[ccp4bb] IDS in PDB

[Italo Carugo Oliviero]

A brief reflection on IDPs



Increasingly, people with a computer science background are analyzing the
data deposited in the Protein Data Bank. In the case of conformation
disorder analyses, they consider residues that are explicitly stated to be
disordered (the old REMAR 465 records). This is not quite correct as there
are two problems.

- The first is that some crystallographers consider “visible,” and deposit
their coordinates, even amino acids that have stratospheric B-factors, so
large as to indicate that those amino acids are definitely “invisible” in
electronic density maps.

- The second problem has to do with crystallographic resolution. The amount
of “invisible” amino acids increases as the crystallographic resolution
decreases. At low resolution, electron density maps are often not very
detailed, and some parts of them cannot be interpreted. But this does not
mean that the amino acids found there are definitely “invisible.” It simply
means that resolution might be insufficient.

Editors and reviewers may find it useful to keep these considerations in
mind when evaluating articles on conformational disorder submitted by
scientists that lack a structural biology background. Or is there something
else that can be done?



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Re: [ccp4bb] unable to fit the 11-amino-acid peptide

[Gregory Verdon]

Hi,

1) maybe work on refining the protein structure first, so that your
residual maps improve in quality.
2) Maybe only part of the peptide is ordered? Can you assign part of the
sequence? Starting a bulky aromatic (e.g. W/Trip)?
3) do you have a way to QC your peptide? Is it still 11 residues in your
crystallisation solution?

Cheers
Greg


On Thu, 27 Feb 2025, 21:10 Manjula Ramu,  wrote:

> Dear all,
>
> I recently solved a complex structure of a protein with an 11-amino-acid
> phosphopeptide at 2.58 Å resolution. The asymmetric unit contains two
> protein chains, and the difference map shows positive green density (Fo-Fc
> positive difference density) for the peptide. However, the density is not
> well-defined, making manual fitting of the peptide challenging.
>
> I have two key questions:
>
>1. *How can I generate a 3D model of the 11-residue phosphopeptide?*
>2. *What options are available for fitting the peptide into the
>electron density?*
>
> I would greatly appreciate any guidance or suggestions to help complete my
> structure. I have attached the png file from the coot.
>
> 
>
> Thanks and Regards,
>
> *Manjula *
>
>
>
>
>
> 
>
> --
>
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Re: [ccp4bb] 3D/Stereoscopic hardware options in 2025?

[Diana Tomchick]

Hi,

Sorry, I haven’t had time to read all the posts in this thread, but do people 
think that these fancy new lightfield displays will be the preferred route for 
3D visualization in the future?

For more information, see

https://www.arch.tamu.edu/app/uploads/2021/10/FoVI3D_DeepDrive.pdf

Has anyone had any experience with one of these displays?

Diana

**
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On Feb 27, 2025, at 1:05 AM, Blankenfeldt, Wulf 
 wrote:

External Mail
This email originated from outside of UT Southwestern. Please be cautious.

Report Suspicious
Dear all,

I have just been shocked by our IT department’s announcement that they will 
force us into migration to Win11 very soon. I know I am a dinosaur, but I still 
use and love my old nvidia Quadro/Asus/shutter glasses combi (over 10 years 
old) for hardware stereo viewing of protein structures under Win10. I am afraid 
that this will simply not work anymore once I have been upgraded, since nvdia 
has disabled hardware stereo in its drivers long time ago.

Personally, I cannot understand how modern structural biology can live without 
it and I would love to still be able view structures in “real” 3D.

I know that the ccp4 community is graphics- and tech-savvy, I am therefore 
asking if you know of any modern day and established/sustainable hardware 
solution for 3D viewing in our favorite programs (Coot, PyMol, …).


Thank you in advance for your advice,


Wulf



Prof. Wulf Blankenfeldt
Struktur und Funktion der Proteine (SFPR)

HZI - Helmholtz-Zentrum für Infektionsforschung GmbH

SCIENCE CAMPUS Braunschweig-Süd
Inhoffenstraße 7, 38124 Braunschweig
Tel. +49 5316181-7000
wulf.blankenfe...@helmholtz-hzi.de
www.helmholtz-hzi.de








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Re: [ccp4bb] 3D/Stereoscopic hardware options in 2025?

[Christoph Parthier]

Hi Wulf,

As some folks indicated already: Quad-buffered Stereo using Nvidia 
3DVision shutter glasses still works under Windows 11 - no need to 
despair as long as you still have the proper monitor and shutter glasses...


Just checked it using a new PC with a cheap professional graphics card 
(NVIDIA T400 4GB) and an existing ASUS monitor (with built-in 3D 
emitter, no USB emitter necessary) and recent NVIDIA drivers (572.16). 
The Stereo (3D) settings in the NVIDIA control panel are still there and 
just need to be enabled. The video connection between graphics card 
(miniDP) and the (not so new) ASUS monitor (Dual-Link DVI) is a bit 
cumbersome: first adapter from mini-DP to DP, second (BizLink) adapter 
from DP to Dual-Link DVI (the cheap DP-DVI adapters won't give you the 
120Hz refresh rate that is needed). But it works...


Not sure if the setup would work with an external USB IR emitter though 
(instead of the built-in emitter).


Christoph

 2/27/25 09:48 Pedro Matias wrote:


Hi Wulf,

We never got our NVIDIA 3D to work with Windows 10, only with Windows 
7. The Windows advantage is that the graphics cards are much cheaper 
than those for Linux.


I believe there is a NVIDIA 3D Vision standalone driver that may work 
in Windows 11.


Alternatively, my suggestion would be to use a PC disconnected from 
the internal institute network and keep running Windows 10 on it. File 
transfer would be a bit of an hassle but workable.


Good luck & best regards,

Pedro

On 27/02/2025 07:05, Blankenfeldt, Wulf wrote:


Dear all,

I have just been shocked by our IT department’s announcement that 
they will force us into migration to Win11 very soon. I know I am a 
dinosaur, but I still use and love my old nvidia Quadro/Asus/shutter 
glasses combi (over 10 years old) for hardware stereo viewing of 
protein structures under Win10. I am afraid that this will simply not 
work anymore once I have been upgraded, since nvdia has disabled 
hardware stereo in its drivers long time ago.


Personally, I cannot understand how modern structural biology can 
live without it and I would love to still be able view structures in 
“real” 3D.


I know that the ccp4 community is graphics- and tech-savvy, I am 
therefore asking if you know of any modern day and 
established/sustainable hardware solution for 3D viewing in our 
favorite programs (Coot, PyMol, …).


Thank you in advance for your advice,

Wulf

**Prof. Wulf Blankenfeldt**
Struktur und Funktion der Proteine (SFPR)

HZI - Helmholtz-Zentrum für Infektionsforschung GmbH

SCIENCE CAMPUS Braunschweig-Süd
Inhoffenstraße 7, 38124 Braunschweig
Tel. +49 5316181-7000
wulf.blankenfe...@helmholtz-hzi.de
www.helmholtz-hzi.de





Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 
38124 Braunschweig | www.helmholtz-hzi.de


Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von 
Messling, Bundesministerium für Bildung und Forschung
Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches 
Ministerium für Wissenschaft und Kultur
Wissenschaftlicher Geschäftsführer: Prof. Dr. Josef Penninger - 
Administrativer Geschäftsführer: Christian Scherf

Gesellschaft mit beschränkter Haftung (GmbH)
Sitz der Gesellschaft: Braunschweig
Handelsregister: Amtsgericht Braunschweig, HRB 477

Unsere Hinweise zum Datenschutz finden Sie hier: 
https://www.helmholtz-hzi.de/de/service/datenschutz/





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Re: [ccp4bb] unknown density

[Rafael Marques]

Hi Pavel,

Interesting! I have always been told that one should include only what could be 
seen. In this scenario, I would model hydrogens only if I had a sub 1 A 
resolution or if I had Neutron diffraction data. Thanks for the documentation.

All the best



__

Rafael Marques da Silva

PhD Student – Structural Biology

University of Leicester

Mestre em Física Biomolecular
Universidade de São Paulo

Bacharel em Ciências Biológicas
Universidade Federal de São Carlos

phone: +44 07861 273773

   "A sorte acompanha uma mente bem treinada"



De: Pavel Afonine 
Enviado: domingo, 2 de março de 2025 22:10
Para: Rafael Marques 
Cc: CCP4BB@jiscmail.ac.uk 
Assunto: Re: [ccp4bb] unknown density

Hi Rafael,
Regarding your question about hydrogens: it's a good practice to include them 
using the riding model towards the end of refinement, regardless of resolution. 
Hydrogens make up about half of the model atoms, contribute to the scattering, 
and about 85% of them have geometrically unambiguous positions based on their 
parent atoms. Including hydrogens also helps achieve more sensible model 
geometry by improving non-covalent interactions and reducing steric clashes.

Some notes related to this:
https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2012_01.pdf#page=18

All the best,
Pavel

On Sat, Mar 1, 2025 at 8:20 AM Rafael Marques 
mailto:rafael_mmsi...@hotmail.com>> wrote:
Hi Michael,

It looks like PEG to me too. Have you used a smaller PEG as cryoprotectant. 
Such as PEG 200 or PEG400? Also, as an off topic thing, why are you refining 
hydrogens at this resolution?

Best wishes



__

Rafael Marques da Silva

PhD Student – Structural Biology

University of Leicester

Mestre em Física Biomolecular
Universidade de São Paulo

Bacharel em Ciências Biológicas
Universidade Federal de São Carlos

phone: +44 07861 273773

   "A sorte acompanha uma mente bem treinada"



De: CCP4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> 
em nome de Kennedy, Michael 
mailto:michael.kenn...@miamioh.edu>>
Enviado: quinta-feira, 27 de fevereiro de 2025 19:57
Para: CCP4BB@JISCMAIL.AC.UK 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Assunto: [ccp4bb] unknown density

Hello All,

We recently solved the structure of a protein at 1.8A. There is a large unknown 
density (see attached) at the interface between two protein molecules.

The crystallization buffer was 0.2 M Li Sulfate, 0.1 M Tris,25% PEG 4000, 10% 
glycerol.
The protein purification buffer was 250 mM NaCl, 20 mM Tris, 10% glycerol, 300 
mM imidazole.

Does anyone recognize this ligand or have an idea about what it might be?

thanks

Michael A. Kennedy, PhD

Eminent Scholar and Professor
Department of Chemistry and Biochemistry
106 Hughes Laboratory
Miami University
651 East High Street
Oxford, OH 45056

phone: 513-529-8267
fax: 513-529-5715
email: kenne...@miamioh.edu
webpage: http://chemistry.muohio.edu/kennedy/
google scholars citations: 
https://scholar.google.com/citations?user=7rWzfjkJ
NCBI My Bibliography 
https://www.ncbi.nlm.nih.gov/myncbi/1L3_kwfzxCU/bibliography/public/
Lab Twitter : @Kennedy_Lab



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Re: [ccp4bb] AW: [ccp4bb] 3D/Stereoscopic hardware options in 2025?

[Dirk Kostrewa]

Hi Clemens,


I have a workstation running under Rocky Linux 8 with a Nvidia RTX A4000 
graphics card plus the bracket for the 3-pin mini-DIN connection. The 
last Nvidia driver that both recognizes and activates the Nvidia 3D 
Vision IR emitter is the 525 driver which can be installed from the 
Nvidia CUDA 12.0 repository for Linux. Since driver version 530, the 
Nvidia emitter is recognized, but is not activated anymore upon 
switching to 3D stereo.



Best regards,

Dirk


On 28.02.25 15:13, Clemens Grimm wrote:
There will be no alternative to quad-buffered OpenGL if you want broad 
support of all stereo-capable software. In fact, quad-buffered OpenGL 
is part of the OpenGL specification since the beginning. The Acer 
website says that the SpatialLabs displays require an additional, 
dedicated driver. It seems rather unlikely that this will enable 
quad-buffered OpenGL.


A few years ago, when our 3D vision equipment (which, of 
course, supported quad-buffered OpenGL) stopped working properly after 
a driver update, I had a long conversation with a technical guy from 
Nvidia. He told me that there would be no bug fixes for 3D Vision 
anymore and that driver support would be discontinued soon. From the 
conversation here, it seems however, that 3D vision is still in use 
(with newer drivers?) - could you please post the driver version that 
works for you?


The Nvidia technician also said that quad-buffered OpenGL support will 
continue for professional cards (which I can confirm for the latest 
driver and our dual-monitor stereo display). Since then, we have kept 
the 3D Vision glasses and monitors, but have never tried to see if 
they can be reactivated with a current driver ...


Best,
Clemens




*Von:* CCP4 bulletin board  im Auftrag von 
David J. Schuller 

*Gesendet:* Freitag, 28. Februar 2025 14:19
*An:* CCP4BB@JISCMAIL.AC.UK
*Betreff:* [EXT] Re: [ccp4bb] 3D/Stereoscopic hardware options in 2025?
Strengths and weaknesses.

The AcerSpatialLabsStereoscopic 3D-solutions are lenticular displays. 
Such solutions have existed for quite a while, so it's nothing new. 
They just claim to do it better by using "AI."


Lenticular displays do not require glasses. They have lenses/prisms 
(made of liquid crystals) in front of the pixels, so that of each pair 
of pixels, one is seen by the left eye and one by the right eye.


To do this successfully, the display needs to know where your eyes 
are, to shape the prisms properly. That is purportedly where the AI 
comes in. Only one person can view the screen with this 3D effect at a 
time.

Lenticular displays halve the resolution in one spatial dimension.

---
For comparison, the old CrystalEyes and Nvidia 3D systems use active 
glasses: the lenses of the glasses are shutters made of liquid 
crystals. One shutter is open and one closed, synchronized to the 
display. Left and right images are interlaced to the display in the 
time dimension.


To do this successfully, the display needs to be bright enough. It 
also needs to have a refresh rate of at least 120 Hz so that each eye 
can get 60 Hz viewing. But you get the full spatial resolution of the 
display.


Wearing the glasses, and keeping them charged is somewhat of a 
nuisance. But as many people can view the display at one time as the 
number of pairs of glasses you have.



===
 All Things Serve the Beam
 ===
 David J. Schuller
 modern man in a post-modern world
 MacCHESS, Cornell University
schul...@cornell.edu


*From:* CCP4 bulletin board  on behalf of 
Jeroen Mesters 

*Sent:* Friday, February 28, 2025 04:07
*To:* CCP4BB@JISCMAIL.AC.UK 
*Subject:* Re: [ccp4bb] 3D/Stereoscopic hardware options in 2025?
Hi,

could Acer's newly developed SpatialLabsStereoscopic 3D-solutions i.e. 
3D-monitors offer a way out? Apparently, with the aid of AI, they 
claim it can transform 2D to 3D content.


3D is still alive as CAD and game software developers are currently 
opting for 3D-glasses-free viewing based on OpenXR or SteamVR…


Best

Jeroen
__
Dr. /math. et dis. nat./ Jeroen R. Mesters
Biological Safety Officer (BBS)
Deputy, Lecturer, Program Coordinator Infection Biology
Visiting Professorship in Biophysics - University South Bohemia

attachment.png

University of Lübeck
Center for Structural and Cell Biology in Medicine
Institute of Biochemistry
Ratzeburger Allee 160
23562 Lübeck

Tel +49 451 3101 3105
https://orcid.org/-0001-8532-6699

Am 27.02.2025 um 08:05 schrieb Blankenfeldt, Wulf
:

Dear all,

I have just been shocked by our IT department’s announcement that
they wil

Re: [ccp4bb] AW: [ccp4bb] 3D/Stereoscopic hardware options in 2025?

[Dirk Kostrewa]

Just to clarify: Gnome never worked with 3D stereo in the past 
(gnome-shell is incompatible with switching off compositing), which is 
why is used XFCE. 3D stereo with Gnome works to my knowledge only under 
Fedora and more recent Red Hat Enterprise Linux versions (or clones of 
it). Unfortunately, I don't remember, since which versions Fedora and 
RHEL support  3D stereo with Gnome. Switching to stereo/mono in 
Fedora/RHEL with Gnome also takes a couple of seconds with an on-screen 
message about the switching process.



Best regards,

Dirk


On 03.03.25 09:10, Dirk Kostrewa wrote:


Hi Wim,


we had the problem with smeared/unreadable scroll-able menus in Coot 
with activated 3D stereo both under Debian 11 and Rocky Linux 8 using 
XFCE. This does not happen with Rocky Linux 8 using Gnome. I think, it 
has something to do with a different way of switching to 3D stereo 
under Gnome, such, that all non-stereo windows behave as if 3D stereo 
is not active, presumably by applying different compositing in 
stereo/non-stereo windows (but I'm not sure about this).



Best regards,

Dirk


On 28.02.25 16:47, Wim Burmeister wrote:


Hello,

we have a Linux installation with Debian 12 / Xfce 4.18 Gtk 3.24.38 
using the Nvidia driver version 470.256.02 and a Quadro M4000 
Graphics card, which still works (Chimera, PyMol, Coot), besides a 
minor bug in Coot pull-down menus.


Best,

Wim


On 28/02/2025 15:13, Clemens Grimm wrote:
There will be no alternative to quad-buffered OpenGL if you 
want broad support of all stereo-capable software. In fact, 
quad-buffered OpenGL is part of the OpenGL specification since the 
beginning. The Acer website says that the SpatialLabs displays 
require an additional, dedicated driver. It seems rather unlikely 
that this will enable quad-buffered OpenGL.


A few years ago, when our 3D vision equipment (which, of 
course, supported quad-buffered OpenGL) stopped working properly 
after a driver update, I had a long conversation with a technical 
guy from Nvidia. He told me that there would be no bug fixes for 3D 
Vision anymore and that driver support would be discontinued soon. 
From the conversation here, it seems however, that 3D vision is 
still in use (with newer drivers?) - could you please post the 
driver version that works for you?


The Nvidia technician also said that quad-buffered OpenGL support 
will continue for professional cards (which I can confirm for the 
latest driver and our dual-monitor stereo display). Since then, we 
have kept the 3D Vision glasses and monitors, but have never tried 
to see if they can be reactivated with a current driver ...


Best,
Clemens




*Von:* CCP4 bulletin board  im Auftrag von 
David J. Schuller 

*Gesendet:* Freitag, 28. Februar 2025 14:19
*An:* CCP4BB@JISCMAIL.AC.UK
*Betreff:* [EXT] Re: [ccp4bb] 3D/Stereoscopic hardware options in 2025?
Strengths and weaknesses.

The AcerSpatialLabsStereoscopic 3D-solutions are lenticular 
displays. Such solutions have existed for quite a while, so it's 
nothing new. They just claim to do it better by using "AI."


Lenticular displays do not require glasses. They have lenses/prisms 
(made of liquid crystals) in front of the pixels, so that of each 
pair of pixels, one is seen by the left eye and one by the right eye.


To do this successfully, the display needs to know where your eyes 
are, to shape the prisms properly. That is purportedly where the AI 
comes in. Only one person can view the screen with this 3D effect at 
a time.

Lenticular displays halve the resolution in one spatial dimension.

---
For comparison, the old CrystalEyes and Nvidia 3D systems use active 
glasses: the lenses of the glasses are shutters made of liquid 
crystals. One shutter is open and one closed, synchronized to the 
display. Left and right images are interlaced to the display in the 
time dimension.


To do this successfully, the display needs to be bright enough. It 
also needs to have a refresh rate of at least 120 Hz so that each 
eye can get 60 Hz viewing. But you get the full spatial resolution 
of the display.


Wearing the glasses, and keeping them charged is somewhat of a 
nuisance. But as many people can view the display at one time as the 
number of pairs of glasses you have.



===
 All Things Serve the Beam
 ===
 David J. Schuller
 modern man in a post-modern world
 MacCHESS, Cornell University
schul...@cornell.edu


*From:* CCP4 bulletin board  on behalf of 
Jeroen Mesters 

*Sent:* Friday, February 28, 2025 04:07
*To:* CCP4BB@JISCMAIL.AC.UK 
*Subject:* Re: [ccp4bb] 3D/Stereoscopic hardw

Re: [ccp4bb] unable to fit the 11-amino-acid peptide

[Matthew Snee]

Hi

It looks like the peptide is bound close to a  2_fold symmetry axis, which can 
result in mistakes, so try to anchor your peptide registry using regions that 
are away from this axis (turn symmetry on in COOT to make sure you dont build 
it inside itself).

Other than, that its just a case of treating it like any other part of a 
protein that needs rebuilding, and just apply the same iterative process where 
you improve/rebuild the bits you can, and as the maps improve
The more difficult areas become more tractable.
Some of the regions at the top-left of your image look like they may need 
rebuilding for instance, and once you have improved the protein, the peptide 
density may become more interpretable.
The shape of the phosphate should hopefully be visible to help you.

Once the protein part is as good as you think you can manage (and you have 
checked some of the weaker areas for model bias in the maps), then you can 
attempt to recover some of the finer details of your peptide.

I personally use Polders or Phenix FEM maps.   FEM maps can be really good. I'm 
not an expert in how they work, but personally I feel like the results are 
quite dependant on the quality of the phases you start with, so I usually use 
them To try and recover weak sidechain/ligand information in otherwise fairly 
complete models.


Finally, once you think you have built your peptide you can add the 
phosphorylated residue which is (hopefully) in the existing dictionary using 
the "replace residue" tool in Coot I think.

Hope this helps

Matthew.



From: CCP4 bulletin board  on behalf of Manjula Ramu 

Sent: 27 February 2025 21:09
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] unable to fit the 11-amino-acid peptide

Dear all, I recently solved a complex structure of a protein with an 
11-amino-acid phosphopeptide at 2. 58 Å resolution. The asymmetric unit 
contains two protein chains, and the difference map shows positive green 
density (Fo-Fc positive difference
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Dear all,

I recently solved a complex structure of a protein with an 11-amino-acid 
phosphopeptide at 2.58 Å resolution. The asymmetric unit contains two protein 
chains, and the difference map shows positive green density (Fo-Fc positive 
difference density) for the peptide. However, the density is not well-defined, 
making manual fitting of the peptide challenging.

I have two key questions:

  1.  How can I generate a 3D model of the 11-residue phosphopeptide?
  2.  What options are available for fitting the peptide into the electron 
density?

I would greatly appreciate any guidance or suggestions to help complete my 
structure. I have attached the png file from the coot.



Thanks and Regards,

Manjula




[nimhans.kar.nic.in]



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Re: [ccp4bb] AW: [ccp4bb] 3D/Stereoscopic hardware options in 2025?

[Dirk Kostrewa]

Hi Wim,


we had the problem with smeared/unreadable scroll-able menus in Coot 
with activated 3D stereo both under Debian 11 and Rocky Linux 8 using 
XFCE. This does not happen with Rocky Linux 8 using Gnome. I think, it 
has something to do with a different way of switching to 3D stereo under 
Gnome, such, that all non-stereo windows behave as if 3D stereo is not 
active, presumably by applying different compositing in 
stereo/non-stereo windows (but I'm not sure about this).



Best regards,

Dirk


On 28.02.25 16:47, Wim Burmeister wrote:


Hello,

we have a Linux installation with Debian 12 / Xfce 4.18 Gtk 3.24.38 
using the Nvidia driver version 470.256.02 and a Quadro M4000 Graphics 
card, which still works (Chimera, PyMol, Coot), besides a minor bug in 
Coot pull-down menus.


Best,

Wim


On 28/02/2025 15:13, Clemens Grimm wrote:
There will be no alternative to quad-buffered OpenGL if you 
want broad support of all stereo-capable software. In fact, 
quad-buffered OpenGL is part of the OpenGL specification since the 
beginning. The Acer website says that the SpatialLabs displays 
require an additional, dedicated driver. It seems rather unlikely 
that this will enable quad-buffered OpenGL.


A few years ago, when our 3D vision equipment (which, of 
course, supported quad-buffered OpenGL) stopped working properly 
after a driver update, I had a long conversation with a technical guy 
from Nvidia. He told me that there would be no bug fixes for 3D 
Vision anymore and that driver support would be discontinued soon. 
From the conversation here, it seems however, that 3D vision is still 
in use (with newer drivers?) - could you please post the driver 
version that works for you?


The Nvidia technician also said that quad-buffered OpenGL support 
will continue for professional cards (which I can confirm for the 
latest driver and our dual-monitor stereo display). Since then, we 
have kept the 3D Vision glasses and monitors, but have never tried to 
see if they can be reactivated with a current driver ...


Best,
Clemens




*Von:* CCP4 bulletin board  im Auftrag von 
David J. Schuller 

*Gesendet:* Freitag, 28. Februar 2025 14:19
*An:* CCP4BB@JISCMAIL.AC.UK
*Betreff:* [EXT] Re: [ccp4bb] 3D/Stereoscopic hardware options in 2025?
Strengths and weaknesses.

The AcerSpatialLabsStereoscopic 3D-solutions are lenticular displays. 
Such solutions have existed for quite a while, so it's nothing new. 
They just claim to do it better by using "AI."


Lenticular displays do not require glasses. They have lenses/prisms 
(made of liquid crystals) in front of the pixels, so that of each 
pair of pixels, one is seen by the left eye and one by the right eye.


To do this successfully, the display needs to know where your eyes 
are, to shape the prisms properly. That is purportedly where the AI 
comes in. Only one person can view the screen with this 3D effect at 
a time.

Lenticular displays halve the resolution in one spatial dimension.

---
For comparison, the old CrystalEyes and Nvidia 3D systems use active 
glasses: the lenses of the glasses are shutters made of liquid 
crystals. One shutter is open and one closed, synchronized to the 
display. Left and right images are interlaced to the display in the 
time dimension.


To do this successfully, the display needs to be bright enough. It 
also needs to have a refresh rate of at least 120 Hz so that each eye 
can get 60 Hz viewing. But you get the full spatial resolution of the 
display.


Wearing the glasses, and keeping them charged is somewhat of a 
nuisance. But as many people can view the display at one time as the 
number of pairs of glasses you have.



===
 All Things Serve the Beam
 ===
 David J. Schuller
 modern man in a post-modern world
 MacCHESS, Cornell University
schul...@cornell.edu


*From:* CCP4 bulletin board  on behalf of 
Jeroen Mesters 

*Sent:* Friday, February 28, 2025 04:07
*To:* CCP4BB@JISCMAIL.AC.UK 
*Subject:* Re: [ccp4bb] 3D/Stereoscopic hardware options in 2025?
Hi,

could Acer's newly developed SpatialLabsStereoscopic 3D-solutions 
i.e. 3D-monitors offer a way out? Apparently, with the aid of AI, 
they claim it can transform 2D to 3D content.


3D is still alive as CAD and game software developers are currently 
opting for 3D-glasses-free viewing based on OpenXR or SteamVR…


Best

Jeroen
__
Dr. /math. et dis. nat./ Jeroen R. Mesters
Biological Safety Officer (BBS)
Deputy, Lecturer, Program Coordinator Infection Biology
Visiting Professorship in Biophysics - University South Bohemia

attachment.png

University of Lübeck
Ce

Re: [ccp4bb] Peptide design

[Abhishek A. Jalan]

That is true. The MPNN is implemented in the RFdiffusion notebook with
validation via alphafold.


On Fri, Feb 28, 2025 at 8:28 PM Jurgen Bosch  wrote:

> You need Protein MPNN, otherwise you’ll just get a poly-glycine chain
>
> Jürgen
> ___
> Jürgen Bosch, PhD, MBA
> Center for Global Health & Diseases
> Case Western Reserve University
> Cleveland, OH 44106
> https://www.linkedin.com/in/jubosch/
>
> CEO & Co-Founder at InterRayBio, LLC
>
>
>
> On Feb 28, 2025, at 1:57 PM, Abhishek A. Jalan 
> wrote:
>
> RFdiffusion is a good starting point.
> Best,
> Abhishek
>
> On Fri, Feb 28, 2025 at 7:47 PM careinaedgo...@yahoo.com <
> 02531c126adf-dmarc-requ...@jiscmail.ac.uk> wrote:
>
>> Dear all
>> This post is a bit off topic but I wonder if anyone could help direct me
>> to a good tool to use for designing novel peptides with affinity for a
>> certain protein?
>> Kind regards Careina
>>
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
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>>
>
> --
>
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Re: [ccp4bb] IDS in PDB

[Pavel Afonine]

Greetings,

It's hard to disagree with this! Resolution, occupancies, and B factors
only indirectly suggest what's visible and what isn't — and they can be
especially difficult to interpret correctly for non-specialists. Perhaps a
local confidence measure — similar to pLDDT for predicted models — could
address this by condensing into a single number everything we know about
the model quality and how well it fits the data, computed per atom or per
residue.

All the best,
Pavel

On Mon, Mar 3, 2025 at 7:21 AM Italo Carugo Oliviero <
olivieroitalo.car...@unipv.it> wrote:

> A brief reflection on IDPs
>
>
>
> Increasingly, people with a computer science background are analyzing the
> data deposited in the Protein Data Bank. In the case of conformation
> disorder analyses, they consider residues that are explicitly stated to be
> disordered (the old REMAR 465 records). This is not quite correct as there
> are two problems.
>
> - The first is that some crystallographers consider “visible,” and deposit
> their coordinates, even amino acids that have stratospheric B-factors, so
> large as to indicate that those amino acids are definitely “invisible” in
> electronic density maps.
>
> - The second problem has to do with crystallographic resolution. The
> amount of “invisible” amino acids increases as the crystallographic
> resolution decreases. At low resolution, electron density maps are often
> not very detailed, and some parts of them cannot be interpreted. But this
> does not mean that the amino acids found there are definitely “invisible.”
> It simply means that resolution might be insufficient.
>
> Editors and reviewers may find it useful to keep these considerations in
> mind when evaluating articles on conformational disorder submitted by
> scientists that lack a structural biology background. Or is there
> something else that can be done?
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



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Re: [ccp4bb] unknown density

[Pavel Afonine]

Hi Rafael,

This is progressively getting further off-topic, so we may consider
continuing this conversation off-list or under a different subject line.

You are correct that "one should include only what could be seen". However:

a) "What could be seen" is not always necessarily a hefty green blob on an
Fo-Fc map, and
b) Hydrogens are a bit of a special case.

As I hinted previously, about 85% of hydrogen atoms (those without
rotational degrees of freedom) can be unambiguously assigned to their
positions. They are present in actual structures and do contribute to
scattering, as including them reduces R — which might align with your
definition of "what could be seen" here. Adding hydrogens as a riding model
does not introduce additional refinable parameters, while still accounting
for their scattering contribution.

This is very different from modeling entities such as flexible loops — if
you don't see density in the map, there's no reliable way to trace the loop
because it may adopt many geometrically plausible conformations. Without
data (i.e., map density for the loop), you simply cannot know where to
place it — so you may consider not including it in the model.

Additionally, including hydrogen atoms makes surrounding atoms aware of
them, preventing steric clashes. After all, this is how MolProbity
validation works — it automatically adds hydrogens to your model before
calculating metrics like Clashscore. By including hydrogens upfront, you
proactively reduce the risk of steric clashes, while without them, the only
meaningful way to resolve a clash reported by MolProbity would be to add
hydrogens and re-refine the model.

All the best,
Pavel


On Mon, Mar 3, 2025 at 3:12 AM Rafael Marques 
wrote:

> Hi Pavel,
>
> Interesting! I have always been told that one should include only what
> could be seen. In this scenario, I would model hydrogens only if I had a
> sub 1 A resolution or if I had Neutron diffraction data. Thanks for the
> documentation.
>
> All the best
>
>
>
> __
>
> Rafael Marques da Silva
>
> PhD Student – Structural Biology
>
> University of Leicester
>
> Mestre em Física Biomolecular
> Universidade de São Paulo
>
> Bacharel em Ciências Biológicas
> Universidade Federal de São Carlos
>
> phone: +44 07861 273773
>
> *   "A sorte acompanha uma mente bem treinada"*
> **
>
> --
> *De:* Pavel Afonine 
> *Enviado:* domingo, 2 de março de 2025 22:10
> *Para:* Rafael Marques 
> *Cc:* CCP4BB@jiscmail.ac.uk 
> *Assunto:* Re: [ccp4bb] unknown density
>
> Hi Rafael,
> Regarding your question about hydrogens: it's a good practice to include
> them using the riding model towards the end of refinement, regardless of
> resolution. Hydrogens make up about half of the model atoms, contribute to
> the scattering, and about 85% of them have geometrically unambiguous
> positions based on their parent atoms. Including hydrogens also helps
> achieve more sensible model geometry by improving non-covalent interactions
> and reducing steric clashes.
>
> Some notes related to this:
>
> https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2012_01.pdf#page=18
>
> All the best,
> Pavel
>
> On Sat, Mar 1, 2025 at 8:20 AM Rafael Marques 
> wrote:
>
> Hi Michael,
>
> It looks like PEG to me too. Have you used a smaller PEG as
> cryoprotectant. Such as PEG 200 or PEG400? Also, as an off topic thing, why
> are you refining hydrogens at this resolution?
>
> Best wishes
>
>
>
> __
>
> Rafael Marques da Silva
>
> PhD Student – Structural Biology
>
> University of Leicester
>
> Mestre em Física Biomolecular
> Universidade de São Paulo
>
> Bacharel em Ciências Biológicas
> Universidade Federal de São Carlos
>
> phone: +44 07861 273773
>
> *   "A sorte acompanha uma mente bem treinada"*
> **
>
> --
> *De:* CCP4 bulletin board  em nome de Kennedy,
> Michael 
> *Enviado:* quinta-feira, 27 de fevereiro de 2025 19:57
> *Para:* CCP4BB@JISCMAIL.AC.UK 
> *Assunto:* [ccp4bb] unknown density
>
> Hello All,
>
> We recently solved the structure of a protein at 1.8A. There is a large
> unknown density (see attached) at the interface between two protein
> molecules.
>
> The crystallization buffer was 0.2 M Li Sulfate, 0.1 M Tris,25% PEG 4000,
> 10% glycerol.
> The protein purification buffer was 250 mM NaCl, 20 mM Tris, 10% glycerol,
> 300 mM imidazole.
>
> Does anyone recognize this ligand or have an idea about what it might be?
>
> thanks
>
> Michael A. Kennedy, PhD
>
> Eminent Scholar and Professor
> Department of Chemistry and Biochemistry
> 106 Hughes Laboratory
> Miami University
> 651 East High Street
> Oxford, OH 45056
>
> phone: 513-529-8267
> fax: 513-529-5715
> email: kenne...@miamioh.edu
> webpage: http://chemistry.muohio.edu/kennedy/
> goo