Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

Hi Harry, Thanks for sharing this. I already read and endorsed the letter. However, I do have a comment - since one of the letter signatories was a reviewer of the paper, wouldn't the shortcomings described in the letter be grounds for rejection of the manuscript? Best regards, Pedro On

Re: [ccp4bb] what happened to Molprobity

Hi Gerlind, As far as I know, Molprobity in PHENIX is standalone and does not use the server. Can you check with a previous PHENIX version if that problem persists? Best regards, Pedro On 30/04/2024 12:25, Gerlind Sulzenbacher wrote: Dear all, The Molprobity server appears to be not

Re: [ccp4bb] Difficult Molecular replacement

But curiously, all the 4 best solutions correspond to a SG with a 21 screw along b. And amazingly none of the TF solutions is rejected due to clashes. On 21/02/2024 12:20, Eleanor Dodson wrote: Lots of comments, but it would be easier to actually look at your integrated data! Some of the

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Difficult Molecular replacement

Hi Marco, Further to Zhen's comment, that can also happen if you have a cusp containing one of the reciprocal lattice axes. The SG may be P212121 but one of the 21 is never located due to the missing data. You will always sort of get a solution from MR but you should look at the Z-score of

Re: [ccp4bb] Problem running CCP4I2 in CCP4 8 * SOLVED

ost-modern world MacCHESS, Cornell University schul...@cornell.edu *From:* CCP4 bulletin board on behalf of Pedro Matias *Sent:* Tuesday, January 30, 2024 9:17 AM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] Proble

Re: [ccp4bb] Problem running CCP4I2 in CCP4 8

this error before on linux mint/ubuntu. Did you also updated the OS? Cheers, Arnaud On 30/01/2024 11:43, Pedro Matias wrote: ⚠ External sender. Take care when opening links or attachments. Do not provide your login details. Dear All, After updating CCP4 to version 8, CCP4I2 stopped working

Re: [ccp4bb] Problems updating CCP4 via CCP4i

wrote: Dear Pedro, you can start the graphical update manager from command line with ccp4um you can also run updates without the GUI using ccp4um -auto Hope this helps, Christian Am 30.01.24 um 12:40 schrieb Pedro Matias: Dear All, I am no longer able to update CCP4 via CCP4i When

Re: [ccp4bb] Problems updating CCP4 via CCP4i

board on behalf of Pedro Matias *Sent:* Tuesday, January 30, 2024 6:40 AM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] Problems updating CCP4 via CCP4i Dear All, I am no longer able to update CCP4 via CCP4i When I click on "Proceed" Instead of opening the update window, I get back

[ccp4bb] Problem running CCP4I2 in CCP4 8

Dear All, After updating CCP4 to version 8, CCP4I2 stopped working with the following error message: Running CCP4i2 browser from: /home/pxsoft/ccp4/ccp4-8.0/lib/python3.7/site-packages/ccp4i2 Python 3.7.12 (default, Jan  6 2022, 21:30:12) [GCC 8.2.1 20180905 (Red Hat 8.2.1-3)] Qt version

[ccp4bb] Problems updating CCP4 via CCP4i

Dear All, I am no longer able to update CCP4 via CCP4i When I click on "Proceed" Instead of opening the update window, I get back to exactly this view. Is it possible to update CCP4 via the command line? I haven't tried using CCP4I2 because it doesn't work on my PC (separate e-mail).

Re: [ccp4bb] 3D viewing on PC

With the demise of NVIDIA 3D Vision, you may need to revert to the old split stereo viewers, at least until a decent VR system is implemented. On 12/10/2023 12:21, Jon Cooper wrote: Hello Oliviero If you look in the ccp4bb archive (my apologies if you already have) there are quite a few

Re: [ccp4bb] Win 10 DHCP-Server to assign fixed IP-address

Hi Tim, Why do you need a DHCP server? Can't you configure a fixed IP address on the Oxford Cryo 800? Check out this site for a possible alternative: https://www.dhcpserver.de/cms/ But if you can connect via USB instead, it's probably better to buy a cable. We have an older 700 and it is

[ccp4bb] CryoEM group Leader position at ITQB NOVA - deadline December 21, 2022

are given. Applications should be sent until December 21^st , 2022 On behalf of the ITQB NOVA Direction, Pedro Matias -- Industry and Medicine Applied Crystallography Macromolecular Crystallography Unit ___ Phones : (351-21) 446-9100 Ext. 1669 (351-21

Re: [ccp4bb] Error while running BLEND

one of the modernisation things which changed from 2 -> 3 An older version of ccp4 would probably still work - version 7.something Looks like BLEND needs to be updated… Best wishes Graeme On 11 Oct 2022, at 15:30, Pedro Matias wrote: Dear All, I am trying to run BLEND on a series of XDS files in MTZ

[ccp4bb] Error while running BLEND

t;dataset_",sfx],"") AttributeError: module 'string' has no attribute 'join' whether I run BLEND from CCP4I or the command line. Any help will be much appreciated! Pedro Matias -- Industry and Medicine Applied Crystallography Macromolecular Crystallography Unit

[ccp4bb] Call for expressions of interest for independent researchers to establish a new group,in CryoEM-based Structural Biology at the ITQB NOVA

https://www.itqb.unl.pt/~matias/About_ITQB.html Best regards, Pedro Matias <https://www.itqb.unl.pt/~matias/About_ITQB.html>** -- Industry and Medicine Applied Crystallography Macromolecular Crystallography Unit ___ Phones : (351-21) 446-9100 Ext. 1669 (351-

Re: [ccp4bb] ccp4 installation problem

Hi Marcin, If you are not logged on as root I think you need to run the installer with sudo Hope this helps, Pedro Matias Em 06/09/2022 13:33, Marcin Jaciuk escreveu: Dear All, After upgrading to newest Ubuntu 22.04 I am trying to install ccp4 via Package Manager with /opt directory

Re: [ccp4bb] Problem with understanding mtz and hkl files of S SAD data

yze the mtz file and HKL file. I donot know how to solve this problem as well. Kindly guide me if I went wrong anywhere here. On Tue, May 10, 2022 at 5:49 PM Pedro Matias wrote: Hi there, I assume you processed the data with XDS. If so, you can use xdsconv to convert the file other form

Re: [ccp4bb] Problem with understanding mtz and hkl files of S SAD data

Hi there, I assume you processed the data with XDS. If so, you can use xdsconv to convert the file other formats, including mtz To analyze (view?) an mtz file you can use mtzdump. MTZ2Various is a format conversion program, just like xdsconv. You can convert directly to SCALEPACK format

[ccp4bb] Announcing the 7th European Crystallographic School - 10-15 July 2022 in Lisbon, Portugal

form can be accessed at: https://ecs7.events.chemistry.pt/ Best regards, Pedro Matias -- Industry and Medicine Applied Crystallography Macromolecular Crystallography Unit ___ Phones : (351-21) 446-9100 Ext. 1669 (351-21) 446-9669 (direct) Fax : (351-21

[ccp4bb] Research Engineer - Transmission Electron Microscopy at the INL in Braga, Portugal

tps://careers.inl.int/our-vacancies/?p=job%2FoIccifw8> Best Regards, Pedro Matias -- Industry and Medicine Applied Crystallography Macromolecular Crystallography Unit ___ Phones : (351-21) 446-9100 Ext. 1669 (351-21) 446-9669 (direct) Fax : (351-21) 44

Re: [ccp4bb] chain on 2-fold axis?

Dear Peer, This is indeed a very strange situation. If you have a molecule sitting on a crystallographic 2-fold, it would almost certainly overlap with its symmetry-related copy. A more exotic solution would be a 2-fold disorder around the axis, with each chain having a 50% occupancy, but I

Re: [ccp4bb] S=O converted to S-OH during refinement

That's right. The S-OH configuration is imposed by the CIF dictionary for the ligand that you are using in REFMAC. You can edit the dictionary with e.g., jligand, save a local copy and feed that copy to REFMAC - it will override the library definition of the ligand. On 25/06/2021 10:58,

Re: [ccp4bb] Converting data set to another format?

There is a  Nonius/Bruker software that converts the images and writes out the undistorted frames. Many years ago we also tried to use MOSFLM and XDS to process our Proteum images (Bruker) but even with this transformation we could not do it, so in the end we gave up. Regards, Pedro Às

Re: [ccp4bb] B-factors very high

Dear Silvia, In addition to your high-B values I would also worry about your high R/R-free values - I suggest running your dataset through xtriage to check for twinning (or look carefully at the output of your data processing - it should also include some checks for twinning). The B-value

Re: [ccp4bb] Tiny rocks on my CX100 shipping dewar

It does not look like absorbent material and why should it be outside the dewar and not all over the pucks? I concur with Jürgen - it does look like gravel. Às 16:18 de 04/12/2020, Jurgen Bosch escreveu: That looks like gravel from the driveway where the dewar was tossed around Jürgen On

Re: [ccp4bb] Coot 0.9.2 in CCP4 - quad-buffered stereo broken?

Hi All, How can a noob user do that? Will CCP4 release a patched Coot binary? Pedro Às 15:25 de 25/11/2020, Christian Becke escreveu: Dear Paul, Am 25.11.20 um 12:05 schrieb Paul Emsley: On 23/11/2020 15:21, Pedro Matias wrote: In the latest coot update (to 0.9.2) in CCP4 the quad

[ccp4bb] Coot 0.9.2 in CCP4 - quad-buffered stereo broken?

Hi All, In the latest coot update (to 0.9.2) in CCP4 the quad-buffered stereo doesn't seem to work. The NVIDIA emitter turns on but the stereo picture does not appear when the glasses are turned on. Strangely enough, the only coot update I can find in the updates list is to 0.9.1 in 7.1.007

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

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: >>

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

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

Re: [ccp4bb] COOT over SSH

This is a known problem when accessing recent Linux releases remotely via ssh -X. The default X-server configuration has changed and openGL applications no longer work. Supposedly it should be possible to revert the server behaviour with a flag on startup but I haven't been able to do so. I

Re: [ccp4bb] PyMOL now packaged as a snap on Linux

Well, I can't get it to work in FC30 - I installed FC30 on a virtual machine and managed to install both snapd and pymol-oss but pymol does not run as a command. Am I missing something rather obvious? Pedro Às 12:46 de 03/06/2019, Matic Kisovec escreveu: > Hi, > > thank you very much for this.

Re: [ccp4bb] PyMOL now packaged as a snap on Linux

Hi Darren et al., The snap doesn't seem to work with older Linux distros. I have FC23 on my machine and even after installing snapd as per instructions found on the web, the snap install does not work. I wonder if anyone had better luck with these older Linux distributions... Pedro Às 12:01 de

Re: [ccp4bb] 3D

Reading the news piece, I would hardly consider the present-day VR headsets to be "affordable" - except perhaps for the PSVR. With the added downside that they are single-user. When can we expect a CootVR release ? Às 15:45 de 11/03/2019, Joern Krausze escreveu: > > The legacy drivers will not

Re: [ccp4bb] 3D stereo and (pymol) Win 10

15, rue René Descartes > F-67084 STRASBOURG cedex > +33.3.8841.7109 > E-mails: p.be...@ibmc-cnrs.unistra.fr > <mailto:p.be...@ibmc-cnrs.unistra.fr>, philippe_be...@yahoo.fr > <mailto:philippe_be...@yahoo.fr> > URLs: http://www-ibmc.u-strasbg.fr/ , > http://www-ibmc.u-

Re: [ccp4bb] 3D stereo and (pymol) Win 10

7084 STRASBOURG cedex >> +33.3.8841.7109 >> E-mails: p.be...@ibmc-cnrs.unistra.fr >> <mailto:p.be...@ibmc-cnrs.unistra.fr>, philippe_be...@yahoo.fr >> <mailto:philippe_be...@yahoo.fr> >> URLs: http://www-ibmc.u-strasbg.fr/ , >> http://www-ibmc.u-stra

Re: [ccp4bb] FW: [ccp4bb] old data - headers

Hi Dean, I reckon that it is an ADSC Quantum 4 or 4R CCD detector. If you open the images with mosflm or adxv you should see the characteristic 2x2 tile pattern. Note how the header format is similar to the one you posted from the ESRF. Pedro Às 10:21 de 31/01/2019, Dean Derbyshire escreveu: >

Re: [ccp4bb] old data

It helps to know the filename extension. Opening the image with adxv may also provide clues as to the detector type. Às 09:42 de 31/01/2019, graeme.win...@diamond.ac.uk escreveu: > Hi Dean > > Usually there is a serial number buried somewhere in the header - many are > text headers though some

Re: [ccp4bb] 3D stereo and pymol

Hi all, The problem with COOT stereo and Windows 10 is that the COOT binary is not compatible with the newer OpenGL drivers or somesuch in Windows 10. So, COOT runs fine in Windows 10 but crashes if you enter hardware stereo mode. However, PyMOL works fine in stereo in Windows 10. According to

Re: [ccp4bb] Pointless and Aimless interface in Proteum 3 (Bruker)

directly into CCP4. Best wishes, Pedro Matias Às 13:15 de 08/01/2019, Jens Hj örleifsson escreveu: > I have seen there is a possibility to run Pointless and Aimless inside the > Proteum 3 software, but after installing CCP4 I am unable to find it. Does > anyone know how to

Re: [ccp4bb] Joint CCP4 and ESF-EACBM Newsletter number 31

contents are here: > ftp://ftp.ccp4.ac.uk/ccp4/newsletter/nov_94/ > Best wishes, > Tomas > > On Wed, Jul 11, 2018 at 9:01 AM Pedro Matias <mailto:mat...@itqb.unl.pt>> wrote: > > Dear CCP4ers, > > Is there a PDF version of the Joint CCP4 and ESF-EACBM Ne

[ccp4bb] Joint CCP4 and ESF-EACBM Newsletter number 31

Dear CCP4ers, Is there a PDF version of the Joint CCP4 and ESF-EACBM Newsletter number 31 (November 1994)? I can find the summary on the web but not the contents. Thanks in advance, Pedro -- Industry and Medicine Applied Crystallography Macromolecular Crystallography Unit

Re: [ccp4bb] akta explorer and CU 900 PCI controller card

. If your disk is OK it might be possible to transfer the contents directly to a new PC. Hope this helps, Pedro Matias Às 11:42 de 18/05/2018, V F escreveu: > We had a big cooling failure within the cold room and lost the Äkta > controller PC due to excess heat. This *old* but reliable ÄktaEx

Re: [ccp4bb] Crystal structure of an unknown protein

environment and electron density and refine the structure. I'm sure you can submit the refined structure to the PDB even from an unknown protein. Regards, Pedro Matias Às 12:08 de 14/12/2017, Jiyong Su escreveu: > Dear CCP4bb, > > In 2014, I collected a high quality data set from a cryst

Re: [ccp4bb] Atom clashes in active site?

Hi Andrew, One of the atoms should be in altconf A and the other in B. Otherwise the problem remains. Pedro Às 01:48 de 20/12/2016, Andrew Marshall escreveu: > Hi all, > > Thank you for your suggestions. I tried the pdb file edit (making the > offending atoms of both the ligand and the protein

Re: [ccp4bb] Atom clashes in active site?

y refinement for corresponding atoms which may > not be desired. > > Pavel > > > On Mon, Dec 19, 2016 at 12:54 AM, Pedro Matias <mat...@itqb.unl.pt > <mailto:mat...@itqb.unl.pt>> wrote: > > Hi Andrew, > > The simplest way would be to place t

Re: [ccp4bb] Atom clashes in active site?

2.23 AS This trick should cause PHENIX to ignore close distances between atoms in the A and B conformers. Hope this helps, Pedro Matias Às 05:39 de 19/12/2016, Andrew Marshall escreveu: > Hi all, > > I have a structure of a condensing enzyme with substrate bound. The > active s

Re: [ccp4bb] Refinement of Iron-sulphur clusters

refinement (e.g., 1.05 A). In particular, the Fe-S-Fe angles are all set to 90 degrees, when in fact some are smaller and others are larger. This introduces a bias in the final rms angle deviation values. Fe4S4 is a distorted cubane, not a perfect cube. Best regards, Pedro Matias Em 13-10-2014

Re: [ccp4bb] deposited SF (or not)?

Hi, Bernhard, I recently published a paper in JBC that was published online only after the Editorial Office confirmed release of PDB coordinates and structure factors. Maybe those structures you mention are older and their internal checking procedures were not yet fully developed ? Cheers,