[ccp4bb] Refmac problem: Validation and Analysis

[Marian Oliva]

Dear list,
 
I have a problem running the Validation and Analysis in Refmac and I would 
really appreciate any feed-back from your side.
 
I am using CCP4i2 (CCP4-8.0.018 locally running in Ubuntu 20.04.4). 
 
Last time I was using Refmac was in November 2023. At the time, I posted in the 
list an error with the CCP4i2 interface (no responding) that I solved by 
turning off the 3D picture in the reports (as kindly suggested by Stuart 
McNicholas).
 
Now, despite the 3D picture in the reports is off, I still experience ‘some 
delays’ on the interface response, though this is not a major issue. 
 
The real problem I’m experiencing is that after a (apparent) normal termination 
of Refmac (no sign of warnings or error messages), I find no results from the 
Multimeric validation. 
 
Navigating through the jobs folders I have found that in job2 (which I guess 
correspond to the validation) there is:
- no prosmart related files (.out, .pdb, .py). 
- the tables_as_csv_files folder is empty.
- there is no molprobity.log file. Instead, there is a log_mtzjoin.txt file but 
it does not highlight any warning or error either. 
- the program.xml file only contains the heather but otherwise, it is blank 
(which I guess this is the reason it is not running). 
- also, in the param.xml file I found that there are 2 sets of input data 
(instead of one and I don’t know why), where:
-There is no dbFileID for the input F-SIGF data (in any of them)
-In the first one the XYZIN is the XYZIN-coordinated.pdb (instead of 
the xyzout_prosmart_refmac.pdb) and in the second it is the 
xyzout_prosmart_refmac.pdb)
 
Checking the terminal while running refmac I saw the following error message 
that appears just after refmac window state ‘The job is finished’. This error 
repeats multiple times, with variations in the .WebGL-alphanumerical code, from 
time to time and ends as follows. 
 
[3701:3802:0405/112315.960478:ERROR:gles2_cmd_decoder.cc 
(12701)] [.WebGL-0x23e9d90]GL ERROR 
:GL_INVALID_VALUE : glVertexAttrib4f: index out of range

<--- Last few GCs --->

[4500:0xc37]   177121 ms: Scavenge 2518.8 (2529.1) -> 2510.8 (2529.1) 
MB, 0.2 / 0.0 ms  (average mu = 0.980, current mu = 0.948) allocation failure
[4500:0xc37]   177148 ms: Scavenge 2518.8 (2529.1) -> 2510.8 (2529.1) 
MB, 0.2 / 0.0 ms  (average mu = 0.980, current mu = 0.948) allocation failure
[4500:0xc37]   177175 ms: Scavenge 2518.8 (2529.1) -> 2510.8 (2529.1) 
MB, 0.2 / 0.0 ms  (average mu = 0.980, current mu = 0.948) allocation failure


<--- JS stacktrace --->

[4500:4500:0405/112334.605730:FATAL:memory.cc (38)] Out of 
memory. size=0
 
 
Because at the end there is an ‘out of memory’ message, I have increased the 
ram of my computer from 16GB to 32GB but the problem persists. Another piece of 
info is that my computer has 8 CPU but when running CCP4i2 it only uses one.
 
Does anybody have an idea of which could be the problem?
 
Best regards,
Marian




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Re: [ccp4bb] How to make GDP.BeF3 solution ?

[Marian Oliva]

Dear Firdous,

As Matt refers BeF3 mimics the GTP/ATP bound states. For the transition state 
we have used mixtures of AlCl3 and HKF2 in combination with GDP (or ADP) and 
MgCl2 within the buffer. Be aware that depending on the concentrations used of 
each component you get different proportions of AlF3 and AlF4 (Goldstein G. 
1964. Equilibrium distribution of Metal-Fluoride complexes. Analytical 
Chemistry 36:243–244. DOI: https://doi.org/10.1021/ac60207a074). Also, if you 
are thinking on doing some biochemistry (binding affinity or similar), you must 
know about Al3+ contamination in glass material and nucleotide solutions 
(Sternweis PC, Gilman AG. 1982. Aluminum: a requirement for activation of the 
regulatory component of adenylate cyclase by fluoride. PNAS 79:4888–4891. DOI: 
https://doi.org/10.1073/pnas.79.16.4888).

Best,
Marian


> El 4 ene 2024, a las 11:19, Matthew BOWLER  escribió:
> 
> Dear Firdous,
> 
> beryllium fluoride is actually a ground state analogue of GTP as 
> trifluoroberyllate is tetrahedral. To get a transition sate analogue you need 
> either AlF4- or MgF3-. Preparation of these complexes is very easy. The great 
> advantage of metal fluoride transition state analogue and ground state 
> analogue complexes is the fact that all components are present in solution 
> and readily self-assemble in the active site forming stable enzyme complexes 
> that are relevant to the catalytic cycle. The inorganic metal fluoride salts 
> (AlF3, and MgF2) are too insoluble to use; therefore, the fluoride anion and 
> metal cation components must be added from separate stock solutions. Both 
> ammonium fluoride and sodium fluoride are suitable as the source of fluoride 
> and are readily soluble in water. Metal chlorides can be easily dissolved in 
> water at high concentration (0.5 M) and the solutions conserved at -20°C. One 
> of the critical aspects in preparing metal fluoride enzyme complexes is the 
> pH of the resulting solution. In particular, solutions of AlCl3 and BeCl2 are 
> highly acidic (pH 2) samples should be prepared in 100 mM unbuffered Tris 
> base. The optimized sequence of component addition is to add fluoride to the 
> prepared buffer first, then the metal chloride stock.
> 
> Hope this helps, Matt
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> On 02/01/2024 18:53, Firdous Tarique wrote:
>> Hi
>> 
>> I would appreciate it if someone could share with me a step by step protocol 
>> for making a stable GDP.BeF3 solution which is often used as a transition 
>> state analogue for structural studies of a protein complex ? 
>> 
>> Or a vendor from where it can be purchased directly.
>> 
>> Regards
>> 
>> Firdous
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
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>> 
> -- 
> Matthew Bowler
> Project Leader MASSIF1@ESRF
> European Molecular Biology Laboratory
> 71 avenue des Martyrs 
> CS 90181 F-38042 Grenoble
> France
> ===
> Tel: +33 (0) 4.76.20.76.37
> Fax: +33 (0) 4.76.20.71.99
> 
> http://www.embl.fr/
> http://www.esrf.eu/MASSIF1
> https://twitter.com/id30_massif1 
> https://www.embl.org/people/person/mbowler/
> ===
> 
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[ccp4bb] How can I refine the occupancy with Refmac? Revisited

[Marian Oliva]

Dear list,

In my structure there are some residues in alternative conformations that I 
would like to refine. I have mostly run Phenix for refinement but recently, I 
have switched to Refmac and since I have no much of experience I dig into the 
ccp4 archive and found some tips from Eleanor Dodson and James Holton.

I am currently running refmac from ccp4i2 (ccp4-8.0.015). In this interface, 
when you specify partial occupancies group, a table appears where you can set 
Group ID, chain, from residue, to residue, (atom) and, (alt). 

In my case, Group ID is always 1 and I cannot change it into a different value, 
which is contrary to what James shared in his examples (shown below)

# typical lysozyme
% refmac_occupancy_setup.com <http://refmac_occupancy_setup.com/> 193l.pdb
occupancy refine
occupancy group id 1 chain A residue 1 alt A
occupancy group id 2 chain A residue 1 alt B
occupancy group id 3 chain A residue 59 alt A
occupancy group id 4 chain A residue 59 alt B
occupancy group id 5 chain A residue 86 alt A
occupancy group id 6 chain A residue 86 alt B
occupancy group id 7 chain A residue 109 alt A
occupancy group id 8 chain A residue 109 alt B
occupancy group alts complete  1 2
occupancy group alts complete  3 4
occupancy group alts complete  5 6
occupancy group alts complete  7 8

My first questions are
- If you do not introduce any value in the table, can refmac recognize 
alternative conformations from the input pdb and refine them?
- Could it be that there issome issue in my setup for running Refmac? No idea 
about where the mistake is. 

Any help will be really appreciate.

Best,
Marian

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

phone: 0034 91 1097301
e-mail: mar...@cib.csic.es

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[ccp4bb] ccp4i2 refmac: results interface not responding

[Marian Oliva]

Dear list,

I’m having an issue with my CCP4i2 interface and I wonder if I can get some 
feed-back from your side.

When running refmac the results window gets stuck meaning that if I try to move 
between the different menus (per cycle statistics, outliers identify, etc.) the 
window does not respond and I get the following error message:

[4358:4398:0905/152516.813938:ERROR:gles2_cmd_decoder.cc 
<http://gles2_cmd_decoder.cc/>(12701)] [.WebGL-0xe008d0]GL ERROR 
:GL_INVALID_VALUE : glVertexAttrib4f: index out of range

I am running ccp4-8.0.15 locally. Initially my machine had Ubuntu 20.04.6 LTS 
but now I have upgraded to Ubuntu 22.04.3 LTS and the error persists

This happens if I close and open again ccp4i2, if I re-start the computer, if I 
open the program from a terminal window or by double clicking the icon. 

Before holidays I was running ccp4-7.1.018 and I didn’t have this problem.

Any feed-back will be really appreciate

Best regards,
Marian

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

phone: 0034 91 1097301
e-mail: mar...@cib.csic.es

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Re: [ccp4bb] cif file for ALF3O

[Marian Oliva]

Dear Jinyu,

Are you sure you have AlF3? I mean, when you prepare your mixture to get AlF3 
actually you produce AlF3 and AlF4 (Goldstein, 1964). Indeed depending on the 
initial concentration of F ion you used you may have a 50% of AlF3 and 50% of 
AlF4, and any of them could be bound to your protein. I cannot say from the 
image you sent but at certain resolutions it is easier to notice the difference 
due to geometry and F - Al distances.

Best,
Marian

> El 15 ago 2023, a las 2:31, Friday  escribió:
> 
> Dear CCP4 community,
> 
> I have a question for how to generate the correct cif file for a chemical 
> that I can't find the correct  geometry for. Basically we used ALF3 for 
> mimicking the 3rd phosphate of a nucleotide and the water molecule is clearly 
> attacking the 3rd phosphate (ALF3) and formed a covalent bond to the ALF3 
> (basically we have a leaving group of ALF3O. How do I make the correct cif 
> for this compound, I can't find this kind of compound anyway.  Please see the 
> density of the CF3O in below.
> 
> Your suggestions are highly appreciated.
> 
> Jinyu
> 
> 
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[ccp4bb] Covalent link with AceDRG

[Marian Oliva]

Dear all,

I'm having an issue running AceDRG for making a covalent link between a 
compound (with a double bond) and a target His (linking atom NE2). 

I am running the program in ccp4i2 (ccp4-7.1.018). I have, of course, include 
the .cif file of the compound (obtained from SMILE using eLBOW) and specify the 
atom I want to link with the His. As this atom is involved in a double bond I 
also specify to change the order of bond between this atom and the next one 
into single. Finally, I set that the order of bond between linking atoms is 
single.

The program run and the link is stablished between the atom of the compound and 
the His NE2 BUT, the double bond within the compound is still there. 

I’m not sure what can be happening and any help will be really appreciated.

Best,
Marian 


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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

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> 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 
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> 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 
> <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 
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> remitente y borrar el mensaje recibido.
>  
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> contain confidential and privileged information for the sole use of the 
> designated recipient named above. Distribution, reproduction or any other use 
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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 
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> 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

[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 
<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 
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[ccp4bb] S-hexylglutathione

[Marian Oliva]

Hi,

does anybody know how to prepare a solution of S-hexylglutathione?. I  
have tried DMSO, DMF, Ethanol and buffer pH7.5 but it was impossible.  
I know that it is soluble at pH 10.0 but I need it at a concentration  
200mM and pH 7.5.


Thanks

Marian


Dr. Marian Oliva-Blanco
MRC-LMB
Structural Studies
Hills Road
Cambridge CB2 2QH (UK)
+44 (0) 1223 252 969
[EMAIL PROTECTED]