Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

Wankowicz From: CCP4 bulletin board on behalf of Krieger, James M Sent: Monday, May 13, 2024 10:22 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility It definitely is impressive but it also has clear limitations On 13

Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility I tried it yesterday and I was really shocked by how fast it is. When I was preparing to submit my second job, the first one was already finished, which made me think that I was definitely doing somethin

Re: [ccp4bb] Request for help in optimizing Coot for AMD 5950x CPU and RX6600XT GPU hardware PC

From: Otsile Mojanaga Sent: Monday, May 13, 2024 3:29 PM To: Paul Emsley Subject: RE: [ccp4bb] Request for help in optimizing Coot for AMD 5950x CPU and RX6600XT GPU hardware PC Dear Paul/All Thank you for the response. I am on Windows 11 and I tried looking around Coot to see where I could

Re: [ccp4bb] What could these crystals be?

Hello, what is in the purification buffer? Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent from Proton Mail mobile Original Message On 13 May 2024, 15:15, 张慧欣 wrote: > Hi all > We have been trying with no success to crystalize a protein. Recently we got > these stra

Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

Is it just me who is really impressed by it? Am I missing something? Get Outlook for Android<https://aka.ms/AAb9ysg> From: CCP4 bulletin board on behalf of Rafael Marques Sent: Monday, May 13, 2024 3:13:16 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4b

Re: [ccp4bb] Fwd: AlphaFold3 Transparency and Reproducibility

I tried it yesterday and I was really shocked by how fast it is. When I was preparing to submit my second job, the first one was already finished, which made me think that I was definitely doing something wrong. Probably I was...Best wishes Rafael Marques On 13 May 2024 09:53, Harry Powell <193

Re: [ccp4bb] Request for help in optimizing Coot for AMD 5950x CPU and RX6600XT GPU hardware PC

On 13/05/2024 13:03, Otsile Mojanaga wrote: Dear All I have been using coot as part of my normal workflow but since last week I have been having issues with Coot after I built my own PC which contains the following Hardware: CPU - AMD Ryzen 9 5950X 16-Core Processor - 16 Cores, 32 Threads

Re: [ccp4bb] coot - how to define a keyboard shortcut for "update NCS ghosts with local match" ?

On 13/05/2024 11:23, Laurent Maveyraud wrote: Hello, I like the function "update NCS ghosts with local match" found in the calculate/NCT tools menu. It's really helpful when NCS is not really strict. However, I find it clumsy that you have to go in a submenu to get it, so I would like to defin

Re: [ccp4bb] Postdoctoral position at the Sussex Drug Discovery Centre

Dear ccp4bb community, There are just a few days left to apply for this position - deadline 17th of May. Many thanks We have a postdoctoral position available to join the Drug Discovery team at the Sussex Drug Disc

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 13

Re: [ccp4bb] ccp4i2 stopped working (no startup) - advice?

Renato and Stuart McNicholls wrote exactly the right thing: deleting this file resolved the issue. Thank you very much! -Original Message- From: CCP4 bulletin board On Behalf Of Renato Weiße Sent: 08 May 2024 16:44 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] ccp4i2 stopped working

Re: [ccp4bb] Ubuntu and Coot

bulletin board on behalf of Tom Peat <b7e4a7a8af49-dmarc-requ...@jiscmail.ac.uk> Sent: Thursday, May 9, 2024 9:29 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Ubuntu and Coot You don't often get email from b7e4a7a8af49-dmarc-requ...@jiscmail.ac.uk. Learn why this is impo

Re: [ccp4bb] Ubuntu and Coot

letin board on behalf of Martin Malý Sent: Wednesday, May 8, 2024 5:31 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Ubuntu and Coot Dear Tom, I am using basically the same setup (Linux Mint 21.3 Xfce based on Ubuntu 22.04, CCP4 8.0.019 including Coot 0.9.8.93). Everything works well

Re: [ccp4bb] [EXTERNAL]Re: [ccp4bb] Modeling Disulfide Bond Occupancies

Thank you so much From: Eleanor Dodson Date: Monday, May 6, 2024 at 3:30 PM To: Liliana Margent Cc: CCP4BB@jiscmail.ac.uk Subject: [EXTERNAL]Re: [ccp4bb] Modeling Disulfide Bond Occupancies ***ATTENTION: This email came from an external source. Do not open attachments or click on links from

Re: [ccp4bb] ccp4i2 stopped working (no startup) - advice?

Hi Andrea, concerning Log #1: there is a log file /home/athorn/.CCP4I2/status/status_1710775099.ccp4i2_status.xml, which is probably empty. If it is, then deleting it should resolve the error. I have seen this problem from time to time on students laptops, but could not figure out, for wh

Re: [ccp4bb] Ubuntu and Coot

Dear Tom, I am using basically the same setup (Linux Mint 21.3 Xfce based on Ubuntu 22.04, CCP4 8.0.019 including Coot 0.9.8.93). Everything works well on my computer. I did not have any issues with Coot even in CCP4 8.0.017. I am sorry I don't know the reason of the error... Cheers, Martin O

Re: [ccp4bb] Multiple ligand simultaneous docking

Haddock certainly has support for this HADDOCK Web Server science.uu.nl [favicon.ico] But I have not run it myself… regards Gary

Re: [ccp4bb] Modeling Disulfide Bond Occupancies

Do not know what the resolution is here, try an anisotropic refinement of the Cys side chains first to see if this solves your problem. __ Dr. math. et dis. nat. Jeroen R. Mesters University of Lübeck https://orcid.org/-0001-8532-6699 Am 06.05.2024 um 21:48 schrieb Eleanor Dodson <176a9d

Re: [ccp4bb] Modeling Disulfide Bond Occupancies

In the CCP4 program refmac5, you specify occupancy groups and then specify how to refine them.  The setup, afaik, is not automatic. Documentation for how to do it is here: http://www.ysbl.york.ac.uk/refmac/data/refmac_keywords.html#Occupancy You may also find this link helpful? https://www.mail

Re: [ccp4bb] Modeling Disulfide Bond Occupancies

But are there two conformations of the disulphide? or one disulphide and one broken link? Eleaor On Mon, 6 May 2024 at 20:42, Dr. Kevin M Jude wrote: > I have done this in shelxl or phenix refinement, you can define occupancy > groups (or free variables in shelxl) so that 472A and 384A are one g

Re: [ccp4bb] Modeling Disulfide Bond Occupancies

I have done this in shelxl or phenix refinement, you can define occupancy groups (or free variables in shelxl) so that 472A and 384A are one group, 472B and 384B are another. Pretty sure there is a similar solution in refmac. Though also if the 384A rotamer doesn’t clash with the 472B rotamer, y

Re: [ccp4bb] Modeling Disulfide Bond Occupancies

Well - I turn off occupancy refinement once there is a sort of consensus.. Disulphides often break after long exposures and you see the positive and negative blobs clearly. I must admit I usually just set 0.5 as occ , fix the surviving disulphide link and let the B values suggest a better ratio tha

Re: [ccp4bb] update manager

J. Schuller Sent: Sunday, May 5, 2024 10:01 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] update manager ccp4um does not work for me. # ccp4um /usr/local/xtal/ccp4_master/ccp4-8.0/libexec/python3.7: error while loading shared libraries: libcrypt.so.1: cannot open shared object file: No

Re: [ccp4bb] update manager

ccp4um does not work for me. # ccp4um /usr/local/xtal/ccp4_master/ccp4-8.0/libexec/python3.7: error while loading shared libraries: libcrypt.so.1: cannot open shared object file: No such file or directory --- I recently updated from Scientific Linux 7 to Alma 9. I don't know if this is part of

Re: [ccp4bb] PDB validation - oligosacchides

Hi Natalie, comp_id needs to be a valid CCD ID, in this case 'GLC'. Not sure why/how the invalid value 'GLC-b-D' was generated. Let us know if you need further assistance, Deborah On 03/05/2024 22:25, Natalie Losada wrote: I am validating a structure with two sucrose molecules. I am gettin

Re: [ccp4bb] PDB validation - oligosacchides

Natalie If you send me the model file off-list I can help. BTW, there is a Phenix specific BB that can help with all things Phenix. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235

Re: [ccp4bb] Diffraction Methods 2024

Dear All, A reminder that this meeting is taking place in July - we have an interesting programme coming together in both the main research methods conference and the associated seminar, details are on the meeting page at: https://events.gwdg.de/event/650/ Many thanks to all those who have alr

Re: [ccp4bb] Linking 2 different alternate conformation CYS residue to main chain

Thank you all for your help :) The only way I could solve it was to manually edit the PDB after placing both conformations as desired. Briefly: i) Make "2CO" read in the PDB as a real alternate conformation: change resi number (same as CYS), name ("B2CO" - conf B). ii) Change "OXT" atom name to "

Re: [ccp4bb] what happened to Molprobity

Dear Martin, Mark and Pedro for your replies which have been helpful. Hopefully, here speaking for the hole community, the disfunctioning of the server is just a temporary problem. All the best, Gerlind On 30/04/2024 13:47, Martin Malý wrote: Ce mail provient de l'extérieur, restons vigilants

Re: [ccp4bb] Virtual Registration for 10th CCP-EM Spring Symposium & BCI User Meeting 30th April - 2nd May 2024

Dear all, BCI and Spring Symposium is now live! If you'd like to join virtually any time over the few days please register here for full joining instructions: https://cvent.me/Q1QANv Or you can drop in following the Zoom links in the full schedule here: https://www.ccpem.ac.uk/downloads/sympo

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 funct

Re: [ccp4bb] what happened to Molprobity

same here, the website http://molprobity.biochem.duke.edu/index.php loads, but when trying uploading a pdb file nothing happens. Hopefully it is just a temporary glitch. Mark van Raaij Dpto de Estructura de Macromoleculas, lab 20B Centro Nacional de

Re: [ccp4bb] what happened to Molprobity

Dear Gerlind, The MolProbity analysis is included in the 'Multimeric validation' task and also in the refinement task in CCP4i2 - just be sure to have the current version 8.0.019. In Phenix GUI, I can still find such a task: Crystals -> Validation and map-based comparison -> Comprehensive va

Re: [ccp4bb] Instruct Biennial Structural Biology Conference: Last Chance to Register

Prof. em. Gebhard F.X. Schertler Strukturbiologie ETH Zürich ERC Investigator Head of Biology and Chemistry Division Paul Scherrer Institut OSRA 007 CH-5232 Villigen PSI gebhard.schert...@psi.ch phone +41 56 310 4265 Am 29.04.2024 um 10:14 schrieb ccp4mail :  D

Re: [ccp4bb] Linking 2 different alternate conformation CYS residue to main chain

Dear Filipa and Nicholas, I confirm that in the current CCP4 version 8.0.019, refmacat is integrated in the ccp4i2 refinement task - now the task is called "Refmacat/Refmac5". Cheers, Martin On 29/04/2024 17:30, Nicholas Clark wrote: Hi Filipa,

Re: [ccp4bb] replacement for Scientific Linux

Hello, I don’t know if crystallographic software is commonly GPU-accelerated. Most software we use to process cryoEM data is and requires CUDA, which only works on Nvidia hardware with their driver. Also seems to be the case for a lot of deep learning software. Like it or not, it’s simply a fac

Re: [ccp4bb] refmac5 version 5.8.0425 corrupts B-factors..?

That result looks really bizarre but it is hard to make a sensible comment without more details..maybe you could attach the whole log file for the refmac run. What input reflection dAta are you using ? You couldn’t have picked up a Sharpened set by any chance? (It is always good practice to make

Re: [ccp4bb] refmac5 version 5.8.0425 corrupts B-factors..?

Dear Martin, one suspicion comes to my mind: could it be a "computer problem" in the sense that you are using different computing environments for the two calculations (arpWarp vs standalone refmac5)? That could lead to different decimal separators ("." versus a ","; see https://en.wikipedia.o

Re: [ccp4bb] replacement for Scientific Linux

Hi Harry, same here. Actually we skipped RHEL8 and its alternatives, so moved directly from CentOS7 to Rocky9. We are happy with that decision. Best wishes, Kay On Fri, 26 Apr 2024 15:57:46 +, Andy Purkiss wrote: >Hi Harry, > >We've been migrating to Rocky Linux as it is built on RHEL in

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] add ligand with AceDRG

t; -Original Message- > From: CCP4 bulletin board On Behalf Of Gerard Bricogne > Sent: Friday, April 26, 2024 11:47 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [EXTERNAL] Re: [ccp4bb] add ligand with AceDRG > > EXTERNAL EMAIL: Use caution before replying, clicking links, and

Re: [ccp4bb] add ligand with AceDRG

Use the search tab at the RCSB web site, type in a 3 letter code, and if it has been used for a ligand then it will appear as a Chemical Component. Thanks to Phil, I am on vacation in Mexico and cut and pasting URLs is a pain on an iPhone. Diana Sent from my iPhone On Apr 26, 2024, at 9:07 A

Re: [ccp4bb] replacement for Scientific Linux

Hi Harry, I started using Debian about 10-15 years ago, and never changed my opinion since. I had tested various others before, like redhat, suse, ubuntu etc. The stable version of Debian is indeed very stable, as there are no version changes, only bug fixes etc. The new release is about every thr

Re: [ccp4bb] replacement for Scientific Linux

If you want to keep as close to scientific linux as possible, I would suggest Alma or Rocky Linux. Those were the two options my group considered when the writing was on the wall for scientific linux and we were ramping up our workstations. We ended up going with Alma, but I'm not sure it is any be

Re: [ccp4bb] replacement for Scientific Linux

Hello Harry Any of the top 50 on distrowatch.com will basically be fine and the next 20 or so on the list will probably be fine. Then you start getting into the twilight zone. I am sure that will help greatly to narrow down your choice ;-0 Best wishes, Jon Cooper. jon.b.coo...@protonmail.com S

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] add ligand with AceDRG

letin board On Behalf Of Gerard Bricogne Sent: Friday, April 26, 2024 11:47 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [EXTERNAL] Re: [ccp4bb] add ligand with AceDRG EXTERNAL EMAIL: Use caution before replying, clicking links, and opening attachments. Dear Oliver and CCP4BB readers, This obsoleted LIG

Re: [ccp4bb] replacement for Scientific Linux

Hi Harry, We've been migrating to Rocky Linux as it is built on RHEL in a similar way to Scientific Linux. Most things compiled on Centos 7 (our default for a while) work in Rocky Linux version 9. For compilers etc., I use the Software Collections / devtoolsets to run later versions than the de

Re: [ccp4bb] add ligand with AceDRG

Dear Oliver and CCP4BB readers, This obsoleted LIG came from PDB entry 1JVP deposited in 2001 by Jean-Michel Rondeau working at Novartis. He must simply have been the first person to deposit a structure in which the ligand was called LIG ... . That molecule is now called 89E, but as Phil showed, t

Re: [ccp4bb] add ligand with AceDRG

Hi Stefanie, If you want to try Grade2 (for a non-confidential ligand) then this is easy to do using the Grade Web Server https://grade.globalphasing.org/ We have altered our default "3-letter code” (aka PDB chemical component ID) to “LIG”. The reserved PDB two letter codes 01 to 99 are also

Re: [ccp4bb] add ligand with AceDRG

Thanks for the feedback, I will let PDBe developers know that this is causing confusion and that LIG should not return results. Kind regards, Deborah On 26/04/2024 16:11, Garib Murshudov wrote: On this website: https://www.ebi.ac.uk/pdbe-srv/pdbechem/ If you search for LIG it returns a ligan

Re: [ccp4bb] add ligand with AceDRG

Indeed, as Diana points out: PDB's own components.cif defines LIG as: _chem_comp.id LIG _chem_comp.name "3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H11 N3" So they probably should fix that. Also that c

Re: [ccp4bb] add ligand with AceDRG

On this website: https://www.ebi.ac.uk/pdbe-srv/pdbechem/ If you search for LIG it returns a ligand. With small letters it says: The chemical component you are trying to view (LIG) has been obsoleted. You have been redirected to the component wh

Re: [ccp4bb] add ligand with AceDRG

Hi Diana, Could you please clarify where you are searching? LIG is obsolete and definitely not in use. Cheers, Deborah On 26/04/2024 15:40, Diana Tomchick wrote: But I think that is a mistake, if you search for LIG in the PDB, it brings up a definite ligand that has that 3-letter code. Dia

Re: [ccp4bb] add ligand with AceDRG

But I think that is a mistake, if you search for LIG in the PDB, it brings up a definite ligand that has that 3-letter code. Diana Sent from my iPhone On Apr 26, 2024, at 8:04 AM, Deborah Harrus wrote:  Dear all, Just to clarify, "LIG" is also a reserved code, so it's safe to use. See ht

Re: [ccp4bb] add ligand with AceDRG

Dear all, Just to clarify, "LIG" is also a reserved code, so it's safe to use. See https://www.wwpdb.org/news/news?year=2023#656f4404d78e004e766a96c6 Kind regards, Deborah Harrus PDBe On 25/04/2024 16:04, Diana Tomchick wrote: The PDB has reserved the following codes for unknown ligands: D

Re: [ccp4bb] add ligand with AceDRG

Thank you Paul. I did not think about it. Stefanie, could you please send the log file to me? Regards Garib > On 26 Apr 2024, at 14:17, Paul Emsley wrote: > > > On 25/04/2024 13:01, FREITAG-POHL, STEFANIE wrote: >> >> >> >> I have trouble adding a ligand with AceDRG in CCP4i2 into my refi

Re: [ccp4bb] COOT 1.1 and DNA mutation

On 26/04/2024 02:44, Paul Emsley wrote: On 25/04/2024 16:07, Simon Vecchioni wrote: Paul, Many thanks for fixing the [simple mutate] button for DNA in v1.1.08--works like a charm! I would ask about two other DNA features-- 1) The [add terminal residue] button seems unresponsive for DNA,

Re: [ccp4bb] add ligand with AceDRG

On 25/04/2024 13:01, FREITAG-POHL, STEFANIE wrote: I have trouble adding a ligand with AceDRG in CCP4i2 into my refinement: I put in a smilesstring and the ligand is written ok, but since I can only chose already 'taken' 3-letter-codes the refinement always crashes as there is a clash with

Re: [ccp4bb] add ligand with AceDRG

to make sure that it is not related to your ccp4 installation. Best regards Cyprian Cyprian Cukier, Ph.D. Head of Structural Biology Selvita S.A. From: CCP4 bulletin board On Behalf Of Garib Murshudov Sent: Friday, April 26, 2024 1:48 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] add

Re: [ccp4bb] add ligand with AceDRG

Refmac by itself should not care about duplicated residue names in the monomer library. It takes the last monomer. There should be something on the interface preventing this. Longer than three letters should be available from the next release of ccp4. New acedrg and Refmacat should be able to d

Re: [ccp4bb] add ligand with AceDRG

Dear all, thank you so much for all your suggestions. Unfortunately, nothing helped. Whatever 3-letter code I choose Refmac is complaining that there is a clash with an already existing ligand (even DRG, LIG, numbers) and AceDRG in CCP4i2 insists on 3 letters. I am not quite sure how to bypass

Re: [ccp4bb] COOT 1.1 and DNA mutation

On 25/04/2024 16:07, Simon Vecchioni wrote: -- Paul, Many thanks for fixing the [simple mutate] button for DNA in v1.1.08--works like a charm! I would ask about two other DNA features-- 1) The [add terminal residue] button seems unresponsive for DNA, I see what you mean. From the termina

Re: [ccp4bb] COOT 1.1 and DNA mutation

Paul, Many thanks for fixing the [simple mutate] button for DNA in v1.1.08--works like a charm! I would ask about two other DNA features-- 1) The [add terminal residue] button seems unresponsive for DNA, and is often quite useful; 2) There was a button chain in v0.8.9 to add base pair restraints

Re: [ccp4bb] add ligand with AceDRG

The PDB has reserved the following codes for unknown ligands: DRG INH 01 - 99 Using one of these should not cause you the described problems. I successfully used 99 just last week. If you try to use 999 or LIG these will not work, there are ligands assigned to those codes. Diana Sent from

Re: [ccp4bb] add ligand with AceDRG

Hi Stefanie, If you could run from command-lines, it will be easy to solve this problem. try from command-line, type acedrg -i "your_smiles_string" -r your_3_letter_code -o your_out_file_name For example, acedrg -i "C[C@@H](C(=O)O)N" -r UNL -o UNL You will get a file called UNL.cif, which

Re: [ccp4bb] add ligand with AceDRG

Hi Stefanie, Why can you only use "taken" three letter codes? In the "output monomer" box, you should be able to enter whatever you'd like for the "Three letter code for output monomer". In the attached image, this is shown as "DRG" but can be changed to any 3 letter code of your choice. Obviously

Re: [ccp4bb] add ligand with AceDRG

Hi Stefanie, Can you manually edit the restraints file using TextEdit and find and replace and the pdb file of course? Other option is to use Grade or Grade2 and the smiles string if you have this software installed. I often find this easier than ccp4i2. Best regards and good luck! Maria >

Re: [ccp4bb] add ligand with AceDRG

Hi Stefanie, In CCP4Cloud, the equivalent task will generate the files using a 'free', unused code, if nothing is entered in the relevant box. However, not sure if CCP4I2's task will do the same, but worth trying. Hope this helps, Andy From: CCP4 bulletin boar

Re: [ccp4bb] Microscope camera

Have you considered a Raspberry Pi with camera, or camera mount with your existing lens: https://www.raspberrypi.com/products/#cameras-and-displays Photos and livestream will be easy to set up. You could try motioneye to give you a livestream and take pictures on demand, or at defined time in

Re: [ccp4bb] Microscope camera

Dear Pat, we are facing the same problem and the most effective solution I found is to print support for smartphones, which today offer incredibly good cameras. Here are two examples of open access designs: https://www.openocular.com/ https://bioceednews.w.uib.no/2020/12/07/3d-printing-a-smart

Re: [ccp4bb] Microscope camera

Hi Pat Depends on how much you want to spend. I’d start with a web search for “webcam astrophotography”, which should show options on how to remove a webcam’s lens and mount the cam (not the kens, of course!) on another optical instrument. Back in the day, I had a Philips webcam that had a scr

Re: [ccp4bb] disordered cysteine

C.UK Objet : Re: [ccp4bb] disordered cysteine Ce mail provient de l'extérieur, restons vigilants Dear Oliviero, For sure cysteines can be disordered. Sometimes you can find one conformation reduced and another conformation oxidised if the cysteine is solvent exposed. Also in well-resolved

Re: [ccp4bb] disordered cysteine

Dear Oliviero, Resending the message since I am not sure you got it. For sure cysteines can be disordered. Sometimes you can find one conformation reduced and another conformation oxidised if the cysteine is solvent exposed. Also in well-resolved structures you can see a cysteine taking part in

Re: [ccp4bb] disordered cysteine

Dear Oliviero, For sure cysteines can be disordered. Sometimes you can find one conformation reduced and another conformation oxidised if the cysteine is solvent exposed. Also in well-resolved structures you can see a cysteine taking part in a disulphide bond, but only partially, one conformatio

Re: [ccp4bb] Request for assistance with structure solution

Thank you @Yehudi BLOCH, Kay for the help.  Kind Regards, Adewumi Adeyeye, (PhD Candidate)Department of Biochemistry, Genetics, and Microbiology Structural Biology Group, Room 3-7, Agricultural Sciences Building, University of Pretoria c/o University & Lynnwood Roads Hatfield Pretoria 0083

Re: [ccp4bb] Rescale merged data?

Dear all, Just to reiterate that wwPDB can accept multiple data blocks of data before and after process, and the first block should be the one that used for the refinement of the deposited coordinates. Kind regards, Deborah On 18/04/2024 13:37, Randy John Read wrote: I haven’t deposited an

Re: [ccp4bb] Rescale merged data?

Hi Clemens I’m “quite”* surprised. Do the authors of these programs offer any explanation as to why the scaling programs (given that these are the ones that usually provide F/I information for subsequent programs) bother to calculate sigmas if they’re going to be ignored? Harry * for “quite”

Re: [ccp4bb] Rescale merged data?

Dear Randy, Harry et al, sorry for replying to several emails in one message - but as always, everything is connected ;-) On Thu, Apr 18, 2024 at 10:02:40AM +, Randy John Read wrote: > I’d like to add my strong agreement to what Robbie said, but also point > out a wrinkle. When the PDB runs v

Re: [ccp4bb] Refmac problem: Validation and Analysis

Dear Marian, This issue regarding validation report in refmac task has been fixed in the latest update 8.0.019. Please let us know if the problem persists. Best wishes, Martin On 05/04/2024 13:19, Jon Agirre wrote: Dear Marian, Thanks for your report. I'm sorry you're having to deal with this

Re: [ccp4bb] Rescale merged data?

your favorite >>> refinement program. >>> My personal convention is to use CC1/2 = 0.30 as the point to which retain >>> data and = 2 as the nominal resolution of the dataset. If you have >>> the HKL2000 scaling log, you should be able to retrieve this inform

Re: [ccp4bb] Rescale merged data?

esday, April 17, 2024 4:12 PM To: Hekstra, Doeke Romke Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Rescale merged data? Sure thing. A former student left somewhere between 30-50 datasets but they scaled the data to the detector corners (or maybe edge) in HKL2000. There are many of the

Re: [ccp4bb] Rescale merged data?

sed on some criterion or another. > > > > Best, Doeke > > > > From: Matt Mcleod > > Sent: Wednesday, April 17, 2024 4:12 PM > > To: Hekstra, Doeke Romke > > Cc: CCP4BB@JISCMAIL.AC.UK > > Subject: Re: [ccp4bb] Rescale merged data? > > > > S

Re: [ccp4bb] Rescale merged data?

> on some criterion or another. > > Best, Doeke > > From: Matt Mcleod > Sent: Wednesday, April 17, 2024 4:12 PM > To: Hekstra, Doeke Romke > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Rescale merged data? > > Sure thing. > > A former student left

Re: [ccp4bb] Rescale merged data?

> Sent: Wednesday, April 17, 2024 4:12 PM > To: Hekstra, Doeke Romke > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Rescale merged data? > > Sure thing. > > A former student left somewhere between 30-50 datasets but they scaled the > data to the detector corners

Re: [ccp4bb] Rescale merged data?

should be able to retrieve this information. I frankly wish we’d just deposit all data in the PDB rather than truncate based on some criterion or another.   Best, Doeke   From: Matt Mcleod Sent: Wednesday, April 17, 2024 4:12 PM To: Hekstra, Doeke Romke Cc: CCP4BB@JISCMAIL.AC.UK Subject: R

Re: [ccp4bb] Rescale merged data?

est, Doeke > > > > *From:* Matt Mcleod > *Sent:* Wednesday, April 17, 2024 4:12 PM > *To:* Hekstra, Doeke Romke > *Cc:* CCP4BB@JISCMAIL.AC.UK > *Subject:* Re: [ccp4bb] Rescale merged data? > > > > Sure thing. > > > > A former student left somewhere

Re: [ccp4bb] Rescale merged data?

, Doeke Romke Cc: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Rescale merged data? Sure thing. A former student left somewhere between 30-50 datasets but they scaled the data to the detector corners (or maybe edge) in HKL2000. There are many of the high-resolution bins with no reflections in

Re: [ccp4bb] Rescale merged data?

Sure thing. A former student left somewhere between 30-50 datasets but they scaled the data to the detector corners (or maybe edge) in HKL2000. There are many of the high-resolution bins with no reflections in them. He then went forward and merged this data, presumably in HKL2000 again and did h

Re: [ccp4bb] Rescale merged data?

L pm xzx Have a grea lol On Wednesday, April 17, 2024, 1:59 PM, Hekstra, Doeke Romke wrote: Hi Matt, It would be helpful if you could describe your case in more detail. Do you want to change the resolution cutoff after scaling? Do you want to keep more data? Fewer? Or do you mean something

Re: [ccp4bb] Rescale merged data?

Hi Matt, It would be helpful if you could describe your case in more detail. Do you want to change the resolution cutoff after scaling? Do you want to keep more data? Fewer? Or do you mean something different such as truncation to generate amplitudes, application of anisotropic resolution cutof

Re: [ccp4bb] Request for assistance with structure solution

good detective work indeed! Kay On Tue, 16 Apr 2024 14:40:15 +0100, Yehudi BLOCH wrote: >Dear Adewumi > >I'm afraid the 85% complete dataset is a contaminant as well. >PDB 2r6s and related entries for E.coli Gab protein have near identical unit >cell parameters. The autoprocessed (?) .mtz file

Re: [ccp4bb] Request for assistance with structure solution

Dear Adewumi I'm afraid the 85% complete dataset is a contaminant as well. PDB 2r6s and related entries for E.coli Gab protein have near identical unit cell parameters. The autoprocessed (?) .mtz file you attached also solves with this E.coli protein. I suppose that if you rerun XDS with the giv

Re: [ccp4bb] Staff position at UCSC

Dear Structural Biology community, Just a friendly reminder that we are still seeking applications for the new staff scientist position (specialist series) available within the Department of Chemistry and Biochemistry at UC Santa Cruz. The scientist will work with users of the Biomolecular Cryo-E

Re: [ccp4bb] iNEXT/3D-Bioinfo AI in structural biology workshop announcement

Dear all, Just a reminder that there are only 10 days left until abstract submission closes. Abstracts will be considered for oral and poster presentations. Please register and send your abstract before 25 April 2024. Website: https://instruct-eric.org/events/ai-approaches-in-structural-biology

Re: [ccp4bb] Parameters for phenix.refine in phenix 1.21

Dear Dennis, As Elke wrote, some parameters were changed... I'm not sure but I think that now definitions are even more sensitive to be specified hierarchically. I would try to this: phenix.refine model.pdb data.mtz params.def where params.def are: data_manager {   fmodel {     xray_data {   

Re: [ccp4bb] Parameters for phenix.refine in phenix 1.21

Hi, If you indeed run phenix.refine --show-defaults=3 you will see that many parameter names have been changed as compared to 1.20, e.g. refinement.input.xray_data.r_free_flags.generate has been replaced by data_manager.fmodel.xray_data.r_free_flags.generate I haven't checked all of your par

Re: [ccp4bb] "pandda.analyse ground_state_datasets=" fails with "Error: No shell partitions generated"

Hi Filippo, try reducing the number of min_build_datasets: pandda.analyse min_build_datasets=20 ... The default value is 30 (you can see this by running pandda.analyse --show-defaults). HTH, Christian Am 12.04.24 um 10:00 schrieb Filippo Vascon: Hi, I am experiencing the same issue runni

Re: [ccp4bb] Request for assistance with structure solution

Good morning Adewumi Adeyeye, I'll look at the problem but I need the raw data. Please upload the *.h5 files from this crystal to some cloud service, and send me the link. Best wishes, Kay Am 12.04.24 um 10:40 schrieb Adewumi Adeyeye: Good day, I am writing to seek your help with resolving

Re: [ccp4bb] "pandda.analyse ground_state_datasets=" fails with "Error: No shell partitions generated"

Hi, I am experiencing the same issue running pandda with 30 ground-state datasets and 26 datasets obtained in the presence of different ligands. As already reported by Christian, the pandda run exits with "No shell partitions generated" error. Does anybody know how to overcome this problem?

Re: [ccp4bb] Resolution discrepancy between MTZ file and Refinement

Hi Thank you Pavel for your input. Venkat On Wed, Apr 10, 2024 at 1:44 AM Pavel Afonine wrote: > Hi, > every time you run phenix.refine it may exclude some reflections from > refinement per Read 1999 (Acta Cryst. (1999). D55, 1759-1764). Usually the > number of reflections omitted ranges from

Re: [ccp4bb] Voidoo cavity volume tool: cavity.lib file

I can see the file here: https://github.com/martynwinn/Uppsala-Software-Factory/tree/master/voidoo Hope that will help. Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent from Proton Mail mobile Original Message On 10 Apr 2024, 12:05, Ankur Kumar Singh wrote: > Dear A

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