[ccp4bb] Resolution Discrepancy in Data Set

Hello all, I hope this message finds you well. In my current data set, I’ve encountered a discrepancy between the completeness in the high-resolution shells in merged statistics vs the refinement statistics. For example, when I look at my merged statistics file, output by Xia2 dials, the

[ccp4bb] CBMS Lecture Series - Erik Debler - January 24; 13:30 (EST)

You are cordially invited to join the Center for Biomolecular Structure Lecture Series ……….. Erik Debler Thomas Jefferson University WEDNESDAY, January 24, 13:30 (EST) "Hybrid methods to investigate the mechanism of Dot1 histone-modifying enzymes in kinetoplastid parasites"

[ccp4bb] Phenix version 1.21 released

The Phenix developers are pleased to announce that version 1.21 of Phenix is now available (build 1.21-5207). Binary installers for Linux, Mac OSX, and Windows (under Windows Subsystem for Linux), and the source installer, are available at the download site:

[ccp4bb] Applications for RapiData at SSRL 2024 still open!

Hi everyone, Applications for the 2024 edition of RapiData at SSRL are still open. The course will be held at the Stanford Synchrotron Radiation Lightsource (SSRL) located on the SLAC National Accelerator Laboratory campus in Menlo Park, CA, from April 29 to May 4, 2024. Please visit

Re: [ccp4bb] problem running ccp4mg: ugly and useless graphics

Dear Stuart, I did test that (removing the .CCP4MG2 directory and its contents) and it gave the same ugly graphics. There are problems with Alma Linux and the "Secure Boot" on this Hewlett Packard Z4 computer. This I have noticed. The secure boot option wants to load a signed graphics

Re: [ccp4bb] problem running ccp4mg: ugly and useless graphics

Dear Fred, Many apologies for your difficulties. My first thought is that perhaps CCP4MG's lighting settings are completely messed up. This can be tested by removing completely the folder: $HOME/.CCP4MG2 If this does not work, then further investigation will be required. Also, in CCP4 we are

[ccp4bb] problem running ccp4mg: ugly and useless graphics

Dear all, Perhaps a reader of the bb will have a solution for this problem. ccp4 is version 8.0 and is up to date. All graphics programs (coot, but also other non-ccp4 software such as chimeraX, Pymol...) run fine on the Alma-Linux 9.3 system. There is a problem however with ccp4mg: the

[ccp4bb] Permanent position in structural biology at the Micalis institute (Université Paris-Saclay)

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Re: [ccp4bb] Manual setting of config file in PyRx

Postdoctoral scholarship (2 years) within Structural Biology of Switchable Proteins from Directed Evolution The Magnus Wolf-Watz laboratory has an opening for a two-year postdoctoral scholarship. We are searching enthusiastic candidates that will focus on structure determination and

[ccp4bb] NOW HIRING: Structural Proteomics position at Human Technopole, Milano

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[ccp4bb] Manual setting of config file in PyRx

Greetings to all. I am screening around 500 compounds using Pyrx. I wanted to know if it is possible to use my old Config file without manually moving the grid box in PyRx. Any assistance in this regard would be very helpful. Thank you, Regards. Thripthi S.

[ccp4bb] Post-doc opportunity in RNA structure

Dear All, Please see the link below for details about a post-doc (Research Fellow) position in RNA structure, based in the group of Prof. Teresa Carlomagno at the University of Birmingham. Research Fellow in RNA Structure

[ccp4bb] i2run ProvideAsuContents Problem

To whom it may concern, I am currently working with CCP4 version 8.0.016 on an Ubuntu 22.04 system. In my efforts to follow the guidelines provided in the documentation (https://ccp4i2.gitlab.io/rstdocs/i2run/i2run.html), I have encountered an issue. Specifically, I have encountered a problem

[ccp4bb] Structural Biology activities at the ESRF User meeting 2024

Dear CCP4ers, The ESRF User Meeting for 2024 is scheduled to be held onsite from 5th to 7th February. https://www.esrf.fr/home/events/conferences/2024/user-meeting-2024.html This edition includes three Tutorials related to Structural Biology: -    Monday 5th, 9:00 - 12:30 (hybrid event): The

Re: [ccp4bb] Poor correlation coefficient of model to cryo-EM map.

The clash score is also impressively high. Your map may have the incorrect hand. Have you tried flipping it? Best wishes Reza From: CCP4 bulletin board on behalf of Martyn Winn - STFC UKRI <7c0f4d7fc2b7-dmarc-requ...@jiscmail.ac.uk> Sent: 10 January 2024

Re: [ccp4bb] Poor correlation coefficient of model to cryo-EM map.

THere must be some error in the calculation of the CC - or you are over optimistic about what constitutes a fit! What does the COOT density fit show? Eleanor On Wed, 10 Jan 2024 at 09:54, Martyn Winn - STFC UKRI < 7c0f4d7fc2b7-dmarc-requ...@jiscmail.ac.uk> wrote: > You can also try the

[ccp4bb] wwPDB News: Resources for Supporting the Extended PDB ID Format (pdb_00001abc)

Dear all, wwPDB anticipates that all the four character PDB accession codes (PDB ID) will be consumed by 2029. With the continuous growth of PDB archive, wwPDB has revised the PDB accession code format by extending its length and prepending “PDB” (e.g., "1abc" will become "pdb_1abc").

Re: [ccp4bb] Poor correlation coefficient of model to cryo-EM map.

You can also try the CCPEM list for more cryoEM-orientated advice https://www.jiscmail.ac.uk/CCPEM and look in CCP-EM for more fitting, refinement, validation tools. Certainly, the map doesn’t look 3A, unless you have filtered it for these pictures. The CC for the middle and C-terminal domains

Re: [ccp4bb] Poor correlation coefficient of model to cryo-EM map.

You can also try the CCPEM list for more cryoEM-orientated advice https://www.jiscmail.ac.uk/CCPEM and look in CCP-EM for more fitting, refinement, validation tools. Certainly, the map doesn’t look 3A, unless you have filtered it for these pictures. The CC for the middle and C-terminal domains

Re: [ccp4bb] Poor correlation coefficient of model to cryo-EM map.

Are you confident that your 3 Å resolution is correct? The map in the picture you supplied looks more like 5 Å, and the model vs. map FSC at 0.5 is apparently 20 Å (?).BasilGesendet mit der mobilen Mail AppAm 10.01.24 um 05:57 schrieb Ketul Saharan

Re: [ccp4bb] Poor correlation coefficient of model to cryo-EM map.

Hi Ketul, CCmask evaluates the cross-correlation between your experimental map and the map that is calculated from the model. If you look at the formula, the map calculated from the model involves, among other things, atomic coordinates, B factors, and occupancies. This means that even if the

[ccp4bb] Poor correlation coefficient of model to cryo-EM map.

Dear CCP4 community, I am building a structure model from ~3.0 Å resolution cryo-EM map. The structure consists of seven chains, with each chain containing an N-, middle, and C-terminal domain. Although I attempted to directly fit the Alfa-fold model, it became evident that the protein exhibited

Re: [ccp4bb] RMSD per residue graph for multiple aligned PDB files

Dear All, Thank you very much to everyone who replied, both on and off the mailing list (Andy Karplus and Ensemblator from his team; Joseph Ellaway and his scripts available at https://github.com/Joseph-Ellaway/per-residue-distance). As I was analysing conformations of the same protein from the

[ccp4bb] Recruiting: Science Coordinator - antiviral discovery (14 Jan)

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[ccp4bb] Robert Langridge obit

His work was mostly before my time, but I just saw this obituary of Robert Langridge, founder of the UCSF computer graphics laboratory.

[ccp4bb] MRC funded - senior research technician position

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[ccp4bb] Applications Open for Director, RCSB Protein Data Bank

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Re: [ccp4bb] [External] Re: [ccp4bb] alternatives to Consurf server

Hello, ChimeraX can also color an atomic model by sequence conservation score: https://www.rbvi.ucsf.edu/chimerax/data/conservation-coloring/conservation-coloring.html This tutorial uses an output from ConSurf, but as far as I understand any multiple sequence alignment can serve as the source

[ccp4bb] Instruct-ERIC Structure Meets Function Webinar 29

Dear all, Register now for the 29th edition of the Instruct-ERIC Structure Meets Function webinar series, taking place 11:00 CET on 23 January. Register Here

[ccp4bb] School on Single molecule biophysics in cell lysates, 13-17 May 2024, IBT, Vestec, Czech Republic

Dear colleagues, The registration to a specialized course - Basic level school of MOSBRI is open. Find all the relevant details on this page https://www.mosbri.eu/training/basic-level-schools/bls2/ This basic-level school is aimed at biologists, biophysicists, biochemists, structural biologists,

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

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

Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

Dear colleagues, Thank you to everyone who responded. Here is a short summary: 1.Refmac using isotropic B-factors with tight restraints 2. Add a TLS in refinement may help. Best wishes, chenzhonghao...@163.com From: Tom Peat Date: 2024-01-07 10:57 To: CCP4BB Subject: Re: [ccp4bb]

Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

Hello All, I think we are all in agreement that it depends on resolution, or more specifically the amount of experimental data one has versus how many atoms one has in the model to refine. There is also no question that structures have become better over the decades due to more and better

Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

Hi All, I believe it depends on the resolution. At sufficiently low resolution, it may not be too unreasonable to assume that the main chain atoms of a residue have the same B factors, and its side chain atoms also share the same B factor (different from the main chain). Why? Simply because your

Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

Hi Tom,I think restraints do change the data/parameter ratio, but how much is not straightforward. In, at least, the context of the Hamilton test restraints change the degrees of freedom which translates into a change of the effective data/parameter ratio. It is treated as adding extra

Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

Hello Robbie, Thanks for the stats and description of what has been done. I think this puts us back into the realm of restraints versus constraints and what is possible when trying to reduce the number of parameters to be refined. Although grouped B-factors don't capture the reality of side

Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

Hi Robbie and everyone, Perhaps some clustering of the structure could be used to define TLS groups rather than using chains. A spectral clustering based on Gaussian network model normal modes seems to work fairly well for defining dynamical domains, for example. In some cases these may be

Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

Hi Tom, At 3A the median number of reflections per atom is 3.4 which is indeed lower than 4. So in unrestrained refinement the data/parameter ratio is indeed worse than 1. This is where the effect of the restraints really matter and starting from a flat B-factor model is interesting. This is

Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

It appears that Zhonghao might be worried about his data to parameter ratio. At 3 A, one can easily be in a situation where one has fewer reflections than four times the number of atoms (X, Y, Z plus B). I like the idea of starting out with the average B (or even Wilson B) and then doing TLS as

[ccp4bb] How do I restrain B values?

I thought it was possible to stop B values on bonded atoms from fluctuating wildly? But I am quite unable to follow the newly formatted documentation.. To unsubscribe from the CCP4BB list, click the following link:

Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

One wonders who those "many people" are. You may not want to use them as your go-to reference for refinement techniques.Anyway, Refmac cannot do grouped B-factor refinement, but you are not missing out on anything. As Eleanor implied, one-per-residue B-factors give unrealistic results. You are

Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

Dear Prof. Dr. Dodson and all CCP4 community, Thanks for your reply. Just now, I used baverage. I found that it can average the B factor but not refine it. This function does not fit my requirement, because my resolution is low as 3 A. Many people said that Refmac5 overrefines the

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

Some blast from the past: Facility management came in full hazmat suits to decommission the old multiwire detectors with the large Be windows. https://www.ruppweb.org/Garland/gallery/Ch8/pages/Biomolecular_Crystallography_Fig_8-07.htm Anyhow, got one on the DOE Beryllium worker’s list.

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

Hi Firdous Can you ask Trilink biotechnologies if they can make it for you very good experience many speciality materials made Disclaim: i do not work with them or have any financial connections with them I think jena discontinued this item

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

Be aware that beryllium is also quite toxic. https://en.wikipedia.org/wiki/Acute_beryllium_poisoning Diana ** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry UT Southwestern Medical Center 5323 Harry Hines Blvd. Rm.

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

Nb, dissolution of BeCl2 in water is quite exothermic and releases HCl vapor, you will want to prepare that stock in a fume hood. Best wishes Kevin From: CCP4 bulletin board on behalf of Matthew BOWLER Date: Thursday, January 4, 2024 at 2:19 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re:

Re: [ccp4bb] [External] Re: [ccp4bb] alternatives to Consurf server

Hi Andre, I don't know if anyone mentioned Conservation-Colab, although it maps the conservation onto an AF model. https://zenodo.org/records/10062829 Cheers, Nick Nicholas Schnicker, PhD Director, Protein & Crystallography Facility Adjunct Assistant Professor, Molecular Physiology &

Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?

Hmmm - I am not sure about the value of this - one expects the longer floppier side chains to have very different B values for the CB than the OE2.. The program BAVERAGE gives you a plot of mean B value residue by residue.. *baverage* - averages B over main and side chain atoms SYNOPSIS¶

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Re: [ccp4bb] RMSD per residue graph for multiple aligned PDB files

AFAIK the CCP4 tools “superpose” and “gesamt” both give tables of per-residue RMSD Harry > On 5 Jan 2024, at 10:49, Tomas Malinauskas > wrote: > > Dear All, > > I apologize for asking a somewhat off-topic question. > > I have multiple aligned PDB files loaded in PyMOL, each representing >

Re: [ccp4bb] RMSD per residue graph for multiple aligned PDB files

Dear Thomas, Just have a look at this paper where we have made three-dimensional sketches of both backbone and side chain RMSDs: https://pubmed.ncbi.nlm.nih.gov/34988429 The illustrations were done with Chimera, but "B-factor" plots with PyMOL can be generated,at least for the backbone

[ccp4bb] RMSD per residue graph for multiple aligned PDB files

Dear All, I apologize for asking a somewhat off-topic question. I have multiple aligned PDB files loaded in PyMOL, each representing different conformations of the same protein. I'm interested in creating a graph displaying RMSD per residue, similar to those shown at

[ccp4bb] Can Refmac5 refine temperature factor residue by group?

Dear CCP4 community,  I found that Refmac5 refined the temperature factor only by four modes (see the bottom of the attached figure). However, no grouped B-factor (one or two per residue instead of one per atom) was found.  Actually, PHENIX and CNS can do it. But we are not familiar with both

[ccp4bb] wwPDB News: Time-stamped Copies of PDB and EMDB Archives

Dear all, A snapshot of the PDB Core archive (ftp://ftp.wwpdb.org,https://s3.rcsb.org) as of January 2, 2024 has been added toftp://snapshots.wwpdb.org,https://s3snapshots.rcsb.org(AWS), andftp://snapshots.pdbj.org. Snapshots have been archived annually since 2005 to provide readily

Re: [ccp4bb] alternatives to Consurf server

You can also map conservation with VMD, if memory serves (have not done this in quite a while). On Thu, Jan 4, 2024 at 9:34 AM Roberto Steiner < 2497b6493202-dmarc-requ...@jiscmail.ac.uk> wrote: > ConservFold from the Rodrigues lab at Warwick is something that you might > consider. >

Re: [ccp4bb] alternatives to Consurf server

ConservFold from the Rodrigues lab at Warwick is something that you might consider. https://www.rodrigueslab.com/resources Roberto A Steiner www.steinerlab.org https://twitter.com/steiner_lab roberto.stei...@kcl.ac.uk Randall

Re: [ccp4bb] alternatives to Consurf server

Hi Andre, I recently prepared a Consurf-like figure using conservation scores pulled from alignments in JalView. You would follow instructions for running data2bfactor.py in PyMOL, feeding the conservation scores to replace your model's B factor column. Then set up a color ramp like you would use

[ccp4bb] alternatives to Consurf server

Dear CCP4ers, Wishing you all a Happy New Year! You may have noticed that the Consurf server has been down since the conflicts in the Middle East began. Does anyone know of alternative tools that can provide similar results? Best regards. Andre S. Godoy, PhD  Universidade de São Paulo

Re: [ccp4bb] "LINK" and "REMARK 290" of pdb file

Dear Qixu, You can take a look at existing entries which have link records between 1_555 and another symmetry molecule. For example 5BQC which has various of these. mmCIF: # loop_ _struct_conn.id _struct_conn.conn_type_id _struct_conn.pdbx_leaving_atom_flag _struct_conn.pdbx_PDB_id

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

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

Re: [ccp4bb] Glide fails to generate accurate docking pose

You could a) change the force field used b) increase the docking resolution c) switch to a different program e.g. FRED from OpenEye d) examine if you limited the amount of generated confirmers for your ligand. If you have two or three rotatable bonds you can easily generate >1000. And it seems

[ccp4bb] Glide fails to generate accurate docking pose

Greetings to all. I am trying to dock a co crystallized ligand using GLIDE. The co crystallized ligand is a big molecule with multiple rotatable bonds. GLIDE is unable to regenerate the ligand pose. I tried limiting the rotatable bonds, but in vain. I would be grateful to receive any advice or

[ccp4bb] CCPBioSim Industry Talk - Kuano AI

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[ccp4bb] How to make GDP.BeF3 solution ?

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

Re: [ccp4bb] Input from the community for panel session: Crystallography is Dead! Long Live Crystallography!

Hi, “… Liv[ing] Crystallography” implies leveraging dynamics through time-resolved studies… But, competing for beamtime at synchrotrons and XFELs can restrict access to those systems that pass PRP scrutiny and likely have multi-method preliminary data from crystalline samples/slurries.

Re: [ccp4bb] Input from the community for panel session: Crystallography is Dead! Long Live Crystallography!

Happy New Year to everybody ! Health and peace ! Hi, Nicholas, Actually, the title : “Crystallography is Dead. Long Live Crystallography!” made me laugh. As you can find in Wikipedia : [ https://en.wikipedia.org/wiki/The_king_is_dead,_long_live_the_king! |

[ccp4bb] Open PhD positions in graduate school on microbial substrate conversion

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[ccp4bb] Input from the community for panel session: Crystallography is Dead! Long Live Crystallography!

Hello, and happy new year! Tomorrow evening, we will have a panel discussion at the CCP4 study weekend about the future of crystallography, called “Crystallography is Dead. Long Live Crystallography!” [https://en.wikipedia.org/wiki/The_king_is_dead,_long_live_the_king]. Whether you’re

Re: [ccp4bb] what is isomorphous?

Ahh yes. I still have the very helpful email I got from Dame Louise Johnson in 2010.  I don't think she would mind my quoting it here: Dear James I was sorry to miss you when you were at Diamond - I was in Germany. The story of the two forms of lysozyme crystals goes back to about 1964 when

[ccp4bb] "LINK" and "REMARK 290" of pdb file

Dear all, I'm working on the refinement of a crystal structure. In the structure, one crystal packing interface is mediated by a compound with two coordinate covalent bonds to two macromolecules from different asymmetric units. Thus I need to specify two "LINK" records in the head of pdb file.

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Re: [ccp4bb] nearestcell

Dear all, a short summary: - SAUC and the Phenix tool worked well. - SIMBAD was also pointed out to me, but it stops with an error message both in my local CCP4 installation and in "CCP4 online". - The https://app.strubi.ox.ac.uk/nearest-cell/nearest-cell.cgi alternative to

Re: [ccp4bb] nearestcell

That is a live link to sauc, but I have not updated the database from the PDB in a while. Let me know if there is an urgent need for an update, Otherwise I am planning one for March. I normally build the database from COD and the PDB, but if CCDC wishes, we can add the CSD to the mix. For the

Re: [ccp4bb] nearestcell

Hi Kay, http://flops.arcib.org:8084/sauc-1.1.1/ similar to the nearest-cell server, which seems to change its link and is harder to find (or stale link) https://app.strubi.ox.ac.uk/nearest-cell/nearest-cell.cgi HTH, Mike On Wed, Dec 27, 2023 at 1:39 PM Kay Diederichs <

Re: [ccp4bb] nearestcell

Hi Kay, to address "(...) not elsewhere (...)", in Phenix GUI go to Tools then down to "Search PDB symmetry...". I've never used it myself nor do I know who added it in Phenix but from the description it looks like what you're looking for. Let us know if you have any problems with it. All the

Re: [ccp4bb] nearestcell

Are you thinking of "othercell" ? On 12/27/2023 10:38 AM, Kay Diederichs wrote: Dear all, I seem to remember a tool called "nearestcell", a command-line equivalent of the Oxford Nearest-Cell web server which appears to be offline. However I cannot locate that tool in CCP4 nor elsewhere. Can

[ccp4bb] nearestcell

Dear all, I seem to remember a tool called "nearestcell", a command-line equivalent of the Oxford Nearest-Cell web server which appears to be offline. However I cannot locate that tool in CCP4 nor elsewhere. Can anyone point me to it or give alternatives, please? (I did try the PDB's advanced

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Re: [ccp4bb] Query on density fitting to phosphate

Hello, happy Boxing day. Re: "The inappropriate identification of an ion as PO4(-3) will significantly degrade the quality of any electrostatic potential one calculates from the model." A couple of comments. I always deleted solvents and counter-ions, etc, when doing this sort of thing, given

Re: [ccp4bb] Query on density fitting to phosphate

Everyone should bear in mind the following when considering the presence of an ionizable anion at a protein binding site: 1. The ionizable ion will exist in solution in a equilibrium distribution of ionization states, depending on the solution pH, and will exchange between them rapidly

Re: [ccp4bb] Query on density fitting to phosphate

Back to the value of an anomalous map - IF the anomalous data is good enough to give a significant peak at a sulphur position, you might expect to get a peak at a well ordered phosphate- if no sulphur peaks not much hope... On Mon, 25 Dec 2023 at 19:51, Tom Peat <

Re: [ccp4bb] Query on density fitting to phosphate

Hello Dale, Thank you for the correction/ clarification. I think this is still a tricky question, as in solution, this is an average state and one doesn't have a stable hydrogen (or two) sitting discretely on the phosphate. More specifically, the hydrogens are coming off and popping back on

Re: [ccp4bb] Relion issue with MPI

I see that you used 3 GPU and 3 MPI as you posted commands on GitHub as below command : which relion_refine_mpi --continue Refine3D/job006/run_it000_optimiser.star --o Refine3D/job008/run --dont_combine_weights_via_disc --no_parallel_disc_io --preread_images --pool 3 --pad 1 --particle_diameter

Re: [ccp4bb] [External] Re: [ccp4bb] Relion issue with MPI

Try separating the MPI process and threads. For example if you have 4 GPUs, use 0,1:2,3. You can do this in ‘Which GPUs to use’ under compute tab. Additionally, use a scratch directory and do not put particles in RAM. You can skip padding and gridding as well. Hope this helps! Suparno. Sent

Re: [ccp4bb] [External] Re: [ccp4bb] Relion issue with MPI

It was reported by me but the problem was not solved. I thought ccp4bb has much bigger user base and may be someone has experienced this issue. It is something related to os (rocky linux) or mpi in my computer. Data set is not a problem as i can process same data set with exactly same parameters

Re: [ccp4bb] CCP4BB Digest - 21 Dec 2023 to 22 Dec 2023 (#2023-324) (out of office)

Thank you for your e-mail. I am out of office until January 2nd, 2024. I will respond to your e-mail as soon as possible upon my return. For urgent matters please contact: b...@boku.ac.at Thank you for your understanding. With kind regards, Elisabeth Laurent >>> CCP4BB automatic digest system

Re: [ccp4bb] Relion issue with MPI

Hi, First of all, please report details of your hardware and your job. - Type of GPU - Number of GPU - GPU memory size - Box size - Number of threads - Number of MPI processes - Full command line Do you get the same error in ALL datasets (including our tutorial dataset) or only on this

[ccp4bb] Relion issue with MPI

Hi I am trying to use relion and I am getting error when trying to use mpi (for 3d classification and 3D auto-refine). ERROR: out of memory in /home/lvantol/relion5/relion/src/acc/cuda/custom_allocator.cuh at line 436 (error-code 2) in:

[ccp4bb] Postdoc opportunity at the PSI of Switzerland.

Dear Colleagues, The Laboratory of Biomolecular Research at the Paul Scherrer Institute (PSI), Switzerland, is advertising for a Postdoc position from the NanoArgovia Programm of the Swiss Nanoscience Institute (SNI). This project is granted for one year and extendable to 2 years. The

[ccp4bb] Two-year postdoctoral position in time-resolved crystallography at IBS in Grenoble

Dear all, We have an immediate opening for a two-year postdoctoral researcher in SNaX team of the DYNAMOP group at the Institute for Structural Biology in Grenoble (France). The successful candidate will work on the development and optimization of bio-scavengers towards toxic organophosphorus

Re: [ccp4bb] what is isomorphous?

Hello All, I think Randy makes a very good point here- it depends on what you are trying to do with your data sets. If you are trying to merge them, 'isomorphous' is important for this to work. If you are using them for cross crystal averaging, being less isomorphous is better (more signal).

Re: [ccp4bb] what is isomorphous?

Thank you all. What I gather from this (please correct me) is: a. that for the intensities what matters is effectively whether s * delta_r is smaller than about 0.25--that is the fourier components at high resolution should not cover corresponding atoms that have shifted by

Re: [ccp4bb] what is isomorphous?

I think we’ve strayed a bit from Doeke’s original question involving crystals A, B and C, where I think the consensus opinion would be that we would refer to crystal C as not being isomorphous to either A or B. On the question of what “isomorphous” means in the context of related crystals, I’m

Re: [ccp4bb] what is isomorphous?

Hello Harry, I think this is the paper you mean: https://scripts.iucr.org/cgi-bin/paper?S0365110X56002552 They gave depressingly low estimates of how much the cell dimensions could change in order for isomorphous replacement to still work. In reality, unit cells can shrink and swell, but the

Re: [ccp4bb] what is isomorphous?

Hi Didn’t Francis Crick have something to say about this in the early 1950s? I’m sure it was published but off the top of my mind I can’t think where (one of the more “established” members of this community will be able to give chapter and verse)! If you want to read something a little more

Re: [ccp4bb] what is isomorphous?

Hi Doeke, you can take the coordinates of B and do a rigid body refinement against the data from A. If this map is sufficient to reproduce model A (including model building and more refinement cycles), then B is isomorphous to A. You can do this the other way round, and the result may not be the

Re: [ccp4bb] what is isomorphous?

The Drenth rule of thumb makes sense. Whether 2 in the macromolecular sense isomorphous structures are isomorphous, is a matter or resolution, and it has to do with the reciprocal space overlap function aka G-function. So up to a certain resolution, 2 data sets may be isomorphous, but at high

Re: [ccp4bb] what is isomorphous?

According to Jon, Isomorphous Replacement ALWAYS works, because it is only supposed to be isomorphous. Isomorphous difference maps can ALWAYS be calculated with sensible results, because the unit cells of the reference and the time-resolved data are only supposed to be isomorphous. Something is

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