Indeed! Scientists in the Soviet Bloc got paid for publishing their scientific
papers (and maybe for citations as well - not sure about that one)! We need to
change the current system! Although these changes could be accompanied by many
other pleasant virtues of the Soviet regime.
Petr
> On
Petr Leiman
University of Texas Medical Branch
Department of BMB
Basic Sciences Building 6.600D
301 University Blvd
Galveston, TX 77555-0647
Cell: 832 908 6635
Office: 409 747 2078
https://scsb.utmb.edu/faculty/Leiman.asp
> On Dec 16, 2017, at 4:42 PM, Anastassis Perrakis <a
If your signal goes all the way to the half Nyquist frequency, oversample your
map to have the pixel size equal to 1/3rd of the highest resolution. Your map
will look much better in coot. Real space fitting will work much better as
well.
Best,
Petr
> On May 17, 2017, at 11:24 AM, MyeongSeon
A small erratum is needed unfortunately. The sequence identity of 4UHV to 2P5Z
is 19% (but not the exceptional 15% as I wrote originally). Nevertheless,
Phaser successfully finding a solution for a 19% SI model is no small feat.
> On Mar 16, 2016, at 09:48, Petr Leiman <petr.lei...@e
.
On 03/12/2015 08:49 PM, Petr Leiman wrote:
Dear Community,
What is the reason of placing the CCP4 PATH and other path-related variables
in front of existing variables? This forces a linux system to use
CCP4-distributed wish in all applications by default. Note that the ccp4i
script calls CCP4
caused by CCP4 wish.
Would it be possible to append CCP4 path variables by default instead of rather
rudely jumping in front of the queue?
Thank you,
Petr
--
Petr Leiman
EPFL
BSP 415
CH-1015 Lausanne
Switzerland
Office: +41 21 69 30 441
Mobile: +41 79 538 7647
Fax: +41 21 69 30 422
://pva.scripps.edu/program.html
The all-inclusive registration fee is rather modest considering that the site
is a 4-star resort hotel and all talks will take place in a large congress hall.
Hope to see you in Les Diablerets!
Sincerely,
Petr Leiman
--
Petr Leiman
Laboratory of Structural Biology
On Apr 24, 2014, at 11:39, Petr Leiman
petr.lei...@epfl.chmailto:petr.lei...@epfl.ch wrote:
Dear All,
We are looking for an explanation for a very strange observation.
Problem:
We have two fully independent data sets (two different crystals), in which the
Bijvoet Difference Fourier map peak
much,
Petr
--
Petr Leiman
EPFL
BSP 415
CH-1015 Lausanne
Switzerland
Office: +41 21 69 30 441
Mobile: +41 79 538 7647
Fax: +41 21 69 30 422
today and we can simply ignore it.
Petr
Petr Leiman
EPFL
Switzerland
On 04/02/2014 04:39 AM, Edward A. Berry wrote:
Encouraged by recent help from the BB in filling in gaps in my
understanding, maybe I can get help with another question:
At the top of page 121 in Blundell and Johnson
275339
--
Petr Leiman
EPFL
BSP 415
CH-1015 Lausanne
Switzerand
Office: +41 21 69 30 441
Mobile: +41 79 538 7647
Fax: +41 21 69 30 422
know why you find this feature
extremely useful?
Best wishes,
Randy Read
On 2 Jul 2013, at 18:41, Petr Leiman petr.lei...@epfl.ch wrote:
I have just found out that phaser v. 2.5.2 in ccp4 6.3.0-021 does not
output columns with HL coefficients. I cannot find a combination of
buttons
has not been discovered and fixed already. If there
is a reason to this new output column behavior, it would be very useful
to hear this reason.
Sincerely,
Petr
--
Petr Leiman
EPFL
BSP 415
CH-1015 Lausanne
Switzerand
Office: +41 21 69 30 441
Mobile: +41 79 538 7647
Fax: +41 21 69 30 422
/ribspline.html
Best wishes,
Petr
--
Petr Leiman
EPFL
BSP 415
CH-1015 Lausanne
Switzerland
Office: +41 21 69 30 441
Mobile: +41 79 538 7647
Fax: +41 21 69 30 422
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UKmailto:CCP4BB@JISCMAIL.AC.UK]
on behalf of Jason Vertrees
[jason.vertr
and additional information please contact Prof. Petr Leiman
(petr.lei...@epfl.chmailto:petr.lei...@epfl.ch)
---
Petr Leiman
EPFL
BSP 415
CH-1015 Lausanne
Switzerland
Office: +41 21 69 30 441
Mobile: +41 79 538 7647
Fax: +41 21 69 30 422
to block emails with 1+MB attachments?
Thank you,
Petr
Prof. Petr Leiman
EPFL
BSP-415
CH-1015 Lausanne
Switzerland
On Mar 27, 2013, at 5:22 PM, Tom Van den Bergh wrote:
Dear members of ccp4bb,
I need some help with the refinement of my structure of a variant of mRFP
Since this is now public domain knowledge and if this gets ever published, Phil
has my vote to be the first author!
Petr
On Mar 27, 2013, at 6:09 PM, Phil Jeffrey wrote:
That's quite brave - shipping your entire structure to people that could be
actual competitors. But it was fun to play
or CCP4BB.
Thank you,
Petr
On Nov 22, 2012, at 3:04 PM, Petr Leiman wrote:
Dear all,
Hgen GUI does not start (the error message is below). The CCP4 version is
6.3.0-009 (64 bit). The system is 2.6.35-32-generic #67-Ubuntu SMP x86_64
GNU/Linux. Is this unique to our system
Dear all,
Hgen GUI does not start (the error message is below). The CCP4 version is
6.3.0-009 (64 bit). The system is 2.6.35-32-generic #67-Ubuntu SMP x86_64
GNU/Linux. Is this unique to our system configuration?
Thank you.
Petr
The error message is:
can't use non-numeric string as operand
in the future.
Thank you,
Petr
Petr Leiman
EPFL
BSP-415
CH-1015 Lausanne
Switzerland
(mainly for small molecules) and no known bugs, so I hope
to release it soon. If anyone would like to try it now please send me an
email.
George
On 11/19/2012 02:13 PM, Petr Leiman wrote:
Dear Developers of Coot,
I believe that coot has never been able to display the crystallographic
them, i.e. to move
all (or selected) atoms to be as close in space as possible and only then
calculate the RMSD for the superimposed or all atoms.
Thank you in advance,
Petr
Petr Leiman
EPFL
BPS-415
CH-1015 Lausanne
Suisse
On Jun 19, 2012, at 5:04 PM, Claudia Millán Nebot
On Jun 20, 2012, at 12:38 AM, Jacob Keller wrote:
Is part of your question based there being many ways to superimpose
structures, which there are?
JPK
On Tue, Jun 19, 2012 at 5:34 PM, Petr Leiman petr.lei...@epfl.ch wrote:
Would anyone be kind enough to explain what kind of information
Jacob, do not worry. Data collection for a typical crystal takes only 0.75
seconds.
Petr
On May 9, 2012, at 5:18 PM, Jacob Keller wrote:
I saw something online about the EIGER 16M: 201 GB of data per second! Is that
number correct?
JPK
On Wed, May 9, 2012 at 9:58 AM, Meitian Wang
.
The presence of high NCS does not guarantee a success even if your initial
model is good as described in Section 9 here:
http://www.ncbi.nlm.nih.gov/pubmed/11526317
Petr
--
Petr Leiman
EPFL
IPSB-LBBS
BSP-415
CH-1015 Lausanne
Suisse
It would be so much more convenient to call these techniques (MAD, SAD, etc.)
by their inventor's name. This would simplify things immensely simultaneously
eliminating CCP4BB MADisagreements.
Although in our days of copyrights wars, the journals and perhaps conferences
where these methods
to receive this message twice...
Dale Tronrud
On 1/19/2012 12:51 PM, Petr Leiman wrote:
It would be so much more convenient to call these techniques (MAD, SAD,
etc.) by their inventor's name. This would simplify things immensely
simultaneously eliminating CCP4BB MADisagreements
Dear Bostjan,
There is Chimera for almost anything you can think of. Search for
Structure-Based Sequence Alignment on this page:
http://www.cgl.ucsf.edu/chimera/features.html
Petr
On Dec 8, 2011, at 6:39 AM, Bostjan Kobe wrote:
Consurf will do this for you.
Bostjan
---
Bostjan Kobe
Do I feel stupid! My previous message about Chimera should have been addresses
to Yuri Pompeu, but not to Bostjan Kobe.
Sincerely,
Petr
On Dec 8, 2011, at 6:26 AM, Yuri Pompeu wrote:
I once saw a figure showing the protein as surface, but instead of having it
coloured by atom type
or
herman.schreu...@sanofi.com wrote:
I am not sure that sending links is the way to go. Our company blocks many
websites that it considers not of professionel interest and were employees
may spend too much time.
What a brilliant idea! If only this could be implemented in academia. Our Ph.D.
For the second time today I have to apologize. In no way I wanted to discourage
anyone and especially people new to crystallography from posting questions to
this BB. Especially good thoughtful questions.
Sincerely,
Petr
On Dec 8, 2011, at 5:24 PM, Petr Leiman wrote:
herman.schreu
Dear Tim,
I agree with you completely. The question then becomes why does the automatic
weighting scheme in refmac allow R and R-free to run away from each other by 8%
in a 1.1 A resolution structure?
Petr
On Dec 8, 2011, at 6:50 PM, Tim Gruene wrote:
-BEGIN PGP SIGNED MESSAGE-
That lmgtfy.com is as almost as cool as HHpred.
Thanks for a very useful piece of information!
Petr
On Nov 3, 2011, at 2:06 PM, Tim Gruene wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear Zhang Qi,
I like this url: http://www.lmgtfy.com/?q=topology+diagram+protein
which
run it stopped in the middle of TF. The
remedy is to explicitly lower the resolution of the input data (that was a 1.2
A resolution data with a smallish unit cell).
I can provide the log files and the mtz file if necessary.
Sincerely,
Petr
---
Petr Leiman
EPFL
IPSB-LBBS
BSP
Dear all,
What is the status of Denzo/HKL2000 availability/support for the Pilatus 6M
detector?
Thank you,
Petr
Apologies for suggesting a non-CCP4 solution, but UCSF Chimera can do that and
more (interactively!):
Tools - Higher Order Structure - Unit cell
Petr
On Jun 30, 2011, at 2:52 PM, Hargreaves, David wrote:
Does anyone have a rigorous method (or script) for generating an extended
lattice
Totally support the statements below. We have had several proteins with A280
absorbance of 0.1 or less (at 1 mg/ml). You _have_ to use Bradford in the
Nanodrop or whatnot to measure the concentration.
Before purchasing the Nanodrop we used a Hellma TrayCell and a normal UV/Vis
instrument.
beam?
Shall we discuss off line (with Jacob) and present our conclusions
when/if we get agreement?
Regards
Colin
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf
Of
Petr Leiman
Sent: 14 April 2011 22:59
To: CCP4BB@JISCMAIL.AC.UK
Subject
People are looking into how to fit the old retired MeV microscopes with pulsed
electron guns (problem is there are very few of those beasts left). If this
works, such a machine will produce equivalent results to FEL but at a fraction
of the cost.
The group at Eindhoven, which Colin had
] On Behalf Of
Petr Leiman
Sent: 14 April 2011 16:23
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Femtosecond Electron Beam
People are looking into how to fit the old retired MeV microscopes with
pulsed electron guns (problem is there are very few of those beasts
left). If this works
Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Petr Leiman
Sent: 14 April 2011 21:07
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Femtosecond Electron Beam
Dear Colin and all interested in the FEL development.
Please look at the figures in the first
Hi Mark,
What about UCSF Chimera? Very easy to use.
http://www.cgl.ucsf.edu/chimera/tutorials/movies08/moviemaking.html
More on the topic:
http://www.cgl.ucsf.edu/chimera/animations/animations.html
Check out the Nuclear pores movie. Amazing stuff. A few years back one had to
pay huge $$$ for
Another vote for Ubuntu.
I have to say that a Live CD version is not a good test of this excellent Linux
distro. We have 3 identical PCs. On two of these the latest version of 10.10
64bit live cd loads to a blank (completely black) screen. Google: blank screen
ubuntu live cd - thankfully there
CHF per
day.
The registration deadline:
October 31, 2009
http://ipsb.epfl.ch/page82078.html
Sincerely,
Petr
-
Petr Leiman
Head of the Laboratory of Structural Biology and Biophysics
Institut de
an older generation Nikon instrument (halogen lamp)
with an objective of a smaller aperture.
Petr
-
Petr Leiman
École Polytechnique Fédérale de Lausanne (EPFL)
Cubotron/BSP-415
CH-1015 Lausanne
Switzerland
- Original Message -
From: Jürgen Bosch jubo
Hello all,
While testing a newly installed ARP/wARP interface (ver. 7.0.1) in ccp4i
(ver. 6.1.0) on Ubuntu (8.10) I noticed that the Fobs and Sigma pull-down
menus are missing from the ARP/wARP Quick Fold window. This is accompanied
by the following error message, which is output in stderr by
A post-doctoral position is available (in the department of Biological
Sciences, Purdue University, Indiana 47907, USA) for structural studies of
viruses and their interaction with host cells. Applicants should have
experience in virus or protein crystallography and in molecular biology.
, biophysics or biochemistry
are encouraged to apply.
The positions are available starting October 1st, 2008.
Applicants are invited to send a CV and a letter of motivation describing
research experience, interests and key accomplishments, and contact
information of two to four referees to Dr. Petr
On behalf of Michael Rossmann:
A post-doctoral position is available in a virus structure laboratory.
Applicants should have experience in computer program development or
adaptation for crystallography or electron microscopy. Please e-mail
applications to Michael Rossmann, [EMAIL PROTECTED]
yes you are right, but I assumed if people see a cloud of condensed
fog over their LN2 bath they should remove that by
a) filling up the bowl completely e.g. some LN2 drips out of the bowl
b) blow the fog away before you dip
I think the original poster meant the relatively low heat conduction
Dear Raja,
Do you seriously believe that you will find help on this board after making
us all download your 2 * 4.1 MB of crap NOT RELATED TO CCP4???
Good luck in your future endeavors!
Petr
- Original Message -
From: Raja Dey [EMAIL PROTECTED]
To: CCP4BB@JISCMAIL.AC.UK
Sent:
- Original Message -
From: Jenny Martin [EMAIL PROTECTED]
To: CCP4BB@JISCMAIL.AC.UK
Sent: Thursday, August 23, 2007 5:46 PM
Subject: Re: [ccp4bb] The importance of USING our validation tools
My question is, how could crystals with 80% or more solvent diffract so
well? The best of the
I just found this old thread in my CCP4 folder.
1. mencoder can convert pymol's quicktime format movies into avi movies.
2. Powerpoint movie handling is beyond ancient and sometimes AVI movies can be
played in MS mediaplayer but Powerpoint would not play them. The remedy is to
use good-sized
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