Re: [ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography

[Frederic Vellieux]

Hi,

In fact the problem was solved with the help of Ivica Dilovic from 
Zagreb who suggested some changes to the shelxl .ins file. After these 
modifications the cryptic error message was still there, but the 
modifications made me try to remove one card. That did it.


So the part that is concerned with this error in the .ins file is as 
follows:


did not work and gave the cryptic error message:
TITL 240223Ru_complex_0m_5 in P1
CELL 1.34139  10.36240  11.17780  13.19300  80.8589  73.7519  71.3166
ZERR2.00   0.00070   0.00080   0.00090   0.0026   0.0023   0.0023
LATT -1
SFAC C H N O CL RU
UNIT 62 64 2 10 2 2
TEMP -163.150
TREF
L.S. 10
EXTI 0.001
WGHT 0.0617
BOND $H
CONF
HTAB
FMAP 2
PLAN 20
FVAR 0.75351

worked and gave no error:
TITL 240223Ru_complex_0m_5 in P1
CELL 1.34139 10.3624 11.1778 13.193 80.8589 73.7519 71.3166
ZERR 2 0.0007 0.0008 0.0009 0.0026 0.0023 0.0023
LATT -1
SFAC C H N O Cl Ru
DISP C 0.0137 0.0067 57.1
DISP Cl 0.3281 0.5435 4162.2
DISP H 0 0 0.6
DISP N 0.0241 0.0134 109.9
DISP O 0.0389 0.0241 193.4
DISP Ru -0.076 2.5955 20068.6
UNIT 62 64 2 10 2 2
L.S. 10
PLAN  10
TEMP -163.15
CONF
BOND $H
HTAB
MORE -1
fmap 2
WGHT 0.1
FVAR 0.25491

I guess it would be much better (from the user's point of view) if 
SHELXL would write on the output what the offending line is.


Also, no indications are given on the SHELX site where the Windows .exe 
files are supposed to go. They must be placed in the directory where the 
GUI (olex2 or WingX) stores its exe file (olex2.exe or wingx.exe). I 
just tried to place them there because I was desperate and it worked.


Cheers, and thanks to everyone for their suggestions.

Fred.

On 2024-03-12 16:12, Kay Diederichs wrote:

Fred,

nobody would be offended if you'd just post your SHELXL .ins file here; 
there are enough experienced crystallographers to spot the mistake.
Best would be if you could pare it down to small size, but such that it 
is still reproducible (my own experience is that this almost always 
makes me find my own mistakes).


But to try and answer your title question, there is the 
bruker-...@g-groups.wisc.edu mailing list.


Best wishes,
Kay



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Re: [ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography

[Fred Vellieux]

Hello again,

I'll try ccp4 for Windows when I am back at home (where Windows "lives" 
in my case).


I have certainly tried shelxle. If I remember well what is provided is a 
.deb file. I used alien to convert that to a .rpm file, and installation 
failed because of issues I can't remember (the Linux flavour here is 
Alma Linux 9, not Debian).


Fred.

On 12/03/2024 10:56, David Waterman wrote:

Hi Fred,

CCP4 distributes the shelxl binary on Linux. I've not checked yet, but 
perhaps it is also part of CCP4 on Windows?


Cheers
-- David


On Tue, 12 Mar 2024 at 09:38, Fred Vellieux 
 wrote:


Hello and thanks for the reply.

My input file came from my checking SHELX manuals and SHELX
instructions on the web, and trying to modify them to suit my case.

I tried olex2 on a Windows computer (somehow olex2 did not run on
my Linux box, and only v1.3 was able to install on that Windows
machine and not the latest v1.5). However, olex2 (the installation
program) does not come with Shelx program executables, and I could
not locate the installers for the shelx software on Windows.

Hence I am running SHELXL in line command mode on my Linux box.

Thank you again,

Fred.

On 12/03/2024 10:12, David Waterman wrote:

Hi Fred,

I find Olex2 and shelxle are both convenient interfaces to SHELXL
refinement, that take care of some of the details of .ins file
format for you. However, maybe you are stuck in the starting
gate, depending on what is malformed in your input file. Where
did your input files come from?

Cheers
-- David


On Tue, 12 Mar 2024 at 09:01, Fred Vellieux
 wrote:

Hi folks,

I have a simple question: is there an electronic bulletin
board for
small-molecule crystallography? I have checked the list of
CCP projects
and there is no CCP-project for small molecule
crystallography in the list.

I am trying to run SHELXL, and it fails with the cryptic
message "** BAD
ATOM OR UNKNOWN INSTRUCTION **".

The alternative for me would be of course to use software
meant for
macromolecular cystallography (that I know) on small molecule
diffraction data. And using the small molecule coordinate files
transformed to a suitable format. I don't know if this is
feasible or
even advised. Probably not.

Thanks,

Fred.

-- 
MedChem, 1st F. Medicine, Charles University

BIOCEV, Vestec, Czech Republic



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BIOCEV, Vestec, Czech Republic


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BIOCEV, Vestec, Czech Republic



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Re: [ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography

[Fred Vellieux]

Hello and thanks for the reply.

My input file came from my checking SHELX manuals and SHELX instructions 
on the web, and trying to modify them to suit my case.


I tried olex2 on a Windows computer (somehow olex2 did not run on my 
Linux box, and only v1.3 was able to install on that Windows machine and 
not the latest v1.5). However, olex2 (the installation program) does not 
come with Shelx program executables, and I could not locate the 
installers for the shelx software on Windows.


Hence I am running SHELXL in line command mode on my Linux box.

Thank you again,

Fred.

On 12/03/2024 10:12, David Waterman wrote:

Hi Fred,

I find Olex2 and shelxle are both convenient interfaces to SHELXL 
refinement, that take care of some of the details of .ins file format 
for you. However, maybe you are stuck in the starting gate, depending 
on what is malformed in your input file. Where did your input files 
come from?


Cheers
-- David


On Tue, 12 Mar 2024 at 09:01, Fred Vellieux 
 wrote:


Hi folks,

I have a simple question: is there an electronic bulletin board for
small-molecule crystallography? I have checked the list of CCP
projects
and there is no CCP-project for small molecule crystallography in
the list.

I am trying to run SHELXL, and it fails with the cryptic message
"** BAD
ATOM OR UNKNOWN INSTRUCTION **".

The alternative for me would be of course to use software meant for
macromolecular cystallography (that I know) on small molecule
diffraction data. And using the small molecule coordinate files
transformed to a suitable format. I don't know if this is feasible or
even advised. Probably not.

Thanks,

Fred.

-- 
MedChem, 1st F. Medicine, Charles University

BIOCEV, Vestec, Czech Republic



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[ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography

[Fred Vellieux]

Hi folks,

I have a simple question: is there an electronic bulletin board for 
small-molecule crystallography? I have checked the list of CCP projects 
and there is no CCP-project for small molecule crystallography in the list.


I am trying to run SHELXL, and it fails with the cryptic message "** BAD 
ATOM OR UNKNOWN INSTRUCTION **".


The alternative for me would be of course to use software meant for 
macromolecular cystallography (that I know) on small molecule 
diffraction data. And using the small molecule coordinate files 
transformed to a suitable format. I don't know if this is feasible or 
even advised. Probably not.


Thanks,

Fred.

--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic



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Re: [ccp4bb] Crystals with DNA

[Fred Vellieux]

Hello,

Overhanging "sticky" ends are mentioned frequently when it comes to 
obtaining infinite helices that are useful in crystallization. For 
example in 
https://home.ccr.cancer.gov/csb/nihxray/Tips-and-Tricks_Crystallization_Protein-DNA_updated.pdf 
.


Cheers,

Fred.

On 09/02/2024 10:59, careinaedgo...@yahoo.com wrote:

Thank you for this insight, Nicolas. It is very helpful.
Yes I have also had a soccer ball shaped crystal that does not 
diffract as well as, and more recently, many plate like crystals but 
they do not diffract either.
I do know I have both protein and DNA in my crystals but I do not 
know, as you say, exactly what is forming the crystal contacts.
Just to be clear, do you say overhangs are helpful? Surely overhangs 
won't promote an infinite helix? If one wants an infinite helix, would 
the DNA not have to be blunt ended?


Sent from Yahoo Mail on Android 



On Thu, Feb 8, 2024 at 4:59 PM, Nicolas Foos
 wrote:

Hello Careina,

In my hands, DNA protein complex crystals may be frustrating, 
because often we get good looking crystals which don't diffract at
all and are actually not easy to improve.

I remember obtaining a lot of crystal looking a bit like "STOP"
road sign (octogonal shape for one axis) which never diffracts.
(Often containing only DNA not well organized)

So long story short, In my hand (transciption factor bound with
homeodomain for example). I had good results with DNA sequence
which results in hoverhangs. The idea was to bet on a "infinit"
DNA helix which should help the packing.

I strongly encouraged you to rely on any other information  you
can have to be sure of what is the best minimal sequence (like
band shift assay). Also if you can purify the entire complex
before crystallization assay (I don't know your protocol, but
ideally, I would prepare the complex prot-DNA and put it on size
exclusion).

The point is, you don't know /a priori /what kind of crystal
packing you will have. It may be only due to protein protein
contact and not related to the DNA directly.

Also, I often get good results with crystal growing condition
containing MPD or PEG (makes me using PEG screen Familly as first
approach).

I invite you to read the Timothy Richmond teams Papers on 
nucleosome they spend some times improving the resolution on very
large complex. (Luger etal 1997).

There is many parameters, DNA sequence also change a bit the DNA
geometry (look for A-tract), You may want to introduce such
sequence to maybe improve the "rigidity".

Also if your DNA fragment are small, be careful with the
temperature. The annealing and the DNA duplex formation is
critical and you should be careful on your procedure.

I remember that small cation like Li, may help too.

HTH


Nicolas


On 08/02/2024 12:25, careinaedgo...@yahoo.com
 wrote:
 Hello all.

I am struggling to get defracting crystals with a protein DNA
complex. The crystals are plentiful but they do not diffract. I am
going back to the grind stone and relookong at my DNA sequence.
Is there any wisdom you could give me with regards to what works
best with DNA in crystals?
From my reading it seems if the length is a multiple of 7 (for B
DNA) and blunt ended, it will stretch over the length of the
crystal and improve crystalisability. But if you want crystals
that diffract better, you will need to play with length and even
making it only one base longer or shorter can make a difference,
even changing the morphology of the crystal? Longer is better than
shorter, and overhangs are good for improving diffraction?
Presumably because they stabilize contacts? It is expensive to
synthesize a while bunch of sequences so I need to be strategic in
my choice. Would appreciate any advice.
Thank you
Careina.



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EMBL Grenoble, McCarthy Team

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Re: [ccp4bb] Solution to [ccp4bb] problem running ccp4mg: ugly and useless graphics

[Fred Vellieux]

Dear all,

In case anyone experiences problems with Alma Linux, NVIDIA graphics 
boards and the NVIDIA graphics driver, here is what worked:


somehow, the nouveau graphics driver seems to sneak back in, even if 
blacklisted. When nouveau is in use, the ugly graphics are obtained with 
ccp4mg.


There are several procedures mentioned on the web to install the NVIDIA 
driver.


This one worked, 
https://www.linuxcapable.com/how-to-install-nvidia-drivers-on-almalinux/ 
. All the nvidia or cuda packages installed by any alternative procedure 
must be removed first.


The other approaches mentioned on the web didn't work in my hands (and 
led to big problems).


The procedure mentioned in linuxcapable seems to set SecureBoot on, and 
then this HP Z4 computer doesn't boot any more. One has to enter the 
BIOS and have "Legacy support enable, Secure boot disable" set (and saved).


Just in case.

Fred.

On 17/01/2024 10:17, Frederic Vellieux wrote:

Dear all,

Perhaps a reader of the bb will have a solution for this problem. ccp4 
is version 8.0 and is up to date. All graphics programs (coot, but 
also other non-ccp4 software such as chimeraX, Pymol...) run fine on 
the Alma-Linux 9.3 system. There is a problem however with ccp4mg: the 
images appearing on the screen are... wrong and quite useless (see 
enclosed png screen capture). There is no error message at program 
startup.


I have disabled and blacklisted the nouveau graphics board driver and 
installed the NVIDIA driver. Made no difference.


So has anyone seen this behaviour before and has a solution to propose?

Thank you.

Regards,

Fred.




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BIOCEV, Vestec, Czech Republic



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Re: [ccp4bb] problem running ccp4mg: ugly and useless graphics

[Fred Vellieux]

Dear Stuart,

I did test that (removing the .CCP4MG2 directory and its contents) and 
it gave the same ugly graphics.


There are problems with Alma Linux and the "Secure Boot" on this Hewlett 
Packard Z4 computer. This I have noticed. The secure boot option wants 
to load a signed graphics driver at boot time and I did not find a way 
to sign the NVIDIA driver (downloaded from the NVIDIA site as a .run 
file for installation) in a way that the system recognizes it. The 
recommended way of installing the NVIDIA driver on the Alma Linux pages 
doesn't allow to run later kernels when they become available (trying 
using dnf or yum and rebooting on a new kernel means a totally bricked 
computer).


So far the only option that seems to work is not to allow Secure Boot 
and not to allow Legacy settings. Otherwise the computer is bricked and 
requires a fresh installation of Linux. I don't know how many times I've 
had to re-install Alma Linux...


Jan Dohnalek mentioned that the ugly graphics could be due to a lack of 
memory problem. I am investigating that.


Cheers,

Fred.

On 1/17/24 11:47, Stuart McNicholas wrote:

Dear Fred,
  Many apologies for your difficulties. My first thought is that 
perhaps CCP4MG's lighting settings are completely messed up. This can 
be tested by removing completely the folder:


$HOME/.CCP4MG2

If this does not work, then further investigation will be required.

Also, in CCP4 we are working on a new graphics program: Moorhen. 
Currently most of our effort has been on model building aspects (it is 
based on Coot), but we are also working on figure preparation and it 
should over the next few months adopt most of the features of CCP4MG.


https://moorhen-coot.github.io/wiki/2023/11/03/Creating-Figures-with-Moorhen.html 
(tutorial)

https://moorhen.org/ (the program)

Best wishes,
Stuart


On Wed, 17 Jan 2024 at 09:17, Frederic Vellieux 
 wrote:


Dear all,

Perhaps a reader of the bb will have a solution for this problem.
ccp4
is version 8.0 and is up to date. All graphics programs (coot, but
also
other non-ccp4 software such as chimeraX, Pymol...) run fine on the
Alma-Linux 9.3 system. There is a problem however with ccp4mg: the
images appearing on the screen are... wrong and quite useless (see
enclosed png screen capture). There is no error message at program
startup.

I have disabled and blacklisted the nouveau graphics board driver and
installed the NVIDIA driver. Made no difference.

So has anyone seen this behaviour before and has a solution to
propose?

Thank you.

Regards,

Fred.




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[ccp4bb] problem running ccp4mg: ugly and useless graphics

[Frederic Vellieux]

Dear all,

Perhaps a reader of the bb will have a solution for this problem. ccp4 
is version 8.0 and is up to date. All graphics programs (coot, but also 
other non-ccp4 software such as chimeraX, Pymol...) run fine on the 
Alma-Linux 9.3 system. There is a problem however with ccp4mg: the 
images appearing on the screen are... wrong and quite useless (see 
enclosed png screen capture). There is no error message at program 
startup.


I have disabled and blacklisted the nouveau graphics board driver and 
installed the NVIDIA driver. Made no difference.


So has anyone seen this behaviour before and has a solution to propose?

Thank you.

Regards,

Fred.




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Re: [ccp4bb] CentOS 7 end of life (july 2024)

[Frederic Vellieux]

Hi and thanks for the reply.

In case others on the bb face the same problem before july 2024, this is 
what I can write about the process of migrating to a more recent Linux 
distro:


"elevate-release", not "elevate-linux"... Poor memory of mine.

The debtakeover and debootstrap route failed with a cryptic message.

The btrfs partition is really preventing direct upgrade to more recent 
RHEL-based distributions (Alma-Linux for example). In the end I 
installed a Debian 12 distribution (the home directory partition was on 
another physical "disk" so it was easy to mount). The root partition fs 
was changed to ext4 in the process.


The one problem I have is that Dassault Systemes' BIOVIA Discovery 
Studio cannot be installed on Debian boxes. Apparently some people 
manage to install it on Ubuntu.


I may try to install Alma-Linux in the end. Just so that I don't need to 
use a Windows PC when Discovery Studio is needed.


Cheers,

Fred.

On 2023-08-30 13:57, Guillaume Gaullier wrote:

Hello,

I have never tried any of the migration tools you listed, so can't
advise on their use.

But regarding your first option of doing a backup, reformatting from
btrfs to a different filesystem, restoring the backup and proceeding
with the upgrade with a non-official tool: you might as well do a
clean install of the new OS (whichever you choose) instead, then
restore your backup.

From my understanding, RHEL derivatives are not designed for automatic
upgrade between major versions, they expect you to backup your /home
and do a clean install. The justification is that they have very long
support (the earlier-than-originally-planned end of life of CentOS is
a consequence of recent policy changes since IBM bought Red Hat, and
hopefully only an outlier), so you only rarely need to do this tedious
clean install and porting of your old configuration.

Debian, on the other hand, is designed to handle upgrades between
major versions (I would still do a backup before attempting this) and
smoothly migrate configuration, so maybe this is the OS you want from
now on.

Backing up data is not too difficult (but check your backups).
Configuration is more difficult, especially because defaults change
between versions, so the configuration files you back up are not
guaranteed to play well with the new system. It is tedious to have to
configure a freshly installed OS, but on the other hand the really
critical pieces of configuration are often not that many, and you
might be better off porting them to a freshly installed system than
trying to keep your old configuration files in place during an
upgrade.

I hope this helps,

Guillaume

-

From: CCP4 bulletin board  on behalf of Fred
Vellieux 
Sent: Friday, August 18, 2023 10:43:34 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] CentOS 7 end of life (july 2024)

Hi,

Other people on this BB may run into the same problem.

CentOS 7 end of life is announced to happen in July 2024.

I have to migrate my Linux box to another Linux "flavour".

I've had a look at the possibilities:

- migrate to another RHEL (rpm-based) Linux, with "elevate-linux" and
"leapp".
Here on this Linux box the problem I have is that the disk partition
mounted as / uses btrfs. btrfs has been deprecated starting at
versions
8 (RHEL8, CentOS 8, Alma etc). This means first to copy all that is
present on / somewhere, change the file system (for example to ext4)
and
restore everything.

- migrate to Debian, that supports btrfs. There are utilities,
"debtakeover" and "debootstrap" that are supposed to install Debian
8.11
(jessie).

Has anyone performed such a migration without data loss (files,
pathways, configurations)? If so I'd like to know what was successful.

Thank you.

Fred.

--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic



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[ccp4bb] CentOS 7 end of life (july 2024)

[Fred Vellieux]

Hi,

Other people on this BB may run into the same problem.

CentOS 7 end of life is announced to happen in July 2024.

I have to migrate my Linux box to another Linux "flavour".

I've had a look at the possibilities:

- migrate to another RHEL (rpm-based) Linux, with "elevate-linux" and 
"leapp".
Here on this Linux box the problem I have is that the disk partition 
mounted as / uses btrfs. btrfs has been deprecated starting at versions 
8 (RHEL8, CentOS 8, Alma etc). This means first to copy all that is 
present on / somewhere, change the file system (for example to ext4) and 
restore everything.


- migrate to Debian, that supports btrfs. There are utilities, 
"debtakeover" and "debootstrap" that are supposed to install Debian 8.11 
(jessie).


Has anyone performed such a migration without data loss (files, 
pathways, configurations)? If so I'd like to know what was successful.


Thank you.

Fred.

--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic



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[ccp4bb] Question about BIOVIA DiscoveryStudio 2021

[Fred Vellieux]

Folks, apologies for the non-CCP4 software question.

I have tried to contact the BIOVIA DiscoveryStudio support team, somehow 
my browser does not allow me to open their "contact form".


I am trying to visualize and perform an analysis on a protein:smaller 
molecule complex. The smaller molecule happens to be a long peptide. 
Whatever I do with the PDB (change ATOM cards to HETATM, change residue 
names to PEP, UNK, LGD, introduce MODEL and ENDMDL cards) 
DiscoveryStudio indicates the input PDB file doesn't contain any ligand.


Would any one in this community have an idea of how to specify that a 
part of a coordinate file is the ligand, so that DiscoveryStudio 2021 
recognises it as such and allows me to proceed?


Thanks,

Fred.

--
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BIOCEV, Vestec, Czech Republic



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Re: [ccp4bb] how to get mol files from PDB and restraint CIF?

[Fred Vellieux]

Hello Frank,

We have to convert betwen file formats very frequently (usually several 
times daily) and:

1) we didn't need any restraints CIF file for that;
2) the tools we are using are
http://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html
https://datascience.unm.edu/tomcat/biocomp/convert

Sometimes the conversion doesn't take place and I have no idea why.

HTH,

Fred.

On 5/19/23 11:28, Frank von Delft wrote:
Hello - as in the subject line, does anybody know of, or have, code 
that will parse (1) a PDB (or mmCIF?) file with a ligand, and (2) the 
restraints CIF file used in refinement, and generate a .mol (or .sdf) 
file?


OpenBabel apparently does not.

I thought the PDB processing tools would, but my collaborator couldn't 
find them.


Any pointers welcome.  (To save us time.)

Thanks!
Frank



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Re: [ccp4bb] ISO model with large groups of atoms in alternative conformations

[Fred Vellieux]

Hello Pavel,

You may want to have a look at PDB structure 6YCR: the macrocyclic 
peptide inhibitor is modelled as two conformations. The entire peptide.


HTH,

Fred.

On 8/24/22 00:02, Pavel Afonine wrote:


Dear community,

I’m looking for an example of a crystal structure where a large group 
of atoms (as large as a whole chain or even a domain) have more than 
one distinct conformation that would require modeling of such 
chain/domain as more than one individual copy, with each copy having 
partial occupancy. I’m not sure if that even exists but if someone can 
share an example that'd be very much appreciated!


Thanks!
Pavel




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[ccp4bb] SUMMARY: displaying residues (as a surface perhaps) for one component of a p-p-i

[Fred Vellieux]

Dear bb members,

My question from yesterday is repeated at the bottom of this email.

What worked is the suggestion by Jan Dohnalek (IBT and CMS, BIOCEV Vestec):

opening a structure file in CCP4MG with the option "interfaces" then 
selecting "residues". A simplified display of the proteins appears with 
the residues involved in the interface. This is followed by a PISA 
calculation from within CCP4MG. The surface of only one of the 
components in the p-p-i can be displayed, which is exactly what I was 
looking for.


Thanks for all the suggestions.

Regards,

Fred.

On 5/31/22 08:12, Fred Vellieux wrote:

Dear bb members,

I am quite certain that someone must have needed to do this already. I 
looked at publications but no details were given concerning how 
figures were prepared.


So here is the problem:

Given a protein protein interface (with the 3D structure of the 
complex available) I am looking for a method allowing me to identify 
and display the interface forming residues of one of the protein 
components. Plus a surface representation of that part, for the 3D 
structure.


Thanks in advance for any tips.

Regards,

Fred. Vellieux


--
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BIOCEV, Vestec, Czech Republic



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[ccp4bb] displaying residues (as a surface perhaps) for one component of a p-p-i

[Fred Vellieux]

Dear bb members,

I am quite certain that someone must have needed to do this already. I 
looked at publications but no details were given concerning how figures 
were prepared.


So here is the problem:

Given a protein protein interface (with the 3D structure of the complex 
available) I am looking for a method allowing me to identify and display 
the interface forming residues of one of the protein components. Plus a 
surface representation of that part, for the 3D structure.


Thanks in advance for any tips.

Regards,

Fred. Vellieux

--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic



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Re: [ccp4bb] Regarding File conversion

[Frederic Vellieux]

Hi,

Last time I needed to do this the most convenient for me was to use 
Coot, with a very large coordinate file. Coot pre v1 (v0 something) to 
read in coordinates in the mmcif format and write out coordinates in the 
PDB format.


HTH,

Fred.

On 2022-04-19 14:01, Abhilasha Thakur wrote:

Hello!!
Greeting of the day,

I want to know regarding file conversion from mcif file format to PDB
format of proteins.
Is there any program or software that can be used to change one format
to another format. KIndly guide me about programs used for file
conversion or any other medium like python script or R script to
convert the file format without changing the coordinates  of the file.


Thankyou

-

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Re: [ccp4bb] [summary] Does anyone know of a "CHARMM bulletin board" ?

[Frederic Vellieux]

Hello,

I am posting this summary in case anyone else encounters the same 
problem. Replies were received from David A. Case, Morpholino Peligro, 
Arunabh Athreya, Tushar R. and Walker Olivier (through Adriana Miele).


The problem: how to get MD runs when you are not a specialist (first 
time you have to "do it") and that it all must be free.


The version of Maestro linked to Desmond is licensed and therefore it 
isn't possible to use it here;


Gromacs: im my hands, trying to compile from source (and therefore get a 
parallelized version) failed, and the version distributed for my Linux 
flavour failed to execute properly the examples given on the internet;


Suggestion to use VMD and NAMD: VMD doesn't install on my Linux box 
somehow and the tutorials I found require both VMD and NAMD;


CHARMM: there was a suggestion to use the CHARMM forum, which may be 
useful? Somehow my registration wasn't accepted by the system and the 
reason isn't made available to the person who tries to register.


Then there was this final suggestion that was useful: CHARMM-GUI.

At first I was trying to use setup.inp and this failed repeatedly.

What worked was pdbreader on the CHARMM-GUI web site, the pdb passes 
through all the stages of preparation and in the end produces two input 
file, one for equilibration (step 4?) and the second one for a MD run 
(step 5?).


Since the CHARMM-GUI web site is a CHARMM web site I chose to produce 
input files for- and run- CHARMM (and not the other software for which 
input files can also be produced): in case of failure(s) I wouldn't know 
if these would be due to incorrect input files being produced or to 
problems with the software on my box. Safest probably.


Thanks to those who replied.

Also note that vi cannot be used as an editor with CHARMM input files. 
Nedit will do but not vi.


Fred.


Hi folks,

Sorry about the non-ccp4 question. I don't know where to ask.

I have to perform MD simulations but I am totally on my own here.
The
one program that appears to be free (in terms of license) seems to
be
CHARMM. GROMACS (testing with the examples found in the internet)
did
not work in my hands so I forget about that.

Charmm somehow looks similar to a program I used to work with,
X-PLOR.
However I haven't found a manual similar to the old XPLOR manual nor
a
web site that can generate the input files as was the case for
X-PLOR.
Neither did I find anywhere a flow chart allowing me to know which
steps
to be performed and in what order.

Hence: does anyone know of an X-PLOR to CHARMM dictionary ? Or a
CHARMM
bulletin board similar to CCP4BB ?

Just to give an example using the CHARMM setup.inp file for a
protein
that has an "ACE" cap at the N-terminus: fails. It complains about
the
ACE cap. Removing the cap solves that problem but then CHARMM fails
because of "HIS". If CHARMM fails because it doesn't like any
amino-acids then I don't know how I can use the program. But still
I'd
like to use it because I have to.

Thanks,

Fred.

--
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BIOCEV, Vestec, Czech Republic






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[ccp4bb] Does anyone know of a "CHARMM bulletin board" ?

[Fred Vellieux]

Hi folks,

Sorry about the non-ccp4 question. I don't know where to ask.

I have to perform MD simulations but I am totally on my own here. The 
one program that appears to be free (in terms of license) seems to be 
CHARMM. GROMACS (testing with the examples found in the internet) did 
not work in my hands so I forget about that.


Charmm somehow looks similar to a program I used to work with, X-PLOR. 
However I haven't found a manual similar to the old XPLOR manual nor a 
web site that can generate the input files as was the case for X-PLOR. 
Neither did I find anywhere a flow chart allowing me to know which steps 
to be performed and in what order.


Hence: does anyone know of an X-PLOR to CHARMM dictionary ? Or a CHARMM 
bulletin board similar to CCP4BB ?


Just to give an example using the CHARMM setup.inp file for a protein 
that has an "ACE" cap at the N-terminus: fails. It complains about the 
ACE cap. Removing the cap solves that problem but then CHARMM fails 
because of "HIS". If CHARMM fails because it doesn't like any 
amino-acids then I don't know how I can use the program. But still I'd 
like to use it because I have to.


Thanks,

Fred.

--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic



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[ccp4bb] cryptic error message trying to use LigPlot on an unknown ligand

[Fred Vellieux]

Hi folks,

I'm trying to run Ligplot on a PDB file that contains a residue with 
type UNL (Unknown Ligand). I hadn't been using LigPlot for perhaps 2 
years now (which means that I had to reinstall, with an expired license, 
and get familiar with it again). I get the following error message 
(rather cryptic):


Calling HBADD ...
Running HBADD
Het Group Dictionary: /components.cif
Temporary PDB file: /tmp/lig7141158588178475829/ligplus.pdb
Command:  /LigPlus/lib/exe_linux/hbadd 
/tmp/lig7141158588178475829/ligplus.pdb /components.cif -wkdir 
/tmp/lig7141158588178475829/
java.io.IOException: Cannot run program "/LigPlus/lib/exe_linux/hbadd": 
error=2, No such file or directory

Other event: state

Would anyone know what to make out of this message ? Otherwise is there 
another piece of software (called "app" nowadays) that could provide me 
with similar drawings ?


At some stage I ran PRODRG, introduced the cif file in the file 
components.cif used by LigPlot (LigPlus). I also replaced the coordinate 
files by those returned by the PRODRG run. Always with the same cryptic 
error message provided by the software (oops, app).


Thanks,

Fred.

--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic



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[ccp4bb] coot & other graphics programs draw too many bonds

[Fred Vellieux]

Hello there,

After running autodock vina on certain small molecules, the graphics 
software I am using (e.g. Pymol, Coot) draws far too many bonds on the 
docked small molecule. See enclosed screen capture.


Is there any way to prevent this from happening? This isn't very 
satisfactory of you wish to produce figures for a presentation or for 
publication.


Ta,

Fred.

--
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BIOCEV, Vestec, Czech Republic




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Re: [ccp4bb] Suggestions to improve resolution of protein crystals

[Fred Vellieux]

Hi,

In addition to all that's been suggested so far: when I was facing such 
problems I always tried the (commercially available) additive screens 
(additive kits, whatever they are called nowadays). This means setting 
up quite a few crystallisation experiments (you already have conditions 
in which crystals grow) and blindly going through the additives. Just in 
case a few of them improve the resolution of your crystals, or even 
provide another crystal form. I've had plenty of success this way. Of 
course the results obtained are not from sessions of hard thinking, what 
could be the cause of the problems with the current crystals etc but who 
cares? It may be that (for example) a small molecule inserts itself in 
the right place to give you the desired result.


Worth trying.

HTH,

Fred.

--
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BIOCEV, Vestec, Czech Republic



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[ccp4bb] Help needed (input files)

[Fred Vellieux]

Hello,

I need to perform some MD calculations and then trajectories of some 
small molecules analyzed.


What I have is
1. protein
2. cofactor (FAD)
3. small molecule (either single O2 atom or single Chlorine atom)
4. crystallographic waters

The software I can access is either Gromacs (with yum install) or 
perhaps Desmond.


I have tried and tried to get this to run (for 6 months perhaps), to no 
avail. The input files located on the web do not work on the version of 
Gromacs provided by the yum install command. The Maestro license 
(required in order to get Desmond to run) is too expensive.


Is there a kind soul somewhere that would have suitable input files that 
would do all the above steps and who'd be willing to pass them on to me?


What needs to be done is:
add waters to the crystallographic waters in order to fill a box of 
suitable size

generate parameter and topology files for each component separately
merge these into global parameter and topology files for the system
run initial Energy Minimization
run M.D. simulations
analize the trajectories of the small molecules.

Thanks in advance.

Fred.

--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic



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[ccp4bb] summary of replies, superimposition of 3D structures using the dsDNA part only

[Fred Vellieux]

Dear all,

I obtained the following suggestions to my query on the BB 
(superimposing two protein:dsDNA structures using the dsDNA structures 
alone for the superposition operation):


- Matthias Barone (fmp-berlin) suggested Chimera, with some instructions 
on "how to do it". He also suggested a program called moloc;


- Anat Bashan (Weizmann) suggested Coot, Calculate, LSQ Superimpose;

- Tim Gruene (univie) suggested Uppsala software factory's lsqman;

- Paul Emsley (MRC-LMB) mentioned that there was no "gesamt" for DNA 
(too bad) and further suggested lsq-improve;


- Jeremy (Tame ?, jt...@yokohama-cu.ac.jp) mentioned a program in c 
called cfit, which he can provide on request.


In the end I used Chimera using the instructions given by Matthias 
Barone and that worked like a charm. So to speak: the result obtained 
was what I wished to find out.


Thanks to all who replied. Superposition using the nucleid acid part of 
complexes can be very informative.


Have a nice day further,

Fred. Vellieux

--
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BIOCEV, Vestec, Czech Republic



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[ccp4bb] superimposition of 3D structures with the DNA part only

[Fred. Vellieux]

Hi folks,

Some of you may have had to do this already. Either in the lab or more 
recently perhaps from home.


I have two structures that I wish to superpose (two protein:dsDNA 
complexes). Not using the protein part, but superposition through the 
dsDNA.


I'm not quite certain what is the "best" way of doing this.

Your suggestions will be appreciated, thanks.

Fred. Vellieux

--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic



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Re: [ccp4bb] current location for the Superimposé web server ?

[Fred Vellieux]

Hello,

Follow up concerning my query to the bb (in case anyone is interested), 
reply received from Robert Preissner through Philip E. Bourne and Joel 
Sussman:


The Superimposé server was stopped in May 2018.

Fred. Vellieux


On 2/28/20 7:47 AM, Fred Vellieux wrote:


*Hello,

I am looking for the Superimposé web server (from Charité, Berlin).
*

*This web server must have moved from the place where it is supposed 
to reside, farnsworth.charite.de , not found.


Does anyone know where this web server resides now ?

TIA,

Fred.
*




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[ccp4bb] current location for the Superimposé web server ?

[Fred Vellieux]

*Hello,

I am looking for the Superimposé web server (from Charité, Berlin).
*

*This web server must have moved from the place where it is supposed to 
reside, farnsworth.charite.de , not found.


Does anyone know where this web server resides now ?

TIA,

Fred.
*




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[ccp4bb] Summary: MD program suitable to compute trajectories of a very small molecule in a protein

[Fred Vellieux]

Dear all,

Thank you for your help.

Here is a summary of the replies received:

---> Neli Fonseca, EBI, suggested the use of Docker containers,
"
https://hub.docker.com/search?q=gromacs=image

https://hub.docker.com/search?q=cp2k=image

https://hub.docker.com/search?q=nwchem=image "

---> Jeroen Mesters, Biochem Uni Lubeck and later Amit Singh pointed at 
the pkgs page for gromacs (Centos 7):


https://centos.pkgs.org/7/epel-x86_64/gromacs-2018.8-1.el7.x86_64.rpm.html

It then became clear why my attempt at "yum install gromacs" followed by 
"which gromacs" returned an error message (the command is "gmx");


---> Chris Roome, mpimf-heidelberg:
"If you're insterested, recently compiled the latest Gromacs 2020, seems 
to work fine.


I compiled GCC v5.5.0 first, and set the LD... and exe path (your path 
will differ of course) here's mine, with tcsh:


setenv LD_LIBRARY_PATH /software/gcc-5/lib64
set path = ( /software/gcc-5/bin $path )

As you say, even with this, cmake picks up the old, system installed 
gcc, so I had to specify on the cmake cmd:


cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON 
-DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=c++ -DGMX_MPI=on 
-DCMAKE_INSTALL_PREFIX=/software/gromacs-2020 -DREGRESSIONTEST_DOWNLOAD


since cmake picks up the old cc even with the correct paths.

I installed the MPI version, so if you want that, you'll need to install 
the openmpi and openmpi-devel packages with yum. Then do a 'module load 
mpi' before the cmake."


--->  Abhik Mukhopadhyay suggested the use of NAMD, 
https://www.ks.uiuc.edu/Research/namd/


---> Eugene Osipov: you can try NAMD, Amber (cost-free CPU-only academic 
version) or Desmond - their installation is simple and they work 
reasonably well.


---> Jack Tanner (U. Missouri-Columbia): "You might want to review the 
literature on using MD to study diffusion of O2/CO in myoglobin." (I had 
started in fact)


[---> Lorenzo Briganti: the reply seems to have been lost along the way].

Hoping this will be useful to others, and thank you once again.

Fred. Vellieux, 1st Faculty of Medicine, Charles University in Prague, 
BIOCEV Vestec site




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[ccp4bb] MD program suitable to compute trajectories of a very small molecule in a protein

[Fred Vellieux]

Dear all,

I need to run MD calculations in order to follow the trajectories of a 
very small molecule inside a protein. From previous calculations (not 
MD) I have starting positions for this small molecule that all seem in 
agreement with a possible path of motion inside the protein.


Now I need to access a MD program (without licensing costs).

I've had a look at the software list provided in Wikipedia (and tried to 
install the software, in succession, alas without success):


cp2k - present for CentOS6 (with yum install ?) but appears to have 
vanished for CentOS7;


gromacs requires a gcc version I don't have (even after having compiled 
and installed a suitable gcc version, cmake complains about the "old 
version" and stops);


NWChem is unhappy with the Python setup and doesn't compile.

I don't know how to solve all these OS version, library, unsuitable 
binary etc problems. In fact I don't know if any of these 3 software 
suites would be suitable for what I have in mind.


Hence would anyone know of a useful MD software suite that would be 
suitable for my purpose and comes with statically linked binaries 
suitable for Intel 64 (Linux) ? Just launch the executable and it runs, 
no questions asked...


Thank you,

Fred.



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[ccp4bb] summary: how to define connectivity, bond types... in PDB files

[Fred Vellieux]

Dear all,

These are the replies received so far:

Daniel Rigden (U. of Liverpool) suggested to do the conversion using 
https://www.webqc.org/molecularformatsconverter.php . It didn't work for 
me, the small molecule may be too complex (error message when reading 
the .mol file);


Petr Kolenko (Czech Technical University in Prague) suggested to use the 
smiles small molecule definition format. molview.org provides a smiles 
string in the place where the URL appears when drawing the molecule and 
then converting it from 2D to 3D.


I located an online smiles translator 
(https://cactus.nci.nih.gov/translate/ ) and used it to generate a pdb 
file that appears to satisfy Pymol (see enclosed screen capture). I 
don't yet know if Pymol will still be happy after docking;


Stephane Rely (ENS Lyon) suggested the use of the prodrg server, and 
drawing the molecule with JME. I haven't tried this approach yet;


Finally, Massimo Degano (San Raffaele Scientific Institute in Milano) 
suggested to read in the pdb in Avogadro and writing it out, with CONECT 
cards written automatically. This didn't work on my system (Avogadro 
doesn't install due to Qt not being in found at the cmake stage, 
although it is present on my system)


Thank you for the prompt responses.

Fred.




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[ccp4bb] Current "best" software for computing volumes of active sites

[Fred Vellieux]

Hi CCP4BBers,

With software constantly changing, new versions arriving to us and new 
software reaching the intended audience, I am looking for the most 
appropriate piece(s) of software to compute the volume of active site 
"cavities" in related 3D structures.


I have tried to use Voidoo however I do not know where to download an 
initial (and fairly comprehensive) cavity.lib file which I'd modify if 
need be. The links on the USF web site appear to be broken.


I am running Linux.

Thanks for the advice,

Fred. Vellieux



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Re: [ccp4bb] Backup of whole synchrotrons

[Fred Vellieux]

Hi,

We already have problems with the volume taken by our standard backups 
(they take too much space and we haven't been able to push the walls 
outwards in the Institute - I don't know why they keep telling us that 
our data should be in some clouds up in the sky). Hence I was wondering 
about space considerations: can the backups of the synchrotrons and 
X-FELs be miniature versions (obtained by clever dehydration methods)? 
If you need to access the backup then simply rehydrate and you'll get 
the full size backup appearing in the garden of your Institute... If 
your Institute doesn't have a garden of the proper size, then it's time 
to talk to the administrator. It should be fairly easy to convice 
her/him that the acquisition of a garden is really a must now.


F.

On 4/1/19 12:22 PM, Robbie Joosten wrote:

Hi Peter,

The copies are only indistinguishable after they have been produced. So there 
has to be good record keeping during production. It's as easy as hanging on to 
rich meta-data. There was another post today on what to store in mmCIF, I'm 
sure we can have another record in there to cover this.
You do touch the subject of FAIR data here, for reproducibility, do we need to 
keep the copy and spawn a new copy with the update? Or can we keep update the 
'original' copy with a well-defined downgrade path. Off course the meta-data 
for the original copy needs to be retained in such a case.
I hope it is obvious to everyone that we have to keep the copies in stasis, we 
cannot have them running around to change all the time. This is not just a 
methodological issue of being able to keep an experiment reproducible, but it 
is also an HR nightmare. It would require a lot of extra salaries. I mean, 
copies have rights and what will the unions think? If only we had thought of 
backing up crystallographers earlier, then we would have a copy of Margaret 
Thatcher to deal with the unions!  Instead, I guess today is a good day to 
invest in cryo-stasis technology.

Cheers,
Robbie

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Peter Keller
Sent: Monday, April 01, 2019 12:04
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Backup of whole synchrotrons

Hi Robbie,

On 01/04/2019 07:23, Robbie Joosten wrote:

I don't think making this GDOR complient is that hard. It's all pretty
well defined what you store (everything), where you store it, and why.
There are some philosophical problems with allowing users to have
their data deleted. Assuming the copy is good enough to reproducing
the experiment. Deleting a copy would constitute murder.

You have correctly identified the underlying philosophical issue: it is a 
variant
of what is now known as the "Teletransportation paradox", see
.

  From the point of view of methods developers like you and me, there is an
additional issue: with insufficient raw data to work with, we are required to
create living experimenters as part of our development work.
For the most accurate results, these should be faithful copies of real
synchrotron visitors and beamline scientists, who in many cases are
personally known to us. How should we handle these copies when we need
to release new or updated methods? Since these copies need to be
indistinguishable from the originals, how can we tell whether we are
upgrading the copy or the original?

Regards,
Peter.

   This means that the

backups have to be stored in a rather libertarian "state" like Sealand
or Somalia.
Keeping that in mind, perrhaps this sort of backup should first be
implemented with the future African synchrotron.

Cheers,
Robbie

On 1 Apr 2019 07:46, "graeme.win...@diamond.ac.uk"
 wrote:

 While this may sound absurd, the principle of incremental backups
 can help out a great deal here. Like Apple’s Time Machine, all we
 need to do is store a copy of the things which have changed rather
 than the entire facility, which reduces the burden by at least a few
 orders of magnitude. Such efficiency savings will I am sure be of
 great interest in this project. Surely though we could save a copy
 of the experimental Eigenstate before the experiment too, offering
 the option of going back and having another go - every
 experimentalists dream!

 I do however take issue with your hypothesis that only the
 experimental equipment need be backed up - surely the experimenters
 also need to be archived, to allow the question “What were you
 thinking??” to be accurately answered when the reviewer’s questions
 come back. Unfortunately due to quantum entanglement issues this
 would probably require archiving the mind-state of dozens of people
 every time you hit “go” with the associated data protection issues -
 I for one would not like to fill in the GDPR section of that EU
 application :-)

 Anyhow, best of luck with your application,

 Graeme

 

Re: [ccp4bb] Experimental phasing vs molecular replacement

[Frederic Vellieux]

Hello,

I think what you are alluding to is model bias in (macromolecular) 
crystallography. What you should consult are the publications associated 
with this topic, and those on the map coefficients used to compute 
electron density maps (e.g. SIGMAA weighting), OMIT maps, current 
refinement techniques...


"Heavy-atom" phasing also suffers (or may suffer) from "imperfections" 
due to the heavy atom model used for phasing. Some of us remember 
ripples in electron density maps.


Fred.

On 2018-12-05 09:07, 香川 亘 wrote:

Dear all,

It is my understanding that experimental phasing (e.g. Se-SAD), in
principle, yields better electron density maps than molecular
replacement for protein regions with weak electron densities
(partially disordered or flexible).  I would appreciate if someone
could provide comments on whether my understanding is correct or not.
If there any good examples or literatures on this issue I would be
grateful to know about it.

I thank you in advance.

Wataru Kagawa


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Re: [ccp4bb] AW: [ccp4bb] [ccp4bb] Oxford University Press

[Vellieux Frédéric]

"how to get grants without papers in Nature. anyone have a solution to that 
one?"

Simple: Once all of us have reviewed enough papers (with the money placed in a 
common pot) we simply buy the Nature Publishing Group. All those having taken 
part get a Nature paper every 4 years to ensure grant money continues to flow 
in.

F.

From: CCP4 bulletin board  on behalf of Hughes, Jon 

Sent: Saturday, June 30, 2018 12:12:50 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] AW: [ccp4bb] [ccp4bb] Oxford University Press

great idea! 2 hours at €200 per hour makes €1000 - sounds like an eminently 
reasonable starting point for negotiations. if the publishers don't like our 
price, they can do the reviewing themselves - and after a while no one will 
bother to buy the resulting rubbish anyhow! in the mean time we put our stuff 
online directly (without wasting our time, for example, still formatting 
reference lists in the 21st century!). we have them over a barrel. the only 
problem i see is how to get grants without papers in Nature. anyone have a 
solution to that one?
one final aspect is: who gets the money? surely the universities etc. should 
get it, not us: the taxpayer pays us already.
best,
jon

-Ursprüngliche Nachricht-
Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Keller, 
Jacob
Gesendet: Samstag, 30. Juni 2018 00:00
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] [ccp4bb] Oxford University Press

The one I don't get is why not pay reviewers? $1000 per review? If you look at 
publishers' profit margins, you will see that they can afford it. I actually 
think the scientific community should go on a "review strike" until reviewers 
get paid.

JPK

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
Desk: (571)209-4000 x3159
Cell: (301)592-7004
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Petr 
Leiman
Sent: Friday, June 29, 2018 4:47 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] [ccp4bb] Oxford University Press

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 Jun 29, 2018, at 8:11 AM, Hughes, Jon  
> wrote:
>
> whose paper? our universities pay subscriptions for these journals and we 
> even pay on top of that for the pages of our publications (even when they're 
> not actually printed!), whilst we review papers for free! sounds like a 
> well-validated way to use taxpayers' money to keep the expensive company cars 
> etc. nice and shiny. why don't universities just require reimbursement for 
> the time we invest to insure that the merchandise is up to standard? €100 per 
> hour would be cheap. seems to me as though some capitalists need to add a few 
> lines to their balance sheets
> best, jon
>
> -Ursprüngliche Nachricht-
> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von
> Robbie Joosten
> Gesendet: Freitag, 29. Juni 2018 13:42
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: Re: [ccp4bb] Oxford University Press
>
> Yes, but think of all the money they miss due to your pirating of their paper 
> ;) It's the typical discussion about whether piracy of copyrighted material 
> leads to loss or gain of revenue. There are a lot of models here, but not 
> necessarily well-validated.
>
> Anyway, if people want to read your papers and cannot get them from
> ResearchGate, I'm sure they can find them on another online
> collection, a hub of some sort ;)
>
> Cheers,
> Robbie
>
>> -Original Message-
>> From: Bernhard Rupp [mailto:hofkristall...@gmail.com]
>> Sent: Friday, June 29, 2018 13:23
>> To: 'Robbie Joosten'; CCP4BB@JISCMAIL.AC.UK
>> Subject: RE: [ccp4bb] Oxford University Press
>>
>> Agreed, but for 10 years old papers this seems a bit of overkill
>>
>>
>>
>> From: CCP4 bulletin board  On Behalf Of Robbie
>> Joosten
>> Sent: Friday, June 29, 2018 12:11
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: Re: [ccp4bb] Oxford University Press
>>
>>
>>
>> Were they open access papers? If they were, than OUP is being too
>> aggressive (IMO), but otherwise it makes sense. I also find the
>> ResearchGate is rather aggressive in bugging you to upload papers
>> that are readily 

[ccp4bb] Announcement: Instruct/CIISB Fragment Screening course in Vestec (Prague area) on April 5 and 6 (arrival on April 4, departure on April 7)

[Vellieux Frédéric]

Dear all,

Just before the end of the year break, before the festive season:

The Centre of Molecular Structure (IBT, Biocev, Vestec, Prague area, Czech 
Republic, one the the two Instruct CZ and CIISB sites) is organising a course 
on April 5 and 6, 2018 (arrival in Vestec on April 4, departure on April 7).

Title: Instruct / CIISB course on fragment screening using crystallography 
laboratory equipment.

The course has two parts: half a day devoted to lectures on April 5 morning, in 
the Biocev auditorium - no registration is needed, everyone is welcome to 
attend the presentations and lectures given by:
Jan Dohnalek (IBT Biocev Vestec)
Andreas Heine (IPC Marburg)
Bohdan Schneider (IBT Biocev Vestec)
Tomas Koval (IBT Biocev Vestec)
Petr Pompach (CMS IBT Biocev Vestec)
Manfred Weiss (Bessy II)
Sameer Velankar (to be confirmed, or another speaker from EBI)
John Darby (Chemistry, U. of York)

The remaining part of the workshop (three half days, April 5 afternoon, April 6 
morning and April 6 afternoon) consist of a "workshop", hands on sessions for 
16 registered participants. This part will be dealing with

-  The initial pre-screening using biophysical methods (Tatsiana 
Charnavets, CMS)

-  Dispensing target protein crystals to a fragment library (Jiri 
Pavlicek, CMS)

-  In situ testing of crystal diffraction, data collection and 
evaluation of the results (Jiri Pavlicek, CMS)

Due to generous Instruct funding, there will be no registration fees for the 16 
registered participants (hands-on sessions), all costs will be covered from the 
first night (April 4 to April 5) in hotel u Krbu in Vestec (ca. 15 minutes walk 
from the Biocev) to the departure from the hotel on April 7 after breakfast. 
For those accepted, of course you are most welcome to arrive earlier and / or 
depart from the Prague area later in order to discover / visit one of Europe's 
most beautiful cities, Prague. There are numerous hotels and "BnB" style 
accomodation available. This isn't part of the course and must be arranged by 
yourselves. Registered participants (and also the people wanting to attend the 
lectures only) must cover the cost of travelling to the venue.

Again, everyone is welcome for the lectures on April 5 morning, in the Biocev 
auditorium

All information (including Course poster) and details can be found on:
http://www.biocev.eu/event/instruct-ciisb-fragment-screening-course/

The deadline for submission of applications is February 9, 2018. Applications 
from laboratories located abroad are especially welcome.

Can you forward this information to anyone you think would be interested ? 
Thanks.

I wish you all a very good festive season.

Fred. Vellieux (Ph.D., HDR)
Centre of Molecular Structure
Institute of Biotechnology
Czech Academy of Sciences, BIOCEV
Prumyslova 595
252 50 Vestec
Czech Republic

Tel +420 325 873 786

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The text of this message and its attachments cannot be considered as a proposal 
to conclude a contract, nor the acceptance of a proposal to conclude a 
contract, nor any other legal act leading to concluding any contract; nor does 
it create any pre-contractual liability on the part of Institute of 
Biotechnology CAS

[ccp4bb] Reminder: Open position for a specialist in biological X-ray techniques, especially SAXS plus XRD and crystallisation

[Vellieux Frédéric]

Dear all,

This is a reminder that there is an open position for a specialist in 
biological X-ray techniques (especially SAXS plus X-ray diffraction and 
crystallisation) at the Centre of Molecular Structure (a CIISB and Instruct 
site) in Vestec, Prague region. The deadline for submission of applications is 
December 15, 2017. Since we have been asked the question: the position is open 
to both EU and non-EU nationals.

Feel free to pass along to colleagues who could be interested in the position. 
The advertisement can also be found on the Instruct web site, 
https://www.structuralbiology.eu/jobs/specialist-in-biological-x-ray-techniques-especially-small-angle-x-ray-scattering-saxs-and-single-cr/
 .

Thank you in advance,

Best regards,

F. Vellieux

Fred. Vellieux (Ph.D., HDR)
Centre of Molecular Structure
Institute of Biotechnology
Czech Academy of Sciences, BIOCEV
Prumyslova 595
252 50 Vestec
Czech Republic

Tel +420 325 873 786


Open position at the Centre of Molecular Structure, Institute of Biotechnology, 
Biocev:

Specialist in biological X-ray techniques, especially small-angle X-ray 
scattering (SAXS) and single crystal X-ray diffraction (plus crystallisation), 
full time

The Centre of Molecular Structure (CMS), part of CIISB (the Czech 
Infrastructure for Integrative Structural Biology) and one of the European 
network ERIC-Instruct sites, is operated by the Institute of Biotechnology CAS 
v.v.i. (Biocev, Vestec, central Bohemia, Czech Republic). The CMS is a 
technology platform providing access to scientific instrumentation and service 
to researchers, mostly working in "life sciences".  Details of the scientific 
equipment and services provided at the CMS can be consulted on 
http://www.biocev.eu/en/corefacilit/centre-of-molecular-structure/ and links 
therein.

We are looking for a specialist in X-ray techniques. The focus of the position 
is to provide excellent service in maintaining and operating a newly acquired 
state-of-the-art SAXS line and partially also the X-ray diffraction and 
crystallisation platform. User support providing training, assistance or 
sometimes full service (depending on the particular case) is also expected.

The successful candidate will also have the opportunity to collaborate in 
exciting research projects involving X-rays (both diffraction and scattering) 
in IBT research groups focused on structural biology. For such additional 
duties (that will represent up to 50% of the time),  practical knowledge of 
protein and nucleic acid purification and crystallisation is a plus. 
Participation to data collection trips at synchrotron radiation beam lines is 
expected.

The applicants (preferably having Ph.D. level experience) must have practical 
experience with bio-SAXS and have a strong interest in providing training and 
assistance to users and students.

The position offered is for an initial period of three years, with the 
possibility of renewal.

Applications (in electronic format, Word document or pdf files preferred) 
including a cover letter, curriculum vitae, and the names and addresses of 
three referees must be sent to the main office of the Institute of 
Biotechnology:

Institute of Biotechnology CAS, v.v.i.
Prumyslova 595
252 50 Vestec
Czech Republic
Phone: +420 325 873 700
E-mail: btu-off...@ibt.cas.cz<mailto:btu-off...@ibt.cas.cz>

Any questions regarding this position can be directed to
Dr Frederic Vellieux, 
frederic.velli...@ibt.cas.cz<mailto:frederic.velli...@ibt.cas.cz>
or Dr Jan Dohnalek, dohna...@ibt.cas.cz<mailto:dohna...@ibt.cas.cz>

Application deadline: 15 December 2017

Expected starting date: within the period January - March 2018
-

Upozornení: Není-li v této zpráve výslovne uvedeno jinak, má tato E-mailová 
zpráva nebo její prílohy pouze informativní charakter. Tato zpráva ani její 
prílohy v zádném ohledu Biotechnologický ústav AV CR, v. v. i. k nicemu 
nezavazují. Text této zprávy nebo jejích príloh není návrhem na uzavrení 
smlouvy, ani prijetím prípadného návrhu na uzavrení smlouvy, ani jiným právním 
jednáním smerujícím k uzavrení jakékoliv smlouvy a nezakládá predsmluvní 
odpovednost Biotechnologického ústavu AV CR, v. v. i.

Disclaimer: If not expressly stated otherwise, this e-mail message (including 
any attached files) is intended purely for informational purposes and does not 
represent a binding agreement on the part of Institute of Biotechnology CAS. 
The text of this message and its attachments cannot be considered as a proposal 
to conclude a contract, nor the acceptance of a proposal to conclude a 
contract, nor any other legal act leading to concluding any contract; nor does 
it create any pre-contractual liability on the part of Institute of 
Biotechnology CAS

[ccp4bb] Open position for a specialist in biological X-ray techniques (SAXS, X-ray diffraction, crystallisation)

[Vellieux Frédéric]

Dear all,

Could you pass the following announcement on to suitable candidates (including 
yourselves, of course) ?

Thank you.

Fred. Vellieux

Fred. Vellieux (Ph.D., HDR)
Centre of Molecular Structure
Institute of Biotechnology
Czech Academy of Sciences, BIOCEV
Prumyslova 595
252 50 Vestec
Czech Republic

Tel +420 325 873 786

Open position at the Centre of Molecular Structure, Institute of Biotechnology, 
Biocev:

Specialist in biological X-ray techniques, especially small-angle X-ray 
scattering (SAXS) and single crystal X-ray diffraction (plus crystallisation), 
full time

The Centre of Molecular Structure (CMS), part of CIISB (the Czech 
Infrastructure for Integrative Structural Biology) and one of the European 
network ERIC-Instruct sites, is operated by the Institute of Biotechnology CAS 
v.v.i. (Biocev, Vestec, central Bohemia, Czech Republic). The CMS is a 
technology platform providing access to scientific instrumentation and service 
to researchers, mostly working in "life sciences".  Details of the scientific 
equipment and services provided at the CMS can be consulted on 
http://www.biocev.eu/en/corefacilit/centre-of-molecular-structure/ and links 
therein.

We are looking for a specialist in X-ray techniques. The focus of the position 
is to provide excellent service in maintaining and operating a newly acquired 
state-of-the-art SAXS line and partially also the X-ray diffraction and 
crystallisation platform. User support providing training, assistance or 
sometimes full service (depending on the particular case) is also expected.

The successful candidate will also have the opportunity to collaborate in 
exciting research projects involving X-rays (both diffraction and scattering) 
in IBT research groups focused on structural biology. For such additional 
duties (that will represent up to 50% of the time),  practical knowledge of 
protein and nucleic acid purification and crystallisation is a plus. 
Participation to data collection trips at synchrotron radiation beam lines is 
expected.

The applicants (preferably having Ph.D. level experience) must have practical 
experience with bio-SAXS and have a strong interest in providing training and 
assistance to users and students.

The position offered is for an initial period of three years, with the 
possibility of renewal.

Applications (in electronic format, Word document or pdf files preferred) 
including a cover letter, curriculum vitae, and the names and addresses of 
three referees must be sent to the main office of the Institute of 
Biotechnology:

Institute of Biotechnology CAS, v.v.i.
Prumyslova 595
252 50 Vestec
Czech Republic
Phone: +420 325 873 700
E-mail: btu-off...@ibt.cas.cz<mailto:btu-off...@ibt.cas.cz>

Any questions regarding this position can be directed to
Dr Frederic Vellieux, frederic.velli...@ibt.cas.cz
or Dr Jan Dohnalek, dohna...@ibt.cas.cz

Application deadline: 15 December 2017

Expected starting date: within the period January - March 2018

-

Upozornení: Není-li v této zpráve výslovne uvedeno jinak, má tato E-mailová 
zpráva nebo její prílohy pouze informativní charakter. Tato zpráva ani její 
prílohy v zádném ohledu Biotechnologický ústav AV CR, v. v. i. k nicemu 
nezavazují. Text této zprávy nebo jejích príloh není návrhem na uzavrení 
smlouvy, ani prijetím prípadného návrhu na uzavrení smlouvy, ani jiným právním 
jednáním smerujícím k uzavrení jakékoliv smlouvy a nezakládá predsmluvní 
odpovednost Biotechnologického ústavu AV CR, v. v. i.

Disclaimer: If not expressly stated otherwise, this e-mail message (including 
any attached files) is intended purely for informational purposes and does not 
represent a binding agreement on the part of Institute of Biotechnology CAS. 
The text of this message and its attachments cannot be considered as a proposal 
to conclude a contract, nor the acceptance of a proposal to conclude a 
contract, nor any other legal act leading to concluding any contract; nor does 
it create any pre-contractual liability on the part of Institute of 
Biotechnology CAS

Re: [ccp4bb] Help needed finding hit condition

[Vellieux Frédéric]

Hello,

Such pH drifts are rather common with crystallisation screens. Have you tried 
to produce other precipitant solutions with ca. 47% PEG 1000, 80 mM Potassium 
bromide but having a pH of (say) 6.2 ? A pH rangle close to that where your 
crystals were obtained. This would mean changing buffering agent to… MES 
perhaps ?

Cheers,

Fred.

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Jonathan 
Bailey
Sent: Monday, July 31, 2017 2:34 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Help needed finding hit condition

Dear CCP4bb community

I apologies for the slightly off topic post.

We have recently had success crystallizing a membrane protein (diffraction > 3 
Å at a synchrotron source) using the in meso method, the hit condition was from 
the Jena Bioscience screen Pi-minimal condition number #57.

Hit condition – 47.1 % w/v PEG1000, 150 mM Tris pH 8.0, 80 mM Potassium bromide

The screen is old and expired 12/20/2013 (lot # JBS00013133), we have tried to 
reproduce the crystals using homemade optimization screens around the hit 
condition but have not had any success. We have tried reproducing the hit using 
a new (not expired) Pi-minimal screen but had no success. We are only able to 
reproduce the crystals using the expired screen and we do not have much of it 
left.

We went back and tested the pH of the condition that had given crystals, the 
expected pH was 7.9 but we found it to be 6 – 6.5 using a pH indicator strip. 
We believe the drop in pH is caused by oxidative degradation of the PEG1000 
resulting in the formation of carboxylic acid species.

We have contacted Jena Bioscience to try and get some of the old screen stock 
but unfortunately they do not have any.

My question is does anyone out there happen to have any expired screen stocks 
of this Pi-minimal condition (#57), ideally from the same lot (lot # 
JB200013133), that they would be willing to send us.

Does anyone have any advice as to how to reproduce the condition? We’ve 
considered bubbling oxygen through and heating the sample to accelerate the 
oxidation process.

King Regards

Jonathan Bailey (PhD student)

Professor Martin Caffrey Lab MS group Trinity College Dublin
-

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Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

[Vellieux Frédéric]

Hello again,

Back in 2001 people still remembered the difference between Rsym and Rmerge. 16 
years later people seem to have forgotten. I will try to dig even more ancient 
references… Archaeology is the name of the game.

http://www.ysbl.york.ac.uk/ccp4bb/2001/msg00383.html

Cheers,

Fred.

From: James Foadi [mailto:james_fo...@yahoo.co.uk]
Sent: Tuesday, July 11, 2017 10:03 AM
To: Vellieux Frédéric <frederic.velli...@ibt.cas.cz>; CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

Hello Frederic. Interesting. Have you got some reference on this to share?

James

Dr James Foadi PhD Diamond Light Source Ltd. Diamond House Harwell Science and 
Innovation Campus Didcot Oxfordshire OX11 0DE United Kingdom office email: 
james.fo...@diamond.ac.uk<mailto:james.fo...@diamond.ac.uk> alternative email: 
j.fo...@imperial.ac.uk<mailto:j.fo...@imperial.ac.uk> personal web page: 
http://www.jfoadi.me.uk

On Tuesday, 11 July 2017, 7:15, Vellieux Frédéric 
<frederic.velli...@ibt.cas.cz<mailto:frederic.velli...@ibt.cas.cz>> wrote:

Hello,

I think this needs a little bit of crystarchaeology.

Rmerge and Rsym used to be different. This was at a time when data sets were 
typically collected from several crystals. Pre-cryo cooling, with data recorded 
on photographic film (Arndt-Wonacott cameras).

Rmerge = agreement R-factor from data from several crystals;
Rsym = agreement R-factor from symmetry-equivalents within one crystal.

[I just type "agreement R-factor" in order not to have to type the formulae]

At that time, people were confused about these two terms.

Nowadays both are (used as) synonyms.

Cheers,

Fred.

-Original Message-
From: CCP4 bulletin board 
[mailto:CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>] On Behalf Of Phil 
Evans
Sent: Monday, July 10, 2017 5:43 PM
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

What is the difference between Rmerge and Rsym - I thought they were the same?
Rrim == Rmeas I think

Phil



> On 10 Jul 2017, at 15:18, John Berrisford 
> <j...@ebi.ac.uk<mailto:j...@ebi.ac.uk>> wrote:
>
> Dear Herman
>
> The new PDB deposition system (OneDep) allows you to enter values for Rmerge, 
> Rsym, Rpim, Rrim and / or CC half. If, during deposition, you do not provide 
> a value for any of these metrics then we will ask you for a value for one of 
> them.
>
> Also, PDB format is a legacy format for the PDB. In 2014 mmCIF became the 
> archive format for the PDB and some large entries are no longer distributed 
> in PDB format. mmCIF is not limited by the constraints of punch cards.
>
> Please see
> https://www.wwpdb.org/documentation/file-formats-and-the-pdb
>
> Regards
>
> John
>
> PDBe
>
>
>
> On 10/07/2017 09:26, 
> herman.schreu...@sanofi.com<mailto:herman.schreu...@sanofi.com> wrote:
>> Dear All,
>>
>> For me this whole discussion is an example of a large number of people 
>> barking at the wrong tree. The real issue is not whether data processing 
>> programs print amongst many quality indicators an Rmerge as well, but the 
>> fact that the PDB and many journals still insist on using the Rmerge as 
>> primary quality indicator. As long as this is true, novice scientist might 
>> be led to believe that Rmerge is the most important quality indicator. As 
>> soon as the PDB and the journals request some other indicator, this will be 
>> over. So that is where we should direct our efforts to.
>>
>> I don't understand at all, why the PDB still insists on an obsolete quality 
>> indicator. However, the PDB format for the coordinates also dates back to 
>> the 1960's to be used with punch cards.
>>
>> My 2 cents.
>> Herman
>>
>>
>>
>> -Ursprüngliche Nachricht-
>> Von: CCP4 bulletin board 
>> [mailto:CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>] Im Auftrag
>> von Edward A. Berry
>> Gesendet: Samstag, 8. Juli 2017 22:31
>> An: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
>> Betreff: Re: [ccp4bb] Rmergicide Through Programming
>>
>> But R-merge is not really narrower as a fraction of the mean value- it just 
>> gets smaller proportionantly as all the numbers get smaller:
>> RMSD of .0043 for R-meas multiplied by factor of 0.022/.027 gives 0.0035 
>> which is the RMSD for Rmerge. The same was true in the previous example. You 
>> could multiply R-meas by .5 or .2 and get a sharper distribution yet! And 
>> that factor would be constant, where this only applies for super-low 
>> redundancy.
>>
>> On 07/08/2017 03:23 PM, James Holton wrote:
>>> The ex

Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

[Vellieux Frédéric]

Hello,

I think this needs a little bit of crystarchaeology.

Rmerge and Rsym used to be different. This was at a time when data sets were 
typically collected from several crystals. Pre-cryo cooling, with data recorded 
on photographic film (Arndt-Wonacott cameras).

Rmerge = agreement R-factor from data from several crystals;
Rsym = agreement R-factor from symmetry-equivalents within one crystal.

[I just type "agreement R-factor" in order not to have to type the formulae]

At that time, people were confused about these two terms.

Nowadays both are (used as) synonyms.

Cheers,

Fred.

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Phil Evans
Sent: Monday, July 10, 2017 5:43 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] AW: [ccp4bb] Rmergicide Through Programming

What is the difference between Rmerge and Rsym - I thought they were the same?
Rrim == Rmeas I think

Phil



> On 10 Jul 2017, at 15:18, John Berrisford  wrote:
>
> Dear Herman
>
> The new PDB deposition system (OneDep) allows you to enter values for Rmerge, 
> Rsym, Rpim, Rrim and / or CC half. If, during deposition, you do not provide 
> a value for any of these metrics then we will ask you for a value for one of 
> them.
>
> Also, PDB format is a legacy format for the PDB. In 2014 mmCIF became the 
> archive format for the PDB and some large entries are no longer distributed 
> in PDB format. mmCIF is not limited by the constraints of punch cards.
>
> Please see
> https://www.wwpdb.org/documentation/file-formats-and-the-pdb
>
> Regards
>
> John
>
> PDBe
>
>
>
> On 10/07/2017 09:26, herman.schreu...@sanofi.com wrote:
>> Dear All,
>>
>> For me this whole discussion is an example of a large number of people 
>> barking at the wrong tree. The real issue is not whether data processing 
>> programs print amongst many quality indicators an Rmerge as well, but the 
>> fact that the PDB and many journals still insist on using the Rmerge as 
>> primary quality indicator. As long as this is true, novice scientist might 
>> be led to believe that Rmerge is the most important quality indicator. As 
>> soon as the PDB and the journals request some other indicator, this will be 
>> over. So that is where we should direct our efforts to.
>>
>> I don't understand at all, why the PDB still insists on an obsolete quality 
>> indicator. However, the PDB format for the coordinates also dates back to 
>> the 1960's to be used with punch cards.
>>
>> My 2 cents.
>> Herman
>>
>>
>>
>> -Ursprüngliche Nachricht-
>> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag
>> von Edward A. Berry
>> Gesendet: Samstag, 8. Juli 2017 22:31
>> An: CCP4BB@JISCMAIL.AC.UK
>> Betreff: Re: [ccp4bb] Rmergicide Through Programming
>>
>> But R-merge is not really narrower as a fraction of the mean value- it just 
>> gets smaller proportionantly as all the numbers get smaller:
>> RMSD of .0043 for R-meas multiplied by factor of 0.022/.027 gives 0.0035 
>> which is the RMSD for Rmerge. The same was true in the previous example. You 
>> could multiply R-meas by .5 or .2 and get a sharper distribution yet! And 
>> that factor would be constant, where this only applies for super-low 
>> redundancy.
>>
>> On 07/08/2017 03:23 PM, James Holton wrote:
>>> The expected distribution of Rmeas values is still wider than that of 
>>> Rmerge for data with I/sigma=30 and average multiplicity=2.0. Graph 
>>> attached.
>>>
>>> I expect that anytime you incorporate more than one source of information 
>>> you run the risk of a noisier statistic because every source of information 
>>> can contain noise.  That is, Rmeas combines information about multiplicity 
>>> with the absolute deviates in the data to form a statistic that is more 
>>> accurate that Rmerge, but also (potentially) less precise.
>>>
>>> Perhaps that is what we are debating here?  Which is better? accuracy or 
>>> precision?  Personally, I prefer to know both.
>>>
>>> -James Holton
>>> MAD Scientist
>>>
>>> On 7/8/2017 11:02 AM, Frank von Delft wrote:
 It is quite easy to end up with low multiplicities in the low resolution 
 shell, especially for low symmetry and fast-decaying crystals.

 It is this scenario where Rmerge (lowres) is more misleading than Reas.

 phx


 On 08/07/2017 17:31, James Holton wrote:
> What does Rmeas tell us that Rmerge doesn't?  Given that we know the 
> multiplicity?
>
> -James Holton
> MAD Scientist
>
> On 7/8/2017 9:15 AM, Frank von Delft wrote:
>> Anyway, back to reality:  does anybody still use R statistics to 
>> evaluate anything other than /strong/ data?  Certainly I never look at 
>> it except for the low-resolution bin (or strongest reflections). 
>> Specifically, a "2%-dataset" in that bin is probably healthy, while a 
>> "9%-dataset" probably Has Issues.
>>
>> In which case, back to Jacob's question:  what does 

Re: [ccp4bb] Incorrect Structure in the PDB

[Vellieux Frédéric]

Hello,

I think it makes sense to have a look at the policy of the PDB concerning 
obsoleting structures:

The publication is retracted. The associated PDB entry will be obsoleted if 
requested by the journal. If a request has not been received, the wwPDB will do 
its best to contact the depositor and co-authors, (former) PIs, journal 
editors, etc. when made aware of the retraction. If the reason(s) for 
retraction were such that the associated PDB entry needs to be made obsolete, 
the wwPDB will obsolete the entry. The citation in the obsoleted entry is the 
published journal retraction.
The structure is incorrect, and the entry author obsoletes the entry. The entry 
must contain a statement as to the reason for obsoleting the structure.
A third-party (such as the employer) requests that the entry is obsoleted 
(e.g., in case of malfeasance). The citation in the obsoleted entry must be a 
published explanation and retraction in a peer-reviewed journal.

Source: https://www.wwpdb.org/documentation/policy

Cheers,

Fred.

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Trevor 
Sewell
Sent: Tuesday, June 27, 2017 8:35 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Incorrect Structure in the PDB


I have come across a key paper in my field that describes an enzyme mechanism. 
Their work is based on a deposited structure – by other authors - that is 
incorrectly interpreted.

Is there a process for removing a demonstrably wrong structure (deposited by 
others) from the PDB and replacing it with a correctly interpreted structure 
based on the original data? Or is there an alternative, and generally 
recognized, way of getting the correct structure in the public domain?

Many thanks for your advice on this matter.

Trevor Sewell

Disclaimer - University of Cape Town This e-mail is subject to UCT policies and 
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to conclude a contract, nor the acceptance of a proposal to conclude a 
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Re: [ccp4bb] Why Does Detwinning Not Work?

[Vellieux Frédéric]

Hello Jacob,

Quoting you, "Please let me know if you have a case where detwinning saved the 
day".

Well you asked for it so here is one example where twinning saved the day: 
"Crystal structure of pb9..." by Flayhan et al. (2014), J. Virol. 88 (2), 
820-828. Without detwinning I think there would have been no crystal structure 
in the end...

Cheers,

Fred.

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Keller, 
Jacob
Sent: Tuesday, October 11, 2016 2:15 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Why Does Detwinning Not Work?

Dear Crystallographers,

Based on some data sets I have looked at and anecdotal-type evidence here and 
there I have gotten the impression that detwinning does not help in structure 
solution. (Please let me know if you have a case where detwinning saved the 
day.) Is there a clear answer to this enigma anywhere, to anyone's knowledge? 
Wouldn't it seem that *any* detwinning would be better than *no* detwinning? I 
understand that the errors explode as one approaches 50% twins and does 
detwinning, but still, I don't think one *loses* information by detwinning, 
right? Take the case of a 33% twin: since the twin-reflections are on average 
about half the intensity of the non-twin, and since they are generally not 
correlated in intensity, isn't this like having noise added at 50% of the 
measured intensity? So why does detwinning make things worse generally? Is 
there something wrong in the assumptions underlying the detwinning algorithm, 
or perhaps something about the calculation that throws things off?

A related sub-enigma: why is MR generally immune to twinning, but anomalous 
methods are susceptible?

All the best,

Jacob Keller

***
Jacob Pearson Keller, PhD
Research Scientist
HHMI Janelia Research Campus / Looger lab
Phone: (571)209-4000 x3159
Email: kell...@janelia.hhmi.org
***

-

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Re: [ccp4bb] Off topic: textbook proteins for crystallization

[Vellieux Frédéric]

Xylose Isomerase is another one.

Cheers,

Fred.

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of WENHE 
ZHONG
Sent: Wednesday, April 20, 2016 11:39 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Off topic: textbook proteins for crystallization

Dear CCP4 members,

We would like to choose some proteins that are “extremely” easy to grow good 
crystals. There is only one protein I can think of which is lysozyme. Do you 
have other candidates that you use as a textbook protein in crystallization?

Thank you.

Kind regards,
Wenhe
-

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Re: [ccp4bb] New crystallization technique

[Vellieux Frédéric]

Hi Bernhard,

We've been thinking along the same lines over here (but then our approach was 
far more "Sci Fi" like than yours, that is truly applicable in a real 
laboratory environment): we were devising ways here to crystallise in space, in 
black holes. Too bad, you beat us at it. Congratulations, really, well 
deserved. I foresee a trip to Stockholm for you in the future.

Anyway now that we have been scooped, we won't be able to publish our 
preliminary results (carried out at CERN): the method indeed works. However, 
crystal growth slows down when approaching the "center" of the black hole (this 
is what our preliminary experiments at CERN have shown), and our mathematical 
modelling indicates that all the macromolecule will have aggregated together to 
form a single "perfect" crystal when gravity is infinite (but then time has 
stopped and we were trying to find innovative ways to solve this time barrier 
of eternity). Strangely enough, modelling has also shown that in the case of 
crystallisation in plates, all the drops would be able to cross the adhesive 
tape to gather into one giant droplet, in which a single perfect giant crystal 
would appear. These crystals would be of sufficient volume even for the latest 
pocket-sized neutron sources. But then, again, too bad: you beat us at it.

Fred.

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank von 
Delft
Sent: Friday, April 1, 2016 7:36 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] New crystallization technique

Sounds awesome.  How do you get the crystals out again?

On 01/04/2016 03:33, Bernhard Rupp (Hofkristallrat a.D.) wrote:
> Hi Fellows,
>
> after quite some tinkering we finally got an exciting new
> crystallization technique to work that has produced exciting results
> in the few cases tested so far.
>
> I attach the first page of the paper. The theory is somewhat involved
> (supplemental material) but the complete letter is available from
> http://www.hofkristallamt.org/Rupp_2016_Phys_Rev_Letters_116(13)_Hyper
> gravit
> y.pdf
>
>
> Best regards, BR
> -
> Bernhard Rupp
> 001 (925) 209-7429
> +43 (676) 571-0536
> b...@ruppweb.org
> http://www.ruppweb.org/
> -
> Physicist are there to find the laws of nature.
> Engineers are there to work around them.
> -
>
-

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contract, nor any other legal act leading to concluding any contract; nor does 
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Re: [ccp4bb] cryo for crystals with CTAB as precipitant

[Vellieux Frédéric]

Hi there,

What about trying the ''olde'' method of a thin layer of oil around the 
crystal? No guarantee whatsoever that this will work but if you don't try it 
you won't know.

Fred.

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Alejandro 
Madrigal Carrillo [amadri...@email.ifc.unam.mx]
Sent: Monday, February 22, 2016 11:00 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] cryo for crystals with CTAB as precipitant

Dear All,


I got crystals using CTAB 10mM as precipitant, but I have had problems with the 
cryoprotectant solution which freezes.  Has anybody collected crystallographic 
data with crystals grown in this detergent? What cryoprotectant do you 
recommend to test?


Two papers report use of glycerol as cryoprotectant (Brown MA et al., 2005; 
glycerol 40% Ren A et al, 2010 ). But at -20oC the reservoir solution plus 
cryoprotectant freezes. I tried with many cryoprotectants  (glycerol 40%, EG 
35%, PEG 400 35%, hexanediol 50%, Sucrose 28%, Xylitol 30%, etc) but solution 
at -20oC looks cloudy or frozen.


Any suggestion will be appreciated.


Thanks in advance,

Alejandro Madrigal Carrillo, M.Sc.
Laboratorio de Biofísica de Biomacromoléculas, 205 sur
Departamento de Bioquímica y Biología Estructural
Instituto de Fisiología Celular
Universidad Nacional Autónoma de México
Circuito Exterior S/N. Ciudad Universitaria
México, D.F., México, 04510
Teléfono: +52 55 5622 5640
-

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Re: [ccp4bb] model bias

[vellieux]

Hello,

I would certainly try the usual approaches (map coefficients that are 
less sensitive to model-bias, i.e. Sigmaa; OMIT maps - there are several 
of these which can be calculated). In addition, you may have a look at 
the approach of Liu and Xiong (2014, J. Mol. Biol. 426, 980-993). It is 
a well known technique (applying a negative temperature factor to 
amplitudes, for map sharpening) but this paper describes a systematic 
study indicating improvement whatever the situation.


As usual in macromolecular crystallography, confidence is gained by the 
use of several approaches.


HTH,

Fred.

On 29/04/15 13:16, Aleksandar Bijelic wrote:

Dear CCP4 users,

I am currently solving a structure (2.8-2.9 A resolution) of a protein 
complexed with a ligand using MR with the apo-form of this protein as 
model (resolution of the model is 2.4). After MR-phasing I performed a 
regular autobuild run giving me good outputs and thus I refined the 
best pdb leading to good values according to R-values and geometry, 
however, the denstiy doesn´t look well (but I think it´s due to the 
moderate resolution). Now I want to get sure if the side chains which 
are involved in the ligand binding are correctly positioned. However, 
the active site is suspicously similar to the active site of the model 
(apo-form) and so I am afraid that this could be due to model bias.  
My question is how to check and to get rid of the bias (if present) at 
this stage (after several refinements). I read the publication of 
Terwilliger about iterative-build OMIT maps but since I am a bloody 
novice in this field I didn´t really understand it. I originally 
thought iterative-build OMIT maps are performed to compare the output 
map with one´s map in order to detect uncertainties, but what to do 
next? Or should I start from the beginning but how to proceed than, 
what should I do (I am using Phenix via GUI) ... Is it possible and 
reasonable to run autobuild with iterative omit map option? Or is it 
only reasonable if experimental phases are available? I didn´t run 
iterative-build OMIT maps yet because I am not sure how to run it 
correctly (what method is the best?) and at my institute the run will 
take more than 1 day and I don´t want to block one computer until I am 
not sure if it is reasonable. I hope you can give me some advice and 
help me. Thank you in advance.


Regards,

Aleks




--
Fred. Vellieux (B.Sc., Ph.D., hdr)

IBS / ELMA
Campus EPN
71 avenue des Martyrs
CS 10090
F-38044 Grenoble Cedex 9
Tel: +33 457428605
Fax: +33 476501890

Re: [ccp4bb] problems with ccp4-6.4.0 occurrences in ccp4-6.5

[vellieux]

Hi there,

Following your kind suggestions, logging out and logging in again solved 
the problem. Thanks !


Fred.

On 23/01/15 18:07, vellieux wrote:

Hello,

I just installed ccp4-6.5

I get an error at run time (relating to $PATH I suppose, see below) 
that still contains occurrences of ccp4-6.4.0 even though the line 
that was supposed to get rid of these was made active in ccp4.setup-csh

# To remove previously added CCP4 directories from the PATH, uncomment:
if $?CCP4 setenv PATH `echo $PATH | sed s,${CCP4}[^:]*:,,g`

The previous distribution of ccp4 (6.4.0) was removed during the 6.5 
installation step. I get this for example when launching ccp4i:


Error in startup script: couldn't read file 
/home/prog/ccp4-6.4.0/share/dbccp4i/ClientAPI/dbClientAPI.tcl: no 
such file or directory

while executing
source [FileJoin [GetEnvPath DBCCP4I_TOP] ClientAPI dbClientAPI.tcl]
(file /home/prog/ccp4-6.5/share/ccp4i/src/projectdirs.tcl line 23)
invoked from within
source [SearchPath TOP src projectdirs.tcl]
(file /home/prog/ccp4-6.5/share/ccp4i/src/system.tcl line 3379)
invoked from within
source [file join $env(CCP4I_TOP) src system.tcl]
(file /home/prog/ccp4-6.5/share/ccp4i/bin/ccp4i.tcl line 79)
invoked from within
source [file join $env(CCP4I_TOP) bin ccp4i.tcl]
(file /home/prog/ccp4-6.5/bin/ccp4i line 12)

and echo $PATH contains the following entry that shouldn't be there:
/home/prog/ccp4-6.4.0/share/xia2/Applications

Would anyone know how to deal with this ?

Thank you in advance,

Fred.




--
Fred. Vellieux (B.Sc., Ph.D., hdr)

IBS / ELMA
Campus EPN
71 avenue des Martyrs
CS 10090
F-38044 Grenoble Cedex 9
Tel: +33 457428605
Fax: +33 476501890

[ccp4bb] problems with ccp4-6.4.0 occurrences in ccp4-6.5

[vellieux]

Hello,

I just installed ccp4-6.5

I get an error at run time (relating to $PATH I suppose, see below) that 
still contains occurrences of ccp4-6.4.0 even though the line that was 
supposed to get rid of these was made active in ccp4.setup-csh

# To remove previously added CCP4 directories from the PATH, uncomment:
if $?CCP4 setenv PATH `echo $PATH | sed s,${CCP4}[^:]*:,,g`

The previous distribution of ccp4 (6.4.0) was removed during the 6.5 
installation step. I get this for example when launching ccp4i:


Error in startup script: couldn't read file 
/home/prog/ccp4-6.4.0/share/dbccp4i/ClientAPI/dbClientAPI.tcl: no such 
file or directory

while executing
source [FileJoin [GetEnvPath DBCCP4I_TOP] ClientAPI dbClientAPI.tcl]
(file /home/prog/ccp4-6.5/share/ccp4i/src/projectdirs.tcl line 23)
invoked from within
source [SearchPath TOP src projectdirs.tcl]
(file /home/prog/ccp4-6.5/share/ccp4i/src/system.tcl line 3379)
invoked from within
source [file join $env(CCP4I_TOP) src system.tcl]
(file /home/prog/ccp4-6.5/share/ccp4i/bin/ccp4i.tcl line 79)
invoked from within
source [file join $env(CCP4I_TOP) bin ccp4i.tcl]
(file /home/prog/ccp4-6.5/bin/ccp4i line 12)

and echo $PATH contains the following entry that shouldn't be there:
/home/prog/ccp4-6.4.0/share/xia2/Applications

Would anyone know how to deal with this ?

Thank you in advance,

Fred.

--
Fred. Vellieux (B.Sc., Ph.D., hdr)

IBS / ELMA
Campus EPN
71 avenue des Martyrs
CS 10090
F-38044 Grenoble Cedex 9
Tel: +33 457428605
Fax: +33 476501890

Re: [ccp4bb] Some advices on model modification

[vellieux]

Hello,

Keeping the waters in a model used for molecular replacement search is 
not a very good idea.


I'd suggest first that you use a program like Chainsaw and possibly 
additional programs to fine-tune your search model to the problem that 
you are trying to solve.


Also, reading material such as the ccp4 study weekend proceedings 
devoted to molecular replacement and similar material (that are 
available on the internet) would be a good idea as well. The problems 
you are encountering have been discussed in the literature.


Fred.


On 06/01/15 13:06, allen price wrote:


Dear all:

I got a dataset at 2.8 angstron. I have tried several ways such as 
phaser, MRBUMP,BALBES,but still can't solve the


data,which means I have to edit my model. Maybe I'd better cut it off 
or delete the water or loop. I really have no


idea,as it is my first time to do such things, I alway used the whole 
model to mr. Could anyone give me some advice?


what kind  of software do you guys use? really need you help!

Best regards,

Allen



--
Fred. Vellieux (B.Sc., Ph.D., hdr)

IBS / ELMA
Campus EPN
71 avenue des Martyrs
CS 10090
F-38044 Grenoble Cedex 9
Tel: +33 457428605
Fax: +33 476501890

Re: [ccp4bb] coot error on a Scientific Linux box (32 bit)

[vellieux]

Hi Tim, hi all,

In fact there was a problem with the graphics driver. Re-installing the 
NVidia Linux driver solved the problem...


So thanks,

Fred.

On 10/12/13 16:18, Tim Gruene wrote:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Fred,

without further info my guess is that you try to run coot through
X11-forwarding of an ssh-connection which sometimes causes this error
message, or you need to recompile your graphics driver, e.g. because
your kernel was updated and the driver was not.

Best,
Tim

On 12/10/2013 03:53 PM, vellieux wrote:

Hi all,

I was wondering if anyone had seen this behaviour with Coot.

Whatever version I was using, or the latest that comes with ccp4
now gives me the following error message. Rather cryptic message
for me.

Thanks,

Fred.

The program 'coot-real' received an X Window System error. This
probably reflects a bug in the program. The error was 'BadWindow
(invalid Window parameter)'. (Details: serial 323 error_code 3
request_code 153 minor_code 4) (Note to programmers: normally, X
errors are reported asynchronously; that is, you will receive the
error a while after causing it. To debug your program, run it with
the --sync command line option to change this behavior. You can
then get a meaningful backtrace from your debugger if you break on
the gdk_x_error() function.) Gtk-Message: Failed to load module
pk-gtk-module Gtk-Message: Failed to load module
canberra-gtk-module coot-exe:
/home/prog/ccp4-6.4.0/bin/coot-real coot-version:
/home/prog/ccp4-6.4.0/bin/coot-real platform: /bin/uname core: #f
No core file found.  No debugging This is not helpful. Please turn
on core dumps before sending a crash report

- -- 
- --

Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

-BEGIN PGP SIGNATURE-
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6QeY2C8XGNlNuwHXWgVA0lY=
=Tqjo
-END PGP SIGNATURE-





--
Fred. Vellieux (B.Sc., Ph.D., hdr)

IBS2 / ELMA
Campus EPN
6 rue Jules Horowitz
F-38042 Grenoble
Tel: +33 457428605
(Fax: +33 438785494)

Re: [ccp4bb] Fwd: undefined edensity blob at glutamine sidechain

[vellieux]

Well the density strongly suggests a Tryptophan side chain.

Sometimes discrepancies (errors) appear in sequences. How certain are 
you of the accuracy of your sequence?


HTH,

Fred.

On 10/12/13 13:44, PriyankMaindola wrote:

​
dear members

i am trying to solve this crystal structure but
​I am puzzled with an​
 undefined  blob
​ that​
​appeared at a glutamine residue after refinement. I have attached 
pics of that below.

Is it a covalent modification of acid-amide side chain..
​... as there is no charged environment around and density seems 
continuous.


​please suggest
​


following reagents were encountered by protein
​ during purification, crystallization and soaking​
:
phenyl methyl sulfonyl fluoride
benzamidine
tris
dtt
​  (could it be cyclized dtt?)​

k[au(cn)2]
acidic pH
isopropanol
citrate
sulfate
phosfate
K+, Na+, Cl-

​ map contour:
2fo-fc: 1rmsd
fo-fc (green): 3 rmsd​


--
*Priyank*



--
Fred. Vellieux (B.Sc., Ph.D., hdr)

IBS2 / ELMA
Campus EPN
6 rue Jules Horowitz
F-38042 Grenoble
Tel: +33 457428605
(Fax: +33 438785494)

[ccp4bb] coot error on a Scientific Linux box (32 bit)

[vellieux]

Hi all,

I was wondering if anyone had seen this behaviour with Coot.

Whatever version I was using, or the latest that comes with ccp4 now 
gives me the following error message. Rather cryptic message for me.


Thanks,

Fred.

The program 'coot-real' received an X Window System error.
This probably reflects a bug in the program.
The error was 'BadWindow (invalid Window parameter)'.
  (Details: serial 323 error_code 3 request_code 153 minor_code 4)
  (Note to programmers: normally, X errors are reported asynchronously;
   that is, you will receive the error a while after causing it.
   To debug your program, run it with the --sync command line
   option to change this behavior. You can then get a meaningful
   backtrace from your debugger if you break on the gdk_x_error() 
function.)

Gtk-Message: Failed to load module pk-gtk-module
Gtk-Message: Failed to load module canberra-gtk-module
coot-exe: /home/prog/ccp4-6.4.0/bin/coot-real
coot-version:
/home/prog/ccp4-6.4.0/bin/coot-real
platform:
/bin/uname
core: #f
No core file found.  No debugging
   This is not helpful.
   Please turn on core dumps before sending a crash report

--
Fred. Vellieux (B.Sc., Ph.D., hdr)

IBS2 / ELMA
Campus EPN
6 rue Jules Horowitz
F-38042 Grenoble
Tel: +33 457428605
(Fax: +33 438785494)

[ccp4bb] Phaser question

[vellieux]

Hiyya all,

I have a question about the latest Phaser output, concerning TFZ = and 
TFZ == .


I do not know how to interpret outputs of the type

TFZ = 5.2 TFZ == 54.1;
TFZ = 5.8 TFZ == 63.0;
TFZ = 6.4 TFZ == 19.7 (these are real TFZ figures coming from Phaser log 
files).


I used to analyse the Phaser output using TFZ, when only a single number 
was given. Now with two figures to consider, I do not know what to think 
of it any more.


Any ideas out there ?

And best wishes for an enjoyable end-of-the-year season (be it in the 
cold or in the sun depending on which side of the planet you sit).


Fred.

--
Fred. Vellieux (B.Sc., Ph.D., hdr)

IBS2 / ELMA
Campus EPN
6 rue Jules Horowitz
F-38042 Grenoble
Tel: +33 457428605
(Fax: +33 438785494)

Re: [ccp4bb] Fwd: [ccp4bb] pdbset

[vellieux]

What about getting rid of the ANISOU records before processing the pdb 
file, with


grep -v ANISOU input.pdb  output.pdb

?

If a program complains about ANISOU records then you use the isotropic 
approximation...


That's what I would do as a quick and dirty fix.

Fred.

On 11/06/13 10:22, Swastik Phulera wrote:



-- Forwarded message --
From: *Swastik Phulera* swastik.phul...@gmail.com 
mailto:swastik.phul...@gmail.com

Date: Tue, Jun 11, 2013 at 1:51 PM
Subject: Re: [ccp4bb] pdbset
To: Tim Gruene t...@shelx.uni-ac.gwdg.de mailto:t...@shelx.uni-ac.gwdg.de


Dear Tim, Miguel
Thanks for your suggestions, the program does work now, but it seems 
that it cant handle AnsioU s . It gives an error:


PDBSET:  *** AnisoU present: cannot reset B ***

Is there any other program which would set minimum bfactors for me.
Also I am looking for a program that would set the maximum occupancy 
to a desired value (It seems that pdbset can only play with the 
minimum values)..




On Tue, Jun 11, 2013 at 12:11 PM, Tim Gruene t...@shelx.uni-ac.gwdg.de 
mailto:t...@shelx.uni-ac.gwdg.de wrote:


-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Swastik Phulera,

after the word 'output.pdb' you must first hit the Enter-key which
takes you into the program pdbset.
Then you type

B_reset Minimum 0
END

and the program runs.
If you wish to do it without interaction, e.g. in a script, you can
use the shell construct '':

pdbset XYZIN input.pdb XYZOUT output.pdb  eof
B_reset MINIMUM 0
eof

Best,
Tim

On 06/11/2013 08:15 AM, Swastik Phulera wrote:
 Dear All, I am trying to use pdbset from the terminal and am
 constantly getting an error:

 [XYZ@NCCS3 110613]$ pdbset XYZIN input.pdb XYZOUT output.pdb
 B_reset MINIMUM 0

 CCP4 library signal ccp4_general:Use: logical name
 file name
 (Error) raised in ccp4fyp  pdbset:  Use: logical name file
 name pdbset:  Use: logical name file name Times: User:
 0.0s System:0.0s Elapsed: 0:00

 Does any one have any idea what's wrong here?


 Swastik Phulera

- --
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

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fG1/zzDml0ynkX8uOBN7S+o=
=2I5+
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--
--
स्वस्तिक फुलेरा
वरिष्ठ अनुसंधान कर्ता
संरचनात्मक जीवविज्ञान प्रयोगशाला
डी. एन. ए. फिंगरप्रिंटिंग एवं निदान केंद्र
हैदराबाद, ५००, ००१

और


राष्ट्रीय कोशिका विज्ञान केंद्र
पुणे विश्वविद्यालय परिसर,
गणेशखिंड
पुना,  ४११,००७



--
--
स्वस्तिक फुलेरा
वरिष्ठ अनुसंधान कर्ता
संरचनात्मक जीवविज्ञान प्रयोगशाला
डी. एन. ए. फिंगरप्रिंटिंग एवं निदान केंद्र
हैदराबाद, ५००, ००१

और

राष्ट्रीय कोशिका विज्ञान केंद्र
पुणे विश्वविद्यालय परिसर,
गणेशखिंड
पुना,  ४११,००७



--
Fred. Vellieux (B.Sc., Ph.D., hdr)
ouvrier de la recherche
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

Re: [ccp4bb] delete subject

[vellieux]

Hello,

I stayed away from this thread until now - the major reason being that I 
was fitting snugly under my quilt.


However I feel compelled to react now: placing your data in a public 
repository (thereby proving that you did the work) also means that a 
colleague, friend or whatever can and will publish your work for 
you. Once your work has been published you cannot publish it again, you 
did the work and the colleague, friend or whatever has in fact 
appropriated your work.


In the world of dreams I was living in until a few moments ago (it was 
night time), this is perhaps the way we should act. In the real world we 
live in, even your colleague upstairs will publish your work if he / 
she has a chance to do it because by doing so he / she will improve his 
/ her career while ensuring that yours doesn't take off.


Fred.

On 28/03/13 01:34, mjvdwo...@netscape.net wrote:
Earlier today, I thought this and did not write it. It is a slightly 
different theme on your suggestion:


I hear there are now (but have not seen examplesof) journals (web 
sites) where you do exactly what Tom did: you put your data there, 
which proves that you did the work (first) and you do not worry 
about the fact that you are making it public before formal 
publication, because making data public is the reason why you got the 
data in the first place. And nobody can claim to have done the work, 
because everybody knows that someone else was first - the web site is 
proof. Theresults are not peer-reviewed of course (even though, in 
the case of CCP4, things are inherently peer-reviewed to some extent, 
that is what he asked us to do). And I hear that there are now 
journals that will accept references to such web sites.


Freely sharing unpublished data on a public forum might well be the 
future, even if in our corner of science this is not yet commonplace.


The pivotal point to Tom is that he can learn from the suggestions 
that have been made. I hope he will. I actually hope that he will 
follow up on the suggestions (privately maybe). Unlike some, I do not 
feel that it was bad to find a big file in my inbox, this is what 
move to is for. I think my reaction was ouch, he did not want to do 
what he just did and it cannot be undone. But maybethis is not true. 
There is definitely value in sharing preliminary data, especially for 
junior people. To have such a function as part of CCP4 might be a very 
good suggestion, but I agree with you that perhaps it should not land 
in its full glory in everyone's mailbox.


Mark



--
Fred. Vellieux (B.Sc., Ph.D., hdr)
ouvrier de la recherche
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

Re: [ccp4bb] process data from two crystals in-house data

[vellieux]

Sorry I am mentioning non-ccp4 software here:

XDS processing (the 2 data sets separately); AIMLESS / TRUNCATE and 
checking the truncate plots to see if there are frames (Batches) that 
should better be discarded; if need be, XDS processing again, XSCALE, 
XDSCONV (option CCP4_F if you only want F, SIGF and FreeRFlag).


HTH,

Fred.

On 28/03/13 11:08, S. Thiyagarajan wrote:

Dear all
I have two data sets, 75 frames each from crystals of the same protein 
- same cell parameters/space group (P4).
I could process them seperately each yielding  90% completeness but 
with poor multiplicity (  2 )


If I merge the data sets using CAD, I loose the data reduction 
statistics of the combined data set.


I do not have HKL2000.

Which (free) tool can handle two different diffraction data sets, 
process them together to give a single final data statistics.


Thanks and regards
Thiyaga



S. Thiyagarajan
Centre of Excellence in Bioinformatics
School of Biotechnology
Madurai Kamaraj University
Madurai - 625021
Ph: +91-9159224881 (cell)



--
Fred. Vellieux (B.Sc., Ph.D., hdr)
ouvrier de la recherche
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

Re: [ccp4bb] Twinning problem

[vellieux]

Hello,

I would suggest to use several tools (in addition to Phenix's) - CCP4's 
detwin, the plots generated by truncate before detwinning, the Yeates 
twinning server and there might be others - to get a good idea of what 
the twinning fraction is.


Here we've had success using CCP4's detwin to detwin diffraction data. 
The resulting mtz file is not equivalent to an mtz file containing data 
recorded from an untwinned crystal - this detwinning operation is not a 
perfectly accurate operation... In our case we used the estimate of the 
twinning fraction obtained from Phenix (which was lower).


HTH,

Fred.

On 26/03/13 15:45, Liang Zhang wrote:

Hi, All,

I got a set of P2(or P21) data for MR. However, the Phenix-Xtriage 
indicated that it could be a pseudo-merohedral twinning. Does anyone 
know how to deal with such kind of twinning problem? Thanks.


Best,

Liang



--
Fred. Vellieux (B.Sc., Ph.D., hdr)
ouvrier de la recherche
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

Re: [ccp4bb] molecular replacement problem.

[vellieux]

On Sat, Mar 23, 2013 at 2:26 PM, Appu kumar
appu.kum...@gmail.com mailto:appu.kum...@gmail.com wrote:

Dear members,

  I am doing a molecular
replacement of a transcription factor whose ligand
binding structure(24000 Da) is available in PDB but not
for the DNA binding(13000 Da). When i am searching for
the two copies from ligand binding domain as a template
model, i am getting very good solution but i am not
getting any density for the DNA binding domain to build
up in density. The space gorup is P 1 21 1 (4) and unit
cell parameters are Unit Cell:   57.43   69.36  105.99
90.00   90.00   90.00. Please guide me how to get the
complete model structure. Table below show the matthews
statistics

 For estimated molecular weight
37000.
Nmol/asym  Matthews Coeff %solvent   P(2.20) P(tot)
_
  1 5.71 78.46 0.00 0.01
  2 2.85 56.91 0.62 0.70
  3 1.90 35.37 0.37 0.29
  4 1.43 13.82 0.00 0.00
_


The phaser molecular replacement gives the following table.
istogram of relative frequencies of VM values
--
   Frequency of most common VM value normalized to 1
   VM values plotted in increments of 1/VM (0.02)

--- relative frequency ---
0.0  0.1  0.2  0.3  0.4 0.5  0.6  0.7  0.8  0.9  1.0
||||| ||||||
   10.00 -
8.33 -
7.14 -
6.25 -
5.56 -
5.00 -
4.55 -
4.17 -
3.85 --
3.57 ---
3.33 --
3.12 --
2.94  (COMPOSITION*1)
2.78 ---
2.63 
2.50 -
2.38 
2.27 --
2.17 ---
2.08 --
2.00 --
1.92 ---
1.85 ---
1.79 ---
1.72 -
1.67 -
1.61 -
1.56 -
1.52 -
1.47 * (COMPOSITION*2)
1.43 -
1.39 -
1.35 -
1.32 -
1.28 -
1.25 -

$TABLE : Cell Content Analysis:
$SCATTER
:N*Composition vs Probability:0|3x0|1:1,2:
$$
N*Composition Probability
$$ loggraph $$
1 0.306066
2 0.00141804
$$

   Most probable VM for resolution = 2.27817
   Most probable MW of protein in asu for resolution =
92664.2

Thank a lot in advance





-- 
Raji Edayathumangalam

Instructor in Neurology, Harvard Medical School
Research Associate, Brigham and Women's Hospital
Visiting Research Scholar, Brandeis University








--
Fred. Vellieux (B.Sc., Ph.D., hdr)
ouvrier de la recherche
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

[ccp4bb] Vote for crystallography

[vellieux]

Dear all,

Britain is organizing an on-line poll of the top 20th century British 
innovations backed by the Science Museum, the Royal Academy etc. Voting 
ends on March 25. The URL for this on-line poll is 
http://www.topbritishinnovations.org/ , then select 1 - Vote for the 
Past innovation.


If you select Order by Most Popular (go) you will see X-ray 
crystallography technique appear on the screen.


Undoubtedly, the Bragg's contribution to the development of X-ray 
crystallography (100 years ago) was essential to shape this Science as 
we practice it today. As macromolecular crystallographers, what is our 
view of the importance of X-ray crystallography as an important 
innovation ? Perhaps it is the time to vote for our fav ? Only two 
days to go before the poll closes.


Thank you,

Fred.

--
Fred. Vellieux (B.Sc., Ph.D., hdr)
ouvrier de la recherche
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

Re: [ccp4bb] Scaling with SCALA high and low resolution data sets

[vellieux]

Dear Kyriacos,

Just one thing to add to this suggestion from Herman:

I personally view and study the plots generated by the SCALA/TRUNCATE or 
AIMLESS/TRUNCATE route after XDS processing (in particular the plot of 
Rmerge values as a function of Batch number) to eliminate deviating 
batches from processing. Once I have done this, XDS/XSCALE/XDSCONV gives 
me very adequate results (you will notice that I am not particularly 
faithful to a single suite of crystallographic software but that I pick 
what I want from each program suite... :-) )


HTH,

Fred.

On 21/03/13 08:41, herman.schreu...@sanofi.com wrote:

Dear Kyriacos,

What kind of high-resolution data do you have?
In my experience, while Scala usually produces excellent results, it often 
fails miserably or even crashes due to too negative intensities in case of low 
redundancy data. E.g. if one does a second high-resolution scan with a high 
swing-out angle with little low-resolution data and friedel mates. I have not 
looked whether Scala could be stabilized by somehow restraining the scale 
factors or switching off some refinement parameters. Since we process with XDS, 
in these cases I use XSCALE for scaling, which does produce very good results.

My recommendation would be to process with XDS. By using the autoProc procedure 
from Global Phasing this is very easy, even for people who are normally not 
able to run a program without a GUI. You will then have to run XSCALE manually, 
which is again trivial once XDS had run correctly.

Good luck!
Herman

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Kyriacos 
Petratos
Sent: Wednesday, March 20, 2013 6:25 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Scaling with SCALA high and low resolution data sets

Dear All,

we have two data sets at about 0.9 and 1.9 Ang. resolution collected from a 
single crystal.
Integration with iMosflm seems to be fine like the scaling within each of the 
data sets.
When we try to merge and scale both of them with 'Scala' we get extremely high 
scale factors for the lower resolution images varying between approximately 30 
and 200!
Do we need to pay attention to some particular options for running the 
program(s)?
Thank you,

Kyriacos
e-mail: petra...@imbb.forth.gr





--
Fred. Vellieux (B.Sc., Ph.D., hdr)
ouvrier de la recherche
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

Re: [ccp4bb] Resolution limit of index in XDS

[vellieux]

Hello,

The way I do it is by manually editing the SPOT.XDS file (generated by 
the COLSPOT step). Spots are arranged by order of decreasing intensity 
in that file. So if you do down the file, select an appropriate 
intensity cutoff and then remove all spots below that value, it will 
have the effect of selecting a resolution cutoff (think of the plot of 
I vs. resolution) but you won't know what cutoff this corresponds to 
unless you do a careful analysis of the resulting SPOT.XDS file.


HTH,

Fred.

On 19/03/13 20:53, Niu Tou wrote:

Dear All,

Is there any command can set the resolution limit for index step in 
XDS? I only found a keyword INCLUDE_RESOLUTION_RANGE, but it looks to 
be a definition of resolution range after index step

as it says:

INCLUDE_RESOLUTION_RANGE=20.0 0.0 !Angstroem; used by 
DEFPIX,INTEGRATE,CORRECT


Thanks!
Niu



--
Fred. Vellieux (B.Sc., Ph.D., hdr)
ouvrier de la recherche
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

Re: [ccp4bb] qtrview command line options

[vellieux]

Wonderful, thanks very much to all the CCP4 team !

[ I have met users who object to command lines and terminals and 
no-clicking, for them if it's not in the GUI it's yuk but I guess 
that you can't have everything :-) ]


Fred.

On 16/03/13 22:16, andrey.lebe...@stfc.ac.uk wrote:

After ccp4 update No 19, Log–files can be opened with qtrview from the command 
line:

logview name.log

This also works for log-files generated with quick scale and quick symmetry 
from imosflm.

If ccp4 database entries do not exist, input and output files will not be shown 
in the viewer
(except for quick scale and quick symmetry files).

Regards

Andrey



On 11 Mar 2013, at 20:06, Lebedev, Andrey (STFC,RAL,SC) wrote:


Hi Ed

Thank you for the suggestion.
We are looking into this and hopefully will provide a solution soon.

Regards

Andrey


On 11 Mar 2013, at 14:26, Ed Pozharski wrote:


Is there some way of opening a log file (specifically, the
pointandscale.log that imosflm bridge to scala generates) with qtrview
from command line?

I tried, of course, this

qtrview pointandscale.log

but it opens empty, no log-file. I tried qtrview -h and qtrview --help
and man qtrview but there is seemingly no documentation.

I found the source code (yes, I can google) and can deduce that
available options at startup are

--log-file
--report-xml
--report-xrt
--inp-file

The only thing that works is

qrtview --log-file pointandscale.log

but that only shows me the log-file itself, i.e. no graphs etc.  I
understand that the program was designed primarily for ccp4 gui and I
know loggraph (and it works).

By the way, checkout instructions for the qtrview repository at

https://fg.oisin.rc-harwell.ac.uk/projects/qtrview/

don't work throwing this error

bzr: ERROR: Connection error: curl connection error (server certificate
verification failed. CAfile: /etc/ssl/certs/ca-certificates.crt CRLfile:
none)
on https://fg.oisin.rc-harwell.ac.uk/anonscm/bzr/qtrview/.bzr/smart

Cheers,

Ed.

--
Hurry up before we all come back to our senses!
  Julian, King of Lemurs



--
Fred. Vellieux (B.Sc., Ph.D., hdr)
ouvrier de la recherche
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

[ccp4bb] Is there an alternative to Java to view the (nice) plots in ccp4i ?

[vellieux]

Hello,

I think the Subject line tells it all.

Former Linux box, Java was installed within a couple of browsers and I 
could view the (nice and useful) plots within ccp4i.


New Linux box, Java {plugin / extension / whatever} is deactivated to 
start with (this Java plugin seems rather difficult to install, whatever 
I have tried has failed so far) with a message indicating that Java is a 
security risk.


Hence I was wondering if there is an alternative to view these nice 
plots on a Linux box nowadays. Something that would not be seen as a 
security threat and be deactivated.


Thanks in advance,

Fred.

--
Fred. Vellieux (B.Sc., Ph.D., hdr)
ouvrier de la recherche
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

Re: [ccp4bb] Is there an alternative to Java to view the (nice) plots in ccp4i ?

[vellieux]

Hello,

Indeed there is a new viewer and it usually works.

But I also have pre 6.3.0 results that I need to view and somehow the 
ccp4i qtRviewer does not manage to load the results...


So I was wondering if there was a Java-free alternative, I do have the 
log files.


Fred.

On 08/03/13 14:04, eugene.krissi...@stfc.ac.uk wrote:

Two months ago, CCP4 deployed a new viewer for annotated result reports (plots 
etc), which does not depend on browsers and java, exactly for reasons that you 
write about. Do you use 6.3.0 with updates, and if yes, does your question mean 
that the new viewer does not work for you? The viewer (QtRView) was released in 
6.3.0-010 already integrated with ccp4i.

Eugene


On 8 Mar 2013, at 12:56, vellieux wrote:


Hello,

I think the Subject line tells it all.

Former Linux box, Java was installed within a couple of browsers and I could 
view the (nice and useful) plots within ccp4i.

New Linux box, Java {plugin / extension / whatever} is deactivated to start 
with (this Java plugin seems rather difficult to install, whatever I have tried 
has failed so far) with a message indicating that Java is a security risk.

Hence I was wondering if there is an alternative to view these nice plots on a 
Linux box nowadays. Something that would not be seen as a security threat and 
be deactivated.

Thanks in advance,

Fred.

--
Fred. Vellieux (B.Sc., Ph.D., hdr)
ouvrier de la recherche
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494





--
Fred. Vellieux (B.Sc., Ph.D., hdr)
ouvrier de la recherche
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

Re: [ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)

[vellieux]

Hi Jon,

Thanks for the feedback. The version I am using (which is not that 
reported in the web page you mention, Version: 4:4.3.2-2) is:

GNU Fortran (GCC) 4.4.6 20120305 (Red Hat 4.4.6-4).

Hence it appears that the bug hasn't been entirely dealt with. Ian 
Tickle was getting segmentation faults (so he may be using gfortran V 
4.3.2-2), I was only getting a binary that crashes due to a missing left 
parenthesis in a FORMAT statement (the parenthesis was there as far as I 
could see...).


Thanks again,

Fred.

On 07/03/13 10:23, Jon Agirre wrote:

Dear Fred,

I would say that you're using a buggy gfortran version
(http://lists.debian.org/debian-gcc/2009/03/msg00070.html). You may
want to check your version with 'gfortran --version' in order to be
sure of it. The '-malign-double' switch provides only a slight
optimization and as you have already proven, it may be removed with
very little impact on performance.

Cheers,

Jon



--
Fred. Vellieux (B.Sc., Ph.D., hdr)
ouvrier de la recherche
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

[ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)

[vellieux]

Hello,

For those who still know the Fortran language and its Fortran 77 
variant, I used to have a g77 compiler here (Linux box), and now on the 
new box it's no longer g77 but gfortran.


When compiling Fortran77 code (these are the flags used for compilation: 
-o ../bin/$1 -std=legacy -Wno-globals -w -O3 -malign-double 
-funroll-loops -ffast-math -fno-second-underscore $1.f , followed by the 
libraries on that same compile line)


I get errors (at run time) of the type:

At line 138 of file program.f (unit = 6, file = 'stdout')
Fortran runtime error: Missing initial left parenthesis in format

When looking at this code (which compiled perfectly well using g77 - I 
removed the flag -fno-globals which doesn't seem to exist any more in 
gfortran) the Fortran code that I see appears to have all parentheses in 
the correct places.


Any idea of what must be done with existing Fortran 77 code in order to 
get it to compile and run with gfortran ? Otherwise any idea which 
compiler should be used to compile Fortran 77 code ?


Thanks in advance,

Fred.

--
Fred. Vellieux (B.Sc., Ph.D., hdr)
ouvrier de la recherche
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

Re: [ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)

[vellieux]

Dear all,

By popular request here is an example of some code where gfortran gives 
run time errors. This is at the very beginning of the program, the first 
write statement where a parenthesis is seen as missing at run time: (the 
first hyphens are not within the Fortran code but there to indicate the 
number of spaces before each character, 6 and nothing more or less).


Also enclosed as part.f herewith (as an attachment)

[I must admit that, somehow, when modifying a Fortran program using vim 
on this new box, the number of characters at the beginning of Fortran 
cards seems to reset to 8 when there are 6 blanks to start with, I have 
no idea why this is so.]


Help most welcome, and I'd hate to have to retype every single program...

Ta,

Fred.

--

  ORDER='A'
  NATM=0
  DO 5,I=1,3
 NGRID(2,I)= 9
 NGRID(3,I)=-9
 XMIN(I)= .
 XMAX(I)=-.
  5  CONTINUE
C
C   OPEN INPUT FILE
C
  WRITE (*,10)
   10 FORMAT(///,25X,'*',
 . /,25X,'*   *',

--
Fred. Vellieux (B.Sc., Ph.D., hdr)
ouvrier de la recherche
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

  ORDER='A'
  NATM=0
  DO 5,I=1,3
NGRID(2,I)= 9
NGRID(3,I)=-9
XMIN(I)= .
XMAX(I)=-.
  5   CONTINUE
C
C OPEN INPUT FILE
C
  WRITE (*,10)
   10 FORMAT(///,25X,'*',
 . /,25X,'*   *',

Re: [ccp4bb] SOLVED [ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)

[vellieux]

Hi all,

Problem solved thanks to Jorge Navaza's suggestion: remove all 
compilation flags but only have -Wall as a compilation flag.


There is no run time error any more and there is no error at compilation 
time. The program runs fine.


Thanks to Thomas Jens, Harry Powell, Ian Tickle, Ian Clifton and 
Bernhard Rupp for their suggestions.


Fred.

On 06/03/13 10:48, vellieux wrote:

Hello,

For those who still know the Fortran language and its Fortran 77 
variant, I used to have a g77 compiler here (Linux box), and now on 
the new box it's no longer g77 but gfortran.


When compiling Fortran77 code (these are the flags used for 
compilation: -o ../bin/$1 -std=legacy -Wno-globals -w -O3 
-malign-double -funroll-loops -ffast-math -fno-second-underscore $1.f 
, followed by the libraries on that same compile line)


I get errors (at run time) of the type:

At line 138 of file program.f (unit = 6, file = 'stdout')
Fortran runtime error: Missing initial left parenthesis in format

When looking at this code (which compiled perfectly well using g77 - I 
removed the flag -fno-globals which doesn't seem to exist any more 
in gfortran) the Fortran code that I see appears to have all 
parentheses in the correct places.


Any idea of what must be done with existing Fortran 77 code in order 
to get it to compile and run with gfortran ? Otherwise any idea which 
compiler should be used to compile Fortran 77 code ?


Thanks in advance,

Fred.




--
Fred. Vellieux (B.Sc., Ph.D., hdr)
ouvrier de la recherche
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

Re: [ccp4bb] SOLVED [ccp4bb] compiling Fortran 77 code on a Linux box (using gfortran ?)

[vellieux]

Hi again Ian and list,

The following flags seem to work fine:
gfortran -o ../bin/$1 -std=legacy -ffixed-format -Wno-globals -w -O3 
-funroll-loops -ffast-math -fno-second-underscore $1.f (followed by the 
library or libraries, compiled with the same flags).


Problem solved as far as I am concerned (until there is yet another 
compiler I guess, next Linux box down the road).


Fred.

On 06/03/13 13:55, Ian Tickle wrote:
Fred, OK I just noticed I didn't have the  -malign-double flag.  With 
that it compiles but on running I get:


Program received signal SIGSEGV: Segmentation fault - invalid memory 
reference.


Backtrace for this error:
#0  0x12244B
#1  0x122A9C
#2  0x473907
#3  0x1BD238
#4  0x1CB4BF
#5  0x80486E2 in MAIN__
Segmentation fault

Without that flag it compiles  runs without error.  So you may want 
to try it just without that flag.


Cheers

-- Ian


--
Fred. Vellieux (B.Sc., Ph.D., hdr)
ouvrier de la recherche
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

[ccp4bb] example script to run SCALA while excluding films (frames)

[vellieux]

Dear all,

We are trying to use the GUI (ccp4i) to run SCALA a second time while 
excluding data frames. In our hands this fails. It could be for a simple 
reason (such as the Batches to be excluded must be separated in the 
list of the GUI by semicolons, colons, commas, whatever... instead of 
blank spaces).


Would anyone have a running SCALA script that corresponds to the GUI 
defaults but that specifically excludes data frames ? The route that was 
followed for data processing was XDS, COMBAT and now SCALA. The first 
run indicated to us what we think is better excluded from the 
processing. If SCALA cannot remove data frames one can write a specific 
jiffy program to exclude specific rotation ranges from the XDS_ASCII.HKL 
file, but I'd prefer to use an existing program if it allows to do what 
I want to do.


Thanks in advance,

Fred.

--
Fred. Vellieux (B.Sc., Ph.D., hdr)
ouvrier de la recherche
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

Re: [ccp4bb] Rfree flag

[vellieux]

Hello,

I think this depends on the type of problem you are facing:

if the 2 crystals are not isomorphous then you cannot have the same 
R-free sets;
if the 2 crystals are isomorphous then either you do not worry about 
keeping the same R-free set (but then the starting structure must be 
perturbed enough to get rid of R-free bias during refinement), or you 
keep the same indices for the reflections in the 2 R-free sets (same 
reflections in your message) in which case there is no R-free bias at 
the beginning of refinement.


By R-free bias I mean this: in your new (liganded) crystal form, there 
are reflections that have seen the Fo's during refinement of the 
native structure but that are in the R-free set in the ligand structure. 
This leads to bias.


HTH,

Fred.

On 28/02/13 06:54, Kavyashree Manjunath wrote:

Dear users,

Is it mandatory to use the same reflections for
Rfree calculations of a ligand bound data as that
of its native?

Thank you
With Regards
Kavya




--
Fred. Vellieux (B.Sc., Ph.D., hdr)
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

Re: [ccp4bb] the matrix format

[vellieux]

Hi,

Emacs, vi, any (text file) editor ? I wouldn't advise a word processing 
program (Word and the likes).


Unless you want to do this on many pdb files in which case writing a 
small program or shell script would be required.


Fred.

On 25/02/13 14:24, Qixu Cai wrote:

Dear Jon,

Thanks for your reply.

The matrix format in the REMARK 290 section of the pdb file 
(download from rcsb.org http://rcsb.org) is :

r11r12r13tx
r21r22r23ty
r31r32r33tz

And I want to extract the matrix information from the pdb file REMARK 
290 section and use the matrix in the pdbset.


so I have to convert the matrix from
r11r12r13tx
r21r22r23ty
r31r32r33tz

to r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz.

How can I do it?

Thanks.

Qixu Cai


Qixu Cai
Email: caiq...@gmail.com mailto:caiq...@gmail.com
School of Life Sciences,
Xiamen University, Fujian, China


2013/2/25 Jon Agirre jon.agi...@gmail.com mailto:jon.agi...@gmail.com

Dear Qixu,

here's an excerpt from the pdbset manual:

TRANSFORM [INVERT] [FRACTIONAL] r11 r12 r13 r21 r22 r23 r31 r32
r33 tx ty tz

I'm not sure what you mean by covert from the pdb file format to
the pdbset format. Please elaborate on this.

Jon

2013/2/25 Qixu Cai caiq...@gmail.com mailto:caiq...@gmail.com:
 Dear all,

 The matrix formats in different program always confuse me.

 The matrix format of the REMARK 290 SMTRY section of pdb file is:

 r11r12r13tx
 r21r22r23ty
 r31r32r33tz

 What's the matrix format accepted by the transform file
keywords of the
 pdbset program?
 is it r11 r12 r13 r21 r22 r23 r31 r32 r33 tx ty tz?
 And how to covert from the pdb file format to the pdbset format?

 What's the matrix format of apply NCS operators in phenix GUI?

 Thanks a lot!

 Qixu Cai



--
Jon Agirre, PhD
Unit of Biophysics (CSIC-UPV/EHU)
http://sourceforge.net/projects/projectrecon/
+34656756888





--
Fred. Vellieux (B.Sc., Ph.D., hdr)
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

Re: [ccp4bb] need some suggestions for crystallization

[vellieux]

I second that. Gently swirling the bottle (very important) before 
pipetting a few microliters (say 100 microliters or whatever).


Dialyse overnight vs 10 mM HEPES 2 mM MgCl2 ph7, then get the protein 
concentration to 10 mg/ml. Set up the drops (sitting drops) versus the 
same buffer with 30% (v/v) MPD. Direct cryo conditions. Depending on the 
material (plastic) used for the sitting drop trays you may find it 
difficult to get crystals out - you'll break up a few - but then no 
messing up to try to find cryo-conditions.


Fred.

On 04/02/13 17:27, Ganesh Natrajan wrote:

Hi David,

You could try the Glucose Isomerase supplied by Hampton. It 
crystallizes under a number of conditions, details of which you can 
find in their manual.



http://hamptonresearch.com/product_detail.aspx?cid=28sid=56pid=56

Ganesh


--
Fred. Vellieux (B.Sc., Ph.D., hdr)
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

Re: [ccp4bb] refmac5 vs phenix refine mixed up

[vellieux]

Well I am not answering your question. What is the (Wilson) B-factor of 
the diffraction data ? I would personally compare the average isotropic 
temperature factor of the model to that of the diffraction data.


And further the aim of refinement is not to reduce the B-factor. The aim 
of refinement is to provide a model that agrees with all data available. 
There are structures around with very high temperature factors (both for 
the diffraction data set and for the model). There is nothing wrong with 
that.


Fred.

On 24/01/13 11:12, rajesh harijan wrote:

Dear All,

   I am working on a perfectly twinned data in space group P31. 
when I refine this data with phenix refine the R/Rfree is 26.6/29.4 
and average B-factor is 38.


I did one test now.
I used phenix refined pdb and refine with refmac5 and got R/Rfree of 
26.2/29.7 and average B-factor is 64.


Now I used refmac5 refined pdb and refined with phenix again. Now 
R/Rfree is 22.1/24.8 and average B-factor is 56.



My question is, why B-factor gone up now and R/Rfree reduced. In which 
refined model should I believe in. If last refined model is true then 
how should I reduce the B-factor?


Thank you
Rajesh

--
---x
With regards
Rajesh K. Harijan
Phd Researcher
Department of Biochemistry,
University of Oulu,
Oulu, Finland- 90014
Off Phone: +358 85531174
Mob: +358 400408258




--
Fred. Vellieux (B.Sc., Ph.D., hdr)
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

Re: [ccp4bb] perfect twin

[vellieux]

Hello,

Yeates twinning server; Phenix (and other possibilities). For 
detwinning, once you have a valid estimate of the twinning fraction 
(plus the twin law) you could use ccp4's detwin (this is the program I 
personally use). I think the name of the latter program tells what it 
does :-) .


Fred.

On 22/01/13 07:25, LISA wrote:

Hi all,
Does anyone know how to check a data is twin and how to detwin?
My data is 3.3 A with space group P6222 or P6422? But I can not solve 
this structue by molecular replacement with the model has 42% sequence 
identity. I am wondering my data maybe twin.

Thanks
Lisa



--
Fred. Vellieux (B.Sc., Ph.D., hdr)
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

[ccp4bb] another piece of sad news

[vellieux]

Dear all,

Another piece of sad news (passed on from George DeTitta and confirmed 
by wikipedia, http://en.wikipedia.org/wiki/Guy_Dodson )


Guy Dodson also passed away on Christmas eve this year (2012).

I assume that some people who knew him more than myself, either from 
York or from the MRC Mill Hill, London will write a eulogy. I just want 
to say that I will miss him.


Fred.

--
Fred. Vellieux (B.Sc., Ph.D., hdr)
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

Re: [ccp4bb] wrong space group or wrong refinement strategy

[vellieux]

Hello,

What about the enantiomorphic space groups (the 4(3) screw axes instead 
of the 4(1) screw axes) ? These cannot be distinguised on the basis of 
structure factor amplitudes (unless you have an anomalous scatterer) nor 
on the basis of the specific extinctions (both screw axes extinguish the 
same reflections).


However molecular replacement distinguishes between the two. I did not 
see any mention of these enantiomorphic space groups in your post hence 
my asking... Phaser allows to test everything. The CCP4 program 
Pointless is also good at letting you know what is the most likely space 
group.


Hence you may have a combination of wrong space group and twinning. I 
can't really say with the information provided. I have had one case 
(also molecular replacement) where I had to test every single space 
group (a hexagonal lattice) in order to hit the correct one (that was 
before the days of Phaser).


Also, with molecular replacement the first thing I do is to compare the 
initial R-f / R-free to the R-factors that are expected for a random 
distribution of atoms in the asymmetric unit (from memory, ca. 0.6). 
Once you have refined, the numbers go down so you can't really say 
anything any more.


Furthermore, sometimes it is necessary to carry out the molecular 
replacement searches with a smaller set of atoms (for example when you 
are expecting to find a tetramer you carry out the searches with a 
dimer, or with a monomer - and sometimes you have the surprise to 
discover that the solvent content of your crystal is quite high and that 
the tetramer is formed by 2 dimers that are related by a 
crystallographic 2-fold axis - or the arrangement of molecules in your 
multimer is different from that in the search model, to sum it up: in 
crystallography, everything goes!).


HTH,

Fred.

On 01/12/12 01:59, ruisher hu wrote:

Hi, Dear CCP4 group,

I recently collect one dataset and indexed as P4 space group. When I 
try to do MR with a tetramer as input, I found the solution file 
suggested P41.


SOLU SET RFZ=5.2 TFZ=10.3 PAK=0 LLG=239 LLG=366 TFZ==20.9
SOLU SPAC P 41
SOLU 6DIM ENSE ensemble1 EULER 50.265 0.217 219.800 FRAC 0.50029 
0.49916 -0.00408 BFAC -0.04000

SOLU ENSE ensemble1 VRMS 0.639
SOLU SET RFZ=5.2 TFZ=10.0 PAK=0 LLG=239 TFZ==11.2 LLG=365
SOLU SPAC P 41
SOLU 6DIM ENSE ensemble1 EULER 128.607 179.813 38.677 FRAC 0.49991 
0.49905 -0.00208 BFAC -0.06264

SOLU ENSE ensemble1 VRMS 0.642

However when I did refinement in phenix, I have some trouble getting 
the R/Rfree down. It complains about some twinning or maybe higher 
symmetry like P422. When I apply twin law, h,-k,-l, I'm able to refine 
to 0.34/0.37 but still, hard to continue the refinement. The strategy 
I used for refinement is xyz coordinates, real-space, individual 
B-factors, occupancies, with NCS restraints and twin law.


So I tried to rescaled into P41212 space group, and run MR again, with 
two chains as an input and found one solution

   SOLU SET  RFZ=4.5 TFZ=9.5 PAK=0 LLG=115 TFZ==10.0 LLG=118 TFZ==10.4
   SOLU SPAC P 41 21 2
   SOLU 6DIM ENSE ET EULER 234.6 0.7 305.0 tel:234.6%200.7%20305.0 
FRAC 1.00 0.49 -0.17 BFAC -0.14

   Ensemble ET RMS variance(s): 0.96

However, when i tried to refine, the Rfree is high as 0.51 at the 
first round. Does this mean this is not the right solution or maybe 
some problems with the space group?Any suggestions for next step? 
Thanks very much.






--
Fred. Vellieux (B.Sc., Ph.D., hdr)
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

Re: [ccp4bb] vitrification vs freezing

[vellieux]

What about introducing the use of Franglais in the crystallographic 
literature ? Ce serait cool !


Fred.

On 16/11/12 11:24, Sebastiano Pasqualato wrote:


Oui bon d'accord, mais il faudra tout de même décider si utiliser 
vitrifiés ou bien congelés...


sorry couldn't resist ;-)

s

On Nov 16, 2012, at 10:54 AM, Tim Gruene wrote:


-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hi James,

I once heard that in (European) law French is the language of choice
because it were the most precise one (which I find easy to believe).
Maybe we should try and convince journals to only accept articles
written in French - not sure, this will improve their quality, though,
comparing my level of French with my level of English ;-)

Lovely discussion,
Tim

--
Fred. Vellieux (B.Sc., Ph.D., hdr)
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

Re: [ccp4bb] Problems with PDB validation

[vellieux]

Hello,

There are examples of regions (such as loops) where the electron density 
is rather poor and does not allow to build a proper model of the 
polypeptide chain (the refinement program cannot fit a satisfactory 
model in that area). Hence you just know that the chain goes through 
there and you cannot fix it. Usually there are relatively high 
temperature factors associated with such regions. This could be what you 
have in your structure. In this case I would deposit and add a remark in 
the header region of the PDB file to explain. If this has been observed 
in other structures then what you observe is consistent with the 
previous observations.


HTH,

Fred.

On 12/11/12 10:54, Krithika Sundaram wrote:


Hi all,


I am currently validating my protein and experiencing a few issues. I 
am unable to fix the torsion angles for eight residues no matter what 
I try. There are 3 models deposited on the PDB website belonging to 
the same protein. Five of the residues’ torsion angles (of the eight) 
 are consistently reported as being problematic by PDB validation 
server for all three models.


I have tried deleting these residues and adding them again after 
refinement, but the problem doesn't disappear. I have spent a few 
weeks looking at this and trying every possible solution to this problem.


Just wondering what else I can try to fix the issues reported!


Thanks in advance.

Regards,

KS




--
Fred. Vellieux (B.Sc., Ph.D., hdr)
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

Re: [ccp4bb] Problems in crystallization

[vellieux]

Hi there,

You could try to go for liquid-liquid interface crystallisation (in  
capillaries). The minimum volume would be no less than 1.5 microl 
protein + 1.5 microl precipitant, i.e. not the volumes used by nanodrop 
robots. Crystallisation under oil (or similar liquids) should also have 
the same effect (no spreading out).


HTH,

Fred.

On 07/11/12 13:07, Eva Bligt-Lindén wrote:

Dear ccp4 users,

I have a problem in the crystallization of my target protein. Whenever 
I set up a vapour diffusion experiment, either hanging or sitting 
drops, the drops spread out. The surface tension is completely lost in 
80-90% of the droplets. Have any one experienced something similar? 
What could be the reason for this strange behaviour? I have tried 
three different commercial screens with 96 condition each and there is 
no difference between the screens. There is no difference between 
manual or robotic setups either. The protein buffer is 40 mM Tris, 2 
mM MgCl2 buffer, pH 7.4. The buffer controls are all ok.


Kind regards,
Eva



Eva Bligt-Lindén (M.Sc.)
PhD student
Structural Bioinformatics Laboratory

Department of Biosciences,
Åbo Akademi University
BioCity, Tykistökatu 6A
FI-20520 Turku
Finland





--
Fred. Vellieux (B.Sc., Ph.D., hdr)
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

Re: [ccp4bb] Faculty positions at Molecular Biophysics Unit, IISc, Bangalore

[vellieux]

Hello,

Indeed, rigged positions do exist. In places where it is compulsory to 
advertise positions but where the person who will get the job has been 
selected in advance and is known already at the time the job 
advertisement appears. This does happen in several countries worldwide.


I do not agree much with ccp4bb wars but India has been known to hire 
Indian citizens only for permanent jobs (with government funding). 
Foreigners (as I was told by Indian scientists - whom I believe) are 
only allowed to be employed on soft money, i.e. fixed term fellowships 
that may be renewed. This is quite different however than claiming (as 
Sham does) that this is a rigged job, I personally do not know (I won't 
be sitting on the panel interviewing the candidates).


But for those (worldwide) who are involved in arranging such rigged 
jobs, perhaps these people should make it clear in advance to the 
candidates: Look, we are only advertising this position because it is 
compulsory. Now if you want to practice giving a presentation of your 
results for a future job interview and come visit us, and perhaps stay 
on for a couple of days to visit the area, we'd be delighted to have you 
around. But do not expect to get a job with us. Just don't repeat this 
to anyone, in fact we are warning you by phone because there will be no 
traces of this conversation ever having taken place. This would be more 
fair to the people who apply - but this is only day dreaming I think.


F.

On 30/10/12 00:33, Phoebe A. Rice wrote:


I have no idea about Bangalore, but I know from personal experience 
that already-filled job ads exist and waste everybody's time.  One of 
the junior faculty jobs I intereviewed for in the 90s at a prestigious 
US medical school turned out to be just such a thing - before I went 
people in the know told me which inside post-doc would get the 
position, faculty turnout to my presentation was low, and even during 
the visit somebody told me they thought it would be an inside deal.  
And in the end, it was.


I had much better things to do with my time.

++

Phoebe A. Rice
Dept. of Biochemistry  Molecular Biology
The University of Chicago

773 834 1723; pr...@uchicago.edu mailto:pr...@uchicago.edu
http://bmb.bsd.uchicago.edu/Faculty_and_Research/

http://www.rsc.org/shop/books/2008/9780854042722.asp



--
Fred. Vellieux (B.Sc., Ph.D., hdr)
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

[ccp4bb] Fwd: email received from Nick Keep...

[vellieux]

With permission from Nick Keep to forward to the bb which I am doing 
right now :-)


If I may add: an organization advertising for a rigged job but not 
reimbursing the candidate's expenses is, in my opinion, wrong doing. I 
have never seen this happen in the UK but this has happened elsewhere...


With this I think we can close the discussion (I do not favour ccp4bb 
wars). And I am in favour of job ads being posted to the bb.


Fred.

 Original Message 
Subject:Re:
Date:   Tue, 30 Oct 2012 10:55:18 +
From:   Nicholas Keep n.k...@mail.cryst.bbk.ac.uk
To: vellieux frederic.velli...@ibs.fr
CC: n.k...@mail.cryst.bbk.ac.uk



Dear Fred,
Sorry did not mean to send a personal post, it was meant to go to the
list which it has now.  I think some discussion of career issues is not
a bad thing for ccp4bb particularly as we allow job adverts.  The
discussion was starting to be a bit negative about recruitment.

What you recount is a truly dreadful story.  Like the original posting I
think one of the major problems was being made to pick up your own
expenses.  Not something that I have come across in the UK. Perhaps a
point that should be made on the list, except I think there is a desire
to shut this line down.

Institutions should at least pay the costs of attendance; they have the
balance of power. There are as I said people who come for interview with
little intention of taking the job, but the faculty at least get a
seminar for the travel costs.

Feel free to post this or a summary if you think it is helpful.
Best wishes
Nick



--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

email n.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the
crystallography entrance
and ring me or the department office from the internal phone by the door

Re: [ccp4bb] Twinned Data

[vellieux]

Hello,

I am afraid that you aren't saying (writing) enough to describe the 
problem(s) you are facing...


Twin fraction ? How many crystals were used to collect the diffraction 
data (remember that there are polar space groups, where c going up is 
different from c going down) etc etc. Without enough information, no 
advice can be provided...


Fred.

On 19/10/12 12:13, Iris Gawarzewski wrote:

Hello everybody,

I collected data to 2.8A with the space group P63 but they seems to be 
twinned. I tried phenix refinement with the twin law I got from 
Xtriage but the model looks quiet weird...


Hope that somebody can help me with this problem.

Kind regards,

Iris
___
Iris Gawarzewski
PhD student
Arbeitskreis Schmitt
Institut für Biochemie
Geb. 26.32.03.21
Heinrich-Heine-Universität Düsseldorf
Universitätsstr. 1
40225 Düsseldorf
-Germany-
Tel: 0049-211-81-13577






--
Fred. Vellieux (B.Sc., Ph.D., hdr)
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

Re: [ccp4bb] Twinned Data - more information

[vellieux]

Well, the first thing I note is that P6(3) is a polar space group.

Hence what I would do myself is the following:

take your crystal 'number 1' (as a reference);

take the results of XDS for crystal number 2 (XDS_ASCII.HKL) and reindex it;

try to see which of the original XDS_ASCII or the reindexed XDS_ASCII 
file gives you the lowest R-sym values, the one with the lowest Rsym's 
has consistent indexing with your 'reference' crystal 1 - normally 
somewhere in the XDS output (forgot where) there is a reindexing card 
mentioned


repeat with crystal 3;

Then you know what is consistent w.r.t. crystal 1. So you take the 3 
files that are appropriate and repeat the XSCALE scaling.


It may very well be that you do not have any twinning but that you have 
not consistently indexed the 3 data sets. Unless you have already taken 
care of consistent indexing but didn't say (write) it.


HTH,

Fred.

On 19/10/12 13:17, Iris Gawarzewski wrote:

Hello everybody,

I collected datasets with a resolution to 2.8A  from 3 crystal grown 
in the same condition. The space group seems to be P63. Statistic of 
XSCALE.LP


 SUBSET OF INTENSITY DATA WITH SIGNAL/NOISE = -3.0 AS FUNCTION OF 
RESOLUTION
 RESOLUTION NUMBER OF REFLECTIONSCOMPLETENESS R-FACTOR 
 R-FACTOR COMPARED I/SIGMA   R-meas  CC(1/2)  Anomal  SigAno   Nano
   LIMIT OBSERVED  UNIQUE  POSSIBLE OF DATA   observed 
 expected  Corr


10.001023 173   204   84.8%   7.4% 
14.1% 1023   10.86 8.1%99.5*   -280.422 156
 6.004199 704   709   99.3%  11.1% 
15.1% 4199   10.4312.1%99.1*   -250.515 640
 4.00   124012131  2137   99.7%  15.5% 
15.5%124009.9117.0%97.7*   -180.6841893
 3.5084291486  1486  100.0%  18.3% 
18.0% 84268.1020.1%96.4*-80.7881259
 3.304630 842   842  100.0%  23.0% 
22.3% 46276.5925.5%94.5*   -130.768 686
 3.1060571121  1121  100.0%  28.3% 
26.3% 60535.5031.4%93.6*-30.829 882
 3.003527 664   664  100.0%  33.7% 
34.2% 35244.5637.5%86.8* 60.827 502
 2.903961 756   756  100.0%  48.4% 
49.5% 39563.2453.8%82.7* 20.784 549
 2.802140 699   862   81.1%  31.6% 
37.4% 20572.5137.7%87.0* 20.789 178
total   463678576  8781   97.7%  17.2% 
18.1%462657.1519.0%98.2*-90.7306745



 I tried Xtriage and got the following:

merohedral twin operator
twin law: h,-h-k,-l
Britton plot: 0.423
H-test: 0.439
Maximum Likelihood Method: 0.457

I have a model with the sequence of my protein and did Phaser_MR 
(Z-score around 4... I know that this is quiet bad...). This solution 
I refined with phenix.refinement using the twin law from Xtriage. 
Rfree is around 0.44 best but the model looks weird...



Greetings,

Iris

___
Iris Gawarzewski
PhD student
Arbeitskreis Schmitt
Institut für Biochemie
Geb. 26.32.03.21
Heinrich-Heine-Universität Düsseldorf
Universitätsstr. 1
40225 Düsseldorf
-Germany-
Tel: 0049-211-81-13577






--
Fred. Vellieux (B.Sc., Ph.D., hdr)
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

[ccp4bb] Only su (root) can get ccp4i to run

[vellieux]

Hi folks,

on my SL6.3 box, only su (root) can lauch and run ccp4i. For other users 
I get this cryptic message,


/home/prog/ccp4-6.3.0/bin/ccp4i: line 4: /wish: No such file or directory
/home/prog/ccp4-6.3.0/bin/ccp4i: line 4: exec: /wish: cannot execute: No 
such file or directory


Anyone out there knows what to do in order to solve this problem ?

Ta.

F.V.

--
Fred. Vellieux (B.Sc., Ph.D., hdr)
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

Re: [ccp4bb] Only su (root) can get ccp4i to run

[vellieux]

Ta very much Tim,

what I did was to edit the ccp4.setup-csh file in order to change the line:
setenv CCP4I_TCLTK /usr/local/bin
into:
setenv CCP4I_TCLTK /home/prog/ccp4-6.3.0/bin

Then the ccp4i GUI window popped up fine. Problem solved. I didn't 
really want to have to su every time I wanted to use ccp4 !


F.

On 09/10/12 10:15, Tim Gruene wrote:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear F.V.,

you should check read permissions of the setup-files (e.g.
$CCP4/include/ccp4-setup.sh). For your user, the variable CCP4 seems
to be set, but CCP4I_TCLTK is not (which should be done in the same
setup-file).

Cheers,
Tim

On 10/09/2012 09:58 AM, vellieux wrote:

Hi folks,

on my SL6.3 box, only su (root) can lauch and run ccp4i. For other
users I get this cryptic message,

/home/prog/ccp4-6.3.0/bin/ccp4i: line 4: /wish: No such file or
directory /home/prog/ccp4-6.3.0/bin/ccp4i: line 4: exec: /wish:
cannot execute: No such file or directory

Anyone out there knows what to do in order to solve this problem ?

Ta.

F.V.

- -- 
- --

Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFQc90XUxlJ7aRr7hoRAp55AJwPMbK1+aPnh4VbUWKkNuqQ2JBoMgCg/vmr
wufUMHQd6kfaOJXzWSWQPzs=
=G4O5
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--
Fred. Vellieux (B.Sc., Ph.D., hdr)
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

Re: [ccp4bb] Professor Dame Louise Johnson

[vellieux]

A very nice picture of Prof. Louise Johnson can be found on

http://www.flickr.com/photos/wellcomeimages/5814718414/

The picture was taken at Diamond's IO2 beam line.

Condolences to her family and friends.

Fred.

Re: [ccp4bb] ideal rms bond length

[vellieux]

Hi there,

acceptable deviations from ideal geometry depends on the resolution of 
the data set. There are several papers dealing with this, including the 
paper describing the tool used in Phenix.


I couldn't find the resolution of the data set used during refinement in 
your mail so it is difficult to compare the data given to that expected 
for a well refined structure at that resolution.


Fred.

PS the figures shown do not seem to be totally unreasonable. The r.m.s. 
deviations concerning the angles could be improved though IMHO - again 
not knowing the resolution of the data set


On 02/10/12 23:49, Faisal Tarique wrote:


Dear all

i request you to please answer my basic query about the ideal 
acceptable rmsbond length obtained during refmac refinement..is the 
data acceptable in mine case which is as follows..



NcycRfactRfree FOM  -LL -LLfree  rmsBOND  
zBOND rmsANGL  zANGL rmsCHIRAL $$

$$
   0   0.2090   0.2079   0.875226315.   11985.5   0.0278  
1.389   2.718  1.261   0.198
   1   0.2064   0.2284   0.850226313.   12201.1   0.0285  
1.427   2.733  1.271   0.204
   2   0.2076   0.2373   0.837226944.   12289.9   0.0248  
1.242   2.598  1.200   0.187
   3   0.2092   0.2429   0.828227495.   12341.7   0.0222  
1.107   2.458  1.128   0.173
   4   0.2100   0.2468   0.822227753.   12372.4   0.0211  
1.053   2.377  1.086   0.166
   5   0.2104   0.2500   0.818227942.   12395.7   0.0204  
1.021   2.326  1.061   0.161
   6   0.2108   0.2522   0.814228075.   12411.5   0.0200  
0.999   2.289  1.042   0.158
   7   0.2111   0.2537   0.812228162.   12421.8   0.0197  
0.984   2.265  1.030   0.156
   8   0.2113   0.2550   0.810228228.   12430.5   0.0194  
0.971   2.243  1.020   0.154
   9   0.2114   0.2559   0.809228300.   12436.1   0.0192  
0.962   2.228  1.012   0.153
  10   0.2116   0.2568   0.808228348.   12441.7   0.0191  
0.957   2.218  1.008   0.152
  11   0.2118   0.2574   0.807228394.   12446.2   0.0190  
0.951   2.210  1.004   0.151
  12   0.2119   0.2581   0.806228421.   12449.6   0.0189  
0.948   2.203  1.001   0.151
  13   0.2119   0.2585   0.805228440.   12452.7   0.0189  
0.944   2.198  0.998   0.150
  14   0.2120   0.2590   0.805228461.   12455.0   0.0188  
0.941   2.194  0.996   0.150
  15   0.2121   0.2593   0.804228480.   12456.9   0.0188  
0.939   2.190  0.995   0.150



--
Regards

Faisal
School of Life Sciences
JNU




--
Fred. Vellieux (B.Sc., Ph.D., hdr)
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

Re: [ccp4bb] Off Topic: help locating CNS data

[vellieux]

As was mentioned, the diffraction data files can be named according to 
the user's wish. But I'd try to locate files with extensions .hkl, .xpl, 
.cv (and .cns? although I have never seen that extension used myself)


Fred.

On 21/09/12 12:10, Rex Palmer wrote:
I have been presented with the problem of locating protein data for a 
structure which was refined here ten years ago with the CNS program.
Unfortunately I have never used this program so do not know what type 
of files I am looking for (or how many files).

Any suggestions please
Rex Palmer
http://www.bbk.ac.uk/biology/our-staff/emeritus-staff
http://rexpalmer2010.homestead.com



--
Fred. Vellieux (B.Sc., Ph.D., hdr)
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494

Re: [ccp4bb] Which Coot for Scientific Linux 6.3

[vellieux]

Hi all,

Well I did it the hard way, i.e. try all versions until I came across 
one version of Coot that runs.


In my hands I did not get a single version to run on SL6.3, 64-bit 
version (Dirk Kostrewa had another experience with SL6.3 64 though).


So I installed SL6.3, 32-bit version, and the version of Coot for Fedora 
core 12 runs and provides me with a proper graphics windows.


I thought I'd keep the bb informed.

F.V.

--
Fred. Vellieux (B.Sc., Ph.D., hdr)
IBS / ELMA
41 rue Jules Horowitz
F-38027 Grenoble Cedex 01
Tel: +33 438789605
Fax: +33 438785494
email: frederic.velli...@ibs.fr

Re: [ccp4bb] diagram of dsDNA

[Fred. Vellieux]

Wow, an email from the future !

[Sorry...]

 Subject:  [ccp4bb] diagram of dsDNA
 From: cuisheng2007 cuisheng2...@yahoo.com.cn
 Date: Mon, October 1, 2012 9:33 am
 To:   CCP4BB@JISCMAIL.AC.UK
 Dear all

 When I was playing around with Nucplot to generate diagram for
 dsDNA/Protein
 complex, the base pairs are displayed as letters. There must be a way of
 showing the bases as squares, a better illustration, but I cannot find a
 way
 of changing it in the nucplot.par. Does anyone know how to deal with it?



 Many thanks!

 Sheng



 Prof.Dr. CUI Sheng

 Institute of Pathogen Biology, CAMSPUMC.

 Building No.7, Bei Gong Da Ruan Jian Yuan,

 Beijing BDA, 100176,

 Beijing, China.

 Email: cuisheng2...@yahoo.com.cn

 Tel. +86 10 67828669

 Fax. +86 10 67855012








-- 
F.M.D. Vellieux (B.Sc., Ph.D., hdr)
IBS / ELMA
41 rue Jules Horowitz
38027 Grenoble Cedex 01
France
Tel: +33 438789605
Fax: +33 438785494

Re: [ccp4bb] NADP binding protein without Rossmann fold.

[Fred. Vellieux]

Hello,

You could look at this family of enzymes,
http://scop.mrc-lmb.cam.ac.uk/scop/data/scop.b.d.jc.b.b.html

[the sulfolactate dehydrogenase-like family]

No Rossman fold there.

HTH,

Fred.

 Dear all,

 I have biochemically characterized one enzyme that can dephosphorylate
 NADP+ / NADPH. Recently, I have also solved the crystal structure of the
 protein with bound NADP+. The important thing is that, the protein do not
 have the Rossmann fold or the dinucleotide binding fold. Can any one
 please
 cite or suggest any other example of such type of anomaly? Is there any
 example of non-classical Rossmann fold bearing proteins?

 Thanks,
 Sudipta.


 Sudipta Bhattacharyya.
 Senior Research Fellow,
 Department of Biotechnology,
 Indian Institute of Technology Kharagpur, India.



-- 
F.M.D. Vellieux (B.Sc., Ph.D., hdr)
IBS / ELMA
41 rue Jules Horowitz
38027 Grenoble Cedex 01
France
Tel: +33 438789605
Fax: +33 438785494

[ccp4bb] question about DM

[Vellieux Frederic]

Hi all,

Just a (naive?) question: how does one manage to introduce (and deal 
with) improper non-crystallographic symmetry in DM ? Or does one has to 
go to DMmulti for that (because, by definition, going from one crystal 
form to another crystal form is improper NCS) ?


Ta,

F. Vellieux

Re: [ccp4bb] Regarding refinement in Refmac5

[Vellieux Frederic]

Hi there,

Not much information provided. How was the initial model refined ? 
Phenix ? It could be a problem with the Refmac refinement protocol 
(difficult to say with so little information) if you switched from 
Phenix to Refmac.


How certain are you 1 - of the space group; 2 - that the crystal wasn't 
twinned ? You can have both and it can be annoying.


Further, at this resolution I think you could use one of the SHELXes 
(forgot the terminology) for refinement, that could be more appropriate.


F.V.

Deepthi wrote:

Hi all

I am working with a small mutant protein which is 56 amino acids long. 
The crystal diffracted at 1.4A0 and the space group is  p3221. I did 
molecular replacement using Phenix software with all the data (1.4A0) 
and got a solution. Phenix did auto building with waters and R-free 
was 0.3123.


I mutated some residues which don't align with the model protein  to 
Alanines. When i change the residues back to their respective side 
chains Refmac5 won't  refine it well. The maps looks clear( you can 
guess its 1.4A0 data) but R-free is shooting up to 0.41. It is not 
accepting any changes to the Phenix generated model. I have no idea 
what is going on. Can anyone help me?


Thank You in advance
Deepthi

[ccp4bb] information received through the AFC: iycr2014

[Vellieux Frederic]

Dear colleagues,

Information just received here through the AFC channels: the UN general 
assembly has declared that 2014 will be the international year of 
crystallography.


Their statement (in French) as an attachment (sorry about including an 
attachment).


F. Vellieux


IYCr-FR.pdf
Description: Adobe PDF document

Re: [ccp4bb] information received through the AFC: iycr2014

[Vellieux Frederic]

The press release in English:

http://www.un.org/News/Press/docs/2012/ga11262.doc.htm

Boaz: perhaps the crystallography congresses and events taking place in 
2014 will be attended by UN peacekeeping force members as well (with 
their blue helmets) ?


F.V.

Boaz Shaanan wrote:
Et alors, what will this mean for us? 


Boaz


Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel

E-mail: bshaa...@bgu.ac.il
Phone: 972-8-647-2220  Skype: boaz.shaanan
Fax:   972-8-647-2992 or 972-8-646-1710

Re: [ccp4bb] information received through the AFC: iycr2014

[Vellieux Frederic]

Do you mean we should crush the helmets and solve the structure of the 
resulting powder blue coloured powder by crystallographic methods ? 
Sounds like a good proposal to be put forward to the UN to help them get 
rid of their used helmets !


David Schuller wrote:

On 07/04/12 08:03, Vellieux Frederic wrote:

The press release in English:

http://www.un.org/News/Press/docs/2012/ga11262.doc.htm

Boaz: perhaps the crystallography congresses and events taking place 
in 2014 will be attended by UN peacekeeping force members as well 
(with their blue helmets) ?


Powder blue, one might say.

Re: [ccp4bb] how to get phase of huge complex

[Vellieux Frederic]

Hi Lisa, hi all,

Please do not discard the alternative method(s) of conventional heavy 
atoms. Co-crystallisation or heavy-atom containing mother liquor soaks. 
You may remember that monster complexes have been solved in the past 
by such methods, and sometimes there are difficulties in crystallising 
the Se-Met version of a protein (the native protein gives crystals, 
the Se-Met version does not). And there is still some work going on 
regarding the development of novel (lanthanide-based) heavy-atom 
compounds that may provide both isomorphous and anomalous differences, 
the anomalous signal being extremely useful in the case of lanthanides 
and can be used on its own to solve 3D structures (one can then go 
back to the structure of the native macromolecule or complex if need be).


See e.g. Talon, R. et al. (2011), J. Sync. Rad. 18, 74-78 (PMID: 21169697)
and
http://www.natx-ray.com/products/catalogue_consum_CSM002.html

HTH,

Fred.

F.M.D. Vellieux (B.Sc., Ph.D., hdr)
Institut de Biologie Structurale J.-P. Ebel CEA CNRS UJF
LBM/ELMA
41 rue Jules Horowitz
38027 Grenoble Cedex 01
France
Tel: +33 (0) 438789605 (direct line), +33 (0) 663482891 (mobile phone)
Fax: +33 (0) 438785494
e-mail: frederic.velli...@ibs.fr

LISA wrote:

Hi all,
 
My work is to solve huge complex containing 4 different proteins and 
total molecular weight is about 300 KD. I can purify the complex by 
co-expression them in E.coli.  This complex contains 8 protein A, 2 
protein B and 1 protein C and D. protein B and protein C  have 
homology structures deposited in PDB database. No homology structure 
available for protein A and D, which contribute 60% of the whole 
molecular weight for the complex. 
 
  Now I am trying to find a way to solve the phase of this 
complex. I am thinking of use sad or mad with se-Met.   There total 
111 Met residues in this complex. Is it possible to solve this complex 
by se-Met? Does someone have experience to solve huge complex 
structure with se-met? It is also very welcome for all the suggestion. 
Thank you.
 
All the best,
 
Lisa

Re: [ccp4bb] P321 space group reindex problem

[Vellieux Frederic]

Hi there,

I am not certain that the thread is P321 space group reindex problem 
any more.


But: trigonal (and hexagonal) space groups are (usually?) polar. The 
cell axis c  can go up or can go down, and in order to get a 
consistent indexing you need to check both indexing systems when you 
scale additional data to your native (the indexing chosen by your first 
crystals defines the standard indexing - I must say that I haven't 
checked in the drawings of the international tables if having c going up 
or going down leads to a difference in that particular space group, 
P321, I'd need to draw both possibilities and check but I'm sorry I do 
not have the time right now - in fact it's too bad that the 
International Tables do not indicate Polar or Non-polar).


For practical purposes, a derivative is considered non isomorphous 
when the differences in unit cell parameters exceed ca. 1% (this is 
because if you take 2 crystals from the same crystallisation drop and 
collect and process diffraction crystals from these 2 crystals, you will 
never get exactly the very same values for the unit cell parameters; 
non-isomorphism effects start at ca. 1% change and you'll never get 2 
perfectly isomorphous crystals - even if you collect diffraction data 
twice from the same crystals you will not get perfect isomorphism).


From the values mentioned, 1% of the cell parameters of the native for 
a and b is 1.81 Angstroem and for c 1.1 Angstroem (the angles do not 
matter for a trigonal space group).


Had you obtained a value for a, b larger than ca. 183 Angstroem, or 
below ca. 109.2 Angstroem (only in the direction indicated by the 
changes mentioned in your mail - I ignored changes in the opposite 
direction) then you would have been able to say that the crystals were 
non-isomorphous to each other. For me they are isomorphous to each other 
and I ignore these small differences in unit cell parameters.


The difference of 3% in Rfactor (I suppose this is |FP - FPH| / |FP|, no 
Sigma character on my keyboard to indicate the summations over h k l) 
is I think due to 2 different chemicals (heavy-atom compounds) in 
derivative 1 and derivative 2. Differences in R-factors at low 
resolutions are often associated with solvent effects, and I think you 
will have 2 different mother liquors and hence 2 different solvents in 
derivative 1 and in derivative 2. That is assuming that derivative 1 and 
derivative 2 were prepared using 2 different chemicals. And typically 
low-resolution data (below 15 Angstroem resolution or so) is kept out 
during phasing by the MIR method.


To locate the heavy atom constellations in the 2 derivatives, you could 
compute and interpret difference Patterson maps - including automated 
interpretation, vector search and the likes -, you could use direct 
methods (the heavy atom constellation is similar to a small molecule 
because there are far fewer atoms there than in the full macromolecule, 
and direct methods work extremely well for small molecules - you would 
need to use the isomorphous differences in order to use direct methods; 
no mention is made of any anomalous signal so I do not know if you could 
this as well).


HTH,

Fred.

Qixu Cai wrote:
Why the 29% Rfactor indicate the derivatives are not isomorphous to 
native dataset?


Native dataset cell constant: 181.39 181.39 110.217 90 90 120
derivative1 cell constant: 181.909 181.909 109.62 90 90 
120Rfactor to native: 26%
derivative2 cell constant: 181.527 181.527 109.32 90 90 
120Rfactor to native: 29%


The Rfactor at low resolution is larger than in high resolution.

Could you please to help me figure out where the heavy atoms had been 
soaked into the crystal?


Thank you very much.

Best wishe,

Qixu Cai





2012/5/30 Laurent Maveyraud laurent.maveyr...@ipbs.fr 
mailto:laurent.maveyr...@ipbs.fr


Hi,

it is therefore likely that your spacegroup is really P321...
hopefully, your data set is not twinned, did you check that ?

You are left with 2 possible indexing schemes, as already
mentionned. Chek scaling derivative / native scaling for each
indexation of the derivative : the lowest Rfactor will likely
indicate the right one.
It appears that you end up with Rfactor of about 29 %, which
suggest that your derivatives are not isomorphous to your native
dataset. How do cell parameters compare for each data set ?
Check also how the Rfactor varies with resolution, you might still
have usefull phasing info at low resolution.

hope this helps

laurent



Le 30/05/2012 07:50, Qixu Cai a écrit :

At first, I processed the data at P3 space group. But after
phenix.xtriage analysis, the Xtriage told me the space group
must be
P321, so I used P321 to process my data, and got an acceptable
Rmerge.

Qixu Cai



2012/5/29 Phil Evans p...@mrc-lmb.cam.ac.uk
mailto:p...@mrc-lmb.cam.ac.uk 

Re: [ccp4bb] P321 space group reindex problem

[Vellieux Frederic]

Hi Ian,

You're right the information is there... but not where I was expecting 
it (on the page corresponding to an individual space group). It had 
never occurred to me that it could be somewhere else.


So thanks, and regards to Jasmine.

Fred.

Ian Tickle wrote:

Hello Fred

On 30 May 2012 07:55, Vellieux Frederic frederic.velli...@ibs.fr wrote:
  

Hi there,



  

But: trigonal (and hexagonal) space groups are (usually?) polar. The cell
axis c  can go up or can go down, and in order to get a consistent
indexing you need to check both indexing systems when you scale additional
data to your native (the indexing chosen by your first crystals defines the
standard indexing - I must say that I haven't checked in the drawings of
the international tables if having c going up or going down leads to a
difference in that particular space group, P321, I'd need to draw both
possibilities and check but I'm sorry I do not have the time right now - in
fact it's too bad that the International Tables do not indicate Polar or
Non-polar).



It does, at least my edition (Vol. A: 5th ed., 2002, Table 10.2.1.2,
p.806) does - ITC has everything you need to know about space groups
(and a lot more besides)!

See also this table that I made where all polar  non-polar SGs are
listed individually:

http://www.ccp4.ac.uk/dist/html/alternate_origins.html

Counting only the non-enantiomorphic ones, PG3 (4 SGs) and PG6 (6 SGs)
are polar, whereas PG321 (3 SGs), PG312 (3 SGs), PG32 (1 SG) and PG622
(6 SGs) are non-polar.  So in all 10 are polar and 13 are non-polar.
A 2-fold axis perp to another axis always implies that there's no
preferred direction along the other axis, so it's non-polar.

Cheers

-- Ian


  

Re: [ccp4bb] question about a dataset with pseudotranslational symmetry

[Frederic VELLIEUX]

Hello,
 
Which version of Phaser are you using ? As you must be aware, not all versions 
of Phaser deal in the most appropriate manner with cases of translational NCS 
if this is what you mean by pseudo translational symmetry. Personally I'd go 
for the latest version of Phaser...
 
HTH,
 
Fred.


 Message du 26/05/12 03:02
 De : Ke, Jiyuan 
 A : CCP4BB@JISCMAIL.AC.UK
 Copie à : 
 Objet : [ccp4bb] question about a dataset with pseudotranslational symmetry
 


Dear All,
 
Recently I collected a data set to about 3.1 angstrom. Using Xtriage program, I 
found a pseudo translational symmetry on the c-axis.  I noticed that overall 
diffraction intensity is weak for this dataset. I wonder if there are flaws in 
the crystal and I have difficulty to solve the structure using phaser. Has 
anyone seen similar cases and any comments and suggestions? Thanks! 
 
Below is some analysis results from the Xtriage.
 
Cell 102.937, 102.937, 203.059, 90, 90, 90,  P422
-
Largest Patterson peak with length larger than 15 Angstrom
Frac. coord.    :    0.000    0.000    0.350
Distance to origin  :   71.133
Height (origin=100) :   48.451
p_value(height) :    8.588e-05
--
Wilson ratio and moments
Acentric reflections
   /^2    :2.568   (untwinned: 2.000; perfect twin 1.500)
   ^2/    :0.728   (untwinned: 0.785; perfect twin 0.885)
       :0.850   (untwinned: 0.736; perfect twin 0.541)
Centric reflections
   /^2    :3.953   (untwinned: 3.000; perfect twin 2.000)
   ^2/    :0.577   (untwinned: 0.637; perfect twin 0.785)
       :1.111   (untwinned: 0.968; perfect twin 0.736)
---
NZ test (0
---
|  Z  | Nac_obs | Nac_theo | Nc_obs | Nc_theo |
---
| 0.0 |   0.000 |    0.000 |  0.000 |   0.000 |
| 0.1 |   0.126 |    0.095 |  0.293 |   0.248 |
| 0.2 |   0.239 |    0.181 |  0.394 |   0.345 |
| 0.3 |   0.327 |    0.259 |  0.471 |   0.419 |
| 0.4 |   0.401 |    0.330 |  0.521 |   0.474 |
| 0.5 |   0.464 |    0.394 |  0.557 |   0.520 |
| 0.6 |   0.518 |    0.451 |  0.597 |   0.561 |
| 0.7 |   0.569 |    0.503 |  0.635 |   0.597 |
| 0.8 |   0.613 |    0.551 |  0.660 |   0.629 |
| 0.9 |   0.648 |    0.593 |  0.683 |   0.657 |
| 1.0 |   0.679 |    0.632 |  0.706 |   0.683 |
---
| Maximum deviation acentric  :  0.071    |
| Maximum deviation centric   :  0.052    |
| |
| _acentric  : +0.054    |
| _centric   : +0.035    |
--
L test for acentric data
using difference vectors (dh,dk,dl) of the form:
(2hp,2kp,3lp)
  where hp, kp, and lp are random signed integers such that
  2 
  Mean |L|   :0.490  (untwinned: 0.500; perfect twin: 0.375)
  Mean  L^2  :0.323  (untwinned: 0.333; perfect twin: 0.200)
  The distribution of |L| values indicates a twin fraction of
  0.00. Note that this estimate is not as reliable as obtained
  via a Britton plot or H-test if twin laws are available.
---
Twinning and intensity statistics summary (acentric data):
Statistics independent of twin laws
  /^2 : 2.568 
  ^2/ : 0.728 
 : 0.850 
  , : 0.490, 0.323
  Multivariate Z score L-test: 0.686
---
 
Jiyuan Ke, Ph.D.
Research Scientist
Van Andel Research Institute
333 Bostwick Ave NE
Grand Rapids, MI 49503