted as  
functional interactions, our validation tools may fail to detect  
errors, etc. Briefly, we need also other data to confront our models to.



Best,


-- Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr
Web: http://www.pangea.org/mol/spip.php?rubrique2







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Re: [ccp4bb] video that explains, very simply, what Structural Molecular Biology is about

[Miguel Ortiz Lombardia]

Le 14 nov. 09 à 19:15, Kjeldgaard Morten a écrit :


On 14/11/2009, at 18.55, Ronald E Stenkamp wrote:

The rumblings here at the Univ. of Washington among the  
computational modelers is that some of their current models might  
be more representative of protein structures in solution than are  
the crystal structure models.  It may take less than a "couple of  
decades" for a reduced emphasis on crystallographic studies.


Molecular models are the result of numbers emerging from computer  
programs. The results of such computations do not reflect anything  
in nature. There's no experimental evidence whatsoever, making  
modelling a very theoretical -- in my eyes uninteresting -- exercise.


For what it's worth, protein molecules in crystal structures, with  
typically > 50% solvent, are already "in solution" to the extent  
that protein molecules are ever "in solution" in their natural  
environment.



Hi,

I think that strong statements and future foretelling are probably not  
very useful to a discussion that is indeed interesting and that will  
be put forward more and more often. Crystal structures are actually  
models themselves. Sure, they are directly backed by experimental data  
against which they can be compared in many ways, what we call  
validation. But as models, they have their own limitations and,  
ultimately, to be useful and trustworthy, they should be backed by  
results from other experimentalists: biochemists, biophysicists, etc.  
Because computational models don't have direct experimental data  
behind them, they need an even stronger external validation. But this  
does not imply that they are useless. Other fields of science progress  
thanks to computational models that help understanding problems and  
pose new, experimentally-testable questions. Biology needs  
computational models as well: about structures and their dynamics,  
biochemical pathways, cell and tissue interplay, etc.


The question of whether theoretical models reflect better the "in  
solution" state is probably a precipitate one (sorry). They should  
first prove that they consistently lead to predictions that are backed  
by data from experiments "in solution", "in vitro" or, better, "in  
vivo". Experimental structural models have proven very useful in  
predicting properties of the macromolecules that they represent. One  
day, computational models may be considered similarly useful.


But I don't think computational modelling will replace experimental  
structure determination. In a way it is not completely true that there  
is no experimental evidence behind computational structural models:  
these models are not made from just first principles, they incorporate  
a lot of empirical knowledge. Thus, modellers need experimental models  
to be improve their own ones and that will probably hold true for  
long. It can be argued that opposite is also true and we,  
structuralist, have something to learn from computational models. I do  
think so.


In the meantime, I think it is in our best interest to keep a dialogue  
between "computational" and "experimental" modellers and avoid the 'we- 
don't-need-you' wars.


Best,


-- Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr
Web: http://www.pangea.org/mol/spip.php?rubrique2







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Re: [ccp4bb] video that explains, very simply, what Structural Molecular Biology is about

[Miguel Ortiz Lombardia]

Le 14 nov. 09 à 10:53, Frederic VELLIEUX a écrit :


Dear Bulletin Board,

The following URL's may help people to understand crystallography  
(this was also pointed out to me by Ines Kahlaoui last night, I am  
so grateful to her):


http://videolectures.net/mit3091f04_sadoway_lec14/ (for the  
Boltzmann distribution)


through to

http://videolectures.net/mit3091f04_sadoway_lec19/

and the lecturer there is a very good lecturer. I haven't slept much  
last night :-) .


Nothing about the maths, but you can't have everything. And people  
usually choke on the maths.


Fred.



Dear all,

On the same vein, let me recommend a series of lectures about symmetry  
from the wonderful MIT OpenCourseWare:


http://ocw.mit.edu/OcwWeb/Materials-Science-and-Engineering/3-60Fall-2005/CourseHome/

The instructor is Prof. Bernhardt Wuensch, from the materials science  
field, so nothing so close to proteins/nucleic acids. But very clear.


You can download those lectures as video podcasts and watch them  
whenever and wherever. There are also plenty of additional readings  
and problem assignments for many of the lecture series. The MIT  
OpenCourseWare is really a treasure! Just explore it, I'm sure anyone  
can find enough material to fill their hard drives.


Best,


-- Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr
Web: http://www.pangea.org/mol/spip.php?rubrique2







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Re: [ccp4bb] {Disarmed} Re: [ccp4bb] sulfur sad phasing

[Miguel Ortiz Lombardia]

Le 11 nov. 09 à 14:26, Jürgen Bosch a écrit :


Dear CCP4 community,
(hijacking the thread)
I so far failed to get a sulfur SAD phased structure and I blamed it  
on the low symmetry space group C2 plus weakish diffraction if you  
don't want to overexpose your crystal and be able to collect 20-30x  
redundancy.
What do the expert think about fine slicing versus "regular" data  
collection for sulfur SAD phasing ?


Thanks,

Jürgen



Hi Jürgen,

You may find this paper interesting:

Lakomek, K., Dickmanns, A., Mueller, U., Kollmann, K., Deuschl, F.,  
Berndt, A., Lubke, T., and Ficner, R. (2009) De novo sulfur SAD  
phasing of the lysosomal 66.3 kDa protein from mouse. Acta Crystallogr  
D Biol Crystallogr, 65: 220–228.


It shows a case where sulfur-SAD worked for a reasonably-sized protein  
crystallized in C2. There was a Xe atom, but its contribution seemed  
to be negligible. No special data collection strategy is mentioned.


Best,


-- Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr
Web: http://www.pangea.org/mol/spip.php?rubrique2







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Re: [ccp4bb] sulfur sad phasing

[Miguel Ortiz Lombardia]

Le 11 nov. 09 à 13:16, Matthias Zebisch a écrit :


Dear bb!

What is the optimal wavelength for Sulfur SAD phasing?
Is it 1.9A or should one go below that to reduce absorption/damage.

Also, would the same wavelength be appropriate to maximize anomalous
scattering to position chlorides, calcium, sulfate in already phased  
structures?


Thanks in advance,

Matthias




Hi Matthias,

We collected a highly-redundant sulfur-SAD data set at 2.0 A  
wavelength. We managed to solve the structure thanks to two of the  
three sulfur atoms present in the protein, plus one chloride ion that  
happened to be bound to it. Radiation damage was an issue, but only  
after anomalous redundancy was higher than 30. With very, very high  
redundancy it was not possible to solve the structure. Thus, in some  
cases, it may be worth trying with less images.


Of course, as Fred said, the precission of the measurements is  
extremely important for sulfur-SAD phasing.


Best,


-- Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel: +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr
Web: http://www.pangea.org/mol/spip.php?rubrique2







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Re: [ccp4bb] Jobs

[Miguel Ortiz Lombardia]

Le 30 sept. 09 à 22:07, Christopher Law a écrit :


I am just wondering if anyone else is getting just a little bit peeved
that the BB is now primarily being used as a jobs board?

--  
Dr. Christopher J. Law,

Queen's University Belfast




Hi Christopher,

Well, I quote from the CCP4 web site:

The bulletin board is routinely used to request information, and to  
inform people about job vacancies, new services and the availability  
of new or updated software.


Considering how volatile has become almost any job in research, I  
think that this use of the board stands among the most useful ones, in  
practice, for the community. If the messages are properly labelled in  
their subjects non-interested people can always filter such messages  
out.


Best,



-- Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel : +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr
Web: http://www.pangea.org/mol/spip.php?rubrique2





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Re: [ccp4bb] trouble with imosflm cell refinement

[Miguel Ortiz Lombardia]

Le 30 sept. 09 à 17:27, Graeme Winter a écrit :


Dear Miguel,

You may find that replacing the ipmosflm binary with the one from
Harry's web page may be more reliable - typically these sorts of
things come down to gfortran or g77 being a little keen in
optimization.

http://www.mrc-lmb.cam.ac.uk/harry/mosflm/

Cheers,

Graeme




Dear Greame,

Indeed, the pre-built binary from Harry's page did the trick.

Thanks!



-- Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel : +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr
Web: http://www.pangea.org/mol/spip.php?rubrique2





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[ccp4bb] trouble with imosflm cell refinement

[Miguel Ortiz Lombardia]

Dear all,

I cannot get imosflm refining any cell, the program simply stalls: all  
you have is the little "E" at the top right rotating, but no messages,  
no errors, no crashes. 'Abort' doesn't have any effect either, nor it  
has the sequence 'Pause'-'Continue'.


I have this problem with:

OS: Mac (intel) 10.5.8
ccp4: 6.1.2-4 (compiled via fink, this is imosflm 1.0.0 with ipmosflm  
7.0.5)


OR:

OS: Mac (intel) 10.5.8
imosflm: 1.0.3-1 (compiled via fink, it also uses ipmosflm 7.0.5)

In the second case there is a warning:


/sw/bin/imosflm: line 204: type: /sw/bin/wish8.5: not found

Environment variable MOSFLM_WISH does not point to
a valid wish8.4 executable!

Testing default wish8.4 executable (/sw/bin/wish8.4).
Running imosflm with default wish8.4 executable (/sw/bin/wish8.4).



which does not prevent the program to otherwise run.

All other functions (indexation, strategy, integration) work.

Any ideas?

Best regards,



-- Miguel

Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932, 163 Avenue de Luminy, 13288 Marseille cedex 9, France
Tel : +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr
Web: http://www.pangea.org/mol/spip.php?rubrique2





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Re: [ccp4bb] heavy atom derivative choice

[Miguel Ortiz Lombardia]

Hi Sebastiano,

Have a look at HATODAS:

http://hatodas.harima.riken.go.jp/


Good luck,


Miguel

Le 15 juil. 09 à 14:33, Sebastiano Pasqualato a écrit :


Hi all,
I've got crystals of a protein of ca 200 residues, with 2 free  
cysteines, 5 histidines, 2 methionines.
We have nice diffraction for the native crystals, that grow in 150  
mM KSCN, 17% PEG 3350, bis tris propane pH 8.8.
We are crystallising the SeMet derivative, but I'm not completely  
sure I will be able to have nice crystals by saturday, when we have  
tunable time at the ESRF.
I was thinking of trying with some heavy atom soaks, but only have  
like 30 crystals, so limited trials allowed!
Which compound would you advice as more likely to work, and thus  
worth testing?

Thanks in advance for the suggestions,
ciao
s



--
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IFOM-IEO Campus
Dipartimento di Oncologia Sperimentale
Istituto Europeo di Oncologia
via Adamello, 16
20139 - Milano
Italy

tel +39 02 9437 5094

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Case 932
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13288 Marseille cedex 9
France
Tel : +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr
Web: http://www.pangea.org/mol/spip.php?rubrique2



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Re: [ccp4bb] Problem with 2 runs in scala

[Miguel Ortiz Lombardia]

Thanks to all who answered!

Removing "RUN 1 reference" did the trick

Another idea was to simply:

EXCLUDE batch 551 to 650

but then, smoothed scaling is not possible (to wide a gap )


Best regards,


Miguel

2009/7/3 Miguel Ortiz Lombardia >:

Dear all,

I'm trying to scale a dataset where 100 frames in the middle (25  
degrees)
are quite bad so I would like to exclude them. Because the angular  
range is
too wide I can only do that by creating two runs. So far, so good.  
The

problem is that even if my input contains these five lines:

 Data line--- run 1 INCLUDE batch 1 to 550
 Data line--- run 2 INCLUDE batch 651 to 720
 Data line--- RUN 1 reference
 Data line--- name run 1 project sls090624 crystal WHALE4 dataset sls
 Data line--- name run 2 project sls090624 crystal WHALE4 dataset sls

scala ends with this error:

  Run 2 has not been assigned to a dataset 

 Scala:  * Error in input *


I'm almost certain I've seen this before, but I don't remember the  
cure... I

would appreciate if someone can help.

Best regards,


Miguel
--
Miguel Ortiz Lombardía
Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932
163 Avenue de Luminy
13288 Marseille cedex 9
France
Tel : +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr
Web: http://www.pangea.org/mol/spip.php?rubrique2




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Miguel Ortiz Lombardía
Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932
163 Avenue de Luminy
13288 Marseille cedex 9
France
Tel : +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr
Web: http://www.pangea.org/mol/spip.php?rubrique2



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[ccp4bb] Problem with 2 runs in scala

[Miguel Ortiz Lombardia]

Dear all,

I'm trying to scale a dataset where 100 frames in the middle (25  
degrees) are quite bad so I would like to exclude them. Because the  
angular range is too wide I can only do that by creating two runs. So  
far, so good. The problem is that even if my input contains these five  
lines:


 Data line--- run 1 INCLUDE batch 1 to 550
 Data line--- run 2 INCLUDE batch 651 to 720
 Data line--- RUN 1 reference
 Data line--- name run 1 project sls090624 crystal WHALE4 dataset sls
 Data line--- name run 2 project sls090624 crystal WHALE4 dataset sls

scala ends with this error:

  Run 2 has not been assigned to a dataset 

 Scala:  * Error in input *


I'm almost certain I've seen this before, but I don't remember the  
cure... I would appreciate if someone can help.


Best regards,


Miguel
--
Miguel Ortiz Lombardía
Architecture et Fonction des Macromolécules Biologiques (UMR6098)
CNRS, Universités d'Aix-Marseille I & II
Case 932
163 Avenue de Luminy
13288 Marseille cedex 9
France
Tel : +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr
Web: http://www.pangea.org/mol/spip.php?rubrique2



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Re: [ccp4bb] problem starting refmac from ccp4i gui

[Miguel Ortiz Lombardia]

Hi,

If you were trying to re-run a job created with ccp4 6.1.0 or earlier,  
this is a known bug. Have a look at:


http://www.ccp4.ac.uk/problems.php#6.1.1-programs

If that is the case, there is a new refmac.tcl file that solves that  
problem.


Best,


Miguel

Le 16 mai 09 à 12:42, Kay Diederichs a écrit :


Boaz,

I recently saw the same message, after installing (binary) 6.1.1 .  
The workaround that seems to work for me is to start a new project  
from scratch.


The "STARTING" problem may have to do with the line
127.0.0.1 localhost.localdomain localhost
missing from /etc/hosts - did you check that?

HTH,

Kay

Boaz Shaanan schrieb:

Hi,
On a newly installed v 6.1.1 I (built from source) I can't get  
refmac to start from the gui (other programs, such as pointless and  
phaser, run fine). The latest patches have also been installed.  
When I start a refmac job that runs file under 6.1.0 (the binary  
built) the job gets stuck and the gui reports 'starting' for the  
job without switching to 'running'. The latest refmac version from  
York is installed (5.0.92) and again, it runs fine under 6.1.0.
These lines appear in the window from which the ccp4i was launched  
after starting the job:

can't set "ATOM(0)": variable isn't array
   while executing
"set [subst $root]([subst $indx0]) """
   (procedure "ExecuteScript" line 50)
   invoked from within
"ExecuteScript $system(SCRIPT)"
   ("script" arm line 8)
   invoked from within
"switch  $system(RUN_MODE) \
 script {
   source [file join $env(CCP4I_TOP) src execute.tcl]
   source [file join $env(CCP4I_TOP) src job_utils..."
   (file "/home/boaz/ccp4/ccp4-6.1.1/ccp4i/bin/ccp4ish.tcl" line 145)
   invoked from within
"source [file join $env(CCP4I_TOP) bin ccp4ish.tcl]"
   (file "/home/boaz/ccp4/ccp4-6.1.1/ccp4i/bin/ccp4ish" line 12)
Does anybody have a clue on what could have gone wrong and how to  
fix the problem ?

Thanks,
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
Phone: 972-8-647-2220 ; Fax: 646-1710
Skype: boaz.shaanan
‎





--
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Architecture et Fonction des Macromolécules Biologiques
UMR6098 ( CNRS, U. de Provence, U. de la Méditerranée )
Case 932
163 Avenue de Luminy
13288 Marseille cedex 9
France
Tel : +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
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Re: [ccp4bb] NCBHT: severe warning

[Miguel Ortiz Lombardia]

Not nice either to air the address of someone who wrote you privately.


Miguel

Le 1 avr. 09 à 22:48, Marius Schmidt a écrit :


Interesting, isn't it? :-), nice person.



F*** Off.. it might be 1st April but most people are not interested
about
your shit sense of humour.. send them to your friends..



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Architecture et Fonction des Macromolécules Biologiques
UMR6098 ( CNRS, U. de Provence, U. de la Méditerranée )
Case 932
163 Avenue de Luminy
13288 Marseille cedex 9
France
Tel : +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr
Web: http://www.pangea.org/mol/spip.php?rubrique2


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Re: [ccp4bb] XDS and ESRF ID23-1 images

[Miguel Ortiz Lombardia]

Hi Ronnie and others,

Le 27 mars 09 à 15:02, Ronnie Berntsson a écrit :

This might be a bit too obvious, but have you checked that the path  
to the images is correct? The path written in the input files  
generated on the beamline reflects where the images were located in  
the file tree there. Does it match where you have the files on your  
own computer?


Yes and no... it looked the same, however there was a hidden extra  
character between the question marks '?' in the template! Not visible  
in 'vim' or 'less' but became apparent with:


cat -tve XDS.INP

So, next time I will read more carefully the error message (there were  
three '?' instead of the four I thought were written in the XDS.INP  
file)


However, that was not all the story.

Le 27 mars 09 à 14:57, Marija Backovic a écrit :

I had a similar problem, and it was because I had played with  
changing some of the detector hardware parameters (NX, NY values in  
the XDS.INP). I know this has nothing to do with the availability of  
images :) Once I set the NX and NY back to the original value,  
defined by the XDS.INP file, the problem was solved. You can find  
the appropriate XDS.INP, corresponding to the detector you used, at http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/XDS.INP



Indeed, some of the detector hardware parameters (NX, NY) in the  
XDS.INP seemed to be incorrect in the input file generated at the beam  
line. The file from the XDSwiki for ID23-1 worked fine once the extra  
character was removed from the template name.


Thanks to all who replied!


Miguel
--
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Architecture et Fonction des Macromolécules Biologiques
UMR6098 ( CNRS, U. de Provence, U. de la Méditerranée )
Case 932
163 Avenue de Luminy
13288 Marseille cedex 9
France
Tel : +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
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[ccp4bb] XDS and ESRF ID23-1 images

[Miguel Ortiz Lombardia]

Dear all,

Not a CCP4 question.
We seem unable to process with XDS a set of images collected at ESRF  
ID23-1.


Images can be open and processed by other software (adxv, mosflm...)  
They have appropriate read permissions and so has the directory where  
we run XDS. We use the latest XDS binaries (VERSION  January 30, 2009)  
or the previous one (expiring next week) for Mac OSX (Intel) and the  
input file for ID23-1 created at the beam line or the one in the  
XDSwiki. In all cases we get this error:


 !!! ERROR !!! Data image does not exist: x2-id23_1_001.img

Any idea of where the problem may be?

Cheers,


Miguel
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Architecture et Fonction des Macromolécules Biologiques
UMR6098 ( CNRS, U. de Provence, U. de la Méditerranée )
Case 932
163 Avenue de Luminy
13288 Marseille cedex 9
France
Tel : +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr
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[ccp4bb] Plasmids and other material [Was: images]

[Miguel Ortiz Lombardia]

Hi,

I mostly agree with Artem, except on one point:

As long as people publish most of the details necessary to reproduce  
the
materials (protein samples and crystals) used in structure  
determination -
the crystals may be reproduced 'by persons skilled in the art'.  
There is no
need to even store or distribute specific plasmid/clone DNA samples  
any more
as long as relevant DNA sequences are retained (thank you, synthetic  
DNA

providers!).


I understand that it may look today like a romantic idea, but good  
science is done in labs that cannot easily pay the fees of those fancy  
synthetic DNA providers. Storage and distribution of this kind of  
material is therefore still important. Of course, there is a limit:  
you cannot be expected to send crystals all around the world, let  
aside other planets. In general, good common sense should be enough,  
from plasmids to images. As Eleanor pointed out, we should keep those  
materials available, because they are primarily our responsibility.


Artem is right in that many reports simply don't provide enough  
information to reproduce the results. The most important reason to  
have such information is not to go against fraud, I am also an  
optimist here, but to be able to reproduce the results so that we can  
produce new results from them. This information should be in the  
papers or in 'supplementary files' or wherever. Some authors when  
contacted will be happy to provide you with the info, but others never  
answer your letters.


Science should be about collaboration and trust, shouldn't it? That  
would make things easier and cheaper. Or we can implement rules and  
more rules like the security freaks do and we all suffer now when  
travelling.



Best,


Miguel
--
Miguel Ortiz Lombardía
Architecture et Fonction des Macromolécules Biologiques
UMR6098 ( CNRS, U. de Provence, U. de la Méditerranée )
Case 932
163 Avenue de Luminy
13288 Marseille cedex 9
France
Tel : +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr
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Re: [ccp4bb] Problem with multiple users running ccp4i on one machine

[Miguel Ortiz Lombardia]

Dear ccp4i developers,

Jumping into this issue a bit late...
I have some criticism to make here, please take them friendly, I make  
them precisely because ccp4i is so useful.


I presume there are good reasons behind the new design of CCP4i and  
its CCP4 DBhandler, but I think you have overlooked the fact that  
multi-processor, multi-user servers are quite common nowadays. Also,  
that many end-users don't know/don't need to know what a sqlite  
database is and will simply let the default preferences turned on,  
unaware of the consequences.


In our lab this has led to people not using the best computer they  
have available, precisely by reasons similar to those raised by Jun  
Dong. I know of another case where a user got its database corrupted  
after getting confused because not being able to see their own  
projects/directories.


I hope that in future versions of ccp4 the multi-users problem will be  
tackled or, at least, the default option is the old direct-access  
behaviour (if completely functional).



With best regards,


Miguel

Le 18 mars 09 à 17:46, Ronan Keegan a écrit :


Dear Jun Dong,

This is a problem with the new mechanism used in CCP4 to store  
project and job data (the CCP4 DBhandler). The quick fix for now is  
to turn it off and use the old mechanism for storing the project  
data. To do this in the CCP4i interface go to "System  
Administration", select "Database Configuration" and un-check the  
radio button that sets the option to connect to the database server  
on start up. Then have all your users restart CCP4i.


Kind regards,

Ronan Keegan
CCP4 Group


Jun Dong wrote:

Dear CCP4 developers,
I just wonder if there will be a fix for this problem. Basically  
when the first user is running ccp4i on a linux server and then  
when the second user tries to run ccp4i on the same linux server,  
the second user will only see the fist user's Directories&ProjectDir.

Best regards, Jun Dong
Division of Structural Biology
The Wellcome Trust Centre for Human Genetics
Oxford University
Roosevelt Drive
Oxford
OX3 7BN
Tel: 01865 287558




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Architecture et Fonction des Macromolécules Biologiques
UMR6098 ( CNRS, U. de Provence, U. de la Méditerranée )
Case 932
163 Avenue de Luminy
13288 Marseille cedex 9
France
Tel : +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
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Re: [ccp4bb] PHENIX & BSS refinement

[Miguel Ortiz Lombardia]

Hi Pavel,

Thanks, it is clear now.
I have a last concern, though. Does phenix impose minimal values to  
the refined ADPs? I guess it does not, for I have found nothing like  
that in the documentation. But, if it does so, are they imposed to the  
individual B-factors or the B-overall is also taken into account? In  
the former case you might have problems with the refinement in a case  
as the one I described in my previous e-mail (coming from a model with  
artificially low, 'residual' B-factors).


Cheers,


Miguel


Le 4 févr. 09 à 18:23, Pavel Afonine a écrit :


Hi Miguel,

Right, but why this happens only in the final bss step ? Why not in  
the first one?


It's arbitrary: one can do it every macro-cycle as well. The main  
idea is to have a total B-factor in ATOM records written out to a  
PDB file.


I have noticed the behaviour described by José when I refine in  
phenix a model previously refined in refmac5 _with_ TLS, so the  
ADPs in the model are actually 'residual' ADPs of refmac5 TLS  
refinement. In these cases, during the refinement in phenix, the  
ADPs seem to be kept at very low values all throughout until they  
abruptly go to the higher, more reasonable values, after the final  
bulk solvent correction step. There may be a good reason for this  
behaviour, but I don't see it. I would appreciate if you could  
elaborate.


Like I said, it is arbitrary. You can store the overall B-factor in  
overall anisotropic scale matrix (B_overall) or in individual atomic  
B-factors; in both cases the total model structure factor
Fmodel = scale_overall * exp(-h*B_overall*ht) * (Fcalc + k_sol *  
exp(-B_sol*s^2) * Fmask)

will remain the same.

Pavel.

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Case 932
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Tel : +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
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Re: [ccp4bb] PHENIX & BSS refinement

[Miguel Ortiz Lombardia]

Hi Pavel,



We have also seen that the B factor jumps up in this last step (see  
bellow).  Is anybody aware of this?


This is because the trace of overall anisotropic scale matrix is  
added to atomic B-factors and subtracted from that matrix. This is  
exactly what CNS does (at least version 1.1).




Right, but why this happens only in the final bss step ? Why not in  
the first one?


I have noticed the behaviour described by José when I refine in phenix  
a model previously refined in refmac5 _with_ TLS, so the ADPs in the  
model are actually 'residual' ADPs of refmac5 TLS refinement. In these  
cases, during the refinement in phenix, the ADPs seem to be kept at  
very low values all throughout until they abruptly go to the higher,  
more reasonable values, after the final bulk solvent correction step.  
There may be a good reason for this behaviour, but I don't see it. I  
would appreciate if you could elaborate.


I was tempted to send this e-mail also to the phenixbb list in case  
someone there could be interested... but cross-posting used to be  
anathema :-)


Best regards,


Miguel
--
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Architecture et Fonction des Macromolécules Biologiques
UMR6098 ( CNRS, U. de Provence, U. de la Méditerranée )
Case 932
163 Avenue de Luminy
13288 Marseille cedex 9
France
Tel : +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr
Web: http://www.pangea.org/mol/spip.php?rubrique2


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Re: [ccp4bb] Google marks CCP4 web site as a potential security threat

[Miguel Ortiz Lombardia]

The same is true for IUCr, Nature, Science, EMBO (!), Wiley, and  
ScienceDirect websites, among many others... including google.com!


Hope it's a (short-lived) bug.

Pedro



The bug is for them to decide what we have or have not to consider as  
a threat and to force us to change our websites as they please. They  
may change their filters in one hour or so and we won't notice this  
behaviour for our favourite, neutral and usually so compliant  
'science' sites. I'm wary of the principle itself of Google shaping  
the internet as they want it to be.


It seems they are free to do all that, but so we are to stop using  
Google.


Best,


Miguel
--
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Architecture et Fonction des Macromolécules Biologiques
UMR6098 ( CNRS, U. de Provence, U. de la Méditerranée )
Case 932
163 Avenue de Luminy
13288 Marseille cedex 9
France
Tel : +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr
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[ccp4bb] Google marks CCP4 web site as a potential security threat

[Miguel Ortiz Lombardia]

Dear all,

While searching for some definition of rotations angles I have bumped  
into this very disagreeable indeed discovery: google adds now a step  
if you want to go to places _they_ consider as potentially dangerous.  
You can proceed that have to copy and paste the address yourself or  
tell the relevant webmasters to do whatever Google wants them to do so  
their pages don't appear as risky. One such place happens to be the  
full ccp4 web site.


In my opinion, the real danger is Google.
Time to switch to another search engine?

In any case, I wanted CCP4 developers and users to know.
( the search was done from a home adsl connection in France )

Best regards,


Miguel
--
Miguel Ortiz Lombardía
Architecture et Fonction des Macromolécules Biologiques
UMR6098 ( CNRS, U. de Provence, U. de la Méditerranée )
Case 932
163 Avenue de Luminy
13288 Marseille cedex 9
France
Tel : +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr
Web: http://www.pangea.org/mol/spip.php?rubrique2


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Re: [ccp4bb] mapping sequence conservation metrics on the B factor column ...

[Miguel Ortiz Lombardia]

Hi Tassos,

I very much like Homolmapper:

http://www.mcb.ucdavis.edu/faculty-labs/lagarias/homolmapper_home/homolmapper%20web%20page.htm

You can map several conserved properties onto your structures, not  
just plain sequence.


Best,


Miguel

Le 29 janv. 09 à 22:25, Anastassis Perrakis a écrit :


Dear all,

I was wondering what is the state of the art for this old dark  
art ... are there any good servers / programs that allow to easily  
upload your own sequence alignments or create a 'transparent'  
alignment (I want to see the alignment first and not a total black  
box) and then allow you to write out sequence conservation based  
either on identity or in e.g a Dayhoff matrix on the B factor column  
for displaying it later in eg Pymol?


To be clear I do not want a structural alignment, but mapping  
sequence alignment of eg a family to a single structure of a family  
member.


Thanks in advance, Tassos

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Architecture et Fonction des Macromolécules Biologiques
UMR6098 ( CNRS, U. de Provence, U. de la Méditerranée )
Case 932
163 Avenue de Luminy
13288 Marseille cedex 9
France
Tel : +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr
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[ccp4bb] ccp4i 6.1.0 and file paths

[Miguel Ortiz Lombardia]

Dear all,

I have a request to the developers of CCP4I. I find very bizarre and  
potentially quite confusing that the default value for file paths is  
not _strictly_ the project directory but, instead, any directory that  
you happen to choose a moment before using 'Full-path', for instance  
(see below). This is especially problematic with output files, of  
course: you often simply write the name of the file (or worse, the  
task interface writes it for you) in its corresponding place, without  
paying attention to whether it goes to the project directory or  
somewhere else. In fact, you, at least I, expect the files to go to  
the project directory. But this may not happen if you chose a "Full  
path" for a particular file five minutes ago or, like it happened  
right now to me, if when you are creating a project you do this:


1) Click too fast and select a directory under the directory you  
actually wanted

2) Realise your mistake
3) Delete in the directory line (that is, without clicking again  
'Browse') the part that you didn't want

4) Open the project.

If you do such thing, the default value for input and output files for  
this new project is... the directory you selected in step 1) and not  
the one you wrote in step 3) What is more surprising is that the  
project directory itself is all right: only the default path for input  
and output files is wrong.


When you work with several projects at the time, as probably many  
people do, this behaviour can result in a lot of mess. I know you can  
always find the files through the CCP4I gui, but sometimes you want to  
access to those files without having to open the interface.


It is OK to allow the user to choose a different path but I think this  
should be a choice explicitly made by the user.


I think in previous versions this behaviour was not observed?

Happy new year to all!
Best,


Miguel

Disclaimer: I need holidays...
--
Miguel Ortiz Lombardía
!!!
!!!  NEW ADDRESS!!!
!!!
Architecture et Fonction des Macromolécules Biologiques
UMR6098, CNRS, Université Aix-Marseille I & II
Case 932
163 Avenue de Luminy
13288 Marseille cedex 9
France
Tel : +33(0) 491 82 55 93
Fax: +33(0) 491 26 67 20
e-mail: miguel.ortiz-lombar...@afmb.univ-mrs.fr
Web: http://www.pangea.org/mol/spip.php?rubrique2


--
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Re: [ccp4bb] Superdex 200 PC columns

[Miguel Ortiz-Lombardia]

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Hi,

You're right, there are two cell path sizes in AKTA systems: 2 mm and 10
mm. I don't know what path had the SMART. You definitely need the second
one if you want to work with low protein concentrations.


Miguel

En/na Juergen Bosch ha escrit:
> Hi all,
> 
> Isn't the flow cell volume the limiting factor for your detection limit
> ? I believe for the "old" Aktas (~5-8 years old) there were two cell
> sizes a laerger one and a smaller one, and I don't think it is the same
> size as in the SMART system. But I might be wrong.
> 
> Jürgen
> 
> [EMAIL PROTECTED] wrote:
> 
>> Hi Robert,
>>
>> In my experience, there is no problem running a SMART column on an AKTA
>> FPLC or Explorer. I have been using the same S75, S200, and Superose6
>> columns on all three systems depending on which one is available that
>> day.
>> I typically load 50 ul sample, between 10-0.01 mg/ml. The peak width I
>> get
>> is ~150ul, with 70-80% of the original concentration at the height of the
>> peak.
>> On the FPLC/Explorer I replace the standard tubing to shorter and more
>> narrow tubing and bypass the conductivity meter to reduce the amount of
>> dead volume.
>> Finally, for the very low protein concentrations, you're better of using
>> the Explorer, which allows you to measure the absorption at 220-230nm.
>>
>>
>> Meindert
>>
>>
>>  
>>
>>> Sorry for perhaps off-topic question but I am writing to ask if
>>> anyone has
>>> experience in using Amersham Superdex 200 PC 3.2/30 columns in
>>> conjuction
>>> with
>>> the Precision Column holder on a standard (not SMART system) AKTA FPLC.
>>> At the
>>> moment using a Superdex 200 10/300 column on a standard AKTA I can get a
>>> reasonable signal from down to about 20 ug protein - I am wondering how
>>> much
>>> less protein I will be able to use with the narrower Superdex 200 PC
>>> 3.2/30
>>> column when I hook it up to the same FPLC via the Precision Column
>>> holder.
>>>
>>>   
>>
>>  
>>
> 
> 

- --
Miguel Ortiz Lombardía
Centro de Investigaciones Oncológicas
C/ Melchor Fernández Almagro, 3
28029 Madrid, Spain
Tel. +34 912 246 900
Fax. +34 912 246 976
e-mail: [EMAIL PROTECTED]
- --
Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que
ce qui est fort fût juste.
Blaise Pascal, Pensées
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Re: [ccp4bb] Superdex 200 PC columns

[Miguel Ortiz-Lombardia]

-BEGIN PGP SIGNED MESSAGE-
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Hi Robert,

I have run those PC 2.3/30 with ~10 ug of protein (of course this
depends on the protein) and still get a useful signal at 280 nm. If you
don't have anything interfering at ~215 nm and your HPLC system can read
at that wavelength, you can even do with less than that. They are very
useful columns, for example to check for interactions, but they need to
be handled with _extra_ care. Your HPLC system as well needs to be very
stable and _really_ clean, especially the photometer cell. You should
use loops of 10-25 ul, though your sample may need to be bigger to avoid
 getting "lost" in dead spaces.

Good luck,


Miguel

En/na Robert Cleverley ha escrit:
> Sorry for perhaps off-topic question but I am writing to ask if anyone has
> experience in using Amersham Superdex 200 PC 3.2/30 columns in conjuction with
> the Precision Column holder on a standard (not SMART system) AKTA FPLC.  At 
> the
> moment using a Superdex 200 10/300 column on a standard AKTA I can get a
> reasonable signal from down to about 20 ug protein - I am wondering how much
> less protein I will be able to use with the narrower Superdex 200 PC 3.2/30
> column when I hook it up to the same FPLC via the Precision Column holder.
> 

- --
Miguel Ortiz Lombardía
Centro de Investigaciones Oncológicas
C/ Melchor Fernández Almagro, 3
28029 Madrid, Spain
Tel. +34 912 246 900
Fax. +34 912 246 976
e-mail: [EMAIL PROTECTED]
- --
Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que
ce qui est fort fût juste.
Blaise Pascal, Pensées
-BEGIN PGP SIGNATURE-
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=yJGX
-END PGP SIGNATURE-

Re: [ccp4bb] rmsd calculation. .

[Miguel Ortiz Lombardia]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Excellent!
Thank you Gerard,


Miguel

Gerard DVD Kleywegt escribió:
>> But my understanding is that Iain's procedure gives the rmsds of the
>> _aligned_ C-alphas, whereas Jenny actually seems to be more interested
>> in those that she excludes from the alignment. I may be wrong, but in
>> these cases, I use lsqman (from DVD) or lsqkab (from ccp4) to superpose
>> the proteins (using one as reference) according to a particular scheme
>> (Jenny's 1-40,60-100) and then write a script to calculate the rmsds for
>> the "interesting" 41-59 residues. There may be an easier way, which I'll
>> be interested to learn about.
> 
> hola miguel,
> 
> i would use the rmsd command in lsqman, like so:
> 
>   read m1 m1.pdb
>   read m2 m2.pdb
>   expl m1 "a1-40 a60-100" m2 "a1 a60"
>   rmsd m1 a41-59 m2 a41
> 
> --gerard
> 
> **
> Gerard J.  Kleywegt
> [Research Fellow of the Royal  Swedish Academy of Sciences]
> Dept. of Cell & Molecular Biology  University of Uppsala
> Biomedical Centre  Box 596
> SE-751 24 Uppsala  SWEDEN
> 
> http://xray.bmc.uu.se/gerard/  mailto:[EMAIL PROTECTED]
> **
>The opinions in this message are fictional.  Any similarity
>to actual opinions, living or dead, is purely coincidental.
> **
> 
> 

- --
Miguel Ortiz Lombardía
Centro de Investigaciones Oncológicas
C/ Melchor Fernández Almagro, 3
28029 Madrid, Spain
Tel. +34 912 246 900
Fax. +34 912 246 976
email: [EMAIL PROTECTED]
www: http://www.pangea.org/mol/spip.php?rubrique2
~~~
Le travail est ce que l'homme a trouvé de mieux
pour ne rien faire de sa vie.  (Raoul Vaneigem)
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Re: [ccp4bb] rmsd calculation. .

[Miguel Ortiz Lombardia]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hi Jenny and Iain,

But my understanding is that Iain's procedure gives the rmsds of the
_aligned_ C-alphas, whereas Jenny actually seems to be more interested
in those that she excludes from the alignment. I may be wrong, but in
these cases, I use lsqman (from DVD) or lsqkab (from ccp4) to superpose
the proteins (using one as reference) according to a particular scheme
(Jenny's 1-40,60-100) and then write a script to calculate the rmsds for
the "interesting" 41-59 residues. There may be an easier way, which I'll
be interested to learn about.

Cheers,


M.

Kerr, Iain escribió:
> Hi Jenny,
> 
>  
> 
> You can do this in LSQMAN (if I’m understanding your question correctly…)
> 
>  
> 
> You’d first superimpose the residues in the “fixed region” to give a
> superimposed core using the ‘EXplicit’ command, eg:
> 
>  
> 
> *LSQMAN > ex m1*
> 
> * Range 1 ? (A1-10) "a4-10 a19-23 a28-36 a44-51 a53-66 a91-97 a106-111 
> a123:126"*
> 
> * Mol 2 ? (M1) m2*
> 
> * Range 2 ? (A1) "a4 a19 a28 a44 a53 a91 a106 a123"*
> 
> * Explicit fit of M1 "A4-10 A19-23 A28-36 A44-51 A53-66 A91-97 A106-111 
> A123:126"*
> 
> * And M2 "A4 A19 A28 A44 A53 A91 A106 A123"*
> 
> * Atom types | CA | N  | C  | O  | CB |*
> 
> * Nr of atoms to match : (295)*
> 
> * The295 atoms have an RMS distance of0.892 A*
> 
> * Rotation:  -0.956932  0.127723 -0.260706*
> 
> * 0.170532 -0.479456 -0.860837*
> 
> *-0.234946 -0.868222  0.437026*
> 
> * Translation : 13.78726.80038.541*
> 
>  
> 
>  
> 
> Then use the “IMProve” command to iteratively improve the fit over all
> CAs…this only works for two molecules at a time though…I guess choose a
> fixed standard to align all the others against. Remember to write out
> the coordinates for the rotated (ie. “m2”) molecules:
> 
>  
> 
> Ø   apply m1 m2
> 
> Ø   wr m2 blah_rotated.pdb
> 
>  
> 
> Then to calculate the RMSDs for just the loop regions compare the
> superimposed molecules to the fixed standard (ie. “m1” is the fixed
> standard, “m2” is your blah_rotated.pdb), explicitly using just the loop
> atoms this time in “m1” and “m2” ranges.
> 
>  
> 
> I’m sure there is an easier way to do this, but works for me.
> 
>  
> 
> HTH,
> 
> Iain
> 
>  
> 
>  
> 
> 
> 
> *From:* CCP4 bulletin board [mailto:[EMAIL PROTECTED] *On Behalf Of
> *Jenny
> *Sent:* Thursday, May 10, 2007 5:46 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] rmsd calculation. .
> 
>  
> 
> Hi, All,
> 
> I have a question about rmsd calculation.
> 
> I have some pdbs (100 residues ) and these pdbs differ pretty much only
> the loop region 40-60. Is there any easy way that I can superimpose the
> fixed region ( 1-40,60-100) and then calculate the rmsd for the loop?I
> need to calculate for each pair, so if there is any script or program
> available to do this quickly, that would be great.
> 
> Thanks.
> 
> Jenny
> 

- --
Miguel Ortiz Lombardía
Centro de Investigaciones Oncológicas
C/ Melchor Fernández Almagro, 3
28029 Madrid, Spain
Tel. +34 912 246 900
Fax. +34 912 246 976
email: [EMAIL PROTECTED]
www: http://www.pangea.org/mol/spip.php?rubrique2
~~~
Le travail est ce que l'homme a trouvé de mieux
pour ne rien faire de sa vie.  (Raoul Vaneigem)
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Re: [ccp4bb] CCP4 GUI

[Miguel Ortiz Lombardia]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hi Martyn,

I was thinking in the "less scary" widgets-based interface for
not-so-used options. If possible, I think that all options should be
available to the interface. This would make the GUI more consistent, in
a way. I know is a lot more work, but I think that this will be
especially appreciated by people newly approaching CCP4 (students or
not). Those of us who worked with these programs from scripts (and rtfm)
know that there are more options than those exported to the GUI. Others
find this situation confusing.

The Expert switch in Preferences would be excellent.

I'm not sure to have understood the maintainability issue... unless you
mean that it can happen that options that become outdated disappear from
the program, so there would be a risk of having their "ghosts" in the
GUI. But normally programs complain when an option is not available,
don't they?

Cheers,


Miguel

Martyn Winn escribió:
> This is timely. We're in the process of a) trying to organise a major
> effort to tidy up the existing ccp4i classic (rather than fire-fighting
> problems), and b) thinking about designing the next generation. Not sure
> which this is. Option b) would be a project over several years. 
> 
> Can you elucidate further. As an expert user, would you want a less
> scary free text box (which is essentially what Run&View Com File is), or
> actual widgets for every option. The latter could be done as a hidden
> folder, made visible according to an Expert switch in Preferences. 
> 
> As developers, we also have to think about long-term maintainability.
> Options, in particular little-used options, can soon become out-of-date.
> 
> m
> 
> 
> On Thu, 2007-05-10 at 12:41 +0200, Miguel Ortiz Lombardia wrote:
>> -BEGIN PGP SIGNED MESSAGE-
>> Hash: SHA1
>>
>> Dear all,
>>
>> I'm a well-known luddite as Eleanor says. However, I shamelessly confess
>> that the CCP4 GUI is great. Not that I think this is necessary here, I'm
>> sure most people agree with that.
>>
>> If I write now is because Martynn's e-mail have reminded me of something
>> I thought once, but forgot to ask for to the ccp4i developpers: perhaps
>> the GUI could have "two faces/modes", a basic one and an expert/advanced
>> one. I understand that they already exist, but the "expert" one is
>> hidden under the "Run&View Com File", while I'm thinking on a real
>> expert GUI-mode. Users should be able to choose one or the other in
>> their defaults, or switch from one to the other on-the-fly.
>>
>> I don't have a particular problem in editing the scripts as it is done
>> now, but I have found that students tend to get a bit nervous about
>> doing it themselves ;-)
>>
>> Cheers,
>>
>>
>> Miguel
>>
>> Martyn Winn escribió:
>>> The level of detail in the GUI is a matter of constant debate. The
>>> underlying programs are far far richer, so the question is how much to
>>> expose in the GUI. We try to get a balance between ease-of-use and
>>> coverage, but it won't always work. BTW I don't think we ever claimed
>>> that ccp4i (or anything else in ccp4) is "finished" ;-)
>>>
>>> Having said that, we're always happy to hear about specific defects in
>>> the GUI. When reporting these to [EMAIL PROTECTED] please give as much
>>> information as possible, in particular knowing the context is always
>>> helpful.
>>>
>>> Cheers
>>> Martyn
>>>
> 

- --
Miguel Ortiz Lombardía
Centro de Investigaciones Oncológicas
C/ Melchor Fernández Almagro, 3
28029 Madrid, Spain
Tel. +34 912 246 900
Fax. +34 912 246 976
email: [EMAIL PROTECTED]
www: http://www.pangea.org/mol/spip.php?rubrique2
~~~
Le travail est ce que l'homme a trouvé de mieux
pour ne rien faire de sa vie.  (Raoul Vaneigem)
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Re: [ccp4bb] CCP4 GUI

[Miguel Ortiz Lombardia]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear all,

I'm a well-known luddite as Eleanor says. However, I shamelessly confess
that the CCP4 GUI is great. Not that I think this is necessary here, I'm
sure most people agree with that.

If I write now is because Martynn's e-mail have reminded me of something
I thought once, but forgot to ask for to the ccp4i developpers: perhaps
the GUI could have "two faces/modes", a basic one and an expert/advanced
one. I understand that they already exist, but the "expert" one is
hidden under the "Run&View Com File", while I'm thinking on a real
expert GUI-mode. Users should be able to choose one or the other in
their defaults, or switch from one to the other on-the-fly.

I don't have a particular problem in editing the scripts as it is done
now, but I have found that students tend to get a bit nervous about
doing it themselves ;-)

Cheers,


Miguel

Martyn Winn escribió:
> The level of detail in the GUI is a matter of constant debate. The
> underlying programs are far far richer, so the question is how much to
> expose in the GUI. We try to get a balance between ease-of-use and
> coverage, but it won't always work. BTW I don't think we ever claimed
> that ccp4i (or anything else in ccp4) is "finished" ;-)
> 
> Having said that, we're always happy to hear about specific defects in
> the GUI. When reporting these to [EMAIL PROTECTED] please give as much
> information as possible, in particular knowing the context is always
> helpful.
> 
> Cheers
> Martyn
> 
> On Thu, 2007-05-10 at 17:39 +0800, Charlie Bond wrote:
>> I would add that I have found the CCP4 development team very receptive 
>> to being informed about specific improvements which could be made, and 
>> even more so to fixes implemented by users themselves.
>>
>> Perhaps an explicit list of the many limitations which need attention 
>> would be useful to the development team.
>>
>> Cheers,
>> Charlie
>>
>>
>> Flip Hoedemaeker wrote:
>>> Hi Simon,
>>>  
>>> Well, X-ray crystallography nowadays often, but certainly not 
>>> always, amounts to running a set of programs with default settings with 
>>> a few mouse clicks in the GUI. The fun part is knowing when you have to 
>>> deviate from default, leave the well travelled paths etc.
>>>  
>>> The GUI is excellent with the straightforward stuff, if this fails you 
>>> actually have the option of editing the generated scripts (run and view 
>>> com file option), or leave the GUI altogether and go to old fashioned 
>>> command mode or your own scripts. Think of the GUI as a welcome 
>>> addition, but not as a panacea for all your crystallography problems, 
>>> and certainly train new crystallographers in such away that they at 
>>> least have an idea what is going on in the "black box"
>>>  
>>> Flip
>>>
>>> 
>>> *From:* CCP4 bulletin board [mailto:[EMAIL PROTECTED] *On Behalf Of 
>>> *Kolstoe S.E.
>>> *Sent:* Thursday, May 10, 2007 11:09
>>> *To:* CCP4BB@JISCMAIL.AC.UK
>>> *Subject:* Re: [ccp4bb] Refmac and B factors
>>>
>>> Thanks very much for the replies, and especially for the link to the 
>>> previous thread on this topic (Eva).
>>>  
>>> Just a comment about the ccp4i GUI in general - pretty much all the 
>>> students in my department are slowly becoming dependant on the GUI 
>>> because it is so much easier to use for those brought up using MS 
>>> windows. However, is it really fair to be distributing the GUI as a 
>>> "finished" product when it has so many limitations, and in this 
>>> particular case is just plain misleading? Although I applaud the idea of 
>>> making crystallography more user friendly, is it not just asking for 
>>> trouble (and bad science) when software is written that gives the 
>>> illusion that things are more straight forward than they actually are?
>>>  
>>> Simon
>>>  
>>>
>>> 
>>> *From:* CCP4 bulletin board [mailto:[EMAIL PROTECTED] *On Behalf Of 
>>> *Eva Kirchner
>>> *Sent:* 09 May 2007 17:37
>>> *To:* CCP4BB@JISCMAIL.AC.UK
>>> *Subject:* Re: [ccp4bb] Refmac and B factors
>>>
>>> Hi Simon,
>>>
>>> you can't stop it - I asked the same question (with some more questions) 
>>> some weeks ago.
>>>
>>> You can find the original email and the tips I got for not-so-good 
>>> resolution B-factor refinement here:
>>> http://www.mail-archive.com/ccp4bb@jiscmail.ac.uk/msg01224.html
>>>
>>> Good luck,
>>> Eva
>>>
>>>
>>> 2007/5/9, Kolstoe S.E. <[EMAIL PROTECTED] 
>>> >:
>>>
>>>
>>> Dear all,
>>>
>>> I have a structure at fairly low resolution that I am trying to refine
>>> with Refmac. I do not want to refine B factors so have arbitrarily set
>>> them all to 20 and then run refmac in the ccp4i GUI after deselecting
>>> the "refine temperature factors" box. However, when I look at the
>>> resulting pdb file my B factors vary from 2 to 90.
>>>
>>> 

Re: [ccp4bb] predicting protease cleavage sites in proteins?

[Miguel Ortiz-Lombardia]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hi Bill,

If you are interested in the physiological, known cleavage sites, you
may also try one of the possible searches at the MEROPS database:

http://merops.sanger.ac.uk/cgi-bin/show_substrate

Cheers,



Miguel

En/na Manish C Pathak ha escrit:
> 
> Hi Bill,
> 
> Peptide cutter does work for several cleavages.
> 
> http://www.expasy.ch/tools/peptidecutter/
> 
> regards
> Manish
> 
> 
> */William Scott <[EMAIL PROTECTED]>/* wrote:
> 
> Hi Citizens:
> 
> What programs/web sites would you recommend for prediction of enzyme
> cleavage sites in a protein sequence?
> 
> Many thanks.
> 
> Bill Scott
> 
> 
> 
> Never miss an email again!
> Yahoo! Toolbar
> 
> alerts you the instant new Mail arrives. Check it out. <
> http://us.rd.yahoo.com/evt=49937/*http://tools.search.yahoo.com/toolbar/features/mail/>
> 

- --
Miguel Ortiz Lombardía
Centro de Investigaciones Oncológicas
C/ Melchor Fernández Almagro, 3
28029 Madrid, Spain
Tel. +34 912 246 900
Fax. +34 912 246 976
e-mail: [EMAIL PROTECTED]
- --
Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que
ce qui est fort fût juste.
Blaise Pascal, Pensées
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Re: [ccp4bb] process SeMet labelled data

[Miguel Ortiz Lombardia]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear ccp4bbers,

I agree with Dirk. I have also noticed that much due to the way X-ray
crystallography is evolving, a lot of students/early-postdocs find
themselves "doing crystallography" in labs without a tradition in
crystallography, even without "real" crystallographers. While we can
criticise such a situation, this is a fact and students shouldn't be
blamed for it.

Having said so, I also think that people, students or not, should try
and post, in their best interest, questions as specific as possible.

As for Shivesh's question, I think this two papers (and references
within) could be helpful:

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?holding=;&db=PubMed&cmd=search&term=Single-wavelength%20anomalous%20diffraction%20phasing%20revisited
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=16855302&query_hl=5&itool=pubmed_DocSum

Cheers,



Miguel

Dirk Kostrewa escribió:
> Hi Mark,
> 
> although Shivesh's question was not very specific, and he should have
> clearly given some more informations about what he would like to know,
> he is probably a beginner in crystallography and simply asked for help
> on this board. Not everyone has always time or is always in the mood to
> answer such questions. In my opinion, it's then better not to respond at
> all than to give an answer like yours that is neither helpful nor funny!
> We all should try to keep a good style here.
> 
> Dirk.
> 
> Mark J. van Raaij wrote:
>> why don't you just send all your images to the ccp4bb, then we'll
>> process them, solve the structure and publish it for you.
>> And we might put you in the acknowledgements, if you are lucky.
>> Mark
>> On 28 Feb 2007, at 16:35, Jonathan Grimes wrote:
>>
>>> Anastassis Perrakis wrote:
 On Feb 28, 2007, at 14:37, shivesh kumar wrote:

> Dear all,
> I have a data set at 2.2A, of the selenomethionene labelled
> protein.How should I process the data.

 Carefully !

> Thanx for the help.
> Shivesh

 Tassos
>>>
>>>
>>>   i am sure what tassos really meant was "Very Carefully !"
>>>
>>>   jon
>>>
>>> -- 
>>> Dr. Jonathan M. Grimes,  Royal Society Research FellowUniversity
>>> Research Lecturer
>>> Division of Structural Biology
>>> Wellcome Trust Centre for Human Genetics
>>> University of Oxford
>>> Roosevelt Drive,
>>> Oxford OX3 7BN, UK
>>>
>>> Email: [EMAIL PROTECTED], Web: www.strubi.ox.ac.uk Tel: (+44)
>>> - 1865 - 287561, FAX: (+44) - 1865 - 287547
>>
>> Mark J. van Raaij
>> Dpto de Bioquímica, Facultad de Farmacia
>> and
>> Unidad de Rayos X, Edificio CACTUS
>> Universidad de Santiago
>> 15782 Santiago de Compostela
>> Spain
>> http://web.usc.es/~vanraaij/
>>
>>
>>
> 
> 

- --
Miguel Ortiz Lombardía
Centro de Investigaciones Oncológicas
C/ Melchor Fernández Almagro, 3
28029 Madrid, Spain
Tel. +34 912 246 900
Fax. +34 912 246 976
email: [EMAIL PROTECTED]
www: http://www.ysbl.york.ac.uk/~mol/
~~~
Le travail est ce que l'homme a trouvé de mieux
pour ne rien faire de sa vie.  (Raoul Vaneigem)
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Re: [ccp4bb] MR in P1 space group

[Miguel Ortiz-Lombardia]

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Hi Uhnsoo,

AMoRe will not run the translation function for the **first** body (an
hetero-dimer in your case) because in P1 the origin is arbitrary and
hence fixed by the first rotation solution. Now, if you think that the
first solution from the rotation function list is not good you can
manually fix another solution in the list and go on. The translation
function will be then calculated for the second and successive bodies
(other hetero-dimers in your case)

I would say that your solution from phaser looks quite compelling, but
then it's strange that molrep didn't come with the same solution. When
you say that your solution from phaser has 4 molecules, do you mean the
four expected hetero-dimers or just two hetero-dimers? If the latter,
perhaps your solution will not refine better because it is too
incomplete. In this case, you could still try to use your partly refined
model to find the other two hetero-dimers.

Cheers,



Miguel

En/na [EMAIL PROTECTED] ha escrit:
> Dear all,
> 
> Recently, I've gotten a 3.1A data set with a P1 space group. Based on a
> Mattchew
> coefficient, I have 4 hetero-dimer molecules in one asymmetric unit.
> Because one
> of the dimers was known already, I tried MR with a program Phaser and
> molrep
> (Amore doesn't calculate a translation function with a P1 space group). 
> Phaser gave
> me a reasonable solution with Z-score closed to 20 and LL-gain over
> 900(molrep
> didn't give me a good solution), and that solution has 4 molecules with
> quite
> reasonable packing with local 2-fold symmetries. I also ran Phaser with
> different wavelength ranges with different truncated forms, and always the
> solutions were the same. However, when I calculated the map, the map was
> still
> messy and I couldn't see a clear density of the other molecules. I also
> ran a
> rigid body refinement and a restrained refinement with different programs
> (refmac and cns), but the R factor didn't drop. I ran DM with ncs
> averaging and
> solvent flattening, still the map wasn't improved. At this moment, we
> are still
> sure that our data set has a P1 space group with good statistics and the
> solution from phaser is quite reasonable.
> 
> Is it possible that P1 space group can be a problem during MR? Do you
> think the
> solution from Phaser is just wrong or did I miss something?
> 
> Any suggestions will be helpful to me.
> 
> Thanks,
> 
> 
> 
> 
> uhnsoo
> 

- --
Miguel Ortiz Lombardía
Centro de Investigaciones Oncológicas
C/ Melchor Fernández Almagro, 3
28029 Madrid, Spain
Tel. +34 912 246 900
Fax. +34 912 246 976
e-mail: [EMAIL PROTECTED]
- --
Et ainsi ne pouvant faire que ce qui est juste fût fort, on a fait que
ce qui est fort fût juste.
Blaise Pascal, Pensées
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Re: [ccp4bb] human cDNA clones?

[Miguel Ortiz Lombardia]

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Hi Andrew,

Can you get cDNA from human cell lines? Perhaps one of your colleagues
can provide you with a few microliters. You can amplify from there all
the genes you need (provided they are transcribed in that cell line;
therefore, better use cDNA from two-three cell lines) We have followed
this approach quite successfully.

Cheers,


Miguel

Andrew Wong escribió:
> Sorry a little offtopic...
> 
> We'r trying to clones a number of putative human proteins for
> crystallization. Besides IMAGE clones from OpenBiosystem, is there any
> the cheaper way of obtaining human cDNA clones? OpenBiosystem is okish,
> ~$100Cdn for each clone, but does get abit expensive when you start
> getting alot.
> 

- --
Miguel Ortiz Lombardía
Centro de Investigaciones Oncológicas
C/ Melchor Fernández Almagro, 3
28029 Madrid, Spain
Tel. +34 912 246 900
Fax. +34 912 246 976
email: [EMAIL PROTECTED]
www: http://www.ysbl.york.ac.uk/~mol/
~~~
Le travail est ce que l'homme a trouvé de mieux
pour ne rien faire de sa vie.  (Raoul Vaneigem)
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Re: nucleic acid helices

[Miguel Ortiz Lombardia]

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Hi Florian,

You can use coot to create an ideal DNA! Simply:

Calculate -> Other Modelling tools -> Ideal DNA/RNA

Another possibility is 3DNA: (http://rutchem.rutgers.edu/~xiangjun/3DNA/)

For analysis you could use 3DNA or Curves
(http://www.ibpc.fr/UPR9080/Curindex.html)

Cheers,


Miguel

Florian Brückner escribió:
> Dear all,
> 
> I am looking for a program or webtool that can create canonical nucleic
> acid helices (like B-form, A-form...) as well as a program that can
> calculate helical parameters from a given helix.
> 
> Thanks in advance,
> 
> Florian.
> 

- --
Miguel Ortiz Lombardía
Centro de Investigaciones Oncológicas
C/ Melchor Fernández Almagro, 3
28029 Madrid, Spain
Tel. +34 912 246 900
Fax. +34 912 246 976
email: [EMAIL PROTECTED]
www: http://www.ysbl.york.ac.uk/~mol/
~~~
Le travail est ce que l'homme a trouvé de mieux
pour ne rien faire de sa vie.  (Raoul Vaneigem)
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