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.

-- 
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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 
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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
<mailto: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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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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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] 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.

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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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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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[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

--
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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.

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

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

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

 

[ccp4bb] Absence of contact between layers in a crystal

[Kerff Fred]

Hello,

Looking at structure 2HR0 (The structure of complement C3b provides insights 
into complement activation and regulation. »,Abdul Ajees, A.,  Gunasekaran, K., 
 Volanakis, J.E.,  Narayana, S.V.,  Kotwal, G.J.,  Krishna Murthy, H.M.;  
(2006) Nature 444: 221-225), I noticed the absence of contacts between layers 
in the crystal. Is it something that has already been observed in other 
crystals?

Best regards,

Fred
-
Frédéric Kerff
Chercheur qualifié F.R.S.-FNRS
Cristallographie des protéines
Centre d'Ingénierie des Protéines
Université de Liège
17, Allée du 6 Août - Bat B5a
4000 Liège (Belgium)
Tel.: +32 (0)4 3663620
Fax: +32 (0)4 3663772



 Le 6 févr. 2015 à 10:12, Tim Gruene t...@shelx.uni-ac.gwdg.de a écrit :
 
 -BEGIN PGP SIGNED MESSAGE-
 Hash: SHA1
 
 Dear Smith,
 
 The sca file most likely does not contain flags. pointless can read
 the sca file, standardise it to ccp4 standards and freerflag marks
 random reflections. You should use the maximum of 500 unique
 reflections or 5% of the unique reflections, whichever is larger.
 
 Best,
 Tim
 
 On 02/06/2015 09:49 AM, Smith Lee wrote:
 Dear All, I have a sca file. Will you please tell me by which
 software or how I can know whether the sca file contains R-free
 tags? If not, by which software or how I can add the R-free tags?
 And how much of the reflections I add the R-free tags? I am looking
 forward to getting your reply. Smith
 
 
 - -- 
 - --
 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)
 
 iD8DBQFU1IWVUxlJ7aRr7hoRAmZHAJ4+6wREnwkFN0EhfErAA0tPSopKKwCgiLdi
 j0JFZac4kAh8twpov71MG84=
 =XN57
 -END PGP SIGNATURE-

Re: [ccp4bb] Absence of contact between layers in a crystal

[Kerff Fred]

Thanks for all the replies and sorry for rerun of a thread. I however have two 
additional questions:
- Why is the pdb still available without any obvious sign of the fraud?
- Why is the paper stil available ?

Fred

-
Frédéric Kerff
Chercheur qualifié F.R.S.-FNRS
Cristallographie des protéines
Centre d'Ingénierie des Protéines
Université de Liège
17, Allée du 6 Août - Bat B5a
4000 Liège (Belgium)
Tel.: +32 (0)4 3663620
Fax: +32 (0)4 3663772



 Le 6 févr. 2015 à 12:16, Randy Read rj...@cam.ac.uk a écrit :
 
 Actually, if you go back through the archive of CCP4-BB from the first time 
 this came up, I think you'll find that there are real crystals with apparent 
 gaps in the packing.  This can arise because of statistical disorder, where 
 there are two or more ways that a statistically-disordered layer in the 
 crystal can mediate the interaction between ordered layers.  So not finding a 
 connected packing is something to look closely at and worry about, but it 
 doesn't necessarily indicate that somebody did a bad job of making up a 
 structure.
 
 Randy
 
 On 6 Feb 2015, at 11:09, Robbie Joosten robbie_joos...@hotmail.com 
 mailto:robbie_joos...@hotmail.com wrote:
 
 Not in real crystal structures ;)
 
 Cheers,
 Robbie
 
 Sent with my Windows Phone
 Van: Kerff Fred mailto:fke...@ulg.ac.be
 Verzonden: ‎6-‎2-‎2015 12:02
 Aan: CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK
 Onderwerp: [ccp4bb] Absence of contact between layers in a crystal
 
 Hello,
 
 Looking at structure 2HR0 (The structure of complement C3b provides 
 insights into complement activation and regulation. »,Abdul Ajees, A.,  
 Gunasekaran, K.,  Volanakis, J.E.,  Narayana, S.V.,  Kotwal, G.J.,  Krishna 
 Murthy, H.M.;  (2006) Nature 444: 221-225), I noticed the absence of 
 contacts between layers in the crystal. Is it something that has already 
 been observed in other crystals?
 
 Best regards,
 
 Fred
 -
 Frédéric Kerff
 Chercheur qualifié F.R.S.-FNRS
 Cristallographie des protéines
 Centre d'Ingénierie des Protéines
 Université de Liège
 17, Allée du 6 Août - Bat B5a
 4000 Liège (Belgium)
 Tel.: +32 (0)4 3663620
 Fax: +32 (0)4 3663772
 
 
 
  Le 6 févr. 2015 à 10:12, Tim Gruene t...@shelx.uni-ac.gwdg.de 
  mailto:t...@shelx.uni-ac.gwdg.de a écrit :
  
  -BEGIN PGP SIGNED MESSAGE-
  Hash: SHA1
  
  Dear Smith,
  
  The sca file most likely does not contain flags. pointless can read
  the sca file, standardise it to ccp4 standards and freerflag marks
  random reflections. You should use the maximum of 500 unique
  reflections or 5% of the unique reflections, whichever is larger.
  
  Best,
  Tim
  
  On 02/06/2015 09:49 AM, Smith Lee wrote:
  Dear All, I have a sca file. Will you please tell me by which
  software or how I can know whether the sca file contains R-free
  tags? If not, by which software or how I can add the R-free tags?
  And how much of the reflections I add the R-free tags? I am looking
  forward to getting your reply. Smith
  
  
  - -- 
  - --
  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)
  
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 --
 Randy J. Read
 Department of Haematology, University of Cambridge
 Cambridge Institute for Medical Research  Tel: + 44 1223 336500
 Wellcome Trust/MRC Building   Fax: + 44 1223 336827
 Hills RoadE-mail: rj...@cam.ac.uk 
 mailto:rj...@cam.ac.uk
 Cambridge CB2 0XY, U.K.   www-structmed.cimr.cam.ac.uk
 

[ccp4bb] Post-doctoral position at York Structural Biology Laboratory / Closing date: 15 January 2013

[Fred Antson]

Dear All,
a Postdoctoral Research Fellow position in structural biology / biochemistry of 
DNA-translocating molecular motors is available from February/March 2013. 
The position is funded by the Wellcome Trust, for 3 years, with potential 
extension, with the starting salary of £29,541 per year. 
Closing date for this post is Tuesday 15 January.
Additional information and full details about the application process can be 
found at https://jobs.york.ac.uk/ 
Please don't hesitate to contact me directly for further information.
Fred Antson / YSBL

[ccp4bb] Different residue type with same number in refmac?

[Fred Kerff]

Hello,

The protein preparation I'm working with is not homogeneous. It comes from a 
natural source and few amino acid are not conserved. Is there a way to take 
this into account in refmac5. In other words having two alternative 
conformations with two different residue names?
Thanks for your help.

Fred
-
Frédéric Kerff
Chercheur qualifié F.R.S.-FNRS
Cristallographie des protéines
Centre d'Ingénierie des Protéines
Université de Liège
17, Allée du 6 Août - Bat B5a
4000 Liège (Belgium)
Tel.: +32 (0)4 3663620
Fax: +32 (0)4 3663772

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

[ccp4bb] two Postdoctoral positions at YSBL

[Fred Antson]

Two Wellcome Trust funded postdoctoral positions are available at York 
Structural Biology Laboratory, to work with Dr Fred Antson. Both  posts are 
available for 3 years, with potential to extend for a further 2-years. 
One project focuses on investigating protein-nucleic acid interactions within 
DNA-translocating molecular motors present in several viruses. This project 
will involve collaboration with Elena Orlova (Birkbeck College, London), Paulo 
Tavares and Leonor Oliveira (Unité de Virologie Moléculaire et Structurale, 
Gif-sur-Yvette), Juan Alonso (Biotecnología Microbiana, Madrid) and Carol 
Robinson (University of Oxford).  The second project will focus on several 
tRNA-modifying enzymes, in particular, structural and functional studies of 
human dihydrouridine synthase implicated in lung cancer. This project is in 
collaboration with Marina Rodnina (Max Planck Institure for Biophysical 
Chemistry, Goettingen) and Eugene Koonin (NCBI/NIH, Bethesda).

Additional information and full details about the application process can be 
found at: 
https://jobs.york.ac.uk/wd/plsql/wd_portal.show_job?p_web_site_id=3885p_web_page_id=154693

Fred Antson
York Structural Biology LaboratoryTel: +44-(0)1904-328255
Department of Chemistry
University of York
York YO10 5DD
UK

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

Re: [ccp4bb] [RESUME] [OFF-TOPIC] Site-Directed Mutagenesis [OFF-TOPIC]

[Fred]

Hi CCP4 list,
Thank you very much for additional messages and references.
Here goes the image of the PCR product before digested and after 
digested and cleaned.

 http://ompldr.org/vY29jbA
The results of the transformation of 3 microL (90 ng) of 
non-mutated/paretal plasmid gave hundreds of colonies; 3 microL of Dpn1 
digested sample gave two colonies only; and transformation of 3 
microL(90 ng) of cleaned product gave 14 colonies.
So, if the amplification is not abundant, chances are that home made 
competent cell will not be transformed with the digested product. Don't 
want start another discussion but, is there any reason for differences 
in the transformation efficiency between the parental and the mutated 
(cleaned) plasmids?

All the Best,
Fred

Em 03-02-2012 16:14, Fred escreveu:

Hi CCP4 list,
Thanks everyone who have answered my post concerning to mutagenesis.
From quick reading most of the answers, the following seems to be a 
consensus:

1) Do not concentrate your PCR product;
2) Too much DNA and/or impurities like salts or whatever can inhibits 
transformation;
3) Purify your PCR product before transformation if possible or use 3 
of 4 microL of it. This is more or less the amount of DNA showed in 
the uploaded image.

Kind regards,
Fred

P.S.: I'll let you know the results.

[ccp4bb] [OFF-TOPIC] Site-Directed Mutagenesis [OFF-TOPIC]

[Fred]

Dear CCP4users biologists,
I'm trying to make a single aa mutant of a 5.7 kb non commercial vector 
with the Agilent's Quick Change Site-Directed Mutagenesis Kit. I have 
strictly followed the instructions manual, however, I could not be able 
to transform bacterial cells with my PCR product. I can observe the 
amplified PCR product before and after DpnI digestion (see image in 
http://ompldr.org/vY2x3aw), but cannot get any colony on LB plates. I'm 
using very fresh super competent cells so that I've got dozens of 
colonies with 60 ng of the parental/non-mutated vector as positive 
control. The bands in the referenced image corresponds to 2.5 microL of 
a 50 microL reaction volume. I usually concentrate it to 4 microL before 
transformation. Also, I've already optimized the primer's temperature 
annealing (best is 62 oC) and I've increased the extension time up to 9 
min. Is there anything else I can try?

Any help is appreciated!
Regards.
Fred

P.S.: Agilent's e-mail support is not working.
P.P.S.: this might not be of other's interest, address the answers, 
please, to my e-mail only.

Re: [ccp4bb] [OFF-TOPIC] Site-Directed Mutagenesis [OFF-TOPIC]

[Fred]

Hi CCP4 list,
Thanks everyone who have answered my post concerning to mutagenesis.
From quick reading most of the answers, the following seems to be a 
consensus:

1) Do not concentrate your PCR product;
2) Too much DNA and/or impurities like salts or whatever can inhibits 
transformation;
3) Purify your PCR product before transformation if possible or use 3 of 
4 microL of it. This is more or less the amount of DNA showed in the 
uploaded image.

Kind regards,
Fred

P.S.: I'll let you know the results.

[ccp4bb] [RESUME]: [ccp4bb] artificial tetramer

[Fred]

Hi there,
Thanks everyone who answered the post entitled artificial tetramer . 
This is a resume of things I have done to build artificial tetramers. 
The following are the steps I have used:
1) Using your helix as model, run Amore scenario get origin shifted 
model with option Reorient Trail Model checked  (From Eleonor 
Dodson):  this will give your helix perfectly oriented into a P1 cell;
2) With pdbset, translate your helix by the desired distance along X and 
apply the desired symmetry to Z (P4 in my case): this will give your 
template;
3) Rename the chain´s template and write a simple script combining 
lskab and pdb_merge in a FOR loop to superimpose to and merge the 
mobile pdb with your template one chain after another.
In principle I was thinking about get a arbitrary point into the cell, 
pass a vector through it and apply the desired symmetry. However, unless 
XFIT, I don't know which program else has these capabilities. So the 
steps described here in are not of general application, but has solved 
my problem.

Best wishes and Marry Xmas,
Fred

Re: [ccp4bb] artificial tetramer

[Fred]

Hi Tim,
Thanks for your replay. All pdb monomers have the same primary sequence 
and a perfect matching long helix, which I have used to superpose the 
coordinates. Such helix is almost straight so that, the idea would be to 
create a vector along the helix main axis, shift this axis to a some 
distance (perhaps minimizing clashes) and apply 4-fold rotation. A 
second step would be to take these into pdbset to make things in batch 
mode. It sounds simple, but don't know the easiest way/programs to do 
that. I can do just the basics in Coot. I remember that Xfit had some 
options to trace vectors inside a cell and give it rotation properties. 
However, Xfit seems to be frozen and integration with pdbset would be 
painful.

Regards,
Fred

Em 14-12-2011 07:32, Tim Gruene escreveu:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hi Fred,

this sentence of yours, All pdb's are superposed by a common sequence
region, which also will be part of the tetramer interface. probably
hides the information which would be necessary for a reasonable answer
to your question.

If you still are stuck, you might post again with a more detailed
description of what you mean.

Cheers, Tim

On 12/13/2011 07:28 PM, Fred wrote:

Dear CCP4bb list,
Thank you very much all of you who have answered my post. I'm really
sorry if I was unclear. Such operation is so unusual that I could be
able to express myself appropriately. From quick reading some replies
(James Stroud and Guillaume Ponchel), it seems is possible do build
artificial tetramers with Coot. Several problems have been raised like
clashes, unusual interfaces and so on.  A second step would be to take
Coot's rotation and translation matrix and apply it to all pdb's in
batch mode with pdbset. All pdb's are superposed by a common sequence
region, which also will be part of the tetramer interface. I'll try to
make things work.
Once more, sorry for any inconvenience and thank you very  much.
Kind regards,
Fred

- -- 
- --

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

GPG Key ID = A46BEE1A

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Re: [ccp4bb] artificial tetramer

[Fred]

Dear CCP4bb list,
Thank you very much all of you who have answered my post. I'm really 
sorry if I was unclear. Such operation is so unusual that I could be 
able to express myself appropriately. From quick reading some replies 
(James Stroud and Guillaume Ponchel), it seems is possible do build 
artificial tetramers with Coot. Several problems have been raised like 
clashes, unusual interfaces and so on.  A second step would be to take 
Coot's rotation and translation matrix and apply it to all pdb's in 
batch mode with pdbset. All pdb's are superposed by a common sequence 
region, which also will be part of the tetramer interface. I'll try to 
make things work.

Once more, sorry for any inconvenience and thank you very  much.
Kind regards,
Fred

[ccp4bb] artificial tetramer

[Fred]

Hi List,
I would like to build an artificial tetramer from a monomer PBD file. 
All that I have is the coordinates it self with CRYST/CELL information 
cards. The artificial 4-fold axis has an arbitrary orientation into the 
cell. I mean, its not parallel to any crystallographic axis and have to 
be at a certain distance of the molecule. This sounds conceptually 
simple, but I would like to do that in batch mode for hundreds of PDB's. 
Could someone, please, tell me the easiest way/program to do that?

Thanks in advance,
Fred

Re: [ccp4bb] artificial tetramer

[Fred]

Hi Tim,
Thanks for your message and sorry if I wasn't clear. I don't have 
neither the axis orientation nor the rotation matrix. I would like to 
create them but don't know how and which program to use. Theoretically a 
have to create a axis (vector) at some distance of the molecule into the 
cell and give it the 4-fold propriety. Quite simple, but don't which 
program to use.

Regards,
Fred


Em 12-12-2011 18:23, Tim Gruene escreveu:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hello Fred,

if you know the rotation matrix, you can use pdbset with its 'rotate'
keyword.
It is not clear to me whether or not you have the rotation matrix or how
you define rotation.

Cheers,
Tim

On 12/12/2011 08:49 PM, Fred wrote:

Hi List,
I would like to build an artificial tetramer from a monomer PBD file.
All that I have is the coordinates it self with CRYST/CELL information
cards. The artificial 4-fold axis has an arbitrary orientation into the
cell. I mean, its not parallel to any crystallographic axis and have to
be at a certain distance of the molecule. This sounds conceptually
simple, but I would like to do that in batch mode for hundreds of PDB's.
Could someone, please, tell me the easiest way/program to do that?
Thanks in advance,
Fred

- -- 
- --

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

GPG Key ID = A46BEE1A

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=tDUj
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Re: [ccp4bb] artificial tetramer

[Fred]

at few Angstrons of the protein.

Em 12-12-2011 19:01, Jacob Keller escreveu:

How do you know where to put the axis?

JPK

On Mon, Dec 12, 2011 at 2:34 PM, Fredccp4bb.l...@gmail.com  wrote:

Hi Tim,
Thanks for your message and sorry if I wasn't clear. I don't have neither
the axis orientation nor the rotation matrix. I would like to create them
but don't know how and which program to use. Theoretically a have to create
a axis (vector) at some distance of the molecule into the cell and give it
the 4-fold propriety. Quite simple, but don't which program to use.
Regards,
Fred


Em 12-12-2011 18:23, Tim Gruene escreveu:


-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hello Fred,

if you know the rotation matrix, you can use pdbset with its 'rotate'
keyword.
It is not clear to me whether or not you have the rotation matrix or how
you define rotation.

Cheers,
Tim

On 12/12/2011 08:49 PM, Fred wrote:

Hi List,
I would like to build an artificial tetramer from a monomer PBD file.
All that I have is the coordinates it self with CRYST/CELL information
cards. The artificial 4-fold axis has an arbitrary orientation into the
cell. I mean, its not parallel to any crystallographic axis and have to
be at a certain distance of the molecule. This sounds conceptually
simple, but I would like to do that in batch mode for hundreds of PDB's.
Could someone, please, tell me the easiest way/program to do that?
Thanks in advance,
Fred


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

GPG Key ID = A46BEE1A

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Version: GnuPG v1.4.10 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFO5mKwUxlJ7aRr7hoRAsyuAKDfnH50sG/EuKiFz7tCzgTUtnZrdQCg3zSn
cqs8GHOu5M3JQahA/CofR1k=
=tDUj
-END PGP SIGNATURE-

Re: [ccp4bb] artificial tetramer

[Fred]

Hi James,
In my first post arbitrary orientation into the cell only means not 
parallel to any crystallographic axis, which would simplify things very 
much. I want to apply the 4-fold axis to the protein coordinates. If I 
have a cell and therefore an origin, I can take a point at any distance 
of the origin, pass a vector/axis through it and take the 3 others 
molecules by symmetry. That's trivial, given the point, the orientation 
and the property of the rotation. Don't know which program to use.

Regards,
Fred



Em 12-12-2011 19:18, James Stroud escreveu:

This is not trivial. Assuming an arbitrary origin, the simplest 4-fold symmetry 
operation (4-fold rotation) has 5 free parameters (translation along the 
symmetry axis is irrelevant). The biggest problem is determining the values for 
these parameters. For example, once you apply the symmetry, your molecule may 
clash with its symmetry mates or not even contact them. And even if you solve 
this latter problem automatically (which is not trivial because of 
irregularity), that leaves a net of 3 parameters describing the orientation of 
the protomer.

James



On Dec 12, 2011, at 1:34 PM, Fred wrote:


Hi Tim,
Thanks for your message and sorry if I wasn't clear. I don't have neither the 
axis orientation nor the rotation matrix. I would like to create them but don't 
know how and which program to use. Theoretically a have to create a axis 
(vector) at some distance of the molecule into the cell and give it the 4-fold 
propriety. Quite simple, but don't which program to use.
Regards,
Fred


Em 12-12-2011 18:23, Tim Gruene escreveu:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hello Fred,

if you know the rotation matrix, you can use pdbset with its 'rotate'
keyword.
It is not clear to me whether or not you have the rotation matrix or how
you define rotation.

Cheers,
Tim

On 12/12/2011 08:49 PM, Fred wrote:

Hi List,
I would like to build an artificial tetramer from a monomer PBD file.
All that I have is the coordinates it self with CRYST/CELL information
cards. The artificial 4-fold axis has an arbitrary orientation into the
cell. I mean, its not parallel to any crystallographic axis and have to
be at a certain distance of the molecule. This sounds conceptually
simple, but I would like to do that in batch mode for hundreds of PDB's.
Could someone, please, tell me the easiest way/program to do that?
Thanks in advance,
Fred


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

GPG Key ID = A46BEE1A

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Version: GnuPG v1.4.10 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

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cqs8GHOu5M3JQahA/CofR1k=
=tDUj
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Re: [ccp4bb] artificial tetramer

[Fred]

I only want to produce an artificial tetramer.



Em 12-12-2011 19:41, Jacob Keller escreveu:

Can you clarify your reason for doing this?

JPK

On Mon, Dec 12, 2011 at 3:36 PM, Fredccp4bb.l...@gmail.com  wrote:

Hi James,
In my first post arbitrary orientation into the cell only means not
parallel to any crystallographic axis, which would simplify things very
much. I want to apply the 4-fold axis to the protein coordinates. If I have
a cell and therefore an origin, I can take a point at any distance of the
origin, pass a vector/axis through it and take the 3 others molecules by
symmetry. That's trivial, given the point, the orientation and the property
of the rotation. Don't know which program to use.
Regards,
Fred



Em 12-12-2011 19:18, James Stroud escreveu:


This is not trivial. Assuming an arbitrary origin, the simplest 4-fold
symmetry operation (4-fold rotation) has 5 free parameters (translation
along the symmetry axis is irrelevant). The biggest problem is determining
the values for these parameters. For example, once you apply the symmetry,
your molecule may clash with its symmetry mates or not even contact them.
And even if you solve this latter problem automatically (which is not
trivial because of irregularity), that leaves a net of 3 parameters
describing the orientation of the protomer.

James



On Dec 12, 2011, at 1:34 PM, Fred wrote:


Hi Tim,
Thanks for your message and sorry if I wasn't clear. I don't have neither
the axis orientation nor the rotation matrix. I would like to create them
but don't know how and which program to use. Theoretically a have to create
a axis (vector) at some distance of the molecule into the cell and give it
the 4-fold propriety. Quite simple, but don't which program to use.
Regards,
Fred


Em 12-12-2011 18:23, Tim Gruene escreveu:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hello Fred,

if you know the rotation matrix, you can use pdbset with its 'rotate'
keyword.
It is not clear to me whether or not you have the rotation matrix or how
you define rotation.

Cheers,
Tim

On 12/12/2011 08:49 PM, Fred wrote:

Hi List,
I would like to build an artificial tetramer from a monomer PBD file.
All that I have is the coordinates it self with CRYST/CELL information
cards. The artificial 4-fold axis has an arbitrary orientation into the
cell. I mean, its not parallel to any crystallographic axis and have to
be at a certain distance of the molecule. This sounds conceptually
simple, but I would like to do that in batch mode for hundreds of
PDB's.
Could someone, please, tell me the easiest way/program to do that?
Thanks in advance,
Fred


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

GPG Key ID = A46BEE1A

-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.10 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

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cqs8GHOu5M3JQahA/CofR1k=
=tDUj
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Re: [ccp4bb] non-symmetric tetramer ? 2nd round

[Fred]

Thanks all of you who promptly replied my question.
I should have been more precise. I was referring to the symmetry of the 
tetrameric particle (point symmetry) at the molecular level not at the 
atomic level. This question has arisen because I have collected some 
SAXS data of my protein in solution and I don't have a molecular model 
to superpose to the experimental envelop. Others experimental data, gel 
filtration and NAT-PAGE, suggest a tetrameric particle. On the other 
side, P1, P2, P222 and P4 experimental envelops are quite different. So, 
I am not sure which symmetry to take. Considering the native state (no 
ligands at all), 4 identical subunits and that the interface of 
oligomarization have to be conserved, I would take P222 or P4. However, 
I can be able to imagine such spacial arrangement without a 4-fold axis 
at the molecular level. Indeed, even my P222 experimental envelop does 
have a 4-fold axis.

I appreciate if you could add some more comments on this.
Thanks in advance,
Fred




On Wed, 28 Jul 2010 15:31:45 -0300

  Fredccp4bb.l...@gmail.com  wrote:
   

Dear CCP4bb,
Could someone please, point me to some references about non-symmetric 
tetramers? If I have a tetramer composed by 4 identical subunits, it'll always 
have a P4 point group symmetry?
Thank in advance,
Tomb
 

Re: [ccp4bb] non-symmetric tetramer ? 2nd round

[Fred]

Of course, 222 has not a 4 axis, otherwise it would be a 4-fold axis. 
But that's the output of the program. P4 exp. model has a 4-fold axis 
along the longest axis, while the P222 MODEL has a 4-fold axis along the 
smallest, which doesn't make any sense. Can you imagine something build 
up with 4 identical subunits and 222 symmtry, but without a 4-fold axis 
at the molecular level (I mean at the envelop resolution level)?



Em 29-07-2010 12:32, Vellieux Frederic escreveu:

Hi,

To quote you: even my P222 experimental envelop does have a 4-fold 
axis - this is not suprising, a particle with 222 symmetry does not 
have 4-fold symmetry. There are 3 mutually perpendicular 2-fold axes 
that intersect at the origin (of the particle, of the molecule) [and 
for the nomenclature, these axes are named the P Q and R axes].


Fred.

Fred wrote:

Thanks all of you who promptly replied my question.
I should have been more precise. I was referring to the symmetry of 
the tetrameric particle (point symmetry) at the molecular level not 
at the atomic level. This question has arisen because I have 
collected some SAXS data of my protein in solution and I don't have a 
molecular model to superpose to the experimental envelop. Others 
experimental data, gel filtration and NAT-PAGE, suggest a tetrameric 
particle. On the other side, P1, P2, P222 and P4 experimental 
envelops are quite different. So, I am not sure which symmetry to 
take. Considering the native state (no ligands at all), 4 identical 
subunits and that the interface of oligomarization have to be 
conserved, I would take P222 or P4. However, I can be able to imagine 
such spacial arrangement without a 4-fold axis at the molecular 
level. Indeed, even my P222 experimental envelop does have a 4-fold 
axis.

I appreciate if you could add some more comments on this.
Thanks in advance,
Fred

Re: [ccp4bb] non-symmetric tetramer ? 2nd round

[Fred]

Clarifying... That's happened because I was talking about the symmetry 
of the SAXS envelop/particle. I understand that if you consider the 
symmetry of the whole particle, say a tetramer of identical subunits, 
you can have the 4-fold axis when asking for 222 symmetry envelop, which 
gives you a 422 envelop. I disagree with you statement there is no 
fundamental reason that a tetramer has to have any particular symmetry. 
Thinking only in the low resolution envelop, that's not true. Try to 
arrange 4 spheres in a non-symmetrical way keeping the same number of 
reciprocal contacts.



Em 29-07-2010 13:17, Phoebe Rice escreveu:

It sounds like you're missing something fundamental about
222 symmetry, but I may be misunderstanding you - there IS
no fourfold.  In fact, I think it is more common for the
subunits within tetramers to be related to one another by
three mutually perpendicular twofolds than a fourfold (e.g.
the favorite classic hemoglobin has no fourfold anywhere).
And there is no fundamental reason that a tetramer has to
have any particular symmetry.
Phoebe


 Original message 
   

Date: Thu, 29 Jul 2010 13:04:02 -0300
From: Fredccp4bb.l...@gmail.com
Subject: Re: [ccp4bb] non-symmetric tetramer ? 2nd round
To: CCP4BB@JISCMAIL.AC.UK

Of course, 222 has not a 4 axis, otherwise it would be a 4-
 

fold axis.
   

But that's the output of the program. P4 exp. model has a 4-
 

fold axis
   

along the longest axis, while the P222 MODEL has a 4-fold
 

axis along the
   

smallest, which doesn't make any sense. Can you imagine
 

something build
   

up with 4 identical subunits and 222 symmtry, but without a
 

4-fold axis
   

at the molecular level (I mean at the envelop resolution
 

level)?
   


Em 29-07-2010 12:32, Vellieux Frederic escreveu:
 

Hi,

To quote you: even my P222 experimental envelop does
   

have a 4-fold
   

axis - this is not suprising, a particle with 222
   

symmetry does not
   

have 4-fold symmetry. There are 3 mutually perpendicular
   

2-fold axes
   

that intersect at the origin (of the particle, of the
   

molecule) [and
   

for the nomenclature, these axes are named the P Q and R
   

axes].
   

Fred.

Fred wrote:
   

Thanks all of you who promptly replied my question.
I should have been more precise. I was referring to the
 

symmetry of
   

the tetrameric particle (point symmetry) at the
 

molecular level not
   

at the atomic level. This question has arisen because I
 

have
   

collected some SAXS data of my protein in solution and I
 

don't have a
   

molecular model to superpose to the experimental
 

envelop. Others
   

experimental data, gel filtration and NAT-PAGE, suggest
 

a tetrameric
   

particle. On the other side, P1, P2, P222 and P4
 

experimental
   

envelops are quite different. So, I am not sure which
 

symmetry to
   

take. Considering the native state (no ligands at all),
 

4 identical
   

subunits and that the interface of oligomarization have
 

to be
   

conserved, I would take P222 or P4. However, I can be
 

able to imagine
   

such spacial arrangement without a 4-fold axis at the
 

molecular
   

level. Indeed, even my P222 experimental envelop does
 

have a 4-fold
   

axis.
I appreciate if you could add some more comments on this.
Thanks in advance,
Fred
 


   

Phoebe A. Rice
Assoc. Prof., Dept. of Biochemistry  Molecular Biology
The University of Chicago
phone 773 834 1723
http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123

RNA is really nifty
DNA is over fifty
We have put them
   both in one book
Please do take a
   really good look
http://www.rsc.org/shop/books/2008/9780854042722.asp
   

Re: [ccp4bb] non-symmetric tetramer ? 2nd round

[Fred]

So, that was my previous question.

Em 29-07-2010 14:14, Phoebe Rice escreveu:

You don't have to keep the same number of symmetrical
contacts.

 Original message 
   

Date: Thu, 29 Jul 2010 14:13:56 -0300
From: Fredccp4bb.l...@gmail.com
Subject: Re: [ccp4bb] non-symmetric tetramer ? 2nd round
To: CCP4BB@JISCMAIL.AC.UK

Clarifying... That's happened because I was talking about
 

the symmetry
   

of the SAXS envelop/particle. I understand that if you
 

consider the
   

symmetry of the whole particle, say a tetramer of identical
 

subunits,
   

you can have the 4-fold axis when asking for 222 symmetry
 

envelop, which
   

gives you a 422 envelop. I disagree with you
 

statement there is no
   

fundamental reason that a tetramer has to have any
 

particular symmetry.
   

Thinking only in the low resolution envelop, that's not
 

true. Try to
   

arrange 4 spheres in a non-symmetrical way keeping the same
 

number of
   

reciprocal contacts.


Em 29-07-2010 13:17, Phoebe Rice escreveu:
 

It sounds like you're missing something fundamental about
222 symmetry, but I may be misunderstanding you - there IS
no fourfold.  In fact, I think it is more common for the
subunits within tetramers to be related to one another by
three mutually perpendicular twofolds than a fourfold
   

(e.g.
   

the favorite classic hemoglobin has no fourfold anywhere).
And there is no fundamental reason that a tetramer has to
have any particular symmetry.
 Phoebe


 Original message 

   

Date: Thu, 29 Jul 2010 13:04:02 -0300
From: Fredccp4bb.l...@gmail.com
Subject: Re: [ccp4bb] non-symmetric tetramer ? 2nd round
To: CCP4BB@JISCMAIL.AC.UK

Of course, 222 has not a 4 axis, otherwise it would be a
 

4-
   


 

fold axis.

   

But that's the output of the program. P4 exp. model has
 

a 4-
   


 

fold axis

   

along the longest axis, while the P222 MODEL has a 4-fold

 

axis along the

   

smallest, which doesn't make any sense. Can you imagine

 

something build

   

up with 4 identical subunits and 222 symmtry, but
 

without a
   


 

4-fold axis

   

at the molecular level (I mean at the envelop resolution

 

level)?

   

Em 29-07-2010 12:32, Vellieux Frederic escreveu:

 

Hi,

To quote you: even my P222 experimental envelop does

   

have a 4-fold

   

axis - this is not suprising, a particle with 222

   

symmetry does not

   

have 4-fold symmetry. There are 3 mutually perpendicular

   

2-fold axes

   

that intersect at the origin (of the particle, of the

   

molecule) [and

   

for the nomenclature, these axes are named the P Q and R

   

axes].

   

Fred.

Fred wrote:

   

Thanks all of you who promptly replied my question.
I should have been more precise. I was referring to the

 

symmetry of

   

the tetrameric particle (point symmetry) at the

 

molecular level not

   

at the atomic level. This question has arisen because I

 

have

   

collected some SAXS data of my protein in solution and
 

I
   


 

don't have a

   

molecular model to superpose to the experimental

 

envelop. Others

   

experimental data, gel filtration and NAT-PAGE, suggest

 

a tetrameric

   

particle. On the other side, P1, P2, P222 and P4

 

experimental

   

envelops are quite different. So, I am not sure which

 

symmetry to

   

take. Considering the native state (no ligands at all),

 

4 identical

   

subunits and that the interface of oligomarization have

 

to be

   

conserved, I would take P222 or P4. However, I can be

 

able to imagine

   

such spacial arrangement without a 4-fold axis at the

 

molecular

   

level. Indeed, even my P222 experimental envelop does

 

have a 4-fold

   

axis.
I appreciate if you could add some more comments on
 

this.
   

Thanks in advance,
Fred

 


   

Phoebe A. Rice
Assoc. Prof., Dept. of Biochemistry   Molecular Biology
The University of Chicago
phone 773 834 1723

   

http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/0
1_Faculty_Alphabetically.php?faculty_id=123
   

RNA is really nifty
DNA is over fifty
We have put them
both in one book
Please do take a
really good look
http://www.rsc.org/shop/books/2008/9780854042722.asp

   

Phoebe A. Rice
Assoc. Prof., Dept. of Biochemistry  Molecular Biology
The University of Chicago
phone 773 834 1723
http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123

RNA is really nifty
DNA is over fifty
We have put them
   both in one book

Re: [ccp4bb] non-symmetric tetramer ? 2nd round

[Fred]

No, constraints do not improved the Chis, but also don't harm them much. 
Which NSDs, from selection or superposition (damsel or damsup)? The 
superposition ones:

 P1
egp1p_04-1.pdb  !! Reference file
egp1p_12-1r.pdb !! NSD =   0.912
egp1p_05-1r.pdb !! NSD =   0.900
egp1p_03-1r.pdb !! NSD =   0.960
egp1p_06-1r.pdb !! NSD =   0.878
egp1p_10-1r.pdb !! NSD =   1.016
egp1p_07-1r.pdb !! NSD =   0.876
egp1p_14-1r.pdb !! NSD =   1.014
egp1p_02-1r.pdb !! NSD =   0.995
egp1p_13-1r.pdb !! NSD =   1.037
egp1p_08-1r.pdb !! NSD =   1.004
egp1p_01-1r.pdb !! NSD =   1.100
egp1p_11-1r.pdb !! NSD =   1.067
egp1p_15-1r.pdb !! NSD =   1.021
egp1p_09-1r.pdb !! NSD =   0.969
 P2
egp2p_08-1.pdb  !! Reference file
egp2p_09-1r.pdb !! NSD =   0.927
egp2p_12-1r.pdb !! NSD =   1.024
egp2p_10-1r.pdb !! NSD =   1.024
egp2p_13-1r.pdb !! NSD =   1.056
egp2p_07-1r.pdb !! NSD =   0.884
egp2p_06-1r.pdb !! NSD =   0.884
egp2p_01-1r.pdb !! NSD =   0.869
egp2p_03-1r.pdb !! NSD =   1.256
egp2p_14-1r.pdb !! NSD =   0.836
egp2p_15-1r.pdb !! NSD =   0.836
egp2p_02-1r.pdb !! NSD =   1.318
egp2p_05-1r.pdb !! NSD =   1.168
egp2p_04-1r.pdb !! NSD =   1.168
 P222
egp22p01-1.pdb  !! Reference file
egp22p13-1r.pdb !! NSD =   1.268
egp22p14-1r.pdb !! NSD =   1.584
egp22p15-1r.pdb !! NSD =   1.584
egp22p02-1r.pdb !! NSD =   1.030
egp22p03-1r.pdb !! NSD =   1.030
egp22p07-1r.pdb !! NSD =   1.442
egp22p06-1r.pdb !! NSD =   1.442
egp22p04-1r.pdb !! NSD =   0.851
egp22p05-1r.pdb !! NSD =   0.851
egp22p08-1r.pdb !! NSD =   0.905
egp22p09-1r.pdb !! NSD =   0.905
egp22p12-1r.pdb !! NSD =   1.392
egp22p10-1r.pdb !! NSD =   1.392
 P4
egp4p_09-1.pdb  !! Reference file
egp4p_07-1r.pdb !! NSD =   0.923
egp4p_08-1r.pdb !! NSD =   0.923
egp4p_05-1r.pdb !! NSD =   0.886
egp4p_02-1r.pdb !! NSD =   0.861
egp4p_01-1r.pdb !! NSD =   0.861
egp4p_03-1r.pdb !! NSD =   0.998
egp4p_04-1r.pdb !! NSD =   0.998
egp4p_06-1r.pdb !! NSD =   1.176
egp4p_13-1r.pdb !! NSD =   1.079
egp4p_12-1r.pdb !! NSD =   1.079
egp4p_14-1r.pdb !! NSD =   0.868
egp4p_15-1r.pdb !! NSD =   0.868
egp4p_10-1r.pdb !! NSD =   1.309
egp4p_11-1r.pdb !! NSD =   1.309
P5
egp5S206-1.pdb  !! Reference file
egp5S202-1r.pdb !! NSD =   0.675
egp5S205-1r.pdb !! NSD =   0.789
egp5S210-1r.pdb !! NSD =   1.044
egp5S212-1r.pdb !! NSD =   0.998
egp5S215-1r.pdb !! NSD =   0.929
egp5S204-1r.pdb !! NSD =   0.740
egp5S201-1r.pdb !! NSD =   1.077
egp5S211-1r.pdb !! NSD =   1.126
egp5S213-1r.pdb !! NSD =   0.773
egp5S209-1r.pdb !! NSD =   1.192
egp5S207-1r.pdb !! NSD =   1.213
egp5S214-1r.pdb !! NSD =   1.270
egp5S208-1r.pdb !! NSD =   0.710



Em 29-07-2010 13:11, Kushol Gupta escreveu:

Fred,

Two cents - I think the P1 SAXS solution should strongly guide your choice
of symmetry constraint above all else in this case: do any of the
symmetry-restrained shape reconstructions *improve* the statistics (chi) and
stability of the shape (NSD) when compared to the P1 result? Also, it sounds
like you have other data - do the theoretical Rs, f/fo, etc of the shapes
generated agree well with your other measurements?

Cheers,
Kushol


Kushol Gupta, Ph.D.
Research Associate
Van Duyne Laboratory - HHMI/Univ. of Pennsylvania School of Medicine
kgu...@mail.med.upenn.edu
215-573-7260 / 267-259-0082


Of course, 222 has not a 4 axis, otherwise

[ccp4bb] non-symmetric tetramer ?

[Fred]

Dear CCP4bb,
Could someone please, point me to some references about non-symmetric 
tetramers? If I have a tetramer composed by 4 identical subunits, it'll 
always have a P4 point group symmetry?

Thank in advance,
Tomb

Re: [ccp4bb] [OFF TOPIC] his-tag doesn't bind

[Fred]

Hi everyone,
Thanks for answer my question. Just to add some more notes regarding to 
my expression system. The insert-vector (pET28) has been sequenced and 
the his-tag is N-terminal. The anti his-tag WB is positive and the 
binding buffer's pH is 8.2 (double-checked).
I had already experienced the same problem before, which I solved just 
increasing urea from 6M to 8M. Now, I have reached GndHCl 6M and no 
binding at all.
I'm currently running a SDS-PAGE with samples eluted from Talon and let 
you know the results.

All the Best,
Fred  




--- Fred /ccp4bb.l...@gmail.com/ schrieb am *Di, 27.1.2009:
*

*Von: Fred ccp4bb.l...@gmail.com
Betreff: [ccp4bb] [OFF TOPIC] his-tag doesn't bind
An: CCP4BB@JISCMAIL.AC.UK
Datum: Dienstag, 27. Januar 2009, 22:00

*

*Hi ccp4 list,
I am trying to purify a his-tag protein by metal affinity chromatography. 
The
protein was expressed in inclusion bodies and its his-tag doesn't bind the
Qiagen Ni resin in denatured conditions (urea 8M or GndHCl 6M). Playing with
NaCl and detergents didn't help much.
Any help is appreciated.
Fred   *

Re: [ccp4bb] [OFF TOPIC] his-tag doesn't bind

[Fred]

Just to let you know. No way, Talon also don't work. I am gonna try the 
GE His-trap column.


Fred wrote:
 Hi everyone,
 Thanks for answer my question. Just to add some more notes regarding 
to my expression system. The insert-vector (pET28) has been sequenced 
and the his-tag is N-terminal. The anti his-tag WB is positive and the 
binding buffer's pH is 8.2 (double-checked).
 I had already experienced the same problem before, which I solved 
just increasing urea from 6M to 8M. Now, I have reached GndHCl 6M and no 
binding at all.
 I'm currently running a SDS-PAGE with samples eluted from Talon and 
let you know the results.

 All the Best,
 Fred


 --- Fred /ccp4bb.l...@gmail.com/ schrieb am *Di, 27.1.2009:
 *

 *Von: Fred ccp4bb.l...@gmail.com
 Betreff: [ccp4bb] [OFF TOPIC] his-tag doesn't bind
 An: CCP4BB@JISCMAIL.AC.UK
 Datum: Dienstag, 27. Januar 2009, 22:00

 *

 *Hi ccp4 list,
 I am trying to purify a his-tag protein by metal affinity 
chromatography. The
 protein was expressed in inclusion bodies and its his-tag 
doesn't bind the
 Qiagen Ni resin in denatured conditions (urea 8M or GndHCl 6M). 
Playing with

 NaCl and detergents didn't help much.
 Any help is appreciated.
 Fred   *

[ccp4bb] [OFF TOPIC] his-tag doesn't bind

[Fred]

Hi ccp4 list,
I am trying to purify a his-tag protein by metal affinity 
chromatography. The protein was expressed in inclusion bodies and its 
his-tag doesn't bind the Qiagen Ni resin in denatured conditions (urea 
8M or GndHCl 6M). Playing with NaCl and detergents didn't help much.

Any help is appreciated.
Fred   

Re: [ccp4bb] Highest shell standards

[Fred. Vellieux]

On Fri, 23 Mar 2007, Edward Berry wrote:

 I believe fft does not by default do this- only if you use the fillin 
 keyword? One place where it might be important is in density 
 modification/ molecular averaging. Molecular averaging can be seen
 as a numerical solution of the MR equations, finding a density map
 which (A) obeys the NCS/intercrystal symmetry and (B) yields the 
 observed F's upon Fourier transformation.  Now if on each cycle
 you set the missing F's to zero, you are requiring it to have
 as part of (B) zero amplitude for the missing reflections, which is
 more restrictive and incorrect. If instead you allow the missing F's
 to float, calculating them on each cycle from the previous map
 using the fillin option, someone has shown (don't have the
 reference handy at the moment) that the F's tend toward the true F's
 (in the case that they weren't really missing but omitted as part
 of the test).
 
 Ed

You have phase scatter plots in Acta Cryst. D51, 575-589 (1995) that show
just that: the map inversion phases from NCS averaging tend toward the
true phases. Since F's are phased quantities and since phases are more
important than amplitudes, non random amplitudes plus non random phases
(both from map inversion of averaged maps) lead to better electron density
maps.

Fred.

-- 

 Fred. Vellieux, esq.

 =
 IBS J.-P. Ebel CEA CNRS UJF / LBM
 41 rue Jules Horowitz
 38027 Grenoble Cedex 01
 France
 Tel: (+33) (0) 438789605
 Fax: (+33) (0) 438785494
 =

Re: [ccp4bb] CNS v1.2 and unwanted introduction of OXT

[Fred. Vellieux]

On Mon, 5 Mar 2007, James Irving wrote:

 Hi Fred,
 
  From memory, this can occur due to long bond lengths in the model being 
 interpreted as chain breaks, try editing the generate.inp or 
 generate_easy.inp script and increase the value for break_cutoff:
 
 {* cutoff distance in Angstroms for identification of breaks *}
 {* the default of 2.5A should be reasonable for most cases. If the input
structure has bad geometry it may be necessary to increase this 
 distance *}
 {===} break_cutoff=2.5;
 
 You may also try switching off the automatic detection of mainchain breaks:
 
 * automatically detect mainchain breaks in proteins based on distance *}
 {* the peptide link at break points will be removed *}
 {+ choice: true false +}
 {===} auto_break=true;
 
 It is also worth checking that the offending residues have their full 
 complement of backbone atoms in appropriate places (not accidentally 
 zapped to far-flung regions of coordinate space).
 
 Cheers,
 James

Hi James,

I tried to increase the parameter value to 3.0 A. The resulting file gives
the same behaviour (and the newly introduced OXTs are within 0.05 A of the
N atom of the following residue) so I think the distances are reasonable.

So unfortunately I think your valuable suggestion does not solve the
problem. On the graphics with Coot the starting model looks fine in these
regions.

I need to keep the automatic mainchain break detection because there are
some gaps in each chain of the model (12 chains in all).

So if there are other suggestions to solve this br of a problem, they
are most welcome!

Fred.

-- 

 Fred. Vellieux, esq.

 =
 IBS J.-P. Ebel CEA CNRS UJF / LBM
 41 rue Jules Horowitz
 38027 Grenoble Cedex 01
 France
 Tel: (+33) (0) 438789605
 Fax: (+33) (0) 438785494
 =

Re: [ccp4bb] CNS v1.2 and unwanted introduction of OXT

[Fred. Vellieux]

On Mon, 5 Mar 2007, Fred. Vellieux wrote:

 Hi James,
 
 I tried to increase the parameter value to 3.0 A. The resulting file gives
 the same behaviour (and the newly introduced OXTs are within 0.05 A of the
 N atom of the following residue) so I think the distances are reasonable.
 
 So unfortunately I think your valuable suggestion does not solve the
 problem. On the graphics with Coot the starting model looks fine in these
 regions.
 
 I need to keep the automatic mainchain break detection because there are
 some gaps in each chain of the model (12 chains in all).
 
 So if there are other suggestions to solve this br of a problem, they
 are most welcome!
 
 Fred.

Hello again,

I believe that I found the cause of the problem and a solution to it:
not by looking at the molecule with Coot but by looking at the separate
PDB input files where the problems occur.

They all share the same features: the chain label used by CNS is kept
along within Coot. For the parts that are modelled de novo using Coot, the
output pdb file does not contain the CNS chain label. It is only at those
positions where there is a discontinuity for chain label present or absent
does CNS introduce an extra OXT atom. I have introduced the missing chain
labels where necessary, and I am testing this right now:

the file produced by the generate script now does not contain added OXT
atoms.

I thought I'd inform the bulletin boards of this annoying feature.

Fred.

-- 

 Fred. Vellieux, esq.

 =
 IBS J.-P. Ebel CEA CNRS UJF / LBM
 41 rue Jules Horowitz
 38027 Grenoble Cedex 01
 France
 Tel: (+33) (0) 438789605
 Fax: (+33) (0) 438785494
 =