Re: [ccp4bb] Help with isomer ligand from PDB database

[Paul Emsley]

On 17/09/2022 15:48, Marion Schuller wrote:
>
>  
>
> Dear CCP4bb community,
>
>  
>
> I am writing regarding a problem with the refinement of an isomer
> ligand. I try to refine a structure which has the ligand “Carba-NAD”
> (as beta isomer) bound. This ligand is already in the pdb database as
> “CNA”. Although the ligand is in its beta-Carba-NAD form in the
> database, it is loaded into WinCoot as alpha isomer. When generating
> the restraints of Carba-NAD (via the grade server, calling it also
> “CNA”), I can load and refine the correct beta isomer ligand as long
> as I provide the grade-generated .cif file otherwise it would refine
> it back to the alpha isomer. Yet, in the preliminary preparation of
> the wwPDB X-ray validation report for structure deposition, the
> message flags up that the ligand “could not be matched to an existing
> wwPDB Chemical Component Dictionary definition”. With an older ccp4
> version in the background, I noticed that WinCoot would however load
> the beta isomer and I am now wondering if this problem lies in the
> .cif file of the new ccp4 library. Is there a possibility to
> check/correct the CNA file in the current ccp4 library or would there
> be a different way for solving this problem? I would be very grateful
> for support and help!
>
>  
>
Dear Marion,

As a rule, if a molecule has a different anomericity it has a different
ligand-id (three-letter-code) in the CCD. It seems to me that you need a
new entry in the CCD. It is a good thing that the wwPDB X-ray validation
flags this up as a ligand that matched with and existing entry.

So take the entry for CNA:

https://files.rcsb.org/ligands/view/CNA.cif

change the stereo_config from S to an R for C2D (I am guessing that that
is the anomeric carbon atom) in the atom table. Then feed that to
Acedrg. (I'd chop off the _pdbx_chem_comp_descriptor block so that that
Acedrg doesn't get distracted by the out of date SMILES).

Using that dictionary your refinement should be smooth sailing.

Upon deposition, the wwPDB will then reward you with one of the last
ever three letter codes - hooray!


Paul





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[ccp4bb] Help with isomer ligand from PDB database

[Marion Schuller]

Dear CCP4bb community,

I am writing regarding a problem with the refinement of an isomer ligand. I try 
to refine a structure which has the ligand "Carba-NAD" (as beta isomer) bound. 
This ligand is already in the pdb database as "CNA". Although the ligand is in 
its beta-Carba-NAD form in the database, it is loaded into WinCoot as alpha 
isomer. When generating the restraints of Carba-NAD (via the grade server, 
calling it also "CNA"), I can load and refine the correct beta isomer ligand as 
long as I provide the grade-generated .cif file otherwise it would refine it 
back to the alpha isomer. Yet, in the preliminary preparation of the wwPDB 
X-ray validation report for structure deposition, the message flags up that the 
ligand "could not be matched to an existing wwPDB Chemical Component Dictionary 
definition". With an older ccp4 version in the background, I noticed that 
WinCoot would however load the beta isomer and I am now wondering if this 
problem lies in the .cif file of the new ccp4 library. Is there a possibility 
to check/correct the CNA file in the current ccp4 library or would there be a 
different way for solving this problem? I would be very grateful for support 
and help!

With kind regards and many thanks in advance,
Marion




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Re: [ccp4bb] help for motion correction

[Suparno]

Hi,

Please check the X and Y of your gain reference file using the e2iminfo.py
command. It is possible that those values do not match those of the
micrographs. If it is indeed that case, you can use the
relion_image_handler options (for example --flipXY) to flip the gain
reference file. Hope this helps!

Best,
Suparno.

On Sat, Jul 16, 2022 at 3:56 PM Jing  wrote:

> Hello All,
>  I have a question about gain reference file. When I try to work on
> Motion Correction on relion 3.1.3, it always reports an error message said
> "the size of image and the size of the gain reference do not match."
> Because of that error, I could not proceed motion correction of my data.
> The cryo EM facility gave me that refence file in dm4 format and I use
> dm2mrc to covert it to mrc file. May I ask which part that I did wrong? How
> to solve that error?
>  Thank you
>
> 
>
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Re: [ccp4bb] help for motion correction

[Martyn Winn - STFC UKRI]

Might be better posted to cc...@jiscmail.ac.uk
m

-Original Message-
From: CCP4 bulletin board  On Behalf Of Jing
Sent: 16 July 2022 20:56
To: ccp4bb 
Subject: [ccp4bb] help for motion correction

Hello All,
 I have a question about gain reference file. When I try to work on Motion 
Correction on relion 3.1.3, it always reports an error message said "the size 
of image and the size of the gain reference do not match." Because of that 
error, I could not proceed motion correction of my data. The cryo EM facility 
gave me that refence file in dm4 format and I use dm2mrc to covert it to mrc 
file. May I ask which part that I did wrong? How to solve that error?
 Thank you



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Re: [ccp4bb] Help with One dimensional electron density calculation

[Pavel Afonine]

For some perhaps relevant discussion please see Appendix B here:

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6096492/pdf/d-74-00531.pdf

Pavel

On Sat, Jul 16, 2022 at 6:17 AM Marcin Wojdyr  wrote:

> On Thu, Jul 14, 2022 at 3:15 AM Pavel Afonine  wrote:
>
> > Map values are calculated using tricubic interpolation. Optionally you
> can choose a less accurate eight-point interpolation (use interpolation
> keyword for this).
> >
>
> I've been wondering which one is better. Tri-cubic is more accurate
> for smoothly changing values, but for noisy data it will amplify the
> noise. Did anyone test if the choice of interpolation method
> (tri-cubic vs tri-linear) makes a practical difference in any
> crystallographic application?
>



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[ccp4bb] help for motion correction

[Jing]

Hello All,
 I have a question about gain reference file. When I try to work on Motion 
Correction on relion 3.1.3, it always reports an error message said "the size 
of image and the size of the gain reference do not match." Because of that 
error, I could not proceed motion correction of my data. The cryo EM facility 
gave me that refence file in dm4 format and I use dm2mrc to covert it to mrc 
file. May I ask which part that I did wrong? How to solve that error?
 Thank you



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Re: [ccp4bb] Help with One dimensional electron density calculation

[Marcin Wojdyr]

On Thu, Jul 14, 2022 at 3:15 AM Pavel Afonine  wrote:

> Map values are calculated using tricubic interpolation. Optionally you can 
> choose a less accurate eight-point interpolation (use interpolation keyword 
> for this).
>

I've been wondering which one is better. Tri-cubic is more accurate
for smoothly changing values, but for noisy data it will amplify the
noise. Did anyone test if the choice of interpolation method
(tri-cubic vs tri-linear) makes a practical difference in any
crystallographic application?



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Re: [ccp4bb] Help with One dimensional electron density calculation

[Paul Emsley]

On 13/07/2022 19:18, Ravikumar wrote:


I would like to calculate One-dimension electron density profiles of 
the different number of ions bound to an ion channel. Are there any 
programs in CCP4/ Phenix which can do the same job as the MAPMAN 
(UPPSALA electron density server) program to extract the electron 
density values to plot electron density values versus pore axis? I 
have attached an example figure.





Here's how to do it in Coot (see attached).


Paul.





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from __future__ import print_function
import math

imol = read_pdb('pdb6qkc.ent')
imol_map = read_ccp4_map('emd_4572.map', 0)
n_steps = 250

start_point = [154, 154, 133]
end_point   = [154, 154, 180]



imol_map_smooth = sharpen_blur_map_with_resampling(imol_map, 0.0, 2.3)
delta = [x - y for x, y in zip(end_point, start_point)]
delta_step = [ x/float(n_steps) for x in delta]
delta_step_size = math.sqrt(sum([x*x for x in delta_step]))

print(delta)
print(delta_step)
print(delta_step_size)

with open('line-of-density.table', 'w') as f:
for i_step in range(n_steps + 1):
p = [x + i_step * y for x, y in zip(start_point, delta_step)]
r = density_at_point(imol_map_smooth, p[0], p[1], p[2])
d = delta_step_size * i_step
f.write('{} {} {} {} {}\n'.format(p[0], p[1], p[2], d, r))

Re: [ccp4bb] Help with One dimensional electron density calculation

[Martyn Winn - STFC UKRI]

Hi,

It’s not clear why you don’t use MAPMAN if that does what you want. If 
availability is the problem, it is still here 
https://github.com/martynwinn/Uppsala-Software-Factory

If you are prepared to do some Python, then 2 other options:

https://mrcfile.readthedocs.io/en/latest/readme.html  allows you to read in MRC 
file to a numpy array, and then you can you can average, interpolate, plot as 
you wish.  If your pore axis is aligned along Z and you want to average over 
the cross section, then this would be relatively straightforward.

https://gemmi.readthedocs.io/en/latest/grid.html  will also read in maps and 
manipulate.  It understands crystal symmetry, if that is what you have. It also 
has functions for interpolation.

HTH
Martyn

From: CCP4 bulletin board  On Behalf Of Ravikumar
Sent: 13 July 2022 19:18
To: ccp4bb 
Subject: [ccp4bb] Help with One dimensional electron density calculation


Dear all,

I would like to calculate One-dimension electron density profiles of the 
different number of ions bound to an ion channel. Are there any programs in 
CCP4/ Phenix which can do the same job as the MAPMAN (UPPSALA electron density 
server) program to extract the electron density values to plot electron density 
values versus pore axis? I have attached an example figure.

Thank you,
Ravikumar.



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Re: [ccp4bb] Help with One dimensional electron density calculation

[Pavel Afonine]

Hi Ravikumar,

next nightly build of Phenix (dev-4661 and up, likely becomes available
tomorrow) found in the usual place

https://phenix-online.org/download/nightly_builds.cgi?show_all=1

will contain the new command line program
called phenix.map_values_along_line.
The program inputs the map (real-space map in mrc format) and Cartesian
coordinates of two points in space, and it outputs map values along the
line connecting these two points.

Example:

phenix.map_values_along_line map.mrc point_1="1.123 2.455 3.765"
point_2="4321 5.567 6.987"

Optionally, you can specify the step that map values are computed at going
from one point to another, by default it is set to 0.01 (use step parameter
for this).
Map values are calculated using tricubic interpolation. Optionally you can
choose a less accurate eight-point interpolation (use interpolation keyword
for this).

Those interested in CCTBX implementation of underlying functionality of
this program grep for 'map_values_along_line_connecting_two_points' that
will find you the function and the test that exemplifies the use of this
function.

Hope this solves your problem, Ravikumar.

Pavel

On Wed, Jul 13, 2022 at 11:19 AM Ravikumar  wrote:

>
> Dear all,
>
>
> I would like to calculate One-dimension electron density profiles of the
> different number of ions bound to an ion channel. Are there any programs in
> CCP4/ Phenix which can do the same job as the MAPMAN (UPPSALA electron
> density server) program to extract the electron density values to plot
> electron density values versus pore axis? I have attached an example
> figure.
>
>
> Thank you,
>
> Ravikumar.
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] Help with One dimensional electron density calculation

[Georg Mlynek]

Dear Pavel,

I guess you know that Billy made cctbx "available" on colab. So 
installing cctbx and python is not needed any more.


https://github.com/phenix-project/Colabs/blob/main/Start_cctbx.ipynb

There are also some descriptions of some modifications to 
the installation so that everything works.


I planned to write a few exercises for the X-ray practical I am holding

For example for students it is often difficult to see how the number of 
reflections change depending on the space group, resolution,  .


The code which is actually from you is implemented, but task description 
is still missing.


One other idea was that student should calculate from a "precision 
image" the unit cell dimensions.


However I got always sidetracked before the course started.

There was a mail from James Holton I think at the beginning of the 
pandemic suggesting to make a centralized teaching source. For practical 
things this could be a starting.


Some other ideas which could be implemented are published here.

https://conference.scipy.org/proceedings/scipy2021/blaine_mooers.html

https://pubmed.ncbi.nlm.nih.gov/34671231/

Br, Georg.



Am 13.07.2022 um 20:28 schrieb Pavel Afonine:

Hi Ravikumar,
this can be easily done in CCTBX, but requires knowing CCTBX and 
Python scripting. I can write a script-example for you, if interested, 
or feel free to give it a try yourself and let me know if you need any 
help.

Pavel

On Wed, Jul 13, 2022 at 11:19 AM Ravikumar  wrote:


Dear all,


I would like to calculate One-dimension electron density profiles
of the different number of ions bound to an ion channel. Are there
any programs in CCP4/ Phenix which can do the same job as the
MAPMAN (UPPSALA electron density server) program to extract the
electron density values to plot electron density values versus
pore axis? I have attached an example figure.


Thank you,

Ravikumar.




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Re: [ccp4bb] Help with One dimensional electron density calculation

[Pavel Afonine]

Hi Ravikumar,
this can be easily done in CCTBX, but requires knowing CCTBX and Python
scripting. I can write a script-example for you, if interested, or feel
free to give it a try yourself and let me know if you need any help.
Pavel

On Wed, Jul 13, 2022 at 11:19 AM Ravikumar  wrote:

>
> Dear all,
>
>
> I would like to calculate One-dimension electron density profiles of the
> different number of ions bound to an ion channel. Are there any programs in
> CCP4/ Phenix which can do the same job as the MAPMAN (UPPSALA electron
> density server) program to extract the electron density values to plot
> electron density values versus pore axis? I have attached an example
> figure.
>
>
> Thank you,
>
> Ravikumar.
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed

[Rafal Dolot]

Dear CCP4 Users,

Thank you very much for all suggestions. Special thanks to Oliver for 
the ready-to-use files. Great job :) Hopefully it will solve my 
problems...


Best wishes,

Rafal
--
|--|
|Rafal Dolot, Ph.D.|
|  |
|Polish Academy of Sciences|
|Centre of Molecular and Macromolecular Studies|
|Division of Bioorganic Chemistry  |
|Macromolecular Crystallography Laboratory |
|Sienkiewicza 112  |
|90-363 Lodz, Poland   |
|Phone: +48(42)6803325 |
|Cell:  +48 502897781  |
|--|



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Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed

[Oliver Smart]

Dear Rafal,

Apologies my email client rather scrambled the text from my previous message, 
so I will send again here

Please find attached (in the previous message!) a restraint CIF file and a 
corresponding PDB file for your FESAN ligand.

Details:

Your ligand FESAN is a difficult test case for all restraint generation and 
refinement programs. It combines two carborane groups with a charged iron atom. 
Carborane groups have unusual chemistry that does not conform to normal valence 
models (they have carbon atoms bonded to six other atoms). Combining these 
groups with an iron atom that is bonded to 12 other atoms makes things even 
more complicated. Starting from a SMILES string is not wise for such a molecule.

Fortunately, such chemistry can be handled by the Grade2 restraint generator, 
that is supplied with BUSTER:

https://gphl.gitlab.io/grade2_docs/ 
Starting from the PDB file you supplied I converted to MOL2 format using CSD 
Mercury. Grade2 can read the MOL2 file and produce restraints (despite RDKit 
not being able to handle carboranes). All bond restraints are based on Mogul 
searches of CSD small molecule structures.

I manually edited the restraint CIF because there were too many bond angles to 
be useful. In the carborane cluster, each non-hydrogen atom is bonded to 5 
others to form an icosahedral shell, so that the bond length restraints alone 
are sufficient to fully define the geometry since all angles are implied. 
Additional bond angle restraints both within the cluster and for the 
12-coordinated FE atom are unnecessary and likely to be counter-productive.

It appears from CSD entries that FESAN is a cation carrying an overall charge 
of +1. But I did not correct this.

Please note that the atom names are slightly different from your PDB file as 
the FE atom has an uppercase atom name.

Unfortunately, the current CCP4 distribution of Coot 0.8.9.2-pre EL (revision 
count 7766) cannot cope this molecule as 'Send in the bond angels! Ahem I mean 
"Regularize Zone (Click two atoms)' produces a lock-up using all the CPU that 
has to be terminated by a kill. But you should be able to do a manual fit in 
Coot. BUSTER has no difficulty refining a structure with such restraints, as 
shown in this test using PDB entry 3I8W with FESAN replacing the CB5 ligand:

(Picture attached to previous message)
I hope that the restraint dictionary works for you.

All the best,

Oliver Smart, Andrew Sharff for BUSTER Developers.


> On 7 Jun 2022, at 08:35, Rafal Dolot  wrote:
> 
> Dear all,
> 
> Thank you very much for all your messages. Unfortunately, I'm still on the 
> same place, as yesterday...
> 
> First of all, I prepared a pdb/cif file of the ligand based on CCDC entry 
> 1176355 containing FESAN molecule. Also, I prepared SMILES file based on 
> SMILES of CB5 ligand (COSAN) available on PDB, where I simply switched Co 
> into Fe atom.
> 
> -> When I tried use acedrg with SMILES, I received an error info:
> 
> Input file: FSM.smi
> Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_27.cif
> Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_27.pdb
> workMode :  12
> Can not generate a molecule from the input SMILES string!
> Check your SMILES or report the bug
> Can not get the element symbols of atoms. Check input file format
> Error : The job stops because of errors
> 
> -> When I tried use acedrg with *pdb/*cif files I received no output files:
> 
> Input file: fsm.cif
> Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_21.cif
> Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_21.pdb
> workMode :  11
> Number of atoms in the cif file  0
> 
> -> When I tried use acedrg with *.mol file I received no output files:
> 
> Input file: fsm.mol
> Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_28.cif
> Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_28.pdb
> workMode :  13
> The system contains atoms of the following elements
> C B   Fe  H
> The input ligands/molecules contains metal or other heavier atoms
> Acedrg currently deals with ligands/molecules with following elements only
> C, N, O, S, P, B, F, Cl, Br, I, H
> The job finishes succesfully
> 
> 
> -> When I tried use prodrg, the program has been crashed:
> 
> The program run with command: cprodrg XYZIN 
> "C:/data_cryst/hsa_fesan_04/fsm.pdb" LIBOUT 
> "C:/data_cryst/hsa_fesan_04/fsm_prodrg1.cif" XYZOUT 
> "C:/data_cryst/hsa_fesan_04/fsm_prodrg1.pdb" MOLOUT 
> "C:/data_cryst/hsa_fesan_04/fsm_prodrg1.mol"
> has failed with error message
> forrtl: severe (157): Program Exception - access violation
> Image  PCRoutineLineSource
> cprodrg.exe7FF623CB058F  Unknown   Unknown  Unknown
> cprodrg.exe7FF623CB05E0  Unknown   Unknown  Unknown
> cprodrg.exe7FF623CAFB4F  Unknown   Unknown  Unknown
> 

Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed

[Fei Long]

Dear Rafal,

Acedrg could not handle with ligands containing metal elements at the
moment. When your input file was a mol file, acedrg gave that information.
For other kind of input format, acedrg should give the same information.
We are checking why it produced those confusing info.

The developments are under way to make acedrg capable of handling with
ligands containing atoms of metal elements.

Sorry about your situations.

Best wishes,

Fei


Dear all,

Thank you very much for all your messages. Unfortunately, I'm still on
the same place, as yesterday...

First of all, I prepared a pdb/cif file of the ligand based on CCDC
entry 1176355 containing FESAN molecule. Also, I prepared SMILES file
based on SMILES of CB5 ligand (COSAN) available on PDB, where I simply
switched Co into Fe atom.

-> When I tried use acedrg with SMILES, I received an error info:

Input file: FSM.smi
Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_27.cif
Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_27.pdb
workMode :  12
Can not generate a molecule from the input SMILES string!
Check your SMILES or report the bug
Can not get the element symbols of atoms. Check input file format
Error : The job stops because of errors

-> When I tried use acedrg with *pdb/*cif files I received no output
files:

Input file: fsm.cif
Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_21.cif
Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_21.pdb
workMode :  11
Number of atoms in the cif file  0

-> When I tried use acedrg with *.mol file I received no output files:

Input file: fsm.mol
Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_28.cif
Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_28.pdb
workMode :  13
The system contains atoms of the following elements
C   B   Fe  H
The input ligands/molecules contains metal or other heavier atoms
Acedrg currently deals with ligands/molecules with following elements
only
C, N, O, S, P, B, F, Cl, Br, I, H
The job finishes succesfully


-> When I tried use prodrg, the program has been crashed:

The program run with command: cprodrg XYZIN
"C:/data_cryst/hsa_fesan_04/fsm.pdb" LIBOUT
"C:/data_cryst/hsa_fesan_04/fsm_prodrg1.cif" XYZOUT
"C:/data_cryst/hsa_fesan_04/fsm_prodrg1.pdb" MOLOUT
"C:/data_cryst/hsa_fesan_04/fsm_prodrg1.mol"
has failed with error message
forrtl: severe (157): Program Exception - access violation
Image  PCRoutineLine
Source
cprodrg.exe7FF623CB058F  Unknown   Unknown
Unknown
cprodrg.exe7FF623CB05E0  Unknown   Unknown
Unknown
cprodrg.exe7FF623CAFB4F  Unknown   Unknown
Unknown
cprodrg.exe7FF623CB008E  Unknown   Unknown
Unknown
cprodrg.exe7FF623C5BDA8  Unknown   Unknown
Unknown
cprodrg.exe7FF623C3204E  Unknown   Unknown
Unknown
cprodrg.exe7FF623CAA81E  Unknown   Unknown
Unknown
cprodrg.exe7FF623CB3144  Unknown   Unknown
Unknown
KERNEL32.DLL   7FFEB3447034  Unknown   Unknown
Unknown
ntdll.dll  7FFEB4A22651  Unknown   Unknown
Unknown
***

-> I am still waiting for tokens from the prodrg web page ;) To be sure,
I used two emails, but with no response...

-> Ok, then I back to way I used years ago... JLigand was a good
solution, but... actually it is not working at all. I'm working under
Windows 10 / CCP4i, and I remember, there was the same issue in previous
version of CCP4.

-> Ok, then I back to the oldest solution -> using Sketcher. The program
is reading my PDB/CIF, but gave a warning when preparing a library, and
of course, no output _mon_lib.cif:

   WARNING : monomer:FSM  - has a minimal description.
   WARNING: there is no metal chirality for:Fe1
   WARNING: coords are not good enough to create Chirality
   WARNING :  /subroutine CALC_VOBSN/

I attached the PDB file containing the ligand of interest. From my
knowledge, it looks correct, but maybe I'm wrong. Have you any idea,
where is a problem?

Best,

Rafal

---
|--|
|Rafal Dolot, Ph.D.|
|  |
|Polish Academy of Sciences|
|Centre of Molecular and Macromolecular Studies|
|Division of Bioorganic Chemistry  |
|Macromolecular Crystallography Laboratory |
|Sienkiewicza 112  |
|90-363 Lodz, Poland   |
|Phone: +48(42)6803325 |
|Cell:  +48 502897781  |
|--|



W dniu 2022-06-06 14:52, Paul Emsley napisał(a):
> Although it may not be apparent, there has been a lot of work going on
> in 

Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed

[Rafal Dolot]

Dear all,

Thank you very much for all your messages. Unfortunately, I'm still on 
the same place, as yesterday...


First of all, I prepared a pdb/cif file of the ligand based on CCDC 
entry 1176355 containing FESAN molecule. Also, I prepared SMILES file 
based on SMILES of CB5 ligand (COSAN) available on PDB, where I simply 
switched Co into Fe atom.


-> When I tried use acedrg with SMILES, I received an error info:

Input file: FSM.smi
Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_27.cif
Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_27.pdb
workMode :  12
Can not generate a molecule from the input SMILES string!
Check your SMILES or report the bug
Can not get the element symbols of atoms. Check input file format
Error : The job stops because of errors

-> When I tried use acedrg with *pdb/*cif files I received no output 
files:


Input file: fsm.cif
Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_21.cif
Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_21.pdb
workMode :  11
Number of atoms in the cif file  0

-> When I tried use acedrg with *.mol file I received no output files:

Input file: fsm.mol
Output dictionary file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_28.cif
Output coordinate file: C:/data_cryst/hsa_fesan_04/hsa_fesan_04_28.pdb
workMode :  13
The system contains atoms of the following elements
C   B   Fe  H
The input ligands/molecules contains metal or other heavier atoms
Acedrg currently deals with ligands/molecules with following elements 
only

C, N, O, S, P, B, F, Cl, Br, I, H
The job finishes succesfully


-> When I tried use prodrg, the program has been crashed:

The program run with command: cprodrg XYZIN 
"C:/data_cryst/hsa_fesan_04/fsm.pdb" LIBOUT 
"C:/data_cryst/hsa_fesan_04/fsm_prodrg1.cif" XYZOUT 
"C:/data_cryst/hsa_fesan_04/fsm_prodrg1.pdb" MOLOUT 
"C:/data_cryst/hsa_fesan_04/fsm_prodrg1.mol"

has failed with error message
forrtl: severe (157): Program Exception - access violation
Image  PCRoutineLine
Source
cprodrg.exe7FF623CB058F  Unknown   Unknown  
Unknown
cprodrg.exe7FF623CB05E0  Unknown   Unknown  
Unknown
cprodrg.exe7FF623CAFB4F  Unknown   Unknown  
Unknown
cprodrg.exe7FF623CB008E  Unknown   Unknown  
Unknown
cprodrg.exe7FF623C5BDA8  Unknown   Unknown  
Unknown
cprodrg.exe7FF623C3204E  Unknown   Unknown  
Unknown
cprodrg.exe7FF623CAA81E  Unknown   Unknown  
Unknown
cprodrg.exe7FF623CB3144  Unknown   Unknown  
Unknown
KERNEL32.DLL   7FFEB3447034  Unknown   Unknown  
Unknown
ntdll.dll  7FFEB4A22651  Unknown   Unknown  
Unknown

***

-> I am still waiting for tokens from the prodrg web page ;) To be sure, 
I used two emails, but with no response...


-> Ok, then I back to way I used years ago... JLigand was a good 
solution, but... actually it is not working at all. I'm working under 
Windows 10 / CCP4i, and I remember, there was the same issue in previous 
version of CCP4.


-> Ok, then I back to the oldest solution -> using Sketcher. The program 
is reading my PDB/CIF, but gave a warning when preparing a library, and 
of course, no output _mon_lib.cif:


  WARNING : monomer:FSM  - has a minimal description.
  WARNING: there is no metal chirality for:Fe1
  WARNING: coords are not good enough to create Chirality
  WARNING :  /subroutine CALC_VOBSN/

I attached the PDB file containing the ligand of interest. From my 
knowledge, it looks correct, but maybe I'm wrong. Have you any idea, 
where is a problem?


Best,

Rafal

---
|--|
|Rafal Dolot, Ph.D.|
|  |
|Polish Academy of Sciences|
|Centre of Molecular and Macromolecular Studies|
|Division of Bioorganic Chemistry  |
|Macromolecular Crystallography Laboratory |
|Sienkiewicza 112  |
|90-363 Lodz, Poland   |
|Phone: +48(42)6803325 |
|Cell:  +48 502897781  |
|--|



W dniu 2022-06-06 14:52, Paul Emsley napisał(a):

Although it may not be apparent, there has been a lot of work going on
in Acedrg development regarding Boron.

One cannot say the same for Coot though and I can reproduce the
behaviour reported by Rafa Dolot. If/when I can fix it, it will be
available in 0.9.8.4.

Paul.

On 06/06/2022 13:24, Boaz Shaanan wrote:


Hi,
In case you don't have a cif file for the ligand, I would load the
SMILES expression into acedrg (or use any other input option) to
create a cif file which 

Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed

[Lucrezia Catapano - MRC LMB]

Hi,

as previously suggested you can use AceDRG to generate a cif file for your
ligand by input different type of files (SMILES, mmCIF, SDF/MOL, and SYBYL
MOL2 files).

You can use the AceDRG command line:
https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/acedrg/acedrg.html

or via ccp4i2, 'Ligands' menu, 'make ligand-AceDRG'.


Regards
Lucrezia
> Dear CCP4 Users,
>
> I am working with data containing a possible complex of protein with
> FESAN (iron bis(1,2-dicarbollide)). Unfortunately, to my knowledge, this
> ligand is not available in PDB. The closest molecule is COSAN (cobalt
> bis(1,2-dicarbollide)), which is labelled as CB5 and is available in two
> PDB entries. I can load this molecule into Coot, but attempts at ligand
> search or refinement of the manually matched molecule result in freezing
> of the Coot window. FESAN is not present in CCDC as a single molecule,
> but only in some complexes. Could you give me some advice on how to
> prepare a new ligand like this one, for incorporation into the protein
> and further refinement?
>
> Best regards,
>
> Rafal Dolot
>
> --
> |--|
> |Rafal Dolot, Ph.D.|
> |  |
> |Polish Academy of Sciences|
> |Centre of Molecular and Macromolecular Studies|
> |Division of Bioorganic Chemistry  |
> |Macromolecular Crystallography Laboratory |
> |Sienkiewicza 112  |
> |90-363 Lodz, Poland   |
> |Phone: +48(42)6803325 |
> |Cell:  +48 502897781  |
> |--|
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing
> list hosted by www.jiscmail.ac.uk, terms & conditions are available at
> https://www.jiscmail.ac.uk/policyandsecurity/
>


Lucrezia Catapano
PhD student
Murshudov Group
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge CB2 0QH
United Kingdom



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Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed

[Paul Emsley]

Although it may not be apparent, there has been a lot of work going on 
in Acedrg development regarding Boron.


One cannot say the same for Coot though and I can reproduce the 
behaviour reported by Rafa Dolot. If/when I can fix it, it will be 
available in 0.9.8.4.


Paul.


On 06/06/2022 13:24, Boaz Shaanan wrote:

Hi,
In case you don't have a cif file for the ligand, I would load the 
SMILES expression into acedrg (or use any other input option) to 
create a cif file which you can then read into Coot.

Cheers,
Boaz
On Jun 6, 2022 15:06, Rafal Dolot  wrote:
Dear CCP4 Users,

I am working with data containing a possible complex of protein with
FESAN (iron bis(1,2-dicarbollide)). Unfortunately, to my knowledge, this
ligand is not available in PDB. The closest molecule is COSAN (cobalt
bis(1,2-dicarbollide)), which is labelled as CB5 and is available in two
PDB entries. I can load this molecule into Coot, but attempts at ligand
search or refinement of the manually matched molecule result in freezing
of the Coot window. FESAN is not present in CCDC as a single molecule,
but only in some complexes. Could you give me some advice on how to
prepare a new ligand like this one, for incorporation into the protein
and further refinement?




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Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed

[Boaz Shaanan]

Hi,
In case you don't have a cif file for the ligand, I would load the SMILES 
expression into acedrg (or use any other input option) to create a cif file 
which you can then read into Coot.
Cheers,
Boaz

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

On Jun 6, 2022 15:06, Rafal Dolot  wrote:
Dear CCP4 Users,

I am working with data containing a possible complex of protein with
FESAN (iron bis(1,2-dicarbollide)). Unfortunately, to my knowledge, this
ligand is not available in PDB. The closest molecule is COSAN (cobalt
bis(1,2-dicarbollide)), which is labelled as CB5 and is available in two
PDB entries. I can load this molecule into Coot, but attempts at ligand
search or refinement of the manually matched molecule result in freezing
of the Coot window. FESAN is not present in CCDC as a single molecule,
but only in some complexes. Could you give me some advice on how to
prepare a new ligand like this one, for incorporation into the protein
and further refinement?

Best regards,

Rafal Dolot

--
|--|
|Rafal Dolot, Ph.D.|
|  |
|Polish Academy of Sciences|
|Centre of Molecular and Macromolecular Studies|
|Division of Bioorganic Chemistry  |
|Macromolecular Crystallography Laboratory |
|Sienkiewicza 112  |
|90-363 Lodz, Poland   |
|Phone: +48(42)6803325 |
|Cell:  +48 502897781  |
|--|



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

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[ccp4bb] Help with preparation of the ligand coordinates/restraints needed

[Rafal Dolot]

Dear CCP4 Users,

I am working with data containing a possible complex of protein with 
FESAN (iron bis(1,2-dicarbollide)). Unfortunately, to my knowledge, this 
ligand is not available in PDB. The closest molecule is COSAN (cobalt 
bis(1,2-dicarbollide)), which is labelled as CB5 and is available in two 
PDB entries. I can load this molecule into Coot, but attempts at ligand 
search or refinement of the manually matched molecule result in freezing 
of the Coot window. FESAN is not present in CCDC as a single molecule, 
but only in some complexes. Could you give me some advice on how to 
prepare a new ligand like this one, for incorporation into the protein 
and further refinement?


Best regards,

Rafal Dolot

--
|--|
|Rafal Dolot, Ph.D.|
|  |
|Polish Academy of Sciences|
|Centre of Molecular and Macromolecular Studies|
|Division of Bioorganic Chemistry  |
|Macromolecular Crystallography Laboratory |
|Sienkiewicza 112  |
|90-363 Lodz, Poland   |
|Phone: +48(42)6803325 |
|Cell:  +48 502897781  |
|--|



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Re: [ccp4bb] help request (synchrotron schedules)

[Marcin Wojdyr]

If you'd be interested in historical synchrotron schedules, they can
be approximately guessed from pdb data, from data collection dates.
Unfortunately, in many entries the dates are random, so there is
significant noise there. Here is how it looks:
https://project-gemmi.github.io/pdb-stats/calendar.html


On Mon, May 2, 2022 at 7:38 PM Artem Evdokimov
 wrote:
>
> Dear CCP4-ers :)
>
> I used to have a handy chart where major synchrotron schedules were all drawn 
> out as lines (across an entire year) with shutdowns and other blackout dates 
> marked such that it was pretty easy to find what synchrotron is open for 
> business at what week/month. This schedule took me a while to assemble since 
> not every synchrotron handily posts their shutdown schedule and one has to 
> call friends and ask around.
>
> Needless to say, being a putz that I am, I eventually lost this lovely 
> document. So, I wonder - does anyone here have something similar that they 
> won't mind sharing? If enough people share (even individual schedules) I am 
> happy to post the resulting schedule back here for everyone to enjoy...
>
> Many thanks!
>
> Artem
>
> - Cosmic Cats approve of this message
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1



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[ccp4bb] help request (synchrotron schedules)

[Artem Evdokimov]

Dear CCP4-ers :)

I used to have a handy chart where major synchrotron schedules were all
drawn out as lines (across an entire year) with shutdowns and other
blackout dates marked such that it was pretty easy to find what
synchrotron is open for business at what week/month. This schedule took me
a while to assemble since not every synchrotron handily posts their
shutdown schedule and one has to call friends and ask around.

Needless to say, being a putz that I am, I eventually lost this lovely
document. So, I wonder - does anyone here have something similar that they
won't mind sharing? If enough people share (even individual schedules) I am
happy to post the resulting schedule back here for everyone to enjoy...

Many thanks!

Artem

- Cosmic Cats approve of this message



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Re: [ccp4bb] Help with interpreting Tyrosine modification

[Jon Cooper]

Hello, yes, that's right. We've all seen guanidinium groups parallel with 
aromatic rings and shielding them from solvent. I think it might approach that 
sort of arrangement in this case. Cheers, Jon.C.

Sent from ProtonMail mobile

 Original Message 
On 1 Feb 2022, 16:52, Krieger, James M wrote:

> Probably arginine and tyrosine do like each other a fair bit. They can form 
> both cation-pi interactions and hydrogen bonds.
> Best wishes
> James
>
>> On 1 Feb 2022, at 16:41, Jon Cooper 
>> <488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Hello, I did wonder if it might be an alternative conformation for the 
>> quanidinium group of that nearby arginine. Being such high resolution, quite 
>> low occupancy groups would show up, I think, but it may just be too far away 
>> and I don't know how much tyrosine and arginine like each other!
>>
>> Sent from ProtonMail mobile
>>
>>  Original Message 
>> On 1 Feb 2022, 09:28, Misba Ahmad < misba.ah...@gmail.com> wrote:
>>
>>> Thank you for your suggestions.
>>> As this is a high resolution structure (1.1Å) I have been refining it with 
>>> anisotropic B-factors.
>>> Placing a propionate or modelling a phosphate at this position blows up 
>>> during the refinement.
>>> I will inform you if I am successful in figuring this out.
>>>
>>> Best
>>> Misbha
>>>
>>> On Sat, Jan 29, 2022 at 7:01 PM SHEPARD William 
>>>  wrote:
>>>
>>>> Dear Misba,
>>>>
>>>> Perhaps it's a silly question, but have you tried to model in propionate? 
>>>> The carboxylate group could make H-bonds to both the Arginine sidechain 
>>>> and the the tyrosine OH group. Propionate should show no anomalous signal.
>>>>
>>>> Just my 2-bits worth.
>>>>
>>>> Cheers,
>>>> Bill
>>>>
>>>> - Original Message -
>>>> From: "Gerard Bricogne" 
>>>> To: CCP4BB@JISCMAIL.AC.UK
>>>> Sent: Saturday, 29 January, 2022 18:34:26
>>>> Subject: Re: [ccp4bb] Help with interpreting Tyrosine modification
>>>>
>>>> Dear Misba,
>>>>
>>>> Thank you for your reply and for the very clear picture. I hope you
>>>> will be able to share the result once the mystery is solved.
>>>>
>>>> With best wishes,
>>>>
>>>> Gerard.
>>>>
>>>> --
>>>> On Sat, Jan 29, 2022 at 03:32:30PM +0100, Misba Ahmad wrote:
>>>>> Dear Gerard,
>>>>> The data were collected at 0.966Å and I can see the anomalous peaks for As
>>>>> at Cysteines which are modified and I have correctly modelled those (see
>>>>> image below). However, at this Tyr, I don't see an anomalous signal.
>>>>>
>>>>> [image: 4.png]
>>>>>
>>>>> On Sat, Jan 29, 2022 at 3:06 PM Gerard Bricogne 
>>>>> wrote:
>>>>>
>>>>> > Dear Misba,
>>>>> >
>>>>> > A wild guess: have you considered the possibility that this extra
>>>>> > density could be a cacodylate adduct? Cacodylate is well known to react
>>>>> > with
>>>>> > thiols - see
>>>>> >
>>>>> >
>>>>> > [https://febs.onlinelibrary.wiley.com/doi/pdfdirect/10.1016/0014-5793(72)80224-2](https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Ffebs.onlinelibrary.wiley.com%2Fdoi%2Fpdfdirect%2F10.1016%2F0014-5793(72)80224-2=04%7C01%7Ckriegerj%40PITT.EDU%7C3bfe6a715d964db88a1c08d9e5a1740e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637793305180888406%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000=quySIsk%2BnzbHh5o3bYoOGbiXsx1ItJGTt3y6aI2oc5M%3D=0)
>>>>> >
>>>>> > Here the chemistry is different but you never know. If your data are
>>>>> > redundant enough that you have good anomalous completeness, and were
>>>>> > collected above the As K-edge (11.8667 keV), it might be a good idea to
>>>>> > compute an anomalous difference Fourier and check for the presence of a
>>>>> > peak
>>>>> > at the same location as the highest one in your ordinary difference map.
>>>>> >
>>>>> > Only a wild guess, though ... .
>>>>> >
>>>>> >
>>>>> > With best wishes,
>>>>> >

Re: [ccp4bb] Help with interpreting Tyrosine modification

[Krieger, James M]

Probably arginine and tyrosine do like each other a fair bit. They can form 
both cation-pi interactions and hydrogen bonds.
Best wishes
James

On 1 Feb 2022, at 16:41, Jon Cooper 
<488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote:

Hello, I did wonder if it might be an alternative conformation for the 
quanidinium group of that nearby arginine. Being such high resolution, quite 
low occupancy groups would show up, I think, but it may just be too far away 
and I don't know how much tyrosine and arginine like each other!


Sent from ProtonMail mobile



 Original Message 
On 1 Feb 2022, 09:28, Misba Ahmad < misba.ah...@gmail.com> wrote:

Thank you for your suggestions.
As this is a high resolution structure (1.1Å) I have been refining it with 
anisotropic B-factors.
Placing a propionate or modelling a phosphate at this position blows up during 
the refinement.
I will inform you if I am successful in figuring this out.

Best
Misbha


On Sat, Jan 29, 2022 at 7:01 PM SHEPARD William 
mailto:william.shep...@synchrotron-soleil.fr>>
 wrote:
Dear Misba,

Perhaps it's a silly question, but have you tried to model in propionate? The 
carboxylate group could make H-bonds to both the Arginine sidechain and the the 
tyrosine OH group. Propionate should show no anomalous signal.

Just my 2-bits worth.

Cheers,
Bill


- Original Message -
From: "Gerard Bricogne" mailto:g...@globalphasing.com>>
To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>
Sent: Saturday, 29 January, 2022 18:34:26
Subject: Re: [ccp4bb] Help with interpreting Tyrosine modification

Dear Misba,

 Thank you for your reply and for the very clear picture. I hope you
will be able to share the result once the mystery is solved.

 With best wishes,

  Gerard.

--
On Sat, Jan 29, 2022 at 03:32:30PM +0100, Misba Ahmad wrote:
> Dear Gerard,
> The data were collected at 0.966Å and I can see the anomalous peaks for As
> at Cysteines which are modified and I have correctly modelled those (see
> image below). However, at this Tyr, I don't see an anomalous signal.
>
> [image: 4.png]
>
> On Sat, Jan 29, 2022 at 3:06 PM Gerard Bricogne 
> mailto:g...@globalphasing.com>>
> wrote:
>
> > Dear Misba,
> >
> >  A wild guess: have you considered the possibility that this extra
> > density could be a cacodylate adduct? Cacodylate is well known to react
> > with
> > thiols - see
> >
> >
> > https://febs.onlinelibrary.wiley.com/doi/pdfdirect/10.1016/0014-5793(72)80224-2<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Ffebs.onlinelibrary.wiley.com%2Fdoi%2Fpdfdirect%2F10.1016%2F0014-5793(72)80224-2=04%7C01%7Ckriegerj%40PITT.EDU%7C3bfe6a715d964db88a1c08d9e5a1740e%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C0%7C637793305180888406%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000=quySIsk%2BnzbHh5o3bYoOGbiXsx1ItJGTt3y6aI2oc5M%3D=0>
> >
> > Here the chemistry is different but you never know. If your data are
> > redundant enough that you have good anomalous completeness, and were
> > collected above the As K-edge (11.8667 keV), it might be a good idea to
> > compute an anomalous difference Fourier and check for the presence of a
> > peak
> > at the same location as the highest one in your ordinary difference map.
> >
> >  Only a wild guess, though ... .
> >
> >
> >  With best wishes,
> >
> >   Gerard.
> >
> > --
> > On Sat, Jan 29, 2022 at 12:18:58PM +0100, Misba Ahmad wrote:
> > > Placing a water molecule satisfies most of the density and forms nice
> > > H-bonds but there is still some residual density left (8.6 and 5.6 rmsd).
> > >
> > > Best
> > > Misbha
> > > [image: 3.png]
> > >
> > >
> > > On Sat, Jan 29, 2022 at 11:05 AM Klaus Futterer 
> > > mailto:k.futte...@bham.ac.uk>>
> > > wrote:
> > >
> > > > Looks more like water molecules. Phosphorylation would give a much
> > bigger
> > > > peak, and shape of density does not fit either. I don't think this is a
> > > > covalent modification. Model some water molecules and see what the
> > > > distances are and what difference density is left.
> > > >
> > > >
> > > > Klaus
> > > >
> > > >
> > > > ===
> > > > Klaus Fütterer, PhD
> > > > Reader in Structural Biology
> > > >
> > > >
> > > > School of Biosciences
> > > > LES CollegeEmail:
> > > > k.f

Re: [ccp4bb] Help with interpreting Tyrosine modification

[Jon Cooper]

Hello, I did wonder if it might be an alternative conformation for the 
quanidinium group of that nearby arginine. Being such high resolution, quite 
low occupancy groups would show up, I think, but it may just be too far away 
and I don't know how much tyrosine and arginine like each other!

Sent from ProtonMail mobile

 Original Message 
On 1 Feb 2022, 09:28, Misba Ahmad wrote:

> Thank you for your suggestions.
> As this is a high resolution structure (1.1Å) I have been refining it with 
> anisotropic B-factors.
> Placing a propionate or modelling a phosphate at this position blows up 
> during the refinement.
> I will inform you if I am successful in figuring this out.
>
> Best
> Misbha
>
> On Sat, Jan 29, 2022 at 7:01 PM SHEPARD William 
>  wrote:
>
>> Dear Misba,
>>
>> Perhaps it's a silly question, but have you tried to model in propionate? 
>> The carboxylate group could make H-bonds to both the Arginine sidechain and 
>> the the tyrosine OH group. Propionate should show no anomalous signal.
>>
>> Just my 2-bits worth.
>>
>> Cheers,
>> Bill
>>
>> - Original Message -
>> From: "Gerard Bricogne" 
>> To: CCP4BB@JISCMAIL.AC.UK
>> Sent: Saturday, 29 January, 2022 18:34:26
>> Subject: Re: [ccp4bb] Help with interpreting Tyrosine modification
>>
>> Dear Misba,
>>
>> Thank you for your reply and for the very clear picture. I hope you
>> will be able to share the result once the mystery is solved.
>>
>> With best wishes,
>>
>> Gerard.
>>
>> --
>> On Sat, Jan 29, 2022 at 03:32:30PM +0100, Misba Ahmad wrote:
>>> Dear Gerard,
>>> The data were collected at 0.966Å and I can see the anomalous peaks for As
>>> at Cysteines which are modified and I have correctly modelled those (see
>>> image below). However, at this Tyr, I don't see an anomalous signal.
>>>
>>> [image: 4.png]
>>>
>>> On Sat, Jan 29, 2022 at 3:06 PM Gerard Bricogne 
>>> wrote:
>>>
>>> > Dear Misba,
>>> >
>>> > A wild guess: have you considered the possibility that this extra
>>> > density could be a cacodylate adduct? Cacodylate is well known to react
>>> > with
>>> > thiols - see
>>> >
>>> >
>>> > https://febs.onlinelibrary.wiley.com/doi/pdfdirect/10.1016/0014-5793(72)80224-2
>>> >
>>> > Here the chemistry is different but you never know. If your data are
>>> > redundant enough that you have good anomalous completeness, and were
>>> > collected above the As K-edge (11.8667 keV), it might be a good idea to
>>> > compute an anomalous difference Fourier and check for the presence of a
>>> > peak
>>> > at the same location as the highest one in your ordinary difference map.
>>> >
>>> > Only a wild guess, though ... .
>>> >
>>> >
>>> > With best wishes,
>>> >
>>> > Gerard.
>>> >
>>> > --
>>> > On Sat, Jan 29, 2022 at 12:18:58PM +0100, Misba Ahmad wrote:
>>> > > Placing a water molecule satisfies most of the density and forms nice
>>> > > H-bonds but there is still some residual density left (8.6 and 5.6 
>>> > > rmsd).
>>> > >
>>> > > Best
>>> > > Misbha
>>> > > [image: 3.png]
>>> > >
>>> > >
>>> > > On Sat, Jan 29, 2022 at 11:05 AM Klaus Futterer 
>>> > > wrote:
>>> > >
>>> > > > Looks more like water molecules. Phosphorylation would give a much
>>> > bigger
>>> > > > peak, and shape of density does not fit either. I don't think this is 
>>> > > > a
>>> > > > covalent modification. Model some water molecules and see what the
>>> > > > distances are and what difference density is left.
>>> > > >
>>> > > >
>>> > > > Klaus
>>> > > >
>>> > > >
>>> > > > ===
>>> > > > Klaus Fütterer, PhD
>>> > > > Reader in Structural Biology
>>> > > >
>>> > > >
>>> > > > School of Biosciences
>>> > > > LES College Email:
>>> > > > k.futte...@bham.ac.uk
>>> > > > University of Birmingham Phone: +44 - 121 - 414
>>> > > > 5895
>>&

Re: [ccp4bb] Help with interpreting Tyrosine modification

[Misba Ahmad]

Thank you for your suggestions.
As this is a high resolution structure (1.1Å) I have been refining it with
anisotropic B-factors.
Placing a propionate or modelling a phosphate at this position blows up
during the refinement.
I will inform you if I am successful in figuring this out.

Best
Misbha


On Sat, Jan 29, 2022 at 7:01 PM SHEPARD William <
william.shep...@synchrotron-soleil.fr> wrote:

> Dear Misba,
>
> Perhaps it's a silly question, but have you tried to model in propionate?
> The carboxylate group could make H-bonds to both the Arginine sidechain and
> the the tyrosine OH group. Propionate should show no anomalous signal.
>
> Just my 2-bits worth.
>
> Cheers,
> Bill
>
>
> - Original Message -
> From: "Gerard Bricogne" 
> To: CCP4BB@JISCMAIL.AC.UK
> Sent: Saturday, 29 January, 2022 18:34:26
> Subject: Re: [ccp4bb] Help with interpreting Tyrosine modification
>
> Dear Misba,
>
>  Thank you for your reply and for the very clear picture. I hope you
> will be able to share the result once the mystery is solved.
>
>  With best wishes,
>
>   Gerard.
>
> --
> On Sat, Jan 29, 2022 at 03:32:30PM +0100, Misba Ahmad wrote:
> > Dear Gerard,
> > The data were collected at 0.966Å and I can see the anomalous peaks for
> As
> > at Cysteines which are modified and I have correctly modelled those (see
> > image below). However, at this Tyr, I don't see an anomalous signal.
> >
> > [image: 4.png]
> >
> > On Sat, Jan 29, 2022 at 3:06 PM Gerard Bricogne 
> > wrote:
> >
> > > Dear Misba,
> > >
> > >  A wild guess: have you considered the possibility that this extra
> > > density could be a cacodylate adduct? Cacodylate is well known to react
> > > with
> > > thiols - see
> > >
> > >
> > >
> https://febs.onlinelibrary.wiley.com/doi/pdfdirect/10.1016/0014-5793(72)80224-2
> > >
> > > Here the chemistry is different but you never know. If your data are
> > > redundant enough that you have good anomalous completeness, and were
> > > collected above the As K-edge (11.8667 keV), it might be a good idea to
> > > compute an anomalous difference Fourier and check for the presence of a
> > > peak
> > > at the same location as the highest one in your ordinary difference
> map.
> > >
> > >  Only a wild guess, though ... .
> > >
> > >
> > >  With best wishes,
> > >
> > >   Gerard.
> > >
> > > --
> > > On Sat, Jan 29, 2022 at 12:18:58PM +0100, Misba Ahmad wrote:
> > > > Placing a water molecule satisfies most of the density and forms nice
> > > > H-bonds but there is still some residual density left (8.6 and 5.6
> rmsd).
> > > >
> > > > Best
> > > > Misbha
> > > > [image: 3.png]
> > > >
> > > >
> > > > On Sat, Jan 29, 2022 at 11:05 AM Klaus Futterer <
> k.futte...@bham.ac.uk>
> > > > wrote:
> > > >
> > > > > Looks more like water molecules. Phosphorylation would give a much
> > > bigger
> > > > > peak, and shape of density does not fit either. I don't think this
> is a
> > > > > covalent modification. Model some water molecules and see what the
> > > > > distances are and what difference density is left.
> > > > >
> > > > >
> > > > > Klaus
> > > > >
> > > > >
> > > > > ===
> > > > > Klaus Fütterer, PhD
> > > > > Reader in Structural Biology
> > > > >
> > > > >
> > > > > School of Biosciences
> > > > > LES CollegeEmail:
> > > > > k.futte...@bham.ac.uk
> > > > > University of Birmingham Phone: +44 - 121
> - 414
> > > > > 5895
> > > > > Birmingham, B15 2TT, UK(voice mail messages
> > > > > will forward to my email inbox)
> > > > >
> > > > > My normal working hours are Mon - Fri 8.30 - 5.30 pm.
> > > > >
> > > > >
> > > > > ===
> > > > > --
> > > > > *From:* CCP4 bulletin board  on behalf of
> > > > > misba.ah...@gmail.com 
> > > > > *Sent:* 29 January 2022 09:45:24
> >

Re: [ccp4bb] Help with interpreting Tyrosine modification

[SHEPARD William]

Dear Misba, 

Perhaps it's a silly question, but have you tried to model in propionate? The 
carboxylate group could make H-bonds to both the Arginine sidechain and the the 
tyrosine OH group. Propionate should show no anomalous signal.

Just my 2-bits worth. 

Cheers, 
Bill


- Original Message -
From: "Gerard Bricogne" 
To: CCP4BB@JISCMAIL.AC.UK
Sent: Saturday, 29 January, 2022 18:34:26
Subject: Re: [ccp4bb] Help with interpreting Tyrosine modification

Dear Misba,

 Thank you for your reply and for the very clear picture. I hope you
will be able to share the result once the mystery is solved.

 With best wishes,

  Gerard.

--
On Sat, Jan 29, 2022 at 03:32:30PM +0100, Misba Ahmad wrote:
> Dear Gerard,
> The data were collected at 0.966Å and I can see the anomalous peaks for As
> at Cysteines which are modified and I have correctly modelled those (see
> image below). However, at this Tyr, I don't see an anomalous signal.
> 
> [image: 4.png]
> 
> On Sat, Jan 29, 2022 at 3:06 PM Gerard Bricogne 
> wrote:
> 
> > Dear Misba,
> >
> >  A wild guess: have you considered the possibility that this extra
> > density could be a cacodylate adduct? Cacodylate is well known to react
> > with
> > thiols - see
> >
> >
> > https://febs.onlinelibrary.wiley.com/doi/pdfdirect/10.1016/0014-5793(72)80224-2
> >
> > Here the chemistry is different but you never know. If your data are
> > redundant enough that you have good anomalous completeness, and were
> > collected above the As K-edge (11.8667 keV), it might be a good idea to
> > compute an anomalous difference Fourier and check for the presence of a
> > peak
> > at the same location as the highest one in your ordinary difference map.
> >
> >  Only a wild guess, though ... .
> >
> >
> >  With best wishes,
> >
> >   Gerard.
> >
> > --
> > On Sat, Jan 29, 2022 at 12:18:58PM +0100, Misba Ahmad wrote:
> > > Placing a water molecule satisfies most of the density and forms nice
> > > H-bonds but there is still some residual density left (8.6 and 5.6 rmsd).
> > >
> > > Best
> > > Misbha
> > > [image: 3.png]
> > >
> > >
> > > On Sat, Jan 29, 2022 at 11:05 AM Klaus Futterer 
> > > wrote:
> > >
> > > > Looks more like water molecules. Phosphorylation would give a much
> > bigger
> > > > peak, and shape of density does not fit either. I don't think this is a
> > > > covalent modification. Model some water molecules and see what the
> > > > distances are and what difference density is left.
> > > >
> > > >
> > > > Klaus
> > > >
> > > >
> > > > ===
> > > > Klaus Fütterer, PhD
> > > > Reader in Structural Biology
> > > >
> > > >
> > > > School of Biosciences
> > > > LES CollegeEmail:
> > > > k.futte...@bham.ac.uk
> > > > University of Birmingham Phone: +44 - 121 - 414
> > > > 5895
> > > > Birmingham, B15 2TT, UK(voice mail messages
> > > > will forward to my email inbox)
> > > >
> > > > My normal working hours are Mon - Fri 8.30 - 5.30 pm.
> > > >
> > > >
> > > > ===
> > > > --
> > > > *From:* CCP4 bulletin board  on behalf of
> > > > misba.ah...@gmail.com 
> > > > *Sent:* 29 January 2022 09:45:24
> > > > *To:* CCP4BB@JISCMAIL.AC.UK
> > > > *Subject:* Re: [ccp4bb] Help with interpreting Tyrosine modification
> > > >
> > > > Hi Tom,
> > > > The protein was expressed in E Coli.
> > > >
> > > > Best
> > > > Misbha
> > > >
> > > > On Sat, 29 Jan 2022, 10:18 Peat, Tom (Manufacturing, Clayton) <
> > > > tom.p...@csiro.au> wrote:
> > > >
> > > >> Hello Misba,
> > > >>
> > > >> Doesn't quite look like a phosphate, maybe O-sulfation?
> > > >> Maybe just as important as the buffer and crystallisation conditions
> > > >> would be how it was expressed? Insect cells?
> > > >>
> > > >> Best of luck, tom
> > > >>
> > > >> Tom Peat, PhD
> > > >>
> > > >> Biomedical Program, CSI

Re: [ccp4bb] Help with interpreting Tyrosine modification

[Gerard Bricogne]

Dear Misba,

 Thank you for your reply and for the very clear picture. I hope you
will be able to share the result once the mystery is solved.

 With best wishes,

  Gerard.

--
On Sat, Jan 29, 2022 at 03:32:30PM +0100, Misba Ahmad wrote:
> Dear Gerard,
> The data were collected at 0.966Å and I can see the anomalous peaks for As
> at Cysteines which are modified and I have correctly modelled those (see
> image below). However, at this Tyr, I don't see an anomalous signal.
> 
> [image: 4.png]
> 
> On Sat, Jan 29, 2022 at 3:06 PM Gerard Bricogne 
> wrote:
> 
> > Dear Misba,
> >
> >  A wild guess: have you considered the possibility that this extra
> > density could be a cacodylate adduct? Cacodylate is well known to react
> > with
> > thiols - see
> >
> >
> > https://febs.onlinelibrary.wiley.com/doi/pdfdirect/10.1016/0014-5793(72)80224-2
> >
> > Here the chemistry is different but you never know. If your data are
> > redundant enough that you have good anomalous completeness, and were
> > collected above the As K-edge (11.8667 keV), it might be a good idea to
> > compute an anomalous difference Fourier and check for the presence of a
> > peak
> > at the same location as the highest one in your ordinary difference map.
> >
> >  Only a wild guess, though ... .
> >
> >
> >  With best wishes,
> >
> >   Gerard.
> >
> > --
> > On Sat, Jan 29, 2022 at 12:18:58PM +0100, Misba Ahmad wrote:
> > > Placing a water molecule satisfies most of the density and forms nice
> > > H-bonds but there is still some residual density left (8.6 and 5.6 rmsd).
> > >
> > > Best
> > > Misbha
> > > [image: 3.png]
> > >
> > >
> > > On Sat, Jan 29, 2022 at 11:05 AM Klaus Futterer 
> > > wrote:
> > >
> > > > Looks more like water molecules. Phosphorylation would give a much
> > bigger
> > > > peak, and shape of density does not fit either. I don't think this is a
> > > > covalent modification. Model some water molecules and see what the
> > > > distances are and what difference density is left.
> > > >
> > > >
> > > > Klaus
> > > >
> > > >
> > > > ===
> > > > Klaus Fütterer, PhD
> > > > Reader in Structural Biology
> > > >
> > > >
> > > > School of Biosciences
> > > > LES CollegeEmail:
> > > > k.futte...@bham.ac.uk
> > > > University of Birmingham Phone: +44 - 121 - 414
> > > > 5895
> > > > Birmingham, B15 2TT, UK(voice mail messages
> > > > will forward to my email inbox)
> > > >
> > > > My normal working hours are Mon - Fri 8.30 - 5.30 pm.
> > > >
> > > >
> > > > ===
> > > > --
> > > > *From:* CCP4 bulletin board  on behalf of
> > > > misba.ah...@gmail.com 
> > > > *Sent:* 29 January 2022 09:45:24
> > > > *To:* CCP4BB@JISCMAIL.AC.UK
> > > > *Subject:* Re: [ccp4bb] Help with interpreting Tyrosine modification
> > > >
> > > > Hi Tom,
> > > > The protein was expressed in E Coli.
> > > >
> > > > Best
> > > > Misbha
> > > >
> > > > On Sat, 29 Jan 2022, 10:18 Peat, Tom (Manufacturing, Clayton) <
> > > > tom.p...@csiro.au> wrote:
> > > >
> > > >> Hello Misba,
> > > >>
> > > >> Doesn't quite look like a phosphate, maybe O-sulfation?
> > > >> Maybe just as important as the buffer and crystallisation conditions
> > > >> would be how it was expressed? Insect cells?
> > > >>
> > > >> Best of luck, tom
> > > >>
> > > >> Tom Peat, PhD
> > > >>
> > > >> Biomedical Program, CSIRO
> > > >> tom.p...@csiro.au
> > > >>
> > > >> --
> > > >> *From:* CCP4 bulletin board  on behalf of
> > Misba
> > > >> Ahmad 
> > > >> *Sent:* Saturday, January 29, 2022 8:12 PM
> > > >> *To:* CCP4BB@JISCMAIL.AC.UK 
> > > >> *Subject:* [ccp4bb] Help with interpreting Tyrosine modification
> > > >>
> > &g

Re: [ccp4bb] Help with interpreting Tyrosine modification

[Gerard Bricogne]

Dear Misba,

 A wild guess: have you considered the possibility that this extra
density could be a cacodylate adduct? Cacodylate is well known to react with
thiols - see 

https://febs.onlinelibrary.wiley.com/doi/pdfdirect/10.1016/0014-5793(72)80224-2

Here the chemistry is different but you never know. If your data are
redundant enough that you have good anomalous completeness, and were
collected above the As K-edge (11.8667 keV), it might be a good idea to
compute an anomalous difference Fourier and check for the presence of a peak
at the same location as the highest one in your ordinary difference map.

 Only a wild guess, though ... .


 With best wishes,

  Gerard.

--
On Sat, Jan 29, 2022 at 12:18:58PM +0100, Misba Ahmad wrote:
> Placing a water molecule satisfies most of the density and forms nice
> H-bonds but there is still some residual density left (8.6 and 5.6 rmsd).
> 
> Best
> Misbha
> [image: 3.png]
> 
> 
> On Sat, Jan 29, 2022 at 11:05 AM Klaus Futterer 
> wrote:
> 
> > Looks more like water molecules. Phosphorylation would give a much bigger
> > peak, and shape of density does not fit either. I don't think this is a
> > covalent modification. Model some water molecules and see what the
> > distances are and what difference density is left.
> >
> >
> > Klaus
> >
> >
> > ===
> > Klaus Fütterer, PhD
> > Reader in Structural Biology
> >
> >
> > School of Biosciences
> > LES CollegeEmail:
> > k.futte...@bham.ac.uk
> > University of Birmingham Phone: +44 - 121 - 414
> > 5895
> > Birmingham, B15 2TT, UK(voice mail messages
> > will forward to my email inbox)
> >
> > My normal working hours are Mon - Fri 8.30 - 5.30 pm.
> >
> >
> > ===
> > --
> > *From:* CCP4 bulletin board  on behalf of
> > misba.ah...@gmail.com 
> > *Sent:* 29 January 2022 09:45:24
> > *To:* CCP4BB@JISCMAIL.AC.UK
> > *Subject:* Re: [ccp4bb] Help with interpreting Tyrosine modification
> >
> > Hi Tom,
> > The protein was expressed in E Coli.
> >
> > Best
> > Misbha
> >
> > On Sat, 29 Jan 2022, 10:18 Peat, Tom (Manufacturing, Clayton) <
> > tom.p...@csiro.au> wrote:
> >
> >> Hello Misba,
> >>
> >> Doesn't quite look like a phosphate, maybe O-sulfation?
> >> Maybe just as important as the buffer and crystallisation conditions
> >> would be how it was expressed? Insect cells?
> >>
> >> Best of luck, tom
> >>
> >> Tom Peat, PhD
> >>
> >> Biomedical Program, CSIRO
> >> tom.p...@csiro.au
> >>
> >> --
> >> *From:* CCP4 bulletin board  on behalf of Misba
> >> Ahmad 
> >> *Sent:* Saturday, January 29, 2022 8:12 PM
> >> *To:* CCP4BB@JISCMAIL.AC.UK 
> >> *Subject:* [ccp4bb] Help with interpreting Tyrosine modification
> >>
> >> Hi all,
> >> I am trying to interpret this strong difference density peak (11.33 rmsd)
> >> that shows up on the tyrosine residue. Any help would be greatly
> >> appreciated.
> >>
> >> Purification buffer: 20mM HEPES pH 7.5, 250mM NaCl, 1mM TCEP, 5mM DTT
> >> Crystallisation condition: Sodium propionate, Sodium cacodylate, BIS-TRIS
> >> propane, PEG 1500
> >>
> >> Best
> >> Misbha
> >> [image: Picture1.png]
> >> [image: Picture2.png]
> >>
> >> --
> >>
> >> To unsubscribe from the CCP4BB list, click the following link:
> >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> >>
> >
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> >
> > To unsubscribe from the CCP4BB list, click the following link:
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> 
> 
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Re: [ccp4bb] help needed with link description

[Rob Nicholls - MRC LMB]

Dear Gerlind,

I'm glad that we were of help! I should point out that the "Make link (click 2 
atoms)" is dangerous as it only generates a LINK record but not a full link 
dictionary - it should only be used for common known links that are present in 
the monomer library. This issue is discussed in section 4.4 of the article I 
posted earlier 
(https://journals.iucr.org/d/issues/2021/06/00/ir5021/index.html). I'd ignore 
Coot's "Make link" tool unless you really know what you're doing. Otherwise, 
I'd favour the AceDRG interfaces as recommended in that article.

Regards,
Rob


> On 3 Jun 2021, at 20:13, Gerlind Sulzenbacher 
>  wrote:
> 
> Dear David and Rob,
> 
> thanks a lot for your help and your suggestions.
> Following your suggestions I found in Coot the very neat solution "Make link 
> (click 2 atoms ...): Much better than my previous dinosaur approach.
> Thanks again and all the best,
> Gerlind
> 
> 
> On 03/06/2021 20:17, David Briggs wrote:
>> Hi Gerlind,
>> 
>> Rob Nicholls gave a talk on how to deal with covalent linkages using AceDrg 
>> at CCP4 study weekend in 2020.
>> 
>> https://youtu.be/p4oTJ0bjD3M <https://youtu.be/p4oTJ0bjD3M>
>> 
>> And Paul Emsley has written up a guide about it...
>> 
>> https://pemsley.github.io/coot/blog/2020/06/30/make-a-link.html 
>> <https://pemsley.github.io/coot/blog/2020/06/30/make-a-link.html> 
>> 
>> Hopefully these will be useful for you.
>> 
>> Good luck,
>> 
>> Dave
>> 
>> --
>> Dr David C. Briggs
>> Senior Laboratory Research Scientist
>> Signalling and Structural Biology Lab
>> The Francis Crick Institute
>> London, UK
>> ==
>> about.me/david_briggs
>> 
>> From: CCP4 bulletin board  
>> <mailto:CCP4BB@JISCMAIL.AC.UK> on behalf of Gerlind Sulzenbacher 
>>  <mailto:gerlind.sulzenbac...@univ-amu.fr>
>> Sent: Thursday, June 3, 2021 7:10:12 PM
>> To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> 
>>  <mailto:CCP4BB@JISCMAIL.AC.UK>
>> Subject: [ccp4bb] help needed with link description
>>  
>> 
>> External Sender: Use caution.
>> 
>> 
>> Dear all,
>> 
>> I am going litteraly mad (or just old).
>> 
>> I would like to make a covalent link between a carbohydrate moiety and
>> and ASP of my well-cheered protein.
>> 
>> The identifier for the carbohydrate moiety is MAD, chain C, res number 1.
>> 
>> The link is established between C5 of MAD and OD2 of ASP 518, chain A.
>> 
>> In the mad_monlib.cif I added the following:
>> 
>> data_link_list
>> loop_
>> _chem_link.id
>> _chem_link.comp_id_1
>> _chem_link.mod_id_1
>> _chem_link.group_comp_1
>> _chem_link.comp_id_2
>> _chem_link.mod_id_2
>> _chem_link.group_comp_2
>> _chem_link.name
>> ASP-MAD  ASP  ..MAD  ..
>>   bond_ASP-OD2_=_MAD-C5
>> #
>> data_link_ASP-MAD
>> #
>> loop_
>> _chem_link_bond.link_id
>> _chem_link_bond.atom_1_comp_id
>> _chem_link_bond.atom_id_1
>> _chem_link_bond.atom_2_comp_id
>> _chem_link_bond.atom_id_2
>> _chem_link_bond.type
>> _chem_link_bond.value_dist
>> _chem_link_bond.value_dist_esd
>>   ASP-MAD  1 OD2 2 C5.   1.3700.040
>> 
>> In the entry PDB file I added the line:
>> 
>> LINKOD2  ASP A 518C5  MAD C 1
>> 
>> The log file of REFMAC tells me
>> 
>> INFO: link is found (not be used) dist=   1.370 ideal_dist= 1.370
>>  ch:AAA  res: 518  ASP  at:OD2 .->ch:CCC  res:
>> 1  MAD  at:C5  .
>> 
>> And the expression "not be used" is certainly the case, as the distance
>> of the covalent bond changes from 1.37 to 1.6 Å.
>> 
>> The data resolution is 1.8 Å.
>> 
>> If somebody could please point out what I am doing wrong, I'd be very
>> grateful.
>> 
>> With best wishes,
>> 
>> Gerlind
>> 
>> 
>> --
>> Gerlind Sulzenbacher
>> Architecture et Fonction des Macromolécules Biologiques
>> UMR7257 CNRS, Aix-Marseille Université
>> Case 932
>> 163 Avenue de Luminy
>> 13288 Marseille cedex 9
>> France
>> Tel +33 491 82 55 66
>> Fax +33 491 26 67 20
>> E-mail: gerlind.sulzenbac...@univ-amu.fr 
>> <mailto:gerlind.sulzenbac...@univ-amu.fr>
>> 
>> 
>> 
>> To unsubscribe

Re: [ccp4bb] help needed with link description

[Gerlind Sulzenbacher]

Dear David and Rob,

thanks a lot for your help and your suggestions.
Following your suggestions I found in Coot the very neat solution "Make 
link (click 2 atoms ...): Much better than my previous dinosaur approach.

Thanks again and all the best,
Gerlind


On 03/06/2021 20:17, David Briggs wrote:

Hi Gerlind,

Rob Nicholls gave a talk on how to deal with covalent linkages using 
AceDrg at CCP4 study weekend in 2020.


https://youtu.be/p4oTJ0bjD3M <https://youtu.be/p4oTJ0bjD3M>

And Paul Emsley has written up a guide about it...

https://pemsley.github.io/coot/blog/2020/06/30/make-a-link.html

Hopefully these will be useful for you.

Good luck,

Dave

--
Dr David C. Briggs
Senior Laboratory Research Scientist
Signalling and Structural Biology Lab
The Francis Crick Institute
London, UK
==
about.me/david_briggs


*From:* CCP4 bulletin board  on behalf of 
Gerlind Sulzenbacher 

*Sent:* Thursday, June 3, 2021 7:10:12 PM
*To:* CCP4BB@JISCMAIL.AC.UK 
*Subject:* [ccp4bb] help needed with link description

External Sender: Use caution.


Dear all,

I am going litteraly mad (or just old).

I would like to make a covalent link between a carbohydrate moiety and
and ASP of my well-cheered protein.

The identifier for the carbohydrate moiety is MAD, chain C, res number 1.

The link is established between C5 of MAD and OD2 of ASP 518, chain A.

In the mad_monlib.cif I added the following:

data_link_list
loop_
_chem_link.id
_chem_link.comp_id_1
_chem_link.mod_id_1
_chem_link.group_comp_1
_chem_link.comp_id_2
_chem_link.mod_id_2
_chem_link.group_comp_2
_chem_link.name
ASP-MAD  ASP  .    .    MAD  .    .
  bond_ASP-OD2_=_MAD-C5
#
data_link_ASP-MAD
#
loop_
_chem_link_bond.link_id
_chem_link_bond.atom_1_comp_id
_chem_link_bond.atom_id_1
_chem_link_bond.atom_2_comp_id
_chem_link_bond.atom_id_2
_chem_link_bond.type
_chem_link_bond.value_dist
_chem_link_bond.value_dist_esd
  ASP-MAD  1 OD2 2 C5    .   1.370 0.040

In the entry PDB file I added the line:

LINK    OD2  ASP A 518    C5  MAD C 1

The log file of REFMAC tells me

INFO: link is found (not be used) dist=   1.370 ideal_dist= 1.370
 ch:AAA  res: 518  ASP  at:OD2 .->ch:CCC  res:
1  MAD  at:C5  .

And the expression "not be used" is certainly the case, as the distance
of the covalent bond changes from 1.37 to 1.6 Å.

The data resolution is 1.8 Å.

If somebody could please point out what I am doing wrong, I'd be very
grateful.

With best wishes,

Gerlind


--
Gerlind Sulzenbacher
Architecture et Fonction des Macromolécules Biologiques
UMR7257 CNRS, Aix-Marseille Université
Case 932
163 Avenue de Luminy
13288 Marseille cedex 9
France
Tel +33 491 82 55 66
Fax +33 491 26 67 20
E-mail: gerlind.sulzenbac...@univ-amu.fr



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Re: [ccp4bb] help needed with link description

[Rob Nicholls - MRC LMB]

Dear Gerlind,

Where did you get your mad_monlib.cif file? It shouldn't be neccesary for you 
to be manually modifying such restraint dictionaries (any more). You can 
generate these using AceDRG, either via CCP4i2 or Coot.

Shameless plug:
https://journals.iucr.org/d/issues/2021/06/00/ir5021/index.html
https://journals.iucr.org/d/issues/2021/06/00/ir5022/index.html

Regards,
Rob






Dr Rob Nicholls
Senior Investigator Scientist
MRC Laboratory of Molecular Biology
Francis Crick Avenue
Cambridge Biomedical Campus
Cambridge CB2 0QH



> On 3 Jun 2021, at 19:10, Gerlind Sulzenbacher 
>  wrote:
> 
> Dear all,
> 
> I am going litteraly mad (or just old).
> 
> I would like to make a covalent link between a carbohydrate moiety and and 
> ASP of my well-cheered protein.
> 
> The identifier for the carbohydrate moiety is MAD, chain C, res number 1.
> 
> The link is established between C5 of MAD and OD2 of ASP 518, chain A.
> 
> In the mad_monlib.cif I added the following:
> 
> data_link_list
> loop_
> _chem_link.id
> _chem_link.comp_id_1
> _chem_link.mod_id_1
> _chem_link.group_comp_1
> _chem_link.comp_id_2
> _chem_link.mod_id_2
> _chem_link.group_comp_2
> _chem_link.name
> ASP-MAD  ASP  ..MAD  ..
>  bond_ASP-OD2_=_MAD-C5
> #
> data_link_ASP-MAD
> #
> loop_
> _chem_link_bond.link_id
> _chem_link_bond.atom_1_comp_id
> _chem_link_bond.atom_id_1
> _chem_link_bond.atom_2_comp_id
> _chem_link_bond.atom_id_2
> _chem_link_bond.type
> _chem_link_bond.value_dist
> _chem_link_bond.value_dist_esd
>  ASP-MAD  1 OD2 2 C5.   1.3700.040
> 
> In the entry PDB file I added the line:
> 
> LINKOD2  ASP A 518C5  MAD C 1
> 
> The log file of REFMAC tells me
> 
> INFO: link is found (not be used) dist=   1.370 ideal_dist= 1.370
> ch:AAA  res: 518  ASP  at:OD2 .->ch:CCC  res:   1  
> MAD  at:C5  .
> 
> And the expression "not be used" is certainly the case, as the distance of 
> the covalent bond changes from 1.37 to 1.6 Å.
> 
> The data resolution is 1.8 Å.
> 
> If somebody could please point out what I am doing wrong, I'd be very 
> grateful.
> 
> With best wishes,
> 
> Gerlind
> 
> 
> -- 
> Gerlind Sulzenbacher
> Architecture et Fonction des Macromolécules Biologiques
> UMR7257 CNRS, Aix-Marseille Université
> Case 932
> 163 Avenue de Luminy
> 13288 Marseille cedex 9
> France
> Tel +33 491 82 55 66
> Fax +33 491 26 67 20
> E-mail: gerlind.sulzenbac...@univ-amu.fr
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing 
> list hosted by www.jiscmail.ac.uk, terms & conditions are available at 
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Re: [ccp4bb] help needed with link description

[David Briggs]

Hi Gerlind,

Rob Nicholls gave a talk on how to deal with covalent linkages using AceDrg at 
CCP4 study weekend in 2020.

https://youtu.be/p4oTJ0bjD3M

And Paul Emsley has written up a guide about it...

https://pemsley.github.io/coot/blog/2020/06/30/make-a-link.html

Hopefully these will be useful for you.

Good luck,

Dave

--
Dr David C. Briggs
Senior Laboratory Research Scientist
Signalling and Structural Biology Lab
The Francis Crick Institute
London, UK
==
about.me/david_briggs


From: CCP4 bulletin board  on behalf of Gerlind 
Sulzenbacher 
Sent: Thursday, June 3, 2021 7:10:12 PM
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] help needed with link description


External Sender: Use caution.


Dear all,

I am going litteraly mad (or just old).

I would like to make a covalent link between a carbohydrate moiety and
and ASP of my well-cheered protein.

The identifier for the carbohydrate moiety is MAD, chain C, res number 1.

The link is established between C5 of MAD and OD2 of ASP 518, chain A.

In the mad_monlib.cif I added the following:

data_link_list
loop_
_chem_link.id
_chem_link.comp_id_1
_chem_link.mod_id_1
_chem_link.group_comp_1
_chem_link.comp_id_2
_chem_link.mod_id_2
_chem_link.group_comp_2
_chem_link.name
ASP-MAD  ASP  ..MAD  ..
  bond_ASP-OD2_=_MAD-C5
#
data_link_ASP-MAD
#
loop_
_chem_link_bond.link_id
_chem_link_bond.atom_1_comp_id
_chem_link_bond.atom_id_1
_chem_link_bond.atom_2_comp_id
_chem_link_bond.atom_id_2
_chem_link_bond.type
_chem_link_bond.value_dist
_chem_link_bond.value_dist_esd
  ASP-MAD  1 OD2 2 C5.   1.3700.040

In the entry PDB file I added the line:

LINKOD2  ASP A 518C5  MAD C 1

The log file of REFMAC tells me

INFO: link is found (not be used) dist=   1.370 ideal_dist= 1.370
 ch:AAA  res: 518  ASP  at:OD2 .->ch:CCC  res:
1  MAD  at:C5  .

And the expression "not be used" is certainly the case, as the distance
of the covalent bond changes from 1.37 to 1.6 Å.

The data resolution is 1.8 Å.

If somebody could please point out what I am doing wrong, I'd be very
grateful.

With best wishes,

Gerlind


--
Gerlind Sulzenbacher
Architecture et Fonction des Macromolécules Biologiques
UMR7257 CNRS, Aix-Marseille Université
Case 932
163 Avenue de Luminy
13288 Marseille cedex 9
France
Tel +33 491 82 55 66
Fax +33 491 26 67 20
E-mail: gerlind.sulzenbac...@univ-amu.fr



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[ccp4bb] help needed with link description

[Gerlind Sulzenbacher]

Dear all,

I am going litteraly mad (or just old).

I would like to make a covalent link between a carbohydrate moiety and 
and ASP of my well-cheered protein.


The identifier for the carbohydrate moiety is MAD, chain C, res number 1.

The link is established between C5 of MAD and OD2 of ASP 518, chain A.

In the mad_monlib.cif I added the following:

data_link_list
loop_
_chem_link.id
_chem_link.comp_id_1
_chem_link.mod_id_1
_chem_link.group_comp_1
_chem_link.comp_id_2
_chem_link.mod_id_2
_chem_link.group_comp_2
_chem_link.name
ASP-MAD  ASP  .    .    MAD  .    .
 bond_ASP-OD2_=_MAD-C5
#
data_link_ASP-MAD
#
loop_
_chem_link_bond.link_id
_chem_link_bond.atom_1_comp_id
_chem_link_bond.atom_id_1
_chem_link_bond.atom_2_comp_id
_chem_link_bond.atom_id_2
_chem_link_bond.type
_chem_link_bond.value_dist
_chem_link_bond.value_dist_esd
 ASP-MAD  1 OD2 2 C5    .   1.370    0.040

In the entry PDB file I added the line:

LINK    OD2  ASP A 518    C5  MAD C 1

The log file of REFMAC tells me

INFO: link is found (not be used) dist=   1.370 ideal_dist= 1.370
    ch:AAA  res: 518  ASP  at:OD2 .->ch:CCC  res:   
1  MAD  at:C5  .


And the expression "not be used" is certainly the case, as the distance 
of the covalent bond changes from 1.37 to 1.6 Å.


The data resolution is 1.8 Å.

If somebody could please point out what I am doing wrong, I'd be very 
grateful.


With best wishes,

Gerlind


--
Gerlind Sulzenbacher
Architecture et Fonction des Macromolécules Biologiques
UMR7257 CNRS, Aix-Marseille Université
Case 932
163 Avenue de Luminy
13288 Marseille cedex 9
France
Tel +33 491 82 55 66
Fax +33 491 26 67 20
E-mail: gerlind.sulzenbac...@univ-amu.fr



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[ccp4bb] Help EMBL-EBI maintain its services: articulating the value of open data

[Gerard DVD Kleywegt]

Dear colleagues,

As a community of structural molecular (and, increasingly, cellular) biologists 
we are fortunate to have a large collection of well-established, well-managed 
and open data resources at our disposal. (Physicists are often impressed when 
they learn that a protein structure deposited in the PDB in the mid-1970s can 
still be loaded into any molecular viewer and analysed and used as if it was 
determined yesterday.) You may have used (or deposited) structural data from 
archives such as the PDB, EMDB, EMPIAR, BMRB or SASBDB, but perhaps also 
sequence data from UniProt, chemical activity data from ChEMBL or maybe 
discovered relevant literature in PubMed or Europe PMC.


EMBL-EBI is involved in operating many of these public data resources (in many 
cases, together with international partners and as part of global 
collaborations). The institute is currently running a survey that aims to 
assess the worldwide value of the bioinformatics resources it offers.


I would like to invite all of you, as well as any other data users in your 
organisation, to participate in this survey. Your input is extremely important 
and will help EMBL-EBI maintain and develop its resources for the global 
scientific community. It would obviously be helpful to have a good 
representation of the structural biology community providing input into this 
process.


The survey can be accessed here:

 https://www.surveymonkey.co.uk/r/EMBL-EBI_Impact_PE

It takes around 15 minutes and closes on 31 March 2021. The results of the 
survey will be anonymised and all personal data treated as confidential.


I recognise there are many demands on your time so I would like to thank you in 
advance for your participation and input.


If you have any questions or comments about the survey please contact 
impactsur...@ebi.ac.uk.


Many thanks and best wishes,

--Gerard

---
Gerard J. Kleywegt, EMBL-EBI, Hinxton, UK
Head of Molecular and  Cellular Structure
ger...@ebi.ac.uk pdbe.org emdb-empiar.org
PA: Roisin Dunloppdbe_ad...@ebi.ac.uk



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Re: [ccp4bb] Help for Twin Refinement in Refmac5 / CCP4i2

[Eleanor Dodson]

I fell into the same trap this week. Apparently if in the first screen you
tick the box Crystal is twinned” the interface resets the input data to
FMEAN (or IMEAN if you have asked to use intensitirs) and you don’t need to
say TWIN .
Semi logical I guess but easy to miss. Eleanor

On Tue, 26 Jan 2021 at 06:42, Parthasarathy Sampathkumar 
wrote:

> Dear All,
>
> Please you may ignore my previous email. TWIN refinement in Refmac5 /
> CCP4i2 worked well once used "HKLOUT_0-observed_data_asIMEAN.mtz" from
> the data-reduction job. I am slowly getting used to the finer-aspects of
> CCP4i2. Previously, I used to have both Intensities and Amplitudes in a
> single MTZ file :-)
>
> Thanks,
> Partha
>
> On Mon, Jan 25, 2021 at 9:47 PM Parthasarathy Sampathkumar <
> spart...@gmail.com> wrote:
>
>> Dear All,
>>
>> I have not had much experience in refining structure using data from
>> twinned crystals and has started using CCP4i2 very recently only.
>>
>> Here is a background:
>> antigen-Fab crystal structure determined by MR first in P4(3)2(1)2 space
>> group with 1-complex molecule in the asymmetric unit (ASU). Later, I
>> reprocessed the data in P4(3) performed MR to search for the 2nd molecule
>> and refined the structure using Refmac5 without the "twin" keyword. With
>> the sequence fully modeled for the two complex molecules in the ASU current
>> Rcryst = 27.8%and Rfree = 33.2%. Unit cell = "59.9, 59.9, 404.5, 90.0,
>> 90.0, 90.0".
>>
>> Twin fraction estimates from Britton plot = 0.47 and from H-test = 0.43,
>> as reported by AIMLESS. Then, attempted TWIN refinement in Refmac5 /
>> CCP4i2 by adding the keyword "twin" in the advanced options. However,
>> getting following error in the log-file:
>>
>>  Error==> array size in mtz_refl_read_int
>> 
>>  Refmac:  Problem with array sizes
>>
>> Does Refmac5 expects intensities here?!!
>> Any help is greatly appreciated.
>>
>> Best Wishes,
>> Partha
>>
>>
>>
>>
>>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] Help for Twin Refinement in Refmac5 / CCP4i2

[Parthasarathy Sampathkumar]

Dear All,

Please you may ignore my previous email. TWIN refinement in Refmac5 /
CCP4i2 worked well once used "HKLOUT_0-observed_data_asIMEAN.mtz" from the
data-reduction job. I am slowly getting used to the finer-aspects of
CCP4i2. Previously, I used to have both Intensities and Amplitudes in a
single MTZ file :-)

Thanks,
Partha

On Mon, Jan 25, 2021 at 9:47 PM Parthasarathy Sampathkumar <
spart...@gmail.com> wrote:

> Dear All,
>
> I have not had much experience in refining structure using data from
> twinned crystals and has started using CCP4i2 very recently only.
>
> Here is a background:
> antigen-Fab crystal structure determined by MR first in P4(3)2(1)2 space
> group with 1-complex molecule in the asymmetric unit (ASU). Later, I
> reprocessed the data in P4(3) performed MR to search for the 2nd molecule
> and refined the structure using Refmac5 without the "twin" keyword. With
> the sequence fully modeled for the two complex molecules in the ASU current
> Rcryst = 27.8%and Rfree = 33.2%. Unit cell = "59.9, 59.9, 404.5, 90.0,
> 90.0, 90.0".
>
> Twin fraction estimates from Britton plot = 0.47 and from H-test = 0.43,
> as reported by AIMLESS. Then, attempted TWIN refinement in Refmac5 /
> CCP4i2 by adding the keyword "twin" in the advanced options. However,
> getting following error in the log-file:
>
>  Error==> array size in mtz_refl_read_int
> 
>  Refmac:  Problem with array sizes
>
> Does Refmac5 expects intensities here?!!
> Any help is greatly appreciated.
>
> Best Wishes,
> Partha
>
>
>
>
>



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[ccp4bb] Help for Twin Refinement in Refmac5 / CCP4i2

[Parthasarathy Sampathkumar]

Dear All,

I have not had much experience in refining structure using data from
twinned crystals and has started using CCP4i2 very recently only.

Here is a background:
antigen-Fab crystal structure determined by MR first in P4(3)2(1)2 space
group with 1-complex molecule in the asymmetric unit (ASU). Later, I
reprocessed the data in P4(3) performed MR to search for the 2nd molecule
and refined the structure using Refmac5 without the "twin" keyword. With
the sequence fully modeled for the two complex molecules in the ASU current
Rcryst = 27.8%and Rfree = 33.2%. Unit cell = "59.9, 59.9, 404.5, 90.0,
90.0, 90.0".

Twin fraction estimates from Britton plot = 0.47 and from H-test = 0.43, as
reported by AIMLESS. Then, attempted TWIN refinement in Refmac5 / CCP4i2 by
adding the keyword "twin" in the advanced options. However, getting
following error in the log-file:

 Error==> array size in mtz_refl_read_int

 Refmac:  Problem with array sizes

Does Refmac5 expects intensities here?!!
Any help is greatly appreciated.

Best Wishes,
Partha



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[ccp4bb] Help us help you: write support for Ultra-XChem beamline in Diamond-II

[Frank von Delft]

Dear all - please *help us help you*:

 * Some of you have used and even liked Diamond's XChem facility for
   crystal-based fragments screening.

 * Some of you have wanted to use it but didn't know how or didn't get
   time.

 * Lots and lots of you hope your crystallography will turn into
   chemical biology and drug discovery.

If you're one of those: *s*how your support for a lighting-fast XChem 
beamline in Diamond-II:


1. Dial in to the webinar next Monday 4pm (/details below/)
2. Sign up to the Interest Group (/here
   
//or
   linked below/)
3. Drop us statements of support (in this form
   

   or linked from here
   
)
4. Retweet this
   


Diamond-II is planning to upgrade and reinvent, by mid-2027; this 
includes new and upgraded beamlines - and rebuilding I04-1 as K04.  It 
should increase XChem throughput up to 15x, which means far bigger XChem 
fragment screens for far more of your projects, and (we conclude) far 
more of your chemical biology and drug discovery, much accelerated (e.g. 
this ).


We're about to submit the science case - and we're seeking as many 
statements of support as possible.


Please spread the word:  circulate to all your colleagues in chemistry 
and drug design and chemical biology - in fact, this touches so many 
discplines, you can probably send to just about everybody you work with...


Thank you for your help!
Frank


Prof Frank von Delft
Professor for Structural Chemical Biology
Principal Beamline Scientist: I04-1/XChem
Diamond Light Source

Principal Investigator: Protein Crystallography
Centre for Medicines Discovery
Oxford University





 Forwarded Message 
Subject:Diamond-II Webinar: K04 Beamline Rebuild for Ultra-XChem
Date:   Mon, 9 Nov 2020 09:54:39 +
From:   Diamond Communications 
Reply-To:   Diamond Communications 
To: frank.von-de...@diamond.ac.uk




 Diamond-II Webinar: K04 Beamline Rebuild for Ultra-XChem

*Monday 16th November 2020, 16:00-17:00
Click here to visit the event page 
*


Dear Colleagues,

Structural and chemical biologists and medicinal chemists are warmly 
invited to this webinar, which will describe the rebuilding of beamline 
I04-1 as K04 for Diamond-II. The project will achieve ultra-high 
throughput XChem fragment screening and thereby help drive routine and 
rapid pre-clinical impact in structure-based drug discovery and chemical 
biology. Diamond-II 
is 
a coordinated programme of development that includes a major upgrade of 
the storage ring to deliver low emittance at higher energy, along with a 
range of rebuilt and enhanced beamlines. The K04/XChem project is part 
of a transformational change for the MX and XChem communities, and 
attendance and feedback are highly encouraged.


*Proposal background*
The K04/XChem flagship builds on the success and oversubscription of the 
XChem fragment screening facility 
, 
developed in tandem with the evolution of beamline I04-1. The facility 
provides a world-unique offering for structure-based drug design, and is 
in heavy academic and industrial demand, with the resilience to support 
significant COVID 
work 
 during 
lockdown.


The Diamond-II machine configuration necessitates removing beamline 
I04-1, providing the opportunity to rebuild it on the new K04 straight, 
delivering a beamline of vastly increased flux and brilliance, along 
with extreme automation. The resulting order-of-magnitude increase in 
throughput will fundamentally shift the scientific scope of 
crystallographic fragment screening. On the one hand, a far larger range 
of classes of drug targets will become viable, even when diffraction is 
weak. On the other hand, routinely large experiments will help achieve 
the coming revolution in rational drug discovery, by allowing all key 
interactions and conformations to be observed in 3D up front, providing 
the raw data that future algorithms will be able to exploit to design 
clinic-ready drug candidates from scratch


*User community input & webinar*
In order to provide you with more 

Re: [ccp4bb] Help needed (input files)

[Alex Payne]

Hi Fred,
Have you tried
http://www.charmm-gui.org/ ? I think this is the easiest way to walk
through setting up input files, and you can have it generate input files
for several different programs.
Cheers,
Alex

On Tue, Aug 4, 2020 at 4:07 AM Fred Vellieux 
wrote:

> 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
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>



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Re: [ccp4bb] Help needed (input files)

[Murpholino Peligro]

Hi.
You can try namd (https://www.ks.uiuc.edu/Research/namd/) It Is free and
there are good tutorials available. HiH

El mar., 4 de agosto de 2020 3:07, Fred Vellieux <
frederic.velli...@lf1.cuni.cz> escribió:

> 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
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>



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Re: [ccp4bb] Help needed (input files)

[Eugene Osipov]

Fred,
you could use the Academic version of Desmond freely available here:
https://www.deshawresearch.com/resources_desmond.html
The only difference from the commercial version is absence of OPLS3e force
field but you still could use GPU.


вт, 4 авг. 2020 г. в 10:08, 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
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
> available at https://www.jiscmail.ac.uk/policyandsecurity/
>


-- 
Evgenii Osipov
Laboratory for Biocrystallography,
Department of Pharmaceutical Sciences,
KU Leuven O



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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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Re: [ccp4bb] Help With Setting up a Stereo view system_walkthrough

[Dirk Kostrewa]

Dear Marian,

for some while, now, in xorg.conf, the entry

Option "Composite" "Disable"

does not work. Please, use instead the entry

Option "COMPOSITE" "Disable"

Cheers,

Dirk.

On 03.08.20 14:54, Marian Oliva wrote:


INSTALING STEREO COOT 3D VISION 2 FROM NVIDIA UNDER UBUNTU

HARDWARE

CARD: NVIDIA QUADRO 4000. Bought second hand in AMAZON. Other Quadro 
NVIDIA cards would get the job done as long as they have the 3-pin DIN 
stereo connector. But this is the cheapest alternative I foundI had to 
buy the PCI Plate got the 3-pin DIN port separately, it was lost from 
the second hand card.


GLASSES: 3D NVIDIA 2 Also bought Second hand in AMAZON

MONITOR:  Asus VG248 Nvidia 3D Ready In this case from Ebay

Connecting the hardware was trivial. But I recommend to first connect 
the VG240 using the Dual Link DVI wire and do the setup with this, 
then you can complicate your life with the second screen.


SOFTWARE IMPORTANT ISSUES.

The installation is not too difficult if you know a couple of tricks, 
but I didn´t:


- You have to correctly install the NVIDIA driver. I used 390.138 
Legacy Linux driver. Not too difficult. Download from here


https://www.nvidia.com/en-us/drivers/unix/

Execute as root.

You will get this message

An incomplete installation of libglvnd was found. All of the essential

libglvnd libraries are present, but on or more optional components are 
missing.


Do you want to install a full copy of libglvnd? This will overwrite

any existing libglvnd libraries.

Answer DON´T INSTALL. Or fully remove libglvnd and reinstall them.

See this Web for other tips.

https://www.berkhanberkdemir.com/2019/07/24/how-to-not-install-nvidia-driver-in-linux.html

3D IS INCOMPATIBLE WITH COMPOSITE EXTENSIONS OF THE DESKTOP manager.

I found a LOT of info in this page

https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo

This should be enough to get stereo working. However, note that there 
is a major issue on linux with window compositing causing stereo 
images to display improperly. This is a problem with the window 
display manager, and is not inherent to Xorg or NVidia. If you try to 
turn on stereo in Coot in a display manager that makes use of the Xorg 
compositing extension (e.g., Gnome3, or Unity in Ubuntu) then what you 
will see when you activate hardware stereo is a slight rotation of the 
view, but stereo remains disabled. In order to get around this 
problem, you must use a display manager that does not make use of 
compositing as part of its eye candy. This author has found the MATE 
desktop to work quite well for this purpose (and may in fact be one of 
the few that still does not use software compositing by default). Note 
that you /do not/ need to disable the Compositing extension in the 
Xorg configuration file to make this work -- this will allow you to 
switch back to Gnome3, Unity, etc when you don't need stereo if you 
prefer! Not disabling the window compositing extension globally allows 
for a more flexible setup depending on your preferred workflow.


I tried to desactivate the COMPOSITE extension in xorg.conf as suggested.

Section "Extensions"
 Option "Composite" "Disable"
EndSection

But all the Desktop Environments I had miserable failed to start.

Then I simply install MATE environment

https://www.omgubuntu.co.uk/2014/08/install-mate-desktop-ubuntu-14-04-lts

Select it and everything worked.

Best luck if you want to repeat my experience!


Marian Oliva
CSIC-Centro de Investigaciones Biológicas Margarita Salas
9, Ramiro de Maeztu
28040-Madrid (Spain)

phone: 0034 91 8373112 (x4380)
e-mail: mar...@cib.csic.es <mailto:mar...@cib.csic.es>

**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los 
ficheros adjuntos, pueden contener información protegida para el uso 
exclusivo de su destinatario. Se prohíbe la distribución, reproducción 
o cualquier otro tipo de transmisión por parte de otra persona que no 
sea el destinatario. Si usted recibe por error este correo, se 
ruega comunicarlo al remitente y borrar el mensaje recibido.


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attachments may contain confidential and privileged information for 
the sole use of the designated recipient named above. Distribution, 
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El 1 ago 2020, a las 16:18, Oganesyan, Vaheh 
<mailto:vaheh.oganes...@astrazeneca.com>> escribió:


Hi Marian,
Are there other numbers or letters in the monitor nameASUS VG248 that 
you used successfully? I’m trying to do the same.

Thank you.
*From:*CCP4 bulletin board <mailto:CCP4BB@JISCMAIL.AC.UK>>*On Behalf Of*Marian Oliva

*Sent:*Thursday, July 30, 2020 8:46 AM
*To:*CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISC

Re: [ccp4bb] Help With Setting up a Stereo view system_walkthrough

[Marian Oliva]

INSTALING STEREO COOT 3D VISION 2 FROM NVIDIA UNDER UBUNTU

HARDWARE

CARD: NVIDIA QUADRO 4000. Bought second hand in AMAZON. Other Quadro NVIDIA 
cards would get the job done as long as they have the 3-pin DIN stereo 
connector. But this is the cheapest alternative I foundI had to buy the PCI 
Plate got the 3-pin DIN port separately, it was lost from the second hand card.

GLASSES: 3D NVIDIA 2 Also bought Second hand in AMAZON

MONITOR:  Asus VG248 Nvidia 3D Ready In this case from Ebay

Connecting the hardware was trivial. But I recommend to first connect the VG240 
using the Dual Link DVI wire and do the setup with this, then you can 
complicate your life with the second screen.

 SOFTWARE IMPORTANT ISSUES.

The installation is not too difficult if you know a couple of tricks, but I 
didn´t:

- You have to correctly install the NVIDIA driver. I used 390.138 Legacy Linux 
driver. Not too difficult. Download from here

https://www.nvidia.com/en-us/drivers/unix/ 
<https://www.nvidia.com/en-us/drivers/unix/>
Execute as root.

You will get this message

An incomplete installation of libglvnd was found. All of the essential

libglvnd libraries are present, but on or more optional components are missing.

Do you want to install a full copy of libglvnd? This will overwrite

any existing libglvnd libraries.

Answer DON´T INSTALL. Or fully remove libglvnd and reinstall them.

See this Web for other tips.

https://www.berkhanberkdemir.com/2019/07/24/how-to-not-install-nvidia-driver-in-linux.html
 
<https://www.berkhanberkdemir.com/2019/07/24/how-to-not-install-nvidia-driver-in-linux.html>
 

3D IS INCOMPATIBLE WITH COMPOSITE EXTENSIONS OF THE DESKTOP manager.

I found a LOT of info in this page

https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo 
<https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo>
This should be enough to get stereo working. However, note that there is a 
major issue on linux with window compositing causing stereo images to display 
improperly. This is a problem with the window display manager, and is not 
inherent to Xorg or NVidia. If you try to turn on stereo in Coot in a display 
manager that makes use of the Xorg compositing extension (e.g., Gnome3, or 
Unity in Ubuntu) then what you will see when you activate hardware stereo is a 
slight rotation of the view, but stereo remains disabled. In order to get 
around this problem, you must use a display manager that does not make use of 
compositing as part of its eye candy. This author has found the MATE desktop to 
work quite well for this purpose (and may in fact be one of the few that still 
does not use software compositing by default). Note that you do not need to 
disable the Compositing extension in the Xorg configuration file to make this 
work -- this will allow you to switch back to Gnome3, Unity, etc when you don't 
need stereo if you prefer! Not disabling the window compositing extension 
globally allows for a more flexible setup depending on your preferred workflow.

 

I tried to desactivate the COMPOSITE extension in xorg.conf as suggested.

Section "Extensions"
 Option "Composite" "Disable"
   EndSection
 

But all the Desktop Environments I had miserable failed to start.

Then I simply install MATE environment

https://www.omgubuntu.co.uk/2014/08/install-mate-desktop-ubuntu-14-04-lts 
<https://www.omgubuntu.co.uk/2014/08/install-mate-desktop-ubuntu-14-04-lts>
Select it and everything worked.

 

Best luck if you want to repeat my experience!   


Marian Oliva
CSIC-Centro de Investigaciones Biológicas Margarita Salas
9, Ramiro de Maeztu
28040-Madrid (Spain)

phone: 0034 91 8373112 (x4380)
e-mail: mar...@cib.csic.es

**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros 
adjuntos, pueden contener información protegida para el uso exclusivo de su 
destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de 
transmisión por parte de otra persona que no sea el destinatario. Si usted 
recibe por error este correo, se ruega comunicarlo al remitente y borrar el 
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**CONFIDENTIALITY NOTICE** This email communication and any attachments may 
contain confidential and privileged information for the sole use of the 
designated recipient named above. Distribution, reproduction or any other use 
of this transmission by any party other than the intended recipient is 
prohibited. If you are not the intended recipient please contact the sender and 
delete all copies.

> El 1 ago 2020, a las 16:18, Oganesyan, Vaheh 
>  escribió:
> 
> Hi Marian,
>  
> Are there other numbers or letters in the monitor name ASUS VG248 that you 
> used successfully? I’m trying to do the same.
>  
> Thank you.
>  
> From: CCP4 bulletin board  <mailto:CCP4BB@JISCMAIL.AC.UK>> On Behalf Of Marian Oliva
> Sent: Thursday, July 30, 2020 8:46 AM
> To: CCP4B

Re: [ccp4bb] Help With Setting up a Stereo view system

[Marian Oliva]

Dear all.

Issue solved. It was a matter of installing the MATE desktop environment. Now 
everything is up and kicking

Thanks a lot for all the help


Marian Oliva
CSIC-Centro de Investigaciones Biológicas Margarita Salas
9, Ramiro de Maeztu
28040-Madrid (Spain)

phone: 0034 91 8373112 (x4380)
e-mail: mar...@cib.csic.es

**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros 
adjuntos, pueden contener información protegida para el uso exclusivo de su 
destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de 
transmisión por parte de otra persona que no sea el destinatario. Si usted 
recibe por error este correo, se ruega comunicarlo al remitente y borrar el 
mensaje recibido.
 
**CONFIDENTIALITY NOTICE** This email communication and any attachments may 
contain confidential and privileged information for the sole use of the 
designated recipient named above. Distribution, reproduction or any other use 
of this transmission by any party other than the intended recipient is 
prohibited. If you are not the intended recipient please contact the sender and 
delete all copies.

> El 30 jul 2020, a las 14:46, Marian Oliva  escribió:
> 
> Dear colleagues.
> 
> I would like to check if some one can help me with the setup of my hardware 
> stereo system in Coot under Ubuntu 14
> 
> With the help of a friend I collect a bunch of second hand stuff.
> 
> 1 NVIDIA 3D Video 2 system.
> 1 Monitor ASUS VG248 conectes through the display port
> 1 NVIDIA QUADRO 4000 video card.
> 
> After connecting everything and having a nightmare to install the Legacy 
> Drivers 390.138
> 
> And following this instructions
> 
> https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo 
> 
> 
> I run nvidia-xconfig --stereo=10
> 
> I connected the emitter both by USB and the DIN 3 pin conector
> I connected the monitor through the Display Port
> 
> I reboot and , the emitter finally shows the green light
> 
> I can run nvidia-settings and I have the control panel
> 
> I see Stereo 3D Vision Stereo but only the left cube running.
> 
> But when I activate hardware stereo nothing works.
> 
> Does anybody have a clue of what to do?
> 
> Thanks in advance,
> 
> Marian
> 
> 
> Marian Oliva
> CSIC-Centro de Investigaciones Biológicas Margarita Salas
> 9, Ramiro de Maeztu
> 28040-Madrid (Spain)
> 
> phone: 0034 91 8373112 (x4380)
> e-mail: mar...@cib.csic.es 
> 
> **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los 
> ficheros adjuntos, pueden contener información protegida para el uso 
> exclusivo de su destinatario. Se prohíbe la distribución, reproducción o 
> cualquier otro tipo de transmisión por parte de otra persona que no sea el 
> destinatario. Si usted recibe por error este correo, se ruega comunicarlo al 
> remitente y borrar el mensaje recibido.
>  
> **CONFIDENTIALITY NOTICE** This email communication and any attachments may 
> contain confidential and privileged information for the sole use of the 
> designated recipient named above. Distribution, reproduction or any other use 
> of this transmission by any party other than the intended recipient is 
> prohibited. If you are not the intended recipient please contact the sender 
> and delete all copies.
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 
> 



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Re: [ccp4bb] Help With Setting up a Stereo view system

[Dirk Kostrewa]

Dear Marian Oliva,

in my experience, MATE, XFCE and Plasma 5/KDE work well with 3D stereo 
if the compositor is disabled. You don't even have to disable COMPOSITE 
in the xorg.conf - for those desktops, it is sufficient to disable 
composite in the respective desktop/compositor/window manager settings 
(tested with Debian Stable and CentOS 8; unfortunately, I can't access 
my documents for more details).


For Gnome 3, the picture is somewhat mixed: the gnome3 shell crashes if 
you disable composite in xorg.conf. However, if you use a recent Fedora 
or CentOS 8 (which is based on relatively recent Fedoras), 3D stereo 
works under Gnome 3 out-of-the-box. Upon switching 3D stereo on/off, you 
will notice a delay of ~1 second, before a message appears that stereo 
has been enabled/disabled. I guess, in these distributions, the 
compositor is somehow switched in the background without crashing the 
session.


Independent of the desktop, for Fedora/CentOS 8, it might be necessary 
to place a udev rule to give write permissions to the USB emitter for 
regular users. So, if 3D stereo works under root, but not under a 
regular user, you should create a rule like 
/etc/udev/rules.d/98-nvstusb.rules, with the contents


# NVIDIA 3D Vision USB IR Emitter
SUBSYSTEM=="usb", ATTR{idVendor}=="0955", ATTR{idProduct}=="0007", 
MODE="0666"


Cheers,

Dirk.


On 30.07.20 14:46, Marian Oliva wrote:

Dear colleagues.

I would like to check if some one can help me with the setup of my 
hardware stereo system in Coot under Ubuntu 14


With the help of a friend I collect a bunch of second hand stuff.

1 NVIDIA 3D Video 2 system.
1 Monitor ASUS VG248 conectes through the display port
1 NVIDIA QUADRO 4000 video card.

After connecting everything and having a nightmare to install the 
Legacy Drivers 390.138


And following this instructions

https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo

I run nvidia-xconfig --stereo=10

I connected the emitter both by USB and the DIN 3 pin conector
I connected the monitor through the Display Port

I reboot and , the emitter finally shows the green light

I can run nvidia-settings and I have the control panel

I see Stereo 3D Vision Stereo but only the left cube running.

But when I activate hardware stereo nothing works.

Does anybody have a clue of what to do?

Thanks in advance,

Marian


Marian Oliva
CSIC-Centro de Investigaciones Biológicas Margarita Salas
9, Ramiro de Maeztu
28040-Madrid (Spain)

phone: 0034 91 8373112 (x4380)
e-mail: mar...@cib.csic.es 

**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los 
ficheros adjuntos, pueden contener información protegida para el uso 
exclusivo de su destinatario. Se prohíbe la distribución, reproducción 
o cualquier otro tipo de transmisión por parte de otra persona que no 
sea el destinatario. Si usted recibe por error este correo, se 
ruega comunicarlo al remitente y borrar el mensaje recibido.


**CONFIDENTIALITY NOTICE** This email communication and any 
attachments may contain confidential and privileged information for 
the sole use of the designated recipient named above. Distribution, 
reproduction or any other use of this transmission by any party other 
than the intended recipient is prohibited. If you are not the intended 
recipient please contact the sender and delete all copies.





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--

***
Dirk Kostrewa
Gene Center Munich
Department of Biochemistry, AG Hopfner
Ludwig-Maximilians-Universität München
Feodor-Lynen-Str. 25
D-81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:+49-89-2180-76998
E-mail: dirk.kostr...@lmu.de
WWW:www.genzentrum.lmu.de
strubio.userweb.mwn.de
***




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Re: [ccp4bb] Help With Setting up a Stereo view system

[Kay Diederichs]

we use the Mate desktop; this interacts well with the composite extension.
HTH
Kay

On Thu, 30 Jul 2020 16:01:20 +0200, Marian Oliva  wrote:

>Thanks Matthias & Pedro,
>
>Yes, this was the initial point. I needed to connect the monitor through a DVI 
>port and not through the display port.
>
>Now all the system are recognized, but I am still stuck and it seems to be the 
>composite extension of the desktop manager
>
>I am using lightdm and I tried to disable composite. But when I disable 
>composite in xorg.conf I got the initial login screen but when I input the 
>password I go back to the initial login screen back.
>
>I read that I should use MATE desktop, but I am unable to install it.  I am 
>not too familiar with Linux. Can you give me any hint of how to change the 
>desktop manager.
>
>I think this is all I need, for the rest the card and the glasses seems to be 
>working fine.
>
>Thanks in advance.
>
>Marian
>
>Marian Oliva
>CSIC-Centro de Investigaciones Biológicas Margarita Salas
>9, Ramiro de Maeztu
>28040-Madrid (Spain)
>
>phone: 0034 91 8373112 (x4380)
>e-mail: mar...@cib.csic.es
>
>**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los 
>ficheros adjuntos, pueden contener información protegida para el uso exclusivo 
>de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro 
>tipo de transmisión por parte de otra persona que no sea el destinatario. Si 
>usted recibe por error este correo, se ruega comunicarlo al remitente y borrar 
>el mensaje recibido.
> 
>**CONFIDENTIALITY NOTICE** This email communication and any attachments may 
>contain confidential and privileged information for the sole use of the 
>designated recipient named above. Distribution, reproduction or any other use 
>of this transmission by any party other than the intended recipient is 
>prohibited. If you are not the intended recipient please contact the sender 
>and delete all copies.
>
>> El 30 jul 2020, a las 15:40, Pedro Matias  escribió:
>> 
>> This may be a problem with the cable, but normally you need to use a DVI 
>> connection between the graphics card and the monitor.
>> 
>>> No dia 30/07/2020, às 14:41, Barone, Matthias  
>>> escreveu:
>>> 
>>> 
>>> Hi Marian
>>> 
>>> I used the quadro 4000 myself and had two Acer monitors connected to it, 
>>> one with display port, one with VGA connector. Only the VGA showed 3D, the 
>>> other would not. Have you tried going analog with this card?
>>> 
>>> best, matthias
>>> 
>>> 
>>> 
>>> Dr. Matthias Barone
>>> 
>>> AG Kuehne, Rational Drug Design
>>> 
>>> Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
>>> Robert-Rössle-Strasse 10
>>> 13125 Berlin
>>> 
>>> Germany
>>> Phone: +49 (0)30 94793-284
>>> 
>>> From: CCP4 bulletin board  on behalf of Marian Oliva 
>>> 
>>> Sent: Thursday, July 30, 2020 2:46:07 PM
>>> To: CCP4BB@JISCMAIL.AC.UK
>>> Subject: [ccp4bb] Help With Setting up a Stereo view system
>>>  
>>> Dear colleagues.
>>> 
>>> I would like to check if some one can help me with the setup of my hardware 
>>> stereo system in Coot under Ubuntu 14
>>> 
>>> With the help of a friend I collect a bunch of second hand stuff.
>>> 
>>> 1 NVIDIA 3D Video 2 system.
>>> 1 Monitor ASUS VG248 conectes through the display port
>>> 1 NVIDIA QUADRO 4000 video card.
>>> 
>>> After connecting everything and having a nightmare to install the Legacy 
>>> Drivers 390.138
>>> 
>>> And following this instructions
>>> 
>>> https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo 
>>> <https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo>
>>> 
>>> I run nvidia-xconfig --stereo=10
>>> 
>>> I connected the emitter both by USB and the DIN 3 pin conector
>>> I connected the monitor through the Display Port
>>> 
>>> I reboot and , the emitter finally shows the green light
>>> 
>>> I can run nvidia-settings and I have the control panel
>>> 
>>> I see Stereo 3D Vision Stereo but only the left cube running.
>>> 
>>> But when I activate hardware stereo nothing works.
>>> 
>>> Does anybody have a clue of what to do?
>>> 
>>> Thanks in advance,
>>> 
>>> Marian
>>> 
>>> 
>>> Marian Oliva
>>> CSIC-Centro de Investi

Re: [ccp4bb] Help With Setting up a Stereo view system

[Pedro Matias]

Hi Marian,

If you need to change the desktop the best option is to install that
Linux flavor from scratch using a live image.

I personally prefer LXDE and it works fine with stereo and I don't have
the composite extension enabled in my xorg.conf.

Look at the /var/log/Xorg.0.log file and see if you can figure out the
problem. If the graphics system is not working, use  to
open a non-graphics shell on your PC, and login as you.

Good luck,

Pedro

P.S. if you want, you can send me the file privately (not to the list)
and I can take a look.

Às 15:01 de 30/07/2020, Marian Oliva escreveu:
> Thanks Matthias & Pedro,
>
> Yes, this was the initial point. I needed to connect the monitor
> through a DVI port and not through the display port.
>
> Now all the system are recognized, but I am still stuck and it seems
> to be the composite extension of the desktop manager
>
> I am using lightdm and I tried to disable composite. But when I
> disable composite in xorg.conf I got the initial login screen but when
> I input the password I go back to the initial login screen back.
>
> I read that I should use MATE desktop, but I am unable to install it.
>  I am not too familiar with Linux. Can you give me any hint of how to
> change the desktop manager.
>
> I think this is all I need, for the rest the card and the glasses
> seems to be working fine.
>
> Thanks in advance.
>
> Marian
>
> Marian Oliva
> CSIC-Centro de Investigaciones Biológicas Margarita Salas
> 9, Ramiro de Maeztu
> 28040-Madrid (Spain)
>
> phone: 0034 91 8373112 (x4380)
> e-mail: mar...@cib.csic.es <mailto:mar...@cib.csic.es>
>
> **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los
> ficheros adjuntos, pueden contener información protegida para el uso
> exclusivo de su destinatario. Se prohíbe la distribución, reproducción
> o cualquier otro tipo de transmisión por parte de otra persona que no
> sea el destinatario. Si usted recibe por error este correo, se
> ruega comunicarlo al remitente y borrar el mensaje recibido.
>  
> **CONFIDENTIALITY NOTICE** This email communication and any
> attachments may contain confidential and privileged information for
> the sole use of the designated recipient named above. Distribution,
> reproduction or any other use of this transmission by any party other
> than the intended recipient is prohibited. If you are not the intended
> recipient please contact the sender and delete all copies.
>
>> El 30 jul 2020, a las 15:40, Pedro Matias > <mailto:mat...@itqb.unl.pt>> escribió:
>>
>> This may be a problem with the cable, but normally you need to use a
>> DVI connection between the graphics card and the monitor.
>>
>>> No dia 30/07/2020, às 14:41, Barone, Matthias >> <mailto:bar...@fmp-berlin.de>> escreveu:
>>>
>>> 
>>>
>>> Hi Marian
>>>
>>> I used the quadro 4000 myself and had two Acer monitors connected to
>>> it, one with display port, one with VGA connector. Only the VGA
>>> showed 3D, the other would not. Have you tried going analog with
>>> this card?
>>>
>>> best, matthias
>>>
>>>
>>> Dr. Matthias Barone
>>>
>>> AG Kuehne, Rational Drug Design
>>>
>>> Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
>>> Robert-Rössle-Strasse 10
>>> 13125 Berlin
>>>
>>> Germany
>>> Phone: +49 (0)30 94793-284
>>>
>>> 
>>> *From:* CCP4 bulletin board >> <mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Marian Oliva
>>> mailto:mar...@cib.csic.es>>
>>> *Sent:* Thursday, July 30, 2020 2:46:07 PM
>>> *To:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
>>> *Subject:* [ccp4bb] Help With Setting up a Stereo view system
>>>  
>>> Dear colleagues.
>>>
>>> I would like to check if some one can help me with the setup of my
>>> hardware stereo system in Coot under Ubuntu 14
>>>
>>> With the help of a friend I collect a bunch of second hand stuff.
>>>
>>> 1 NVIDIA 3D Video 2 system.
>>> 1 Monitor ASUS VG248 conectes through the display port
>>> 1 NVIDIA QUADRO 4000 video card.
>>>
>>> After connecting everything and having a nightmare to install the
>>> Legacy Drivers 390.138
>>>
>>> And following this instructions
>>>
>>> https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo
>>>
>>> I run nvidia-xconfig --stereo=10
>>>
>>> I connec

Re: [ccp4bb] Help With Setting up a Stereo view system

[Marian Oliva]

Thanks Matthias & Pedro,

Yes, this was the initial point. I needed to connect the monitor through a DVI 
port and not through the display port.

Now all the system are recognized, but I am still stuck and it seems to be the 
composite extension of the desktop manager

I am using lightdm and I tried to disable composite. But when I disable 
composite in xorg.conf I got the initial login screen but when I input the 
password I go back to the initial login screen back.

I read that I should use MATE desktop, but I am unable to install it.  I am not 
too familiar with Linux. Can you give me any hint of how to change the desktop 
manager.

I think this is all I need, for the rest the card and the glasses seems to be 
working fine.

Thanks in advance.

Marian

Marian Oliva
CSIC-Centro de Investigaciones Biológicas Margarita Salas
9, Ramiro de Maeztu
28040-Madrid (Spain)

phone: 0034 91 8373112 (x4380)
e-mail: mar...@cib.csic.es

**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros 
adjuntos, pueden contener información protegida para el uso exclusivo de su 
destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de 
transmisión por parte de otra persona que no sea el destinatario. Si usted 
recibe por error este correo, se ruega comunicarlo al remitente y borrar el 
mensaje recibido.
 
**CONFIDENTIALITY NOTICE** This email communication and any attachments may 
contain confidential and privileged information for the sole use of the 
designated recipient named above. Distribution, reproduction or any other use 
of this transmission by any party other than the intended recipient is 
prohibited. If you are not the intended recipient please contact the sender and 
delete all copies.

> El 30 jul 2020, a las 15:40, Pedro Matias  escribió:
> 
> This may be a problem with the cable, but normally you need to use a DVI 
> connection between the graphics card and the monitor.
> 
>> No dia 30/07/2020, às 14:41, Barone, Matthias  
>> escreveu:
>> 
>> 
>> Hi Marian
>> 
>> I used the quadro 4000 myself and had two Acer monitors connected to it, one 
>> with display port, one with VGA connector. Only the VGA showed 3D, the other 
>> would not. Have you tried going analog with this card?
>> 
>> best, matthias
>> 
>> 
>> 
>> Dr. Matthias Barone
>> 
>> AG Kuehne, Rational Drug Design
>> 
>> Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
>> Robert-Rössle-Strasse 10
>> 13125 Berlin
>> 
>> Germany
>> Phone: +49 (0)30 94793-284
>> 
>> From: CCP4 bulletin board  on behalf of Marian Oliva 
>> 
>> Sent: Thursday, July 30, 2020 2:46:07 PM
>> To: CCP4BB@JISCMAIL.AC.UK
>> Subject: [ccp4bb] Help With Setting up a Stereo view system
>>  
>> Dear colleagues.
>> 
>> I would like to check if some one can help me with the setup of my hardware 
>> stereo system in Coot under Ubuntu 14
>> 
>> With the help of a friend I collect a bunch of second hand stuff.
>> 
>> 1 NVIDIA 3D Video 2 system.
>> 1 Monitor ASUS VG248 conectes through the display port
>> 1 NVIDIA QUADRO 4000 video card.
>> 
>> After connecting everything and having a nightmare to install the Legacy 
>> Drivers 390.138
>> 
>> And following this instructions
>> 
>> https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo 
>> <https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo>
>> 
>> I run nvidia-xconfig --stereo=10
>> 
>> I connected the emitter both by USB and the DIN 3 pin conector
>> I connected the monitor through the Display Port
>> 
>> I reboot and , the emitter finally shows the green light
>> 
>> I can run nvidia-settings and I have the control panel
>> 
>> I see Stereo 3D Vision Stereo but only the left cube running.
>> 
>> But when I activate hardware stereo nothing works.
>> 
>> Does anybody have a clue of what to do?
>> 
>> Thanks in advance,
>> 
>> Marian
>> 
>> 
>> Marian Oliva
>> CSIC-Centro de Investigaciones Biológicas Margarita Salas
>> 9, Ramiro de Maeztu
>> 28040-Madrid (Spain)
>> 
>> phone: 0034 91 8373112 (x4380)
>> e-mail: mar...@cib.csic.es <mailto:mar...@cib.csic.es>
>> 
>> **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los 
>> ficheros adjuntos, pueden contener información protegida para el uso 
>> exclusivo de su destinatario. Se prohíbe la distribución, reproducción o 
>> cualquier otro tipo de transmisión por parte de otra persona que no sea el 
>> destinatario. Si usted recibe por error este correo, se ruega comunic

Re: [ccp4bb] Help With Setting up a Stereo view system

[Pedro Matias]

This may be a problem with the cable, but normally you need to use a DVI 
connection between the graphics card and the monitor.

> No dia 30/07/2020, às 14:41, Barone, Matthias  escreveu:
> 
> 
> Hi Marian
> 
> I used the quadro 4000 myself and had two Acer monitors connected to it, one 
> with display port, one with VGA connector. Only the VGA showed 3D, the other 
> would not. Have you tried going analog with this card?
> 
> best, matthias
> 
> 
> 
> Dr. Matthias Barone
> 
> AG Kuehne, Rational Drug Design
> 
> Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
> Robert-Rössle-Strasse 10
> 13125 Berlin
> 
> Germany
> Phone: +49 (0)30 94793-284
> 
> From: CCP4 bulletin board  on behalf of Marian Oliva 
> 
> Sent: Thursday, July 30, 2020 2:46:07 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Help With Setting up a Stereo view system
>  
> Dear colleagues.
> 
> I would like to check if some one can help me with the setup of my hardware 
> stereo system in Coot under Ubuntu 14
> 
> With the help of a friend I collect a bunch of second hand stuff.
> 
> 1 NVIDIA 3D Video 2 system.
> 1 Monitor ASUS VG248 conectes through the display port
> 1 NVIDIA QUADRO 4000 video card.
> 
> After connecting everything and having a nightmare to install the Legacy 
> Drivers 390.138
> 
> And following this instructions
> 
> https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo
> 
> I run nvidia-xconfig --stereo=10
> 
> I connected the emitter both by USB and the DIN 3 pin conector
> I connected the monitor through the Display Port
> 
> I reboot and , the emitter finally shows the green light
> 
> I can run nvidia-settings and I have the control panel
> 
> I see Stereo 3D Vision Stereo but only the left cube running.
> 
> But when I activate hardware stereo nothing works.
> 
> Does anybody have a clue of what to do?
> 
> Thanks in advance,
> 
> Marian
> 
> 
> Marian Oliva
> CSIC-Centro de Investigaciones Biológicas Margarita Salas
> 9, Ramiro de Maeztu
> 28040-Madrid (Spain)
> 
> phone: 0034 91 8373112 (x4380)
> e-mail: mar...@cib.csic.es
> 
> **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los 
> ficheros adjuntos, pueden contener información protegida para el uso 
> exclusivo de su destinatario. Se prohíbe la distribución, reproducción o 
> cualquier otro tipo de transmisión por parte de otra persona que no sea el 
> destinatario. Si usted recibe por error este correo, se ruega comunicarlo al 
> remitente y borrar el mensaje recibido.
>  
> **CONFIDENTIALITY NOTICE** This email communication and any attachments may 
> contain confidential and privileged information for the sole use of the 
> designated recipient named above. Distribution, reproduction or any other use 
> of this transmission by any party other than the intended recipient is 
> prohibited. If you are not the intended recipient please contact the sender 
> and delete all copies.
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
> 
> 
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Re: [ccp4bb] Help With Setting up a Stereo view system

[Barone, Matthias]

Hi Marian

I used the quadro 4000 myself and had two Acer monitors connected to it, one 
with display port, one with VGA connector. Only the VGA showed 3D, the other 
would not. Have you tried going analog with this card?

best, matthias


Dr. Matthias Barone

AG Kuehne, Rational Drug Design

Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Robert-Rössle-Strasse 10
13125 Berlin

Germany
Phone: +49 (0)30 94793-284


From: CCP4 bulletin board  on behalf of Marian Oliva 

Sent: Thursday, July 30, 2020 2:46:07 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Help With Setting up a Stereo view system

Dear colleagues.

I would like to check if some one can help me with the setup of my hardware 
stereo system in Coot under Ubuntu 14

With the help of a friend I collect a bunch of second hand stuff.

1 NVIDIA 3D Video 2 system.
1 Monitor ASUS VG248 conectes through the display port
1 NVIDIA QUADRO 4000 video card.

After connecting everything and having a nightmare to install the Legacy 
Drivers 390.138

And following this instructions

https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo

I run nvidia-xconfig --stereo=10

I connected the emitter both by USB and the DIN 3 pin conector
I connected the monitor through the Display Port

I reboot and , the emitter finally shows the green light

I can run nvidia-settings and I have the control panel

I see Stereo 3D Vision Stereo but only the left cube running.

But when I activate hardware stereo nothing works.

Does anybody have a clue of what to do?

Thanks in advance,

Marian


Marian Oliva
CSIC-Centro de Investigaciones Biológicas Margarita Salas
9, Ramiro de Maeztu
28040-Madrid (Spain)

phone: 0034 91 8373112 (x4380)
e-mail: mar...@cib.csic.es<mailto:mar...@cib.csic.es>

**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros 
adjuntos, pueden contener información protegida para el uso exclusivo de su 
destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de 
transmisión por parte de otra persona que no sea el destinatario. Si usted 
recibe por error este correo, se ruega comunicarlo al remitente y borrar el 
mensaje recibido.

**CONFIDENTIALITY NOTICE** This email communication and any attachments may 
contain confidential and privileged information for the sole use of the 
designated recipient named above. Distribution, reproduction or any other use 
of this transmission by any party other than the intended recipient is 
prohibited. If you are not the intended recipient please contact the sender and 
delete all copies.




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[ccp4bb] Help With Setting up a Stereo view system

[Marian Oliva]

Dear colleagues.

I would like to check if some one can help me with the setup of my hardware 
stereo system in Coot under Ubuntu 14

With the help of a friend I collect a bunch of second hand stuff.

1 NVIDIA 3D Video 2 system.
1 Monitor ASUS VG248 conectes through the display port
1 NVIDIA QUADRO 4000 video card.

After connecting everything and having a nightmare to install the Legacy 
Drivers 390.138

And following this instructions

https://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo 


I run nvidia-xconfig --stereo=10

I connected the emitter both by USB and the DIN 3 pin conector
I connected the monitor through the Display Port

I reboot and , the emitter finally shows the green light

I can run nvidia-settings and I have the control panel

I see Stereo 3D Vision Stereo but only the left cube running.

But when I activate hardware stereo nothing works.

Does anybody have a clue of what to do?

Thanks in advance,

Marian


Marian Oliva
CSIC-Centro de Investigaciones Biológicas Margarita Salas
9, Ramiro de Maeztu
28040-Madrid (Spain)

phone: 0034 91 8373112 (x4380)
e-mail: mar...@cib.csic.es

**NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros 
adjuntos, pueden contener información protegida para el uso exclusivo de su 
destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de 
transmisión por parte de otra persona que no sea el destinatario. Si usted 
recibe por error este correo, se ruega comunicarlo al remitente y borrar el 
mensaje recibido.
 
**CONFIDENTIALITY NOTICE** This email communication and any attachments may 
contain confidential and privileged information for the sole use of the 
designated recipient named above. Distribution, reproduction or any other use 
of this transmission by any party other than the intended recipient is 
prohibited. If you are not the intended recipient please contact the sender and 
delete all copies.




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[ccp4bb] Help to fight COVID-19

[Pramod Kumar]

Dear Structure Biologists,

We have some significant expertise in stabilizing the membrane proteins 
and domains in different kinds of membranous environments such as 
liposomes (small and giant vesicles suitable for biochemical and 
electrophysiological analysis), nanodiscs and malic acid based polymers. 
We are highly proficient for working up to BSL2 level experiments. In 
this tough time of COVID-19 pandemic we would love to 
share/help/collaborate with our expertise to any lab/organization 
interested in developing any kind of fundamental study or therapeutics. 
Please just contact us and we would do our level best.



Pramod Kumar, Ph.D.

Postdoctoral research associate, Grosman Lab

Department of Molecular and Integrative Physiology

University of Illinois at Urban-Champaign.



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[ccp4bb] Help us design PDBe-KB's aggregated views of small molecules

[David Armstrong]

PDBe-KB is a community-driven resource managed by the Protein Data Bank 
in Europe (PDBe) team, integrating functional annotations and structure 
data in the PDB archive. Recently, we started providingaggregated views 
of available structure data and annotations 
for individual proteins. Now, we aim to develop similar aggregated views 
focusing on small molecules (i.e. ligands) in the PDB.


We would like your help to understand what information regarding small 
molecules is useful to you by responding to thisshort survey 
.


The full link to this feedback form is provided below:

https://forms.gle/4Kk5kWLDyKUU5hwE9


Kind Regards,

David Armstrong

--
David Armstrong
Outreach and Training Coordinator
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
Tel: +44 1223 492544




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Re: [ccp4bb] Help please, COOT destroys PDB

[ALEJANDRA ANGELA CARRILES LINARES]

Awesome. Thank you. Just changing the "," to "." did the trick.
Thing is, this setting hadn't been changed before and used to work perfectly.
Thanks again.
Ale




Paul Emsley  escribió:


On 03/07/2019 05:20, ALEJANDRA ANGELA CARRILES LINARES wrote:
I am currently having problems with COOT (running on a Windows 10  
environment).
Thing is, whenever I write a PDB file (save new coordinates), next  
time I open them (whether it is on a Windows or Mac computer),  
bonds are unexistant. I reckon something is wrong when the file is  
written.

How can I sort this out? I didn't have this problem before.
I have reinstalled the new version (0.8.9.2) just to check... but  
same thing happens.


Have you read the WinCoot FAQ?

http://bernhardcl.github.io/coot/wincoot-faq.html

FWIW, I have yet restore the coot web site after it was damaged.

Regards,

Paul.




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Re: [ccp4bb] Help please, COOT destroys PDB

[Paul Emsley]

On 03/07/2019 05:20, ALEJANDRA ANGELA CARRILES LINARES wrote:

I am currently having problems with COOT (running on a Windows 10 environment).
Thing is, whenever I write a PDB file (save new coordinates), next time I open them (whether it is on a 
Windows or Mac computer), bonds are unexistant. I reckon something is wrong when the file is written.

How can I sort this out? I didn't have this problem before.
I have reinstalled the new version (0.8.9.2) just to check... but same thing 
happens.


Have you read the WinCoot FAQ?

http://bernhardcl.github.io/coot/wincoot-faq.html

FWIW, I have yet restore the coot web site after it was damaged.

Regards,

Paul.



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[ccp4bb] Help please, COOT destroys PDB

[ALEJANDRA ANGELA CARRILES LINARES]

Hi there!
I am currently having problems with COOT (running on a Windows 10  
environment).
Thing is, whenever I write a PDB file (save new coordinates), next  
time I open them (whether it is on a Windows or Mac computer), bonds  
are unexistant. I reckon something is wrong when the file is written.

How can I sort this out? I didn't have this problem before.
I have reinstalled the new version (0.8.9.2) just to check... but same  
thing happens.

Thank you very much,
Alejandra Carriles
Instituto Química-Fisica "Rocasolano"
Madrid
Spain



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[ccp4bb] Help for BALBES Results

[Vikram Dalal]

Hi All,

I want to get the phases from balbes. have submitted my data to BALBES
(online ccp4i). I am getting the results in txt file only.

I am not getting the mtz and model result files.

I would be very thankful for suggestions.



Thanks & Regards,



[image: Mailtrack]

Sender
notified by
Mailtrack

07/02/19,
06:44:52 PM



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Re: [ccp4bb] help with TNCS + MR

[Almudena Ponce Salvatierra]

Dear Randy,

thank you very much, I had a look at it and it seems that fortunately it
was one of the "straighforward" cases.

Best,

Almudena

El jue., 14 mar. 2019 a las 14:48, Randy Read () escribió:

> Dear Almu,
>
> We have a discussion on the Phaser Wiki about some of the possibilities
> for tNCS, what you should look for, and what Phaser can handle:
> http://www.phaser.cimr.cam.ac.uk/index.php/Molecular_Replacement#Translational_Non-crystallographic_Symmetry.
> As it explains, if you have one major peak in the native Patterson then
> everything will be pretty automatic, and it can even be straightforward if
> you have several peaks corresponding to multiples of the same underlying
> translation.  If you have some specific questions about your problem after
> you’ve read that and run Phaser on your problem, then let us know!
>
> Best wishes,
>
> Randy
>
> -
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical ResearchTel: +44 1223 336500
> Wellcome Trust/MRC Building Fax: +44 1223 336827
> Hills Road
> E-mail: rj...@cam.ac.uk
> Cambridge CB2 0XY, U.K.
> www-structmed.cimr.cam.ac.uk
>
> > On 14 Mar 2019, at 05:07, Almudena Ponce Salvatierra <
> maps.fa...@gmail.com> wrote:
> >
> > Dear all,
> >
> > I have a dataset with strong TNCS and I would like to know if there are
> a "series of steps" that I could follow in order to find out whether I can
> solve my structure or not.
> >
> > I see on the Phaser wiki that structure determination in the presence of
> TNCS is not fully automated. which steps are those in which my intervention
> should be needed and what do I look for?
> >
> > It is the first time that I deal with this problem and I'd be immensely
> thankful if I could get some hints from those of you who have encountered
> it in the past or understand where in particular I should keep and eye on :)
> >
> > All the best,
> >
> > cheers,
> >
> > Almu
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> >
>
>



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Re: [ccp4bb] help with TNCS + MR

[Eleanor Dodson]

Sorry to plug MOLREP to a Phaser Q, but it does have some simple tNCS
functions which work well for
straightforward cases.

Something to consider:
tNCS can make spacegroup determination based on axial reflection absences
tricky so set a flag to test all SGS in the pointgroup.
For example: (A translation vector of (x,y,1/4) will mean that only
reflections (0,0,l) will be strong for l having a factor of 4 , ie
4,8,12,16,..)

And R factors are typivally higher for crystals with tNCS -- extensive
classes of reflections are weak..

Eleanor



On Thu, 14 Mar 2019 at 13:48, Randy Read  wrote:

> Dear Almu,
>
> We have a discussion on the Phaser Wiki about some of the possibilities
> for tNCS, what you should look for, and what Phaser can handle:
> http://www.phaser.cimr.cam.ac.uk/index.php/Molecular_Replacement#Translational_Non-crystallographic_Symmetry.
> As it explains, if you have one major peak in the native Patterson then
> everything will be pretty automatic, and it can even be straightforward if
> you have several peaks corresponding to multiples of the same underlying
> translation.  If you have some specific questions about your problem after
> you’ve read that and run Phaser on your problem, then let us know!
>
> Best wishes,
>
> Randy
>
> -
> Randy J. Read
> Department of Haematology, University of Cambridge
> Cambridge Institute for Medical ResearchTel: +44 1223 336500
> Wellcome Trust/MRC Building Fax: +44 1223 336827
> Hills Road
> E-mail: rj...@cam.ac.uk
> Cambridge CB2 0XY, U.K.
> www-structmed.cimr.cam.ac.uk
>
> > On 14 Mar 2019, at 05:07, Almudena Ponce Salvatierra <
> maps.fa...@gmail.com> wrote:
> >
> > Dear all,
> >
> > I have a dataset with strong TNCS and I would like to know if there are
> a "series of steps" that I could follow in order to find out whether I can
> solve my structure or not.
> >
> > I see on the Phaser wiki that structure determination in the presence of
> TNCS is not fully automated. which steps are those in which my intervention
> should be needed and what do I look for?
> >
> > It is the first time that I deal with this problem and I'd be immensely
> thankful if I could get some hints from those of you who have encountered
> it in the past or understand where in particular I should keep and eye on :)
> >
> > All the best,
> >
> > cheers,
> >
> > Almu
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> >
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] help with TNCS + MR

[Randy Read]

Dear Almu,

We have a discussion on the Phaser Wiki about some of the possibilities for 
tNCS, what you should look for, and what Phaser can handle: 
http://www.phaser.cimr.cam.ac.uk/index.php/Molecular_Replacement#Translational_Non-crystallographic_Symmetry.
  As it explains, if you have one major peak in the native Patterson then 
everything will be pretty automatic, and it can even be straightforward if you 
have several peaks corresponding to multiples of the same underlying 
translation.  If you have some specific questions about your problem after 
you’ve read that and run Phaser on your problem, then let us know!

Best wishes,

Randy

-
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical ResearchTel: +44 1223 336500
Wellcome Trust/MRC Building Fax: +44 1223 336827
Hills RoadE-mail: 
rj...@cam.ac.uk
Cambridge CB2 0XY, U.K.   
www-structmed.cimr.cam.ac.uk

> On 14 Mar 2019, at 05:07, Almudena Ponce Salvatierra  
> wrote:
> 
> Dear all, 
> 
> I have a dataset with strong TNCS and I would like to know if there are a 
> "series of steps" that I could follow in order to find out whether I can 
> solve my structure or not. 
> 
> I see on the Phaser wiki that structure determination in the presence of TNCS 
> is not fully automated. which steps are those in which my intervention should 
> be needed and what do I look for?
> 
> It is the first time that I deal with this problem and I'd be immensely 
> thankful if I could get some hints from those of you who have encountered it 
> in the past or understand where in particular I should keep and eye on :)
> 
> All the best, 
> 
> cheers, 
> 
> Almu
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 



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[ccp4bb] help with TNCS + MR

[Almudena Ponce Salvatierra]

Dear all,

I have a dataset with strong TNCS and I would like to know if there are a
"series of steps" that I could follow in order to find out whether I can
solve my structure or not.

I see on the Phaser wiki that structure determination in the presence of
TNCS is not fully automated. which steps are those in which my intervention
should be needed and what do I look for?

It is the first time that I deal with this problem and I'd be immensely
thankful if I could get some hints from those of you who have encountered
it in the past or understand where in particular I should keep and eye on :)

All the best,

cheers,

Almu



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Re: [ccp4bb] help needed with a rabbit-head-shaped blob

[Wim Burmeister]

Hello, 
it looks if the density is located around a 2-fold axis. 
It cannot be the superposition of a bis-tris methane molecule bound 
asymmetrically and its symmetry mate ? 
Best 
Wim 


De: "Deborah Harrus"  
À: "CCP4BB"  
Envoyé: Vendredi 2 Novembre 2018 22:14:32 
Objet: [ccp4bb] help needed with a rabbit-head-shaped blob 




Dear all, 

I came across an unidentified rabbit-head-shaped blob and would need help for 
its identification. There are 2 molecules of protein per asymmetric unit but 
there are some differences between the two chains. The blob is located in 
between the two chains, and is surrounded by residues Asp, Pro, and Val. 

The protein, a glycosyltransferase, was expressed in E. coli BL21(DE3) and 
purified on Ni-NTA followed by gel filtration. The purification buffer included 
Sodium phosphate and NaCl. The crystallization condition had Bis-Tris, ammonium 
acetate and PEG 2, and glycerol was used as cryoprotectant. From the size, 
bis-tris was the most probable, but I have tried to fit it and it is not 
convincing. 

The structure is 1.6 angstrom resolution and this is the only thing left to be 
done, it's driving me crazy! 

Pictures attached show the face, bottom and top of the head. 2Fo-Fc is at 1.1 
sigma, Fo-Fc at 3 sigmas. 

Many thanks in advance for your suggestions! 

Regards, 
Deborah. 






= 
Deborah Harrus, PhD. 

University of Oulu / Faculty of Biochemistry and Molecular Medicine 
Aapistie 7 A, 90220 Oulu 
Finland 

office: F123B 
email: deborah.har...@oulu.fi 
phone: +358 50 3502387 / +358 44 2386351 
http://www.oulu.fi/fbmm/node/20603 
= 




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Re: [ccp4bb] help needed with a rabbit-head-shaped blob

[vincent chaptal]

Dear Deborah, Even though you mention differences between your two chains (it 
depends how much), I can't help thinking your  blob looks symmetric. Could 
there be a hidden two fold symmetry? BestVincent 
 Original message From: Deborah Harrus  
Date: 11/2/18  22:14  (GMT+01:00) To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] 
help needed with a rabbit-head-shaped blob 




Dear all,



I came across an unidentified rabbit-head-shaped blob and would need help for 
its identification. There are 2 molecules of protein per asymmetric unit but 
there are some differences between the two chains. The blob is located in 
between the two chains, and
 is surrounded by residues Asp, Pro, and Val.



The protein, a glycosyltransferase, was expressed in E. coli BL21(DE3) and 
purified on Ni-NTA followed by gel filtration. The purification buffer included 
Sodium phosphate and NaCl. The crystallization condition had Bis-Tris, ammonium 
acetate and PEG 2,
 and glycerol was used as cryoprotectant. From the size, bis-tris was the most 
probable, but I have tried to fit it and it is not convincing.



The structure is 1.6 angstrom resolution and this is the only thing left to be 
done, it's driving me crazy!



Pictures attached show the face, bottom and top of the head. 2Fo-Fc is at 1.1 
sigma, Fo-Fc at 3 sigmas.



Many thanks in advance for your suggestions!



Regards,

Deborah.









=

Deborah Harrus, PhD.



University of Oulu / Faculty of Biochemistry and Molecular Medicine

Aapistie 7 A, 90220 Oulu

Finland



office: F123B

email: deborah.har...@oulu.fi

phone: +358 50 3502387 / +358 44 2386351

http://www.oulu.fi/fbmm/node/20603

=






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Re: [ccp4bb] help needed with a rabbit-head-shaped blob

[Tristan Croll]

In all seriousness, it looks like it may be some form of hexose sugar?

 
 
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
 

 

> On 2 Nov 2018, at 21:14, Deborah Harrus  wrote:
> 
> Dear all,
> 
> I came across an unidentified rabbit-head-shaped blob and would need help for 
> its identification. There are 2 molecules of protein per asymmetric unit but 
> there are some differences between the two chains. The blob is located in 
> between the two chains, and is surrounded by residues Asp, Pro, and Val.
> 
> The protein, a glycosyltransferase, was expressed in E. coli BL21(DE3) and 
> purified on Ni-NTA followed by gel filtration. The purification buffer 
> included Sodium phosphate and NaCl. The crystallization condition had 
> Bis-Tris, ammonium acetate and PEG 2, and glycerol was used as 
> cryoprotectant. From the size, bis-tris was the most probable, but I have 
> tried to fit it and it is not convincing.
> 
> The structure is 1.6 angstrom resolution and this is the only thing left to 
> be done, it's driving me crazy!
> 
> Pictures attached show the face, bottom and top of the head. 2Fo-Fc is at 1.1 
> sigma, Fo-Fc at 3 sigmas.
> 
> Many thanks in advance for your suggestions!
> 
> Regards,
> Deborah.
> 
> 
> =
> Deborah Harrus, PhD.
> 
> University of Oulu / Faculty of Biochemistry and Molecular Medicine
> Aapistie 7 A, 90220 Oulu
> Finland
> 
> office: F123B
> email: deborah.har...@oulu.fi
> phone: +358 50 3502387 / +358 44 2386351
> http://www.oulu.fi/fbmm/node/20603
> =
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
> 
> 
> 



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Re: [ccp4bb] help needed with a rabbit-head-shaped blob

[James Gordon]

Or dumbo the elephant.
[Image]

Get Outlook for iOS<https://aka.ms/o0ukef>

From: CCP4 bulletin board  on behalf of Frank Von Delft 

Sent: Saturday, November 3, 2018 7:41:46 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] help needed with a rabbit-head-shaped blob

It's more a Pacman ghost, innit??

Sent from Nine<http://www.9folders.com/>

From: Deborah Harrus 
Sent: Friday, 2 November 2018 21:25
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] help needed with a rabbit-head-shaped blob


Dear all,

I came across an unidentified rabbit-head-shaped blob and would need help for 
its identification. There are 2 molecules of protein per asymmetric unit but 
there are some differences between the two chains. The blob is located in 
between the two chains, and is surrounded by residues Asp, Pro, and Val.

The protein, a glycosyltransferase, was expressed in E. coli BL21(DE3) and 
purified on Ni-NTA followed by gel filtration. The purification buffer included 
Sodium phosphate and NaCl. The crystallization condition had Bis-Tris, ammonium 
acetate and PEG 2, and glycerol was used as cryoprotectant. From the size, 
bis-tris was the most probable, but I have tried to fit it and it is not 
convincing.

The structure is 1.6 angstrom resolution and this is the only thing left to be 
done, it's driving me crazy!

Pictures attached show the face, bottom and top of the head. 2Fo-Fc is at 1.1 
sigma, Fo-Fc at 3 sigmas.

Many thanks in advance for your suggestions!

Regards,
Deborah.



=
Deborah Harrus, PhD.

University of Oulu / Faculty of Biochemistry and Molecular Medicine
Aapistie 7 A, 90220 Oulu
Finland

office: F123B
email: deborah.har...@oulu.fi
phone: +358 50 3502387 / +358 44 2386351
http://www.oulu.fi/fbmm/node/20603
=



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Re: [ccp4bb] help needed with a rabbit-head-shaped blob

[Frank Von Delft]

It's more a Pacman ghost, innit??

Sent from Nine<http://www.9folders.com/>

From: Deborah Harrus 
Sent: Friday, 2 November 2018 21:25
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] help needed with a rabbit-head-shaped blob


Dear all,

I came across an unidentified rabbit-head-shaped blob and would need help for 
its identification. There are 2 molecules of protein per asymmetric unit but 
there are some differences between the two chains. The blob is located in 
between the two chains, and is surrounded by residues Asp, Pro, and Val.

The protein, a glycosyltransferase, was expressed in E. coli BL21(DE3) and 
purified on Ni-NTA followed by gel filtration. The purification buffer included 
Sodium phosphate and NaCl. The crystallization condition had Bis-Tris, ammonium 
acetate and PEG 2, and glycerol was used as cryoprotectant. From the size, 
bis-tris was the most probable, but I have tried to fit it and it is not 
convincing.

The structure is 1.6 angstrom resolution and this is the only thing left to be 
done, it's driving me crazy!

Pictures attached show the face, bottom and top of the head. 2Fo-Fc is at 1.1 
sigma, Fo-Fc at 3 sigmas.

Many thanks in advance for your suggestions!

Regards,
Deborah.



=
Deborah Harrus, PhD.

University of Oulu / Faculty of Biochemistry and Molecular Medicine
Aapistie 7 A, 90220 Oulu
Finland

office: F123B
email: deborah.har...@oulu.fi
phone: +358 50 3502387 / +358 44 2386351
http://www.oulu.fi/fbmm/node/20603
=



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Re: [ccp4bb] help needed with a rabbit-head-shaped blob

[Patrick Loll]

Fig. 2.13 in Gale Rhodes’ “Crystallography Made Crystal Clear” touches on 
rabbit heads and diffraction, and is one of my favorite cartoons (sadly it 
doesn’t directly address your problem).

> On 2 Nov 2018, at 5:14 PM, Deborah Harrus  wrote:
> 
> Dear all,
> 
> I came across an unidentified rabbit-head-shaped blob and would need help for 
> its identification. There are 2 molecules of protein per asymmetric unit but 
> there are some differences between the two chains. The blob is located in 
> between the two chains, and is surrounded by residues Asp, Pro, and Val.
> 
> The protein, a glycosyltransferase, was expressed in E. coli BL21(DE3) and 
> purified on Ni-NTA followed by gel filtration. The purification buffer 
> included Sodium phosphate and NaCl. The crystallization condition had 
> Bis-Tris, ammonium acetate and PEG 2, and glycerol was used as 
> cryoprotectant. From the size, bis-tris was the most probable, but I have 
> tried to fit it and it is not convincing.
> 
> The structure is 1.6 angstrom resolution and this is the only thing left to 
> be done, it's driving me crazy!
> 
> Pictures attached show the face, bottom and top of the head. 2Fo-Fc is at 1.1 
> sigma, Fo-Fc at 3 sigmas.
> 
> Many thanks in advance for your suggestions!
> 
> Regards,
> Deborah.
> 
> 
> =
> Deborah Harrus, PhD.
> 
> University of Oulu / Faculty of Biochemistry and Molecular Medicine
> Aapistie 7 A, 90220 Oulu
> Finland
> 
> office: F123B
> email: deborah.har...@oulu.fi
> phone: +358 50 3502387 / +358 44 2386351
> http://www.oulu.fi/fbmm/node/20603
> =
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 

---
Patrick J. Loll, Ph. D.  
Professor of Biochemistry & Molecular Biology
Drexel University College of Medicine
Room 10-102 New College Building
245 N. 15th St., Mailstop 497
Philadelphia, PA  19102-1192  USA

(215) 762-7706
pjl...@gmail.com
pj...@drexel.edu



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[ccp4bb] Help PDBe to enrich structure data with functional annotations

[Mihaly Varadi]

Dear All,

We would be grateful if you could spend a moment of your time filling 
out this short survey on PDBe-KB 
[https://goo.gl/forms/6jcmDZNXIQm6IZFj2], to help us understand what 
types of additional structure annotations would be useful to you.


PDBe-KB (Protein Data Bank in Europe - Knowledge Base) 
[https://pdbe-kb.org] is a community-driven resource managed by the PDBe 
team, collating functional annotations and predictions for structure 
data in the PDB archive. PDBe-KB is a collaborative effort between PDBe 
and a diverse group of bioinformatics resources and research teams.


Thank you for you time,
Mihaly Varadi

--
Mihaly Varadi, PhD
Scientific Programmer

European Bioinformatics Institute (EMBL-EBI)
Main Building, A2-32, Wellcome Trust Genome Campus, Hinxton, Cambridge, 
UK

Office: +44 (0)1223 494 278
E-mail: mvar...@ebi.ac.uk
Website: www.ebi.ac.uk/about/people/mihaly-varadi



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Re: [ccp4bb] Help with omit map

[Pavel Afonine]

As others suggested, you can use Polder map:

- how-to video tutorial can be found here:

http://www.phenix-online.org/documentation/reference/tutorial_channel.html

- background is described here:

http://journals.iucr.org/d/issues/2017/02/00/ba5254/ba5254.pdf

Pavel


On Tue, Jul 24, 2018 at 3:26 PM, Vikram Dalal 
wrote:

> Hi everyone,
>
>
> I have to generate the omit map of metal and coordinating residues of
> protein structure for the figure.
>
> Which program can be used to generate the omit map for my requirement.
>
>
>
> Thanks & Regards,
>
>
>
>
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] Help with omit map

[Eugene Osipov]

Vikram,
you can use phenix.polder program.

2018-07-24 22:26 GMT+03:00 Vikram Dalal :

> Hi everyone,
>
>
> I have to generate the omit map of metal and coordinating residues of
> protein structure for the figure.
>
> Which program can be used to generate the omit map for my requirement.
>
>
>
> Thanks & Regards,
>
>
>
>
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



-- 
Eugene Osipov
Junior Research Scientist
Laboratory of Enzyme Engineering
Research Center of Biotechnology
Russian Academy of Sciences
Leninsky pr. 33, 119071 Moscow, Russia
e-mail: e.m.osi...@gmail.com



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[ccp4bb] Help with omit map

[Vikram Dalal]

Hi everyone,


I have to generate the omit map of metal and coordinating residues of
protein structure for the figure.

Which program can be used to generate the omit map for my requirement.



Thanks & Regards,



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Re: [ccp4bb] help

[Eleanor Dodson]

Llok at this paper:

Does NMR Mean “Not for Molecular Replacement”? Using NMR-Based Search
Models to Solve Protein Crystal Structures



The references there clainm to give the first instance of success...


And Hi Eleanor

On 5 March 2018 at 13:51, Chandra  wrote:

> Hello all
>
> Does anyone knows of a review that highlights the first examples of the
> use of NMR combined with X-ray crystallography to solve the structures of
> proteins
>
> thanks
>
> chandra
>

[ccp4bb] help

[Chandra]

Hello all

Does anyone knows of a review that highlights the first examples of the 
use of NMR combined with X-ray crystallography to solve the structures 
of proteins


thanks

chandra

Re: [ccp4bb] Help with assigning density

[Prem Prakash]

Is that positive density lying at the symmetry axis ? please check,  if yes
then probably you have to model  the appropriate compound with appropriate
occupancy.

Best

Prem

On Fri, Jan 26, 2018 at 11:10 PM, Vivoli, Mirella <m.viv...@exeter.ac.uk>
wrote:

> Hi Tristan!
> Definitely PEG, in the so called horseshoe shape.
> Cheers,
> Mirella
>
> Get Outlook for Android <https://aka.ms/ghei36>
>
> --
> *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Tristan
> Croll <ti...@cam.ac.uk>
> *Sent:* Friday, January 26, 2018 6:09:01 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Help with assigning density
>
> Yes it can. See 5x49 (residue 603) for a wonderful example.
>
> On 2018-01-26 16:46, Michal Boniecki wrote:
> > I have positive density around lysine residue (image). This density is
> > found in all crystals, and only with this lysine. It is solvent
> > accessible but again not only this one is surface K residue. Can PEG
> > wrap around lysine like this? Maybe someone else have seen similar
> > density and knows what it might be?
> >
> > Thank You
>

Re: [ccp4bb] Help with assigning density

[Vivoli, Mirella]

Hi Tristan!
Definitely PEG, in the so called horseshoe shape.
Cheers,
Mirella

Get Outlook for Android<https://aka.ms/ghei36>


From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Tristan Croll 
<ti...@cam.ac.uk>
Sent: Friday, January 26, 2018 6:09:01 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Help with assigning density

Yes it can. See 5x49 (residue 603) for a wonderful example.

On 2018-01-26 16:46, Michal Boniecki wrote:
> I have positive density around lysine residue (image). This density is
> found in all crystals, and only with this lysine. It is solvent
> accessible but again not only this one is surface K residue. Can PEG
> wrap around lysine like this? Maybe someone else have seen similar
> density and knows what it might be?
>
> Thank You

Re: [ccp4bb] Help with assigning density

[Tristan Croll]

Yes it can. See 5x49 (residue 603) for a wonderful example.

On 2018-01-26 16:46, Michal Boniecki wrote:

I have positive density around lysine residue (image). This density is
found in all crystals, and only with this lysine. It is solvent
accessible but again not only this one is surface K residue. Can PEG
wrap around lysine like this? Maybe someone else have seen similar
density and knows what it might be?

Thank You

Re: [ccp4bb] Help needed to make a clue about ligand

[Allister Crow]

Shankar,

It looks like Acetyl coA to me.

Best wishes,

- Allister


> On 10 Jan 2018, at 04:09, Shankar Prasad Kanaujia  
> wrote:
> 
> Dear All,
> 
> Wishing you all a very happy and prosperous new year 2018
> 
> We have recently solved a structure which contains a huge density in the 
> active site. We modelled a molecule fitting the electron density (please see 
> the attached figures). However, we could not find any known molecule similar 
> to the fitted molecule either in PDB or PubChem databases. Thus, we are not 
> able to correlate its existence in cell.
> 
> The protein was expressed in E. coli cells. The structure is solved at 1.85 
> Angst. We have not added any molecule like this in any step of the 
> experiments.
> 
> Looking forward to having some ways to figure out this problem.
> 
> With best regards,
> Shankar
> 
> 
> -- 
> Shankar Prasad Kanaujia, Ph.D.
> Associate Professor
> Department of Biosciences and Bioengineering
> Indian Institute of Technology Guwahati
> Guwahati - 781039 Assam, India
> Tele: 0361 258 2228
> Fax:  0361 258 2249
> Email: spkanau...@iitg.ernet.in 
> Homepage: http://www.iitg.ernet.in/spkanaujia/ 
> 
> Google Scholar: https://scholar.google.com/citations?user=Zt4JSNYJ=en 
> 
> 

-
Allister Crow
School of Life Sciences
University of Warwick

Re: [ccp4bb] Help needed to make a clue about ligand

[Tristan Croll]

Looks like it could be a G-C dinucleotide?

 
 
Tristan Croll
Research Fellow
Cambridge Institute for Medical Research
University of Cambridge CB2 0XY
 

 

> On 10 Jan 2018, at 04:09, Shankar Prasad Kanaujia  
> wrote:
> 
> Dear All,
> 
> Wishing you all a very happy and prosperous new year 2018
> 
> We have recently solved a structure which contains a huge density in the 
> active site. We modelled a molecule fitting the electron density (please see 
> the attached figures). However, we could not find any known molecule similar 
> to the fitted molecule either in PDB or PubChem databases. Thus, we are not 
> able to correlate its existence in cell.
> 
> The protein was expressed in E. coli cells. The structure is solved at 1.85 
> Angst. We have not added any molecule like this in any step of the 
> experiments.
> 
> Looking forward to having some ways to figure out this problem.
> 
> With best regards,
> Shankar
> 
> 
> -- 
> Shankar Prasad Kanaujia, Ph.D.
> Associate Professor
> Department of Biosciences and Bioengineering
> Indian Institute of Technology Guwahati
> Guwahati - 781039 Assam, India
> Tele: 0361 258 2228
> Fax:  0361 258 2249
> Email: spkanau...@iitg.ernet.in
> Homepage: http://www.iitg.ernet.in/spkanaujia/
> Google Scholar: https://scholar.google.com/citations?user=Zt4JSNYJ=en
> 

Re: [ccp4bb] help identifying unknown density

[Jiyong Su]

Dear Eleanor,
I think the best way is to use Mass spectrum to identify the compound. 
Best regards,
Jiyong


 



在 2017-10-10 00:07:25，Eleanor Dodson <eleanor.dod...@york.ac.uk> 写道：
Any anomalous signal?Eleanor


On 9 October 2017 at 17:05, Gang Dong <gang.d...@univie.ac.at> wrote:
Could it be a formate ion (HCO2−)? _Gang

-Original Message-
 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Stephen 
Cusack
 Sent: Monday, October 09, 2017 5:40 PM
 To: CCP4BB@JISCMAIL.AC.UK
 Subject: [ccp4bb] help identifying unknown density

 Dear All,

 I am refining the crystal structure of an E. coli expressed protein at 
2.65 A resolution. The crystals grew in

 0.1 M MES pH6, 0.7 M sodium formate pH 6. Ni-NTA was used in the purification.

 There are four molecules in the asymmetric unit. A particular histidine in 
each molecular has clear, strong extra density which looks like a metal bonded 
to an imidazole nitrogen (distance approx 2 A) with three other co-ordinating 
atoms in a triangular planar arrangement (see attached screen shot for unbiased 
extra density, atoms are only put in the density for illustrative purposes).

 Has anyone seen anything like this ? Any suggestions ?

 thanks very much

 Stephen

 --

 **
 Dr. Stephen Cusack, FRS
 Head of Grenoble Outstation of the European Molecular Biology Laboratory 
(EMBL) Group leader in structural biology of protein-RNA complexes and viral 
proteins
 **

 Email:  cus...@embl.fr
 Website: http://www.embl.fr
 Tel:(33) 4 76 20 7238Secretary (33) 4 76 20 7123
 Fax:(33) 4 76 20 7199
 Postal address:   EMBL Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 
38042 Grenoble Cedex 9, France
 Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, 71 Avenue 
des Martyrs, 38000 Grenoble, France
 **

[ccp4bb] RE : [ccp4bb] help identifying unknown density

[Cyr Normand]

(I am new to ccp4bb and it is nice to read all those insightful
discussions!)

Dr. Cusack,

Regarding your problem, we have observed a similar phenomenon in the
past with a protein expressed in E. coli and purified using Ni-NTA resin.

We later discovered that the density in the structure was indeed a metal
which was coordinated with histine from the recombinant protein. The
metal was identified to be nickel that likely leached out from the NTA
resin. This protein was not previously known to bind metal ions. We are
now investigating this using other biophysical methods.

To purify the protein, we used some resin in bulk that we loaded
ourselves with nickel. This could be the source of metal ions.

Hope this helps!
Norm

-- 
Normand Cyr, PhD
Postdoctoral Fellow in Structural Biology
Dept of Biochemistry and Molecular Medicine, Université de Montréal
+1-514-343-6111 ext. 5154
https://www.normandcyr.com

De : CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] de la part de Stephen Cusack 
[cus...@embl.fr]
Envoyé : 9 octobre 2017 11:40
À : CCP4BB@JISCMAIL.AC.UK
Objet : [ccp4bb] help identifying unknown density

Dear All,

I am refining the crystal structure of an E. coli expressed protein
at 2.65 A resolution. The crystals grew in

0.1 M MES pH6, 0.7 M sodium formate pH 6. Ni-NTA was used in the
purification.

There are four molecules in the asymmetric unit. A particular histidine
in each molecular has clear, strong extra density which looks like a
metal bonded to an imidazole nitrogen (distance approx 2 A) with three
other co-ordinating atoms in a triangular planar arrangement (see
attached screen shot for unbiased extra density, atoms are only put in
the density for illustrative purposes).

Has anyone seen anything like this ? Any suggestions ?

thanks very much

Stephen

--

**
Dr. Stephen Cusack, FRS
Head of Grenoble Outstation of the European Molecular Biology Laboratory (EMBL)
Group leader in structural biology of protein-RNA complexes and viral proteins
**

Email:  cus...@embl.fr
Website: http://www.embl.fr
Tel:(33) 4 76 20 7238Secretary (33) 4 76 20 7123
Fax:(33) 4 76 20 7199
Postal address:   EMBL Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 
38042 Grenoble Cedex 9, France
Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, 71 Avenue 
des Martyrs, 38000 Grenoble, France
**

Re: [ccp4bb] help identifying unknown density

[CRAIG A BINGMAN]

You may have crystallized an enzyme that uses a phosphoramidate intermediate.

https://en.wikipedia.org/wiki/Phosphoramidate


On Oct 9, 2017, at 10:40 AM, Stephen Cusack 
> wrote:

Dear All,

   I am refining the crystal structure of an E. coli expressed protein at 2.65 
A resolution. The crystals grew in

0.1 M MES pH6, 0.7 M sodium formate pH 6. Ni-NTA was used in the purification.

There are four molecules in the asymmetric unit. A particular histidine in each 
molecular has clear, strong extra density which looks like a metal bonded to an 
imidazole nitrogen (distance approx 2 A) with three other co-ordinating atoms 
in a triangular planar arrangement (see attached screen shot for unbiased extra 
density, atoms are only put in the density for illustrative purposes).

Has anyone seen anything like this ? Any suggestions ?

thanks very much

Stephen

--

**
Dr. Stephen Cusack, FRS
Head of Grenoble Outstation of the European Molecular Biology Laboratory (EMBL)
Group leader in structural biology of protein-RNA complexes and viral proteins
**

Email: cus...@embl.fr
Website: http://www.embl.fr
Tel: (33) 4 76 20 7238Secretary (33) 4 76 20 7123
Fax:(33) 4 76 20 7199
Postal address:   EMBL Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 
38042 Grenoble Cedex 9, France
Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, 71 Avenue 
des Martyrs, 38000 Grenoble, France
**

Re: [ccp4bb] help identifying unknown density

[Federico Forneris]

Any chances for some guadinium leftover from a refolding protocol? 
See second line in fig 1 here, quite similar stacking: 
http://www.mdpi.com/1420-3049/20/5/9214/htm

Best,
F.

Federico Forneris, PhD

The Armenise-Harvard Laboratory of Structural Biology
Dept. Biology and Biotechnology
University of Pavia
Via Ferrata, 9
I-27100 Pavia - ITALY
http://fornerislab.unipv.it






-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Stephen 
Cusack
Sent: lunedì 9 ottobre 2017 17:40
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] help identifying unknown density

Dear All,

 �� I am refining the crystal structure of an E. coli expressed protein 
at 2.65 A resolution. The crystals grew in

0.1 M MES pH6, 0.7 M sodium formate pH 6. Ni-NTA was used in the 
purification.

There are four molecules in the asymmetric unit. A particular histidine 
in each molecular has clear, strong extra density which looks like a 
metal bonded to an imidazole nitrogen (distance approx 2 A) with three 
other co-ordinating atoms in a triangular planar arrangement (see 
attached screen shot for unbiased extra density, atoms are only put in 
the density for illustrative purposes).

Has anyone seen anything like this ? Any suggestions ?

thanks very much

Stephen

-- 

**
Dr. Stephen Cusack, FRS
Head of Grenoble Outstation of the European Molecular Biology Laboratory (EMBL)
Group leader in structural biology of protein-RNA complexes and viral proteins
**

Email:  cus...@embl.fr  
Website: http://www.embl.fr 
Tel:(33) 4 76 20 7238Secretary (33) 4 76 20 7123

Fax:(33) 4 76 20 7199   
Postal address:   EMBL Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 
38042 Grenoble Cedex 9, France
Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, 71 Avenue 
des Martyrs, 38000 Grenoble, France
**

Re: [ccp4bb] help identifying unknown density

[Eleanor Dodson]

Any anomalous signal?
Eleanor

On 9 October 2017 at 17:05, Gang Dong <gang.d...@univie.ac.at> wrote:

> Could it be a formate ion (HCO2−)? _Gang
>
> -Original Message-
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
> Stephen Cusack
> Sent: Monday, October 09, 2017 5:40 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] help identifying unknown density
>
> Dear All,
>
> I am refining the crystal structure of an E. coli expressed protein at
> 2.65 A resolution. The crystals grew in
>
> 0.1 M MES pH6, 0.7 M sodium formate pH 6. Ni-NTA was used in the
> purification.
>
> There are four molecules in the asymmetric unit. A particular histidine in
> each molecular has clear, strong extra density which looks like a metal
> bonded to an imidazole nitrogen (distance approx 2 A) with three other
> co-ordinating atoms in a triangular planar arrangement (see attached screen
> shot for unbiased extra density, atoms are only put in the density for
> illustrative purposes).
>
> Has anyone seen anything like this ? Any suggestions ?
>
> thanks very much
>
> Stephen
>
> --
>
> **
> Dr. Stephen Cusack, FRS
> Head of Grenoble Outstation of the European Molecular Biology Laboratory
> (EMBL) Group leader in structural biology of protein-RNA complexes and
> viral proteins
> **
>
> Email:  cus...@embl.fr
> Website: http://www.embl.fr
> Tel:(33) 4 76 20 7238Secretary (33) 4 76 20 7123
> Fax:(33) 4 76 20 7199
> Postal address:   EMBL Grenoble Outstation, 71 Avenue des Martyrs, CS
> 90181, 38042 Grenoble Cedex 9, France
> Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, 71
> Avenue des Martyrs, 38000 Grenoble, France
> **
>

Re: [ccp4bb] help identifying unknown density

[Gang Dong]

Could it be a formate ion (HCO2−)? _Gang

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Stephen 
Cusack
Sent: Monday, October 09, 2017 5:40 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] help identifying unknown density

Dear All,

I am refining the crystal structure of an E. coli expressed protein at 2.65 
A resolution. The crystals grew in

0.1 M MES pH6, 0.7 M sodium formate pH 6. Ni-NTA was used in the purification.

There are four molecules in the asymmetric unit. A particular histidine in each 
molecular has clear, strong extra density which looks like a metal bonded to an 
imidazole nitrogen (distance approx 2 A) with three other co-ordinating atoms 
in a triangular planar arrangement (see attached screen shot for unbiased extra 
density, atoms are only put in the density for illustrative purposes).

Has anyone seen anything like this ? Any suggestions ?

thanks very much

Stephen

-- 

**
Dr. Stephen Cusack, FRS
Head of Grenoble Outstation of the European Molecular Biology Laboratory (EMBL) 
Group leader in structural biology of protein-RNA complexes and viral proteins
**

Email:  cus...@embl.fr  
Website: http://www.embl.fr 
Tel:(33) 4 76 20 7238Secretary (33) 4 76 20 7123

Fax:(33) 4 76 20 7199   
Postal address:   EMBL Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, 
38042 Grenoble Cedex 9, France
Delivery address: EMBL Grenoble Outstation, Polygone Scientifique, 71 Avenue 
des Martyrs, 38000 Grenoble, France
**

Re: [ccp4bb] Help needed finding hit condition

[khaja faisal tarique]

Hello everyone.

I remember the screen was again from Jenabioscience and this had happened
with one of my protein. The screen was very old and the condition was
peg3350, tris pH 8, lithium sulfate and NaCl as the salt. Hit was obtained
which was never reproducible. Luckily I solved the structure from the hit
itself which diffracted to 2.2A resolution. But it is still a mystery for
us but this is all crystallography is. Strange things happen.

Faisal
Postdoc
PHRI, NJ, USA

On Jul 31, 2017 5:19 PM, "Janet Newman" <janet.new...@csiro.au> wrote:

> ​Hi Jonathan,
>
>
> Hopefully you know about the trick of making any precious condition last
> longer - use the 'magic' solution only in the drop itself, and use the best
> approximation you can make in the reservoir of the experiment (if you are
> doing vapour diffusion)
>
>
> Regards, Janet
>
>
> Janet Newman
> Principal Scientist / Director, Collaborative Crystallisation Centre (C3)
> CSIRO Material Science and Engineering
> 343 Royal Parade
> Parkville.  VIC. 3052
> Australia
> Tel +613 9662 7326 <+61%203%209662%207326>
> Email janet.new...@csiro.au
> --
> *From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Jonathan
> Bailey <baile...@tcd.ie>
> *Sent:* 31 July 2017 22:34
> *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
>

Re: [ccp4bb] Help needed finding hit condition

[Janet Newman]

?Hi Jonathan,


Hopefully you know about the trick of making any precious condition last longer 
- use the 'magic' solution only in the drop itself, and use the best 
approximation you can make in the reservoir of the experiment (if you are doing 
vapour diffusion)


Regards, Janet


Janet Newman
Principal Scientist / Director, Collaborative Crystallisation Centre (C3)
CSIRO Material Science and Engineering
343 Royal Parade
Parkville.  VIC. 3052
Australia
Tel +613 9662 7326
Email janet.new...@csiro.au

From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Jonathan Bailey 
<baile...@tcd.ie>
Sent: 31 July 2017 22:34
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

Re: [ccp4bb] Help needed finding hit condition

[Kevin Jin]

Hi Jonathan,

 Old buffer may have slow evaporation with some side reactions. The
concentration of each component may increase a little bit.  In this case,
 I would consider the condition as the origin for further optimization.
Each component may need to be considered separately.

For 150mM Tris pH 8.000,
The pH and concentration may  have a slight change (increase ?).  I will
try the concentration of 150mM, 155 mM and 160mM. For pH,  pH 8.1 and pH
8.2...

For KBr, the concentration may be 80, 85, 90mM or higher.

For 47.1% w/v PEG1K (Pretty high concentration),
As the result for ring-opening epoxide reaction, it is not very stable
anyway. The reaction always continued. Basic condition made the case even
worse. In this case, the Mn (MW) of PEG1K may not be that average anymore.
It is very possible that the polymer chain is elongated. Of course, the
concentration of PEG is increased too. In the meanwhile, the presence of
KBr may cause further chemical modification on the PEG chains.  You may try
PEG 95--1050 (Sigma P3515), PEG 1305-1595 (Sigma 202136), PEG3K or PEG
3350, etc.


Best,

Kevin

P.S. If you take a look from the top of your old solution in the tube,
what's the color? Slight Yellow? You can use a tube with dd water a
reference.


On Mon, Jul 31, 2017 at 5:34 AM, Jonathan Bailey  wrote:

> 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
>



-- 
Kevin Jin

Sharing knowledge each other is always very joyful..

Website: http://www.jinkai.org/

Re: [ccp4bb] Help needed finding hit condition

[R. Michael Garavito]

Jonathan,

While your claim of oxidative degradation of PEG1000 may be true -- I gather 
you mean that the conversion of the ends of the PEG polymers to aldehydes or 
peroxides, then to carboxylates --  you should check out Fran Jurnak’s old 
paper (Journal of Crystal Growth 76, 577, 1986).  The synthesis of PEG often 
contains some of phosphoric acid due to the way they terminated the chain 
elongation.  It is variable from batch to batch and from supplier to supplier; 
Merck (Germany) is a fairly good source, but Baker/Union Carbide isn't.   
Unless Jena took the time and effort to purify the PEG (see Bill Ray's article 
in the same issue, p. 562), you have another factor that can drop the pH.  You 
might ask where Jena buys their PEG stock.

Also, the way many companies make the screens are not always clear.  Some just 
mix stocks, meaning the pH of the Tris stock (perhaps at 1 M) was pH 8, but 
when diluted down with the other components to make the 150 mM concentration 
for the screen mixture, the pH can be significantly different.  The dilution of 
Tris would drop the pH.

Cheers,

Michael
 

R. Michael Garavito, Ph.D.
Professor of Biochemistry & Molecular Biology
603 Wilson Rd., Rm. 513   
Michigan State University  
East Lansing, MI 48824-1319
Office:  (517) 355-9724 Lab:  (517) 353-9125
FAX:  (517) 353-9334Email:  rmgarav...@gmail.com





> On Jul 31, 2017, at 8:34 AM, Jonathan Bailey  wrote:
> 
> 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 
> 

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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[ccp4bb] Help needed finding hit condition

[Jonathan Bailey]

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

Re: [ccp4bb] help needed to interpret a SRF

[R. Michael Garavito]

Vincent,

You are on the right track.  Notice now that both maps at chi/kappa=180 have 
strong peaks at the y-axis and a “mirror” plane perpendicular to this.This 
is what would be expected for P21, i.e., Y is b/b*.  Then depending on the 
orthogonalization convention of MolRep, the a- and b-axes are in the X-Z plane. 
 Now the two maps are consistent.  So going to an integration radius of 30 Å 
has made a marked improvement in the SRF maps. What Herman has pointed out is 
that you can (and should) explore different integration radii, but always being 
bias towards choosing a MINIMUM radius that gives you a clear and unequivocal 
signal.  

> I'm puzzled by this radius of 30A as I read in the documentation that is 
> corresponds to the approximate radius of the protein. My protein is about 
> 130Ax40A in the closed form to 130Ax70A in the open form according to other 
> structures available. Shouldn't I compute maps with a radius of 70A or more? 
> I'm not posting here these results here as they look more "artsy". 


Absolutely not!  Part of the problem is that almost no one looks at 
Patterson maps now days.  To find NCS, you want to stay within the region of 
Patterson vectors that contains the intermolecular vectors arising from within 
a putative NCS system (say a tetramer), but also contains almost NO 
intermolecular vectors between a tetramer and a neighboring tetramer (from 
within the same or from a different ASU).  I have always followed the rule of 
thumb to start with an integration radius of about 1/2 of the minimum molecular 
dimension (~35 Å in your case, but I have used routinely 20-30 Å for many large 
proteins).  As Herman rightly points out, lowering the integration radius does 
lower the signal, but any noise/signal from cross-peaks can make the maps 
almost impossible to interpret.

Both maps at chi/kappa=180 also have clear peaks in the X-Z plane that are 90 
degrees apart.  What are their peak heights compared to the origin peak?  If 
they are essentially 100%, you may have a P222 crystal system; if not, you may 
have NCS that mimics P222 (all major peaks separated by 90 degrees).  The NCS 
peaks I’ve seen are generally between 50-80% of the origin peak height.  
Finally, the second map at at chi/kappa=180 shows a series of peaks that form a 
"great circle" between the crystallographic b/b* axis and the second peak in 
the X-Z plane.  These could be weak NCS two-folds.  How many NCS systems do you 
suspect in the ASU?

Cheers and good luck,

Michael


R. Michael Garavito, Ph.D.
Professor of Biochemistry & Molecular Biology
603 Wilson Rd., Rm. 513   
Michigan State University  
East Lansing, MI 48824-1319
Office:  (517) 355-9724 Lab:  (517) 353-9125
FAX:  (517) 353-9334Email:  rmgarav...@gmail.com





> On Jun 2, 2017, at 6:05 AM, vincent Chaptal  wrote:
> 
> Hi Michael, 
> 
> thank you for your explanations. 
> 
> On 01/06/2017 15:41, R. Michael Garavito wrote:
>> Vincent,
>> 
>> I see a few of problems with your SRF (the maps) which would impact the 
>> interpretation.  
>> 
>> First you say that both crystals are processed as P21, which you would 
>> expect a very strong peak (100% of your origin peak) on kappa/chi=180 at the 
>> b* axis (one of the major axes of your map); this arises from the 
>> crystallographic symmetry.  Where this axis is depends on what the 
>> conventions are of the program you are using. Your SRF has a major peak 
>> along Z, but is that the b* axis?  (My b* axis is always placed North-South 
>> or your X, á la the Rossmann conventions.  I don’t know the conventions for 
>> Molrep) Then you see major off-axial peaks.  The sad thing about your 
>> off-axial peaks is that they are badly split.
> The datasets were processed by XDS in primitive monoclinic P2 (space group 
> 3), the reindexed to P21 by Aimless as the most probable space group. I just 
> double checked that it is indeed P21, you made me doubt. I tried to look for 
> the conventions for Molrep but couldn't find them, I'm sorry. 
> Following your 3rd comment bellow, I reproduced the maps with a radius of 30A 
> as you suggested (see attached maps). I guess I can see the same features on 
> both maps, with a peak along Y that would correspond to the 2 fold axis (if 
> the convention is turned 90° compared to yours), and 2 off origin peaks along 
> X. The maps from the crystal without additive is an awful mess. I should add 
> that my monomer has an internal 2fold (pseudo)symmetry. Could the two main 
> peaks mean that I have 2 monomers, each with his own 2 fold symmetry? 
> 
> I'm puzzled by this radius of 30A as I read in the documentation that is 
> corresponds to the approximate radius of the protein. My protein is about 
> 130Ax40A in the closed form to 130Ax70A in the open form according to other 
> structures 

[ccp4bb] AW: [ccp4bb] help needed to interpret a SRF

[Herman . Schreuder]

Hi Vincent,

To calculate the best possible (self)rotation function, you want to have as 
many as possible intramolecular vectors (within the search molecule) and as 
little as possible intramolecular vectors (between molecules in the crystal). 
These latter vectors are meaningless (noise) as long as the orientation of your 
search molecule has not been found and you are not calculating a translation 
function.

Even with a small Patterson radius, you will get some intramolecular vectors 
near crystal contacts, but not many. With a large Patterson radius, you will 
get many intramolecular vectors which may obscure your rotation function 
solution.

So in difficult cases, you have to find the optimal radius: if it is too small, 
you won’t get much signal, if the radius is too large, you will get too much 
noise and you won’t see the correct solution either. The number of 
intramolecular vectors you get depend on the crystal packing and the shape of 
your molecule and there are no universally applicable hard rules. In your case 
it might be a good idea to run the (self)rotation function with different 
radii, too see which radius gives the best signal to noise ratio.

Hope this explains things a little,
Best, Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von vincent 
Chaptal
Gesendet: Freitag, 2. Juni 2017 12:05
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] help needed to interpret a SRF

Hi Michael,

thank you for your explanations.
On 01/06/2017 15:41, R. Michael Garavito wrote:
Vincent,

I see a few of problems with your SRF (the maps) which would impact the 
interpretation.

First you say that both crystals are processed as P21, which you would expect a 
very strong peak (100% of your origin peak) on kappa/chi=180 at the b* axis 
(one of the major axes of your map); this arises from the crystallographic 
symmetry.  Where this axis is depends on what the conventions are of the 
program you are using. Your SRF has a major peak along Z, but is that the b* 
axis?  (My b* axis is always placed North-South or your X, á la the Rossmann 
conventions.  I don’t know the conventions for Molrep) Then you see major 
off-axial peaks.  The sad thing about your off-axial peaks is that they are 
badly split.
The datasets were processed by XDS in primitive monoclinic P2 (space group 3), 
the reindexed to P21 by Aimless as the most probable space group. I just double 
checked that it is indeed P21, you made me doubt. I tried to look for the 
conventions for Molrep but couldn't find them, I'm sorry.
Following your 3rd comment bellow, I reproduced the maps with a radius of 30A 
as you suggested (see attached maps). I guess I can see the same features on 
both maps, with a peak along Y that would correspond to the 2 fold axis (if the 
convention is turned 90° compared to yours), and 2 off origin peaks along X. 
The maps from the crystal without additive is an awful mess. I should add that 
my monomer has an internal 2fold (pseudo)symmetry. Could the two main peaks 
mean that I have 2 monomers, each with his own 2 fold symmetry?

I'm puzzled by this radius of 30A as I read in the documentation that is 
corresponds to the approximate radius of the protein. My protein is about 
130Ax40A in the closed form to 130Ax70A in the open form according to other 
structures available. Shouldn't I compute maps with a radius of 70A or more? 
I'm not posting here these results here as they look more "artsy".

All the best
Vincent


The second problem is that the second crystal shows very strong peak (1001% of 
your origin peak) on kappa/chi=180, but at different position (along Y).  The 
control peak is the expected peak which arises from the P21 crystallographic 
symmetry.  If the data sets were processed as P21, they should be indexed with 
the 2-fold axis along b/b*, thus the control peak is the expected peak which 
arises from the P21 crystallographic symmetry.  Once that peak appears in the 
same place on each map, you can then compare the maps with more confidence.

The third problem is that all your maps have the “appearance" of mirror 
symmetry across the x-axis, which would be expected as it is the consequence of 
the P2(1) symmetry and you are looking at a hemisphere.  But it suggests that 
the 2-fold axis is along Y (b/b*). Then map 1 is missing the expected peak on 
kappa/chi=180 at the b* axis.

Final comment is that the maps labeling suggest that the radius of integration 
is 62-66 Å, which is way, way too large, even for an empty unit cell.  If it 
is, reduce it down to 20-30 Å to avoid intermolecular cross-peaks and see if 
the maps become clearer.  I have attached a SRF map from a P21 crystal form 
(radius of integration = 20 Å, resol. = 2.8 Å) with the 2-fold axis indexed 
along b/b* (Y) from polarrfn; note the “appearance" of mirror symmetry 
perpendicular to across the b/b*-axis (North-South or y-axis).

Cheers,

Michael



**

Re: [ccp4bb] help needed to interpret a SRF

[R. Michael Garavito]

Vincent,I see a few of problems with your SRF (the maps) which would impact the interpretation.  First you say that both crystals are processed as P21, which you would expect a very strong peak (100% of your origin peak) on kappa/chi=180 at the b* axis (one of the major axes of your map); this arises from the crystallographic symmetry.  Where this axis is depends on what the conventions are of the program you are using. Your SRF has a major peak along Z, but is that the b* axis?  (My b* axis is always placed North-South or your X, á la the Rossmann conventions.  I don’t know the conventions for Molrep) Then you see major off-axial peaks.  The sad thing about your off-axial peaks is that they are badly split.The second problem is that the second crystal shows very strong peak (1001% of your origin peak) on kappa/chi=180, but at different position (along Y).  The control peak is the expected peak which arises from the P21 crystallographic symmetry.  If the data sets were processed as P21, they should be indexed with the 2-fold axis along b/b*, thus the control peak is the expected peak which arises from the P21 crystallographic symmetry.  Once that peak appears in the same place on each map, you can then compare the maps with more confidence.The third problem is that all your maps have the “appearance" of mirror symmetry across the x-axis, which would be expected as it is the consequence of the P2(1) symmetry and you are looking at a hemisphere.  But it suggests that the 2-fold axis is along Y (b/b*). Then map 1 is missing the expected peak on kappa/chi=180 at the b* axis.Final comment is that the maps labeling suggest that the radius of integration is 62-66 Å, which is way, way too large, even for an empty unit cell.  If it is, reduce it down to 20-30 Å to avoid intermolecular cross-peaks and see if the maps become clearer.  I have attached a SRF map from a P21 crystal form (radius of integration = 20 Å, resol. = 2.8 Å) with the 2-fold axis indexed along b/b* (Y) from polarrfn; note the “appearance" of mirror symmetry perpendicular to across the b/b*-axis (North-South or y-axis).Cheers,Michael

EhaAc_kappa180.pdf
Description: Adobe PDF document

R. Michael Garavito, Ph.D.Professor of Biochemistry & Molecular Biology603 Wilson Rd., Rm. 513   Michigan State University      East Lansing, MI 48824-1319Office:  (517) 355-9724     Lab:  (517) 353-9125FAX:  (517) 353-9334        Email:  rmgarav...@gmail.com

On Jun 1, 2017, at 4:51 AM, vincent Chaptal  wrote:Dear Manfred, attached are the postcript files. VincentOn 01/06/2017 10:19, Manfred S. Weiss wrote:Dear Vincent,it would be good if you post the postscript file as well.It is called molrep_rf.ps or something like that. Cheers, ManfredAm 01.06.2017 um 10:12 schrieb vincent Chaptal:Thank you for your email. the anisotropic resolutions of the datasets are 5.6-7.1A for the best and worst diffracting directions of the crystal without additive, and 4.0-5.8A for the crystal with additive. The two crystals come from the same prep and same drop setup, only differ from the presence of the additive during crystallogenesis. They are indeed two different crystals, I would be curious to know more how to compare these two datasets together as I thought it was not possible with such different cell parameters.  On 31/05/2017 17:12, Eleanor Dodson wrote:Well - you dont give details o f resolution but the sovent content and the peak of 0.51 would suggest a possible dimer in crystal 1Crystal 2 is so different it might well have a dimer in a different orientation.Yes, it could very well be the case. But wouldn't there be a peak as well in the SRF? I would try to see if there was a relationship between Xtal 1 and Xtal 2 - can tell you how I would do that if you are interested..But doesnt mass spec or some such technique suggest whether there is a dimer or not?I am not aware of a way to test by Mass Spec or other techniques the content of the ASU, I would be very interested if anyone can further my knowledge on this. All the bestVincentEleanorSelf Rotation Functions are a) hard to interpret and b) often misleading! On 31 May 2017 at 14:18, vincent Chaptal  wrote:Dear all, I need help interpreting results from a SRF; I am very naïve at interpreting them and would appreciate any pointer... I have 2 crystals, before and after additive during crystallogenesis. They have different cell parameters, and I am wondering if I have a monomer or a dimer in the ASU, and if the additive changed this. crystal w/o additive: P21  114,5  107,6  134,6 beta=95,74    1monomer in the ASU = 80% solvent, 1 dimer in the ASU = 61% solvent. Note that this high solvent content agrees well with the fact that this is a membrane protein, and diffracts both to low resolution and very anisotropic...     SRF from 

Re: [ccp4bb] help needed to interpret a SRF

[vincent Chaptal]

Thank you for your email.

the anisotropic resolutions of the datasets are 5.6-7.1A for the best 
and worst diffracting directions of the crystal without additive, and 
4.0-5.8A for the crystal with additive.


The two crystals come from the same prep and same drop setup, only 
differ from the presence of the additive during crystallogenesis. They 
are indeed two different crystals, I would be curious to know more how 
to compare these two datasets together as I thought it was not possible 
with such different cell parameters.


On 31/05/2017 17:12, Eleanor Dodson wrote:
Well - you dont give details o f resolution but the sovent content and 
the peak of 0.51 would suggest a possible dimer in crystal 1



Crystal 2 is so different it might well have a dimer in a different 
orientation.
Yes, it could very well be the case. But wouldn't there be a peak as 
well in the SRF?


I would try to see if there was a relationship between Xtal 1 and Xtal 
2 - can tell you how I would do that if you are interested..
But doesnt mass spec or some such technique suggest whether there is a 
dimer or not?
I am not aware of a way to test by Mass Spec or other techniques the 
content of the ASU, I would be very interested if anyone can further my 
knowledge on this.


All the best
Vincent


Eleanor
Self Rotation Functions are a) hard to interpret and b) often misleading!


On 31 May 2017 at 14:18, vincent Chaptal > wrote:


Dear all,

I need help interpreting results from a SRF; I am very naïve at
interpreting them and would appreciate any pointer...

I have 2 crystals, before and after additive during
crystallogenesis. They have different cell parameters, and I am
wondering if I have a monomer or a dimer in the ASU, and if the
additive changed this.

*crystal w/o additive:*
P21  114,5  107,6  134,6 beta=95,74
1monomer in the ASU = 80% solvent, 1 dimer in the ASU = 61%
solvent. Note that this high solvent content agrees well with the
fact that this is a membrane protein, and diffracts both to low
resolution and very anisotropic...
SRF from Molrep:

+--+

| theta phi chi P(i)/P(0)|

+--+

| 1 0.00 0.00 0.00 1.00 |

| 2 148.48 0.00 180.00 0.51 |

| 3 161.29 0.00 180.00 0.31 |

| 4 105.34 180.00 180.00 0.30 |

| 5 74.78 -56.26 179.58 0.27 |

| 6 15.14 -163.78 180.00 0.25 |

| 7 67.61 -40.16 180.00 0.24 |

| 8 134.54 -180.00 180.00 0.19 |

| 9 72.33 -37.82 180.00 0.18 |

| 10 69.72 38.92 175.62 0.18 |

| 11 110.28 -141.08 175.62 0.18 |

| 12 96.58 101.90 179.79 0.18 |

| 13 67.04 -15.02 179.71 0.18 |

| 14 62.76 -15.52 179.45 0.17 |

| 15 117.26 164.48 179.45 0.17 |

| 16 68.39 -18.92 179.86 0.17 |

| 17 70.52 -16.51 180.00 0.17 |

| 18 24.05 -162.02 179.98 0.17 |

| 19 78.61 -36.36 180.00 0.17 |

| 20 83.17 78.42 173.34 0.16 |

| 21 96.83 -101.58 173.34 0.16 |

| 22 81.25 -75.03 179.73 0.16 |

| 23 81.81 -17.73 180.00 0.16 |

| 24 11.02 -142.22 180.00 0.16 |

| 25 76.14 -16.64 179.71 0.16 |

| 26 76.56 -16.93 180.00 0.16 |

| 27 162.29 32.44 180.00 0.16 |

| 28 10.03 -136.82 180.00 0.15 |

| 29 68.67 -58.10 179.49 0.15 |

| 30 111.33 121.90 179.49 0.15 |

| 31 62.99 -20.19 180.00 0.14 |

| 32 97.24 145.00 179.78 0.14 |

| 33 99.56 165.86 179.74 0.14 |

| 34 84.27 -82.68 180.00 0.14 |

| 35 84.51 72.76 174.42 0.13 |

+--+



Crystal with additive:
P21

CELL 117.2840 110.3330 155.6880 90. 93.4280 90.

1 monomer in the ASU = 84% solvent, 1 dimer = 68% solvent.

SRF from Molrep:

+--+

| theta phi chi P(i)/P(0)|

+--+

| 1 0.00 0.00 0.00 1.00 |

| 2 59.55 0.00 180.00 0.36 |

| 3 156.11 0.00 180.00 0.29 |

| 4 10.00 -165.58 180.00 0.26 |

| 5 110.22 -180.00 180.00 0.26 |

| 6 12.97 -169.15 180.00 0.23 |

| 7 166.21 -9.06 180.00 0.22 |

| 8 81.64 -9.61 179.74 0.21 |

| 9 86.02 80.72 178.22 0.20 |

| 10 93.98 -99.28 178.22 0.20 |

| 11 5.96 -54.00 180.00 0.19 |

| 12 67.40 -10.81 180.00 0.19 |

| 13 87.10 -94.56 179.91 0.19 |

| 14 147.13 47.70 10.71 0.19 |

| 15 147.13 -47.70 10.71 0.19 |

| 16 87.45 91.04 155.74 0.19 |

| 17 92.55 -88.96 155.74 0.19 |

| 18 5.33 -63.00 180.00 0.19 |

| 19 104.60 169.61 179.59 0.19 |

| 20 88.01 -85.32 179.05 0.18 |

| 21 92.02 94.64 179.68 0.18 |

| 22 87.61 91.31 153.16 0.18 |

| 23 92.39 -88.69 153.16 0.18 |

| 24 6.65 -46.80 180.00 0.18 |

| 25 153.26 36.01 21.16 0.18 |

| 26 153.26 -36.01 21.16 0.18 |

| 27 63.11 -11.30 179.51 0.18 |

| 28 76.82 -5.09 179.61 0.18 |

| 29 87.69 

Re: [ccp4bb] help needed to interpret a SRF

[Eleanor Dodson]

Well - you dont give details o f resolution but the sovent content and the
peak of 0.51 would suggest a possible dimer in crystal 1


Crystal 2 is so different it might well have a dimer in a different
orientation.

I would try to see if there was a relationship between Xtal 1 and Xtal 2 -
can tell you how I would do that if you are interested..
But doesnt mass spec or some such technique suggest whether there is a
dimer or not?

Eleanor
Self Rotation Functions are a) hard to interpret and b) often misleading!


On 31 May 2017 at 14:18, vincent Chaptal  wrote:

> Dear all,
>
> I need help interpreting results from a SRF; I am very naïve at
> interpreting them and would appreciate any pointer...
>
> I have 2 crystals, before and after additive during crystallogenesis. They
> have different cell parameters, and I am wondering if I have a monomer or a
> dimer in the ASU, and if the additive changed this.
>
> *crystal w/o additive:*
> P21  114,5  107,6  134,6 beta=95,74
> 1monomer in the ASU = 80% solvent, 1 dimer in the ASU = 61% solvent. Note
> that this high solvent content agrees well with the fact that this is a
> membrane protein, and diffracts both to low resolution and very
> anisotropic...
> SRF from Molrep:
>
> +--+
>
>  |   theta phi chi P(i)/P(0)|
>
>  +--+
>
>  |   1 0.000.000.001.00 |
>
>  |   2   148.480.00  180.000.51 |
>
>  |   3   161.290.00  180.000.31 |
>
>  |   4   105.34  180.00  180.000.30 |
>
>  |   574.78  -56.26  179.580.27 |
>
>  |   615.14 -163.78  180.000.25 |
>
>  |   767.61  -40.16  180.000.24 |
>
>  |   8   134.54 -180.00  180.000.19 |
>
>  |   972.33  -37.82  180.000.18 |
>
>  |  1069.72   38.92  175.620.18 |
>
>  |  11   110.28 -141.08  175.620.18 |
>
>  |  1296.58  101.90  179.790.18 |
>
>  |  1367.04  -15.02  179.710.18 |
>
>  |  1462.76  -15.52  179.450.17 |
>
>  |  15   117.26  164.48  179.450.17 |
>
>  |  1668.39  -18.92  179.860.17 |
>
>  |  1770.52  -16.51  180.000.17 |
>
>  |  1824.05 -162.02  179.980.17 |
>
>  |  1978.61  -36.36  180.000.17 |
>
>  |  2083.17   78.42  173.340.16 |
>
>  |  2196.83 -101.58  173.340.16 |
>
>  |  2281.25  -75.03  179.730.16 |
>
>  |  2381.81  -17.73  180.000.16 |
>
>  |  2411.02 -142.22  180.000.16 |
>
>  |  2576.14  -16.64  179.710.16 |
>
>  |  2676.56  -16.93  180.000.16 |
>
>  |  27   162.29   32.44  180.000.16 |
>
>  |  2810.03 -136.82  180.000.15 |
>
>  |  2968.67  -58.10  179.490.15 |
>
>  |  30   111.33  121.90  179.490.15 |
>
>  |  3162.99  -20.19  180.000.14 |
>
>  |  3297.24  145.00  179.780.14 |
>
>  |  3399.56  165.86  179.740.14 |
>
>  |  3484.27  -82.68  180.000.14 |
>
>  |  3584.51   72.76  174.420.13 |
>
>  +--+
>
>
>
> Crystal with additive:
> P21
>
> CELL 117.2840 110.3330 155.6880 90. 93.4280 90.
>
> 1 monomer in the ASU = 84% solvent, 1 dimer = 68% solvent.
>
> SRF from Molrep:
>
>  +--+
>
>  |   theta phi chi P(i)/P(0)|
>
>  +--+
>
>  |   1 0.000.000.001.00 |
>
>  |   259.550.00  180.000.36 |
>
>  |   3   156.110.00  180.000.29 |
>
>  |   410.00 -165.58  180.000.26 |
>
>  |   5   110.22 -180.00  180.000.26 |
>
>  |   612.97 -169.15  180.000.23 |
>
>  |   7   166.21   -9.06  180.000.22 |
>
>  |   881.64   -9.61  179.740.21 |
>
>  |   986.02   80.72  178.220.20 |
>
>  |  1093.98  -99.28  178.220.20 |
>
>  |  11 5.96  -54.00  180.000.19 |
>
>  |  1267.40  -10.81  180.000.19 |
>
>  |  1387.10  -94.56  179.910.19 |
>
>  |  14   147.13   47.70   10.710.19 |
>
>  |  15   147.13  -47.70   10.710.19 |
>
>  |  1687.45   91.04  155.740.19 |
>
>  |  1792.55  -88.96  155.740.19 |
>
>  |  18 5.33  -63.00  180.000.19 |
>
>  |  19   104.60  169.61  179.590.19 |
>
>  |  2088.01  -85.32  179.050.18 |
>
>  |  2192.02   94.64  179.680.18 |
>
>  |  2287.61   91.31  153.160.18 |
>
>  |  2392.39  -88.69  153.160.18 |
>
>  |  24 6.65  -46.80  180.000.18 |
>
>  |  25   153.26   36.01   21.160.18 |
>
>  |  26   153.26  -36.01   21.160.18 |
>
>  |  2763.11  -11.30  179.510.18 |
>
>  |  2876.82   -5.09  179.610.18 |
>
>  |  2987.69   91.37  148.720.18 |
>
>  |  30 

[ccp4bb] help needed to interpret a SRF

[vincent Chaptal]

Dear all,

I need help interpreting results from a SRF; I am very naïve at 
interpreting them and would appreciate any pointer...


I have 2 crystals, before and after additive during crystallogenesis. 
They have different cell parameters, and I am wondering if I have a 
monomer or a dimer in the ASU, and if the additive changed this.


*crystal w/o additive:*
P21  114,5  107,6  134,6 beta=95,74
1monomer in the ASU = 80% solvent, 1 dimer in the ASU = 61% solvent. 
Note that this high solvent content agrees well with the fact that this 
is a membrane protein, and diffracts both to low resolution and very 
anisotropic...

SRF from Molrep:

+--+

| theta phi chi P(i)/P(0)|

+--+

| 1 0.00 0.00 0.00 1.00 |

| 2 148.48 0.00 180.00 0.51 |

| 3 161.29 0.00 180.00 0.31 |

| 4 105.34 180.00 180.00 0.30 |

| 5 74.78 -56.26 179.58 0.27 |

| 6 15.14 -163.78 180.00 0.25 |

| 7 67.61 -40.16 180.00 0.24 |

| 8 134.54 -180.00 180.00 0.19 |

| 9 72.33 -37.82 180.00 0.18 |

| 10 69.72 38.92 175.62 0.18 |

| 11 110.28 -141.08 175.62 0.18 |

| 12 96.58 101.90 179.79 0.18 |

| 13 67.04 -15.02 179.71 0.18 |

| 14 62.76 -15.52 179.45 0.17 |

| 15 117.26 164.48 179.45 0.17 |

| 16 68.39 -18.92 179.86 0.17 |

| 17 70.52 -16.51 180.00 0.17 |

| 18 24.05 -162.02 179.98 0.17 |

| 19 78.61 -36.36 180.00 0.17 |

| 20 83.17 78.42 173.34 0.16 |

| 21 96.83 -101.58 173.34 0.16 |

| 22 81.25 -75.03 179.73 0.16 |

| 23 81.81 -17.73 180.00 0.16 |

| 24 11.02 -142.22 180.00 0.16 |

| 25 76.14 -16.64 179.71 0.16 |

| 26 76.56 -16.93 180.00 0.16 |

| 27 162.29 32.44 180.00 0.16 |

| 28 10.03 -136.82 180.00 0.15 |

| 29 68.67 -58.10 179.49 0.15 |

| 30 111.33 121.90 179.49 0.15 |

| 31 62.99 -20.19 180.00 0.14 |

| 32 97.24 145.00 179.78 0.14 |

| 33 99.56 165.86 179.74 0.14 |

| 34 84.27 -82.68 180.00 0.14 |

| 35 84.51 72.76 174.42 0.13 |

+--+



Crystal with additive:
P21

CELL 117.2840 110.3330 155.6880 90. 93.4280 90.

1 monomer in the ASU = 84% solvent, 1 dimer = 68% solvent.

SRF from Molrep:

+--+

| theta phi chi P(i)/P(0)|

+--+

| 1 0.00 0.00 0.00 1.00 |

| 2 59.55 0.00 180.00 0.36 |

| 3 156.11 0.00 180.00 0.29 |

| 4 10.00 -165.58 180.00 0.26 |

| 5 110.22 -180.00 180.00 0.26 |

| 6 12.97 -169.15 180.00 0.23 |

| 7 166.21 -9.06 180.00 0.22 |

| 8 81.64 -9.61 179.74 0.21 |

| 9 86.02 80.72 178.22 0.20 |

| 10 93.98 -99.28 178.22 0.20 |

| 11 5.96 -54.00 180.00 0.19 |

| 12 67.40 -10.81 180.00 0.19 |

| 13 87.10 -94.56 179.91 0.19 |

| 14 147.13 47.70 10.71 0.19 |

| 15 147.13 -47.70 10.71 0.19 |

| 16 87.45 91.04 155.74 0.19 |

| 17 92.55 -88.96 155.74 0.19 |

| 18 5.33 -63.00 180.00 0.19 |

| 19 104.60 169.61 179.59 0.19 |

| 20 88.01 -85.32 179.05 0.18 |

| 21 92.02 94.64 179.68 0.18 |

| 22 87.61 91.31 153.16 0.18 |

| 23 92.39 -88.69 153.16 0.18 |

| 24 6.65 -46.80 180.00 0.18 |

| 25 153.26 36.01 21.16 0.18 |

| 26 153.26 -36.01 21.16 0.18 |

| 27 63.11 -11.30 179.51 0.18 |

| 28 76.82 -5.09 179.61 0.18 |

| 29 87.69 91.37 148.72 0.18 |

| 30 92.31 -88.63 148.72 0.18 |

| 31 86.74 -9.44 179.90 0.17 |

| 32 85.83 80.82 148.49 0.17 |

| 33 94.17 -99.18 148.49 0.17 |

| 34 175.25 57.61 180.00 0.17 |

| 35 4.63 -90.00 180.00 0.17 |

+--+


Can I say that the peak at 0.51 in the crystal without additive is 
significant, concluding that there is probably a dimer in the ASU in 
that crystal, in contrast to the crystal with additive where no peak 
stands out, which would lean towards a monomer in the ASU?


Thank you for your help.
Best
Vincent



--

Vincent Chaptal, PhD

Institut de Biologie et Chimie des Protéines

Drug Resistance and Membrane Proteins Laboratory

7 passage du Vercors

69007 LYON

FRANCE

+33 4 37 65 29 01

http://www.ibcp.fr

Re: [ccp4bb] help with Buccaneer

[Christian Roth]

Depending on the actual thing you want to do. The options vary a lot.
If you have a MR model I strongly recommend gui2 and the MR mode. In that
case you supply the model and Buccaneer runs Refmac in advance to generate
the necessary phase information it needs.
If you have run CRANK2 in gui2  use the experimental phasing option in i2.
If you have external phases import and convert them with the HL converison
task
In i1 use f.e. phi and FOM (form ShelXE as input)
you might wnat tor tun density modification in the cas of NCS or
experimental phasing when this didn't happen already Difficult to say
without so less information.

Cheers

Christian



On Mon, Jan 23, 2017 at 7:52 AM, Vikram Dalal 
wrote:

> Thanks to all for suggestions.
>
>
>

Re: [ccp4bb] help with Buccaneer

[Vikram Dalal]

Thanks to all for suggestions.