Re: [ccp4bb] Workshop on "Temperature in macromolecular crystallo

Dear CCP4 community, of course I got the date wrong: The workshop will happen on Monday, September 23rd 2024... At least you won't have to travel back in time to be able to attend this awesome workshop. Cheers, Dominik Dear CCP4 community, I am excited to announce an upcoming workshop on

Re: [ccp4bb] Studying hydrogen bonding network by neutron diffraction in sample with D2O

Dear Tim, and Arpita and Doeke, Basically structure is not affected (as evidenced by our Fisher and Helliwell database survey in Acta Cryst) but kinetics is affected ie everything is slower in D2O and can thereby be toxic. Greetings John Emeritus Professor John R Helliwell DSc > On 6 Sep 2024,

Re: [ccp4bb] PCD 2024 - Registration extended to Sept 6!

Gentle reminder that registration for PDC 2024 at Cornell U closes today. Register here: https://web.cvent.com/event/f63b17b8-5582-4590-a22a-e6554d119009/register To unsubscribe from the CCP4BB list, click the following li

Re: [ccp4bb] 16th Annual CCP4/APS Crystallographic School (2024) in the US

There are still a few spots available for additional students in our workshop, we have extended the application deadline. If you are interested in joining, please submit your application as soon as possible. Thanks. Charles, Andrey, Garib and Qingping From: C

Re: [ccp4bb] Studying hydrogen bonding network by neutron diffraction in sample with D2O

Hi Doeke, if I remember correctly, D2O is poisonous and bacteria grow with reduced growth rate. The effect of the greater mass may not be totally insignificant. Best, Tim Am 06.09.2024 15:25, schrieb Hekstra, Doeke Romke: Hi Arpita, H and D have the same number of electrons (1). The D nucleus

Re: [ccp4bb] Studying hydrogen bonding network by neutron diffraction in sample with D2O

Hi Arpita, H and D have the same number of electrons (1). The D nucleus has an extra neutron, changing its mass and therefore its vibrational energy levels. That can affect hydrogen bonding patterns, although I would expect the effect to be relatively minor (see e.g. Fisher and Helliwell, Acta

Re: [ccp4bb] Studying hydrogen bonding network by neutron diffraction in sample with D2O

Hello Dr. Mathew, Good day! Thank you for the explanation and for correcting the sloppy mistake for Deuterium electron numbers! Regarding pKa, will there be differences then in the hydrogen bonding patterns between H2O and D2O enriched solutions for pH 6 to 7 range? Best regards, Arpita On Fri

Re: [ccp4bb] Job opportunities at SARomics Biostructures

are a single protein on nextstrain. Nextstrain is now mapping mpox and other emerging infections so useful also in the future. Good luck. Karla Satchell From: CCP4 bulletin board on behalf of Muneer Ahmad Date: Wednesday, September 4, 2024 at 10:45 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re

Re: [ccp4bb] Job opportunities at SARomics Biostructures

Dear All, I'm hoping someone can assist me with accessing or searching for data related to Sara CoV 2 variants. Specifically, I'm interested in the NSP6 protein and would like to identify variants that have been found in different species. If anyone has recommendations for databases, repositories

Re: [ccp4bb] Contact: Hexclude doesn't work?

On Fri, Aug 30, 2024 at 10:33 PM Dr. Kevin M Jude wrote: > > Thanks Jon, these PDB files do have the atom type in column 78. The message > in the output that “Atoms of all types will be used” makes me think that > either my HEXCLUDE keyword is ignored or that I’m using it incorrectly. It's an o

Re: [ccp4bb] Contact: Hexclude doesn't work?

. I’m measuring intermolecular contacts in the ASU. Best wishes Kevin From: Jon Cooper Date: Friday, August 30, 2024 at 1:06 PM To: Dr. Kevin M Jude Cc: CCP4BB Subject: Re: [ccp4bb] Contact: Hexclude doesn't work? Another thing could be if the atom type field is missing in the pdb file. It&#

Re: [ccp4bb] Contact: Hexclude doesn't work?

Another thing could be if the atom type field is missing in the pdb file. It's the optional one on the far right. Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent from Proton Mail Android Original Message On 30/08/2024 20:04, Dr. Kevin M Jude wrote: > I’m trying to

Re: [ccp4bb] Contact: Hexclude doesn't work?

Hello, you could run pdbset with the "exclude hydrogens" card or pdbcur with "delhydrogen". What contacts are you looking for e.g. crystallographic or intramolecular? Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent from Proton Mail Android Original Message On 30/08/

Re: [ccp4bb] CCP49.0 i2run problem

Dear Xin, Sorry, I was wrong in the last reply, the command line argument problem was just bad result of cut and paste from the email. However, I have found a couple of issues which are hopefully addressed in the two attached files. 1) A change to ProvideAsuContents.py to work without a databas

Re: [ccp4bb] CCP49.0 i2run problem

Dear Xin, It appears that the command line arguments are not being parsed properly. I am looking into this right now. I hope to have a fix for you very shortly. Best wishes, Stuart On Fri, 30 Aug 2024 at 06:30, zx2...@connect.hku.hk wrote: > > Hi all, > > I am experiencing some issues with i2r

Re: [ccp4bb] Coot 1.* in CCP4 9

t: Wednesday, August 28, 2024 6:32 PM To: David J. Schuller ; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Coot 1.* in CCP4 9 Hello David, One need not change anything. Just run it from where it is (for now probably best not to override the path while other programs expect coot to be coot

Re: [ccp4bb] Coot 1.* in CCP4 9

y, August 28, 2024 4:54 PM *To:* David J. Schuller ; CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] Coot 1.* in CCP4 9 On 8/28/24 21:53, David J. Schuller wrote: I installed CCP4 9 on Alma 9 Linux. I requested installation of both Coot-0.9.8.95 and Coot-1.1.08. How do I execute the latter?

Re: [ccp4bb] Coot 1.* in CCP4 9

ley Sent: Wednesday, August 28, 2024 4:54 PM To: David J. Schuller ; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Coot 1.* in CCP4 9 On 8/28/24 21:53, David J. Schuller wrote: I installed CCP4 9 on Alma 9 Linux. I requested installation of both Coot-0.9.8.95 and Coot-1.1.08. How do I execute th

Re: [ccp4bb] Coot 1.* in CCP4 9

On 8/28/24 21:53, David J. Schuller wrote: I installed CCP4 9 on Alma 9 Linux. I requested installation of both Coot-0.9.8.95 and Coot-1.1.08. How do I execute the latter? It's in the coot_py3 directory after installation. I believe that Charles has recently made a binary update to 1.1.10.

Re: [ccp4bb] error in error message

During the installation process, at the bottom of the installer: "*Un)istallation in progress ..." istallation => installation === All Things Serve the Beam

Re: [ccp4bb] Multiple binding model in BLI

Dear Mintu, this seems to be quite a particular case. Just a side question before we jump on the octet fitting of the 1:3 model. Do you have any other evidence that your binding partners are binding in 1:3 stoichiometry? Like a biological mechanism for that or any other experimental assay like SEC?

Re: [ccp4bb] Multiple binding model in BLI

Dear Perrakis, Yes, with a 1:3 binding model, I mean stoichiometry with a sequential binding model. The sensogram profile that I am getting clearly suggests that neither it is a 1:1 nor 1:2 stoichiometric binding (at least R-square and RSS values suggest that it might be a 1:3 stoichiometric bindin

Re: [ccp4bb] Multiple binding model in BLI

Dear Chandra, What exactly do you mean by 1:3 or 1:2 binding mode? Is that stoichiometry? Do you need/want to fit a simple binding model with that stoichiometry, a sequential model, or a co-operative model? Graphpad can get you a long way with existing equations when you define the exact probl

Re: [ccp4bb] malware in ccp4?

Hi Andrea, I would suggest that this is probably a false positive down to the way your anti-virus software detects threats. Searching for this particular threat gives several similar examples from even very simple Python code. On my home PC, a scan of the CCP4 installation with Windows Defender

Re: [ccp4bb] Terminating a protein:cmpd covalent adduction using DTT

Dear Yong, I've used both BME and DTT (as well as CoA, Cys, or GSH, etc.) to terminate/exhaust covalent chemistry on Cys residues. It's relatively speaking 'a piece of cake' however one has to keep in mind that if the particular covalent reagent is very highly specific towards a Cys residue in a p

Re: [ccp4bb] Showing Stick Representation In Coot

Thanks Parijat This is exactly what I wanted. Best wishes Firdous On Tue, Aug 27, 2024 at 3:00 PM Parijat Das wrote: > You can use the Draw>Additional representation to do that in coot. > > Regards, > > Parijat > > > On Tue, Aug 27, 2024 at 6:22 PM Firdous Tarique < > kahkashantari...@gmail.c

Re: [ccp4bb] Showing Stick Representation In Coot

That makes sense. Thanks On Tue, Aug 27, 2024 at 2:46 PM Edwin Pozharski wrote: > I don't know the explicit answer to your question, but you can always copy > active site residues into a separate model and use different representation > for that. > > On Tue, Aug 27, 2024 at 8:52 AM Firdous Tari

Re: [ccp4bb] Showing Stick Representation In Coot

I don't know the explicit answer to your question, but you can always copy active site residues into a separate model and use different representation for that. On Tue, Aug 27, 2024 at 8:52 AM Firdous Tarique wrote: > Hello everyone. > > Is there any way to show stick representation of the selec

Re: [ccp4bb] Mini map aide updates

A couple of updates to Mini Map Aide (https://minimapai.de), if anyone likes the idea of looking at maps on mobile phones, although I know many people look at their phones to get away from maps ;- It can now draw symmetry-related molecules based on the space group symbol given in the CRYST1 car

Re: [ccp4bb] Luzzati plots and estimates of coordinate errors in models

Dear Medhanjali,In case of difficulty with the weblink in our J Appl Cryst Online DPI paper that I mentioned, Prof Sekar provides this one:-Diffraction Precision Index (DPI)physics.iisc.ac.inBest wishes,John Emeritus Professor John R Helliwell DScOn 23 Aug 2024, at 21:53, Medhanjali Dasgupta wrot

Re: [ccp4bb] Luzzati plots and estimates of coordinate errors in models

Thank you all for the help! M On Fri, Aug 23, 2024, 1:32 PM Pavel Afonine wrote: > Hi, > > phenix.refine reports it in the log file (coordinate error estimate, not > DPI). > > Pavel > > On Fri, Aug 23, 2024 at 12:45 AM John R Helliwell > wrote: > >> Dear Medhanjali, >> I imagine you would find

Re: [ccp4bb] Luzzati plots and estimates of coordinate errors in models

Hi, phenix.refine reports it in the log file (coordinate error estimate, not DPI). Pavel On Fri, Aug 23, 2024 at 12:45 AM John R Helliwell wrote: > Dear Medhanjali, > I imagine you would find this useful:- > Online_DPI: a web server to calculate the diffraction precision index for > a protein

Re: [ccp4bb] HERCULES 2025 - European School

Hi all, off course there is a mistake in the deadline: it is of course 6 October 2024, not 2023. Best wishes, giorgio On 23/08/2024 11:02, giorgio schiro wrote: *HERCULES 2025**- European School* /Neutron & Synchrotron Radiation Science since 1991/ *2025 **session**:**/9th Marc

Re: [ccp4bb] Luzzati plots and estimates of coordinate errors in models

Dear Medhanjali,I imagine you would find this useful:-Online_DPI: a web server to calculate the diffraction precision index for a protein structurejournals.iucr.orgSee also:-sciencedirect.comBest wishes,John Emeritus Professor John R Helliwell DScOn 22 Aug 2024, at 19:08, Medhanjali Dasgupta wrote

Re: [ccp4bb] CIF file Cannot Open by Coot

Dear All, I sincerely appreciate everyone’s contributions and suggestions—the issue has now been resolved! Following Oliver's instructions, I used the Grad Web Server to obtain the coordinates and restraint files for input, then adjusted the conformation using real-space refinement in Coot. Th

Re: [ccp4bb] current non-commercial version of XDS will expire at end of August

Rather unsurprisingly xia2 will stop working with this version due to some rather inelegant parsing of the INTEGRATE.LP file - the fix is an easy one and will come out in the next-but-one release of dials as the next release was already in progress. An extra couple of spaces and slightly wider c

Re: [ccp4bb] CIF file Cannot Open by Coot

Hi Martin, I hope you are getting on well with one of the restraints for your molecule. But if choose to tweak the restraints to agree with a CSD small molecule structure for BODIPY, then I thought I should let you know that the structure you have downloaded YOWVOW has a high R-factor 10.29% >

Re: [ccp4bb] CIF file Cannot Open by Coot

, Martin From: CCP4 bulletin board on behalf of Jon Cooper <488a26d62010-dmarc-requ...@jiscmail.ac.uk> Date: Monday, August 19, 2024 at 14:24 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] CIF file Cannot Open by Coot ⚠ Caution: External sender I made your cif into a pdb (attached)

Re: [ccp4bb] CIF file Cannot Open by Coot

Dear Martin, My approach to your problem is to download an MOL2 of the small-molecule compound from WebCSD rather than the small-molecule CIF file. MOL2 files have the advantage that both the coordinates and the CCDC-curated bond orders are included in the file. MOL2 files can be read by AceDRG

Re: [ccp4bb] CIF file Cannot Open by Coot

Monday, August 19, 2024 at 6:43 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] CIF file Cannot Open by Coot Dear All, Thank you all for your help. I’ve tried several approaches to input this file, including changing the format to mmCIF, importing it as coordinates, and checking the restr

[ccp4bb] Your restraint file from acedrg Re: [ccp4bb] CIF file Cannot Open by Coot

Dear all, The attached is a restraint file generated by aceDRG, using your 713483.txt as the input file. The latest version of aceDRG, currently not released yet and under the final testing, can generate restraint or dictionary files of ligands using input files in form of small molecule cif

Re: [ccp4bb] CIF file Cannot Open by Coot

> Martin >> >> From: CCP4 bulletin board on behalf of Jon Cooper >> <488a26d62010-dmarc-requ...@jiscmail.ac.uk> >> Date: Monday, August 19, 2024 at 14:24 >> To: CCP4BB@JISCMAIL.AC.UK >> Subject: Re: [ccp4bb] CIF file Cannot Open by Coot >> &

Re: [ccp4bb] CIF file Cannot Open by Coot

On 19/08/2024 14:42, Hu, Wenhao wrote: Dear Jon, Thank you so much for all your effort! I really appreciate it. I’ve just tried to load the files, but unfortunately, it still won’t open and continues to show the error message I’ve attached here. Martin, These are not restraints. They a

Re: [ccp4bb] CIF file Cannot Open by Coot

ay, August 19, 2024 at 14:24 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] CIF file Cannot Open by Coot > > ⚠ Caution: External sender > > I made your cif into a pdb (attached) which looks OK. Maybe worth trying with > that. > > Best wishes, Jon Cooper. > jon.b

Re: [ccp4bb] CIF file Cannot Open by Coot

of Jon Cooper <488a26d62010-dmarc-requ...@jiscmail.ac.uk> Date: Monday, August 19, 2024 at 14:24 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] CIF file Cannot Open by Coot ⚠ Caution: External sender I made your cif into a pdb (attached) which looks OK. Maybe worth trying with that.

Re: [ccp4bb] CIF file Cannot Open by Coot

Dear All, Thank you all for your help. I’ve tried several approaches to input this file, including changing the format to mmCIF, importing it as coordinates, and checking the restraints in the file. However, I am still unable to install the experimental ligand structure into the protein. It see

[ccp4bb] Coot keybinding [was Re: [ccp4bb] libcheck]

On 15/08/2024 17:14, Petr Pachl wrote: [And now this part] Also two off topic questions regarding coot-1 and coot. I tried to transfer some of my keybindings and settings to coot-1 "language". The language is Python (well, one of them is). Unfortunately, there is not a good web resource for

Re: [ccp4bb] libcheck

On 16/08/2024 09:06, Andrea Smith wrote: Dear Paul, Dear Andrea, my molecule can't be too big for libcheck as I used libcheck successfully for molecules of exactly the same size before. I said "too big" - what libcheck actually says is that your molecule is too _complex_ (particularly in

Re: [ccp4bb] libcheck

Dear Paul,   my molecule can't be too big for libcheck as I used libcheck successfully for molecules of exactly the same size before. Now, only one atom is different, but this atom is a heavy metal and therefore Acedrg won't work (also any program I tried to use with SMILES code just gives nons

Re: [ccp4bb] 16th Annual CCP4/APS Crystallographic School (2024) in the US

Please note that we are still accepting applications, interested students are encouraged to apply before the deadline. A draft program is available at the course website. Charles, Andrey and Qingping From: CCP4 bulletin board on behalf of Qingping Xu <292f

Re: [ccp4bb] CIF file Cannot Open by Coot

On 8/15/24 16:08, Hu, Wenhao wrote: Hi Paul, I’ve attached screenshots that show the error message from Coot, along with the contents of the line that the message refers to. Since this CIF file contains experimental data and restrains that would be difficult to rebuild in other software, I’

Re: [ccp4bb] libcheck

On 8/15/24 17:14, Petr Pachl wrote: Hi Paul, so there is not way how to generate cif file when we have precise ideal structure (given from quantum chemistry calculations)? [This part first] That's right (if by that you mean that you (only) have coordinates and elements) - not in the CCP4 Ec

Re: [ccp4bb] libcheck

Hi Paul, so there is not way how to generate cif file when we have precise ideal structure (given from quantum chemistry calculations)? Also two off topic questions regarding coot-1 and coot. I tried to transfer some of my keybindings and settings to coot-1 "language". However as I understand not

Re: [ccp4bb] CIF file Cannot Open by Coot

: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] CIF file Cannot Open by Coot Hi Paul, Thank you for your reply. I’ve attached screenshots that show the error message from Coot, along with the contents of the line that the message refers to. Since this CIF file contains experimental data and

Re: [ccp4bb] libcheck

On 8/15/24 09:01, Andrea Smith wrote: -- Dear all, Dear Andrea, I successfully used libcheck to generate libraries for my ligands a couple of months ago. Now I wanted to use it again and it is giving me an error. Moreover, even though I select COOR Y and LCOOR N, libcheck uses COOR N and

Re: [ccp4bb] CIF file Cannot Open by Coot

solutions to successfully import this file into Coot. Any help you can provide would be greatly appreciated. Best regards, Martin From: Paul Emsley Sent: Thursday, August 15, 2024 3:09 PM To: Hu, Wenhao ; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] CIF file Cannot

Re: [ccp4bb] CIF file Cannot Open by Coot

On 8/15/24 15:01, Tang, Jiazhi wrote: -- It happens sometimes when you can not open the downloaded cif files properly. One solution is to draw the compound yourself in Chemdraw, copy the smiles and generate the cif in Elbow within the phenix suit or other ligand software within ccp4. Just

Re: [ccp4bb] CIF file Cannot Open by Coot

It happens sometimes when you can not open the downloaded cif files properly. One solution is to draw the compound yourself in Chemdraw, copy the smiles and generate the cif in Elbow within the phenix suit or other ligand software within ccp4. Just be careful if the ligand contains ions, which c

Re: [ccp4bb] CIF file Cannot Open by Coot

On 8/15/24 14:44, Martin Hu wrote: Dear [Recipient's Name], Dear [Correspondent's Name], I have downloaded a CIF file of a ligand of interest directly from WebCSD, which was originally obtained from experimental crystallography research, and attempted to import it into Coot. However, Coot

Re: [ccp4bb] DLS/CCP4 data analysis workshop 2024

Hi folks, Here's a reminder that applications are open for the 11th joint Diamond-CCP4 MX workshop, and remain open for just over one more month. But with holidays, conferences and all the other distractions of summer, why not get your application in sooner rather than later? :) Best wishes, -- D

Re: [ccp4bb] CCP4 database transfer to new computer

Never mind. I figured it out. From: CCP4 bulletin board On Behalf Of Poland, Brad Sent: Thursday, August 8, 2024 2:39 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [EXTERNAL] [ccp4bb] CCP4 database transfer to new computer Hi all. Does anyone know how to transfer my current CCP4 database to a new comp

Re: [ccp4bb] Phenix real space refine getting lost ...

A 2 gigabyte map is a very big one. Maybe it needs resampling or cropping down to something in the megabyte range. Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent from Proton Mail Android Original Message On 07/08/2024 09:24, Klemens Wild wrote: > Dear community

Re: [ccp4bb] Richard Pauptit, 1954-2024

That's a good obituary, but I don't think it quite communicates how funny - and quirky - Richard was. I remember him once giving an introduction to an invited speaker that went on for around 25 mins. I know he had ambitions to become a rock star in his 60s - did he also want to be a stand-up comi

Re: [ccp4bb] Three years postdoc position at University of Kent

Dear all, As it is the holiday season, I have extended the deadline for the 3-year postdoc position in my lab until 21st August. Please see the link to apply and share it if you know someone who would be interested. https://www.jobs.ac.uk/job/DJA996/research-associate Best wishes, Mohinder

Re: [ccp4bb] Off topic: Nobel prize stats

Forgot to credit the Nobel Prize website :The Nobel Prize in Chemistry 1946nobelprize.org-BWL To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

Re: [ccp4bb] Off topic: Nobel prize stats

The Nobel Prize in Chemistry 1946 James Batcheller Sumner “for his discovery that enzymes can be crystallized” Prize share: 1/2 John Howard Northrop and Wendell Meredith Stanley "for their preparation of enzymes and virus proteins in a pure form" Prize share 1/2 jointly Thought it might be w

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

stal. Perhaps I'm way off on this > one > > Best wishes, > Reza > -- > *From:* CCP4 bulletin board on behalf of John R > Helliwell > *Sent:* 02 August 2024 11:47 AM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [EXTERNAL] Re: [ccp4

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

way off on this one Best wishes, Reza From: CCP4 bulletin board on behalf of John R Helliwell Sent: 02 August 2024 11:47 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [EXTERNAL] Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold e

Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

, Vaheh wrote:    Yes, it is and I like the definition of shared “trash bin”. It    will have more physical meaning if we can separate those    contributions into separate bins.    Vaheh    *From:* Pavel Afonine    >    *Sent:* Tuesday, July 30, 2024 1:51 PM    *To:* Ogan

Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

red “trash bin”. It will have >> more physical meaning if we can separate those contributions into separate >> bins. >> >> >> >> Vaheh >> >> >> >> >> >> >> >> *From:* Pavel Afonine >> *Sent:* Tuesday, July 30, 2024 1:5

Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

physical meaning if we can separate those contributions into separate bins. Vaheh *From:* Pavel Afonine *Sent:* Tuesday, July 30, 2024 1:51 PM *To:* Oganesyan, Vaheh *Cc:* CCP4BB@jiscmail.ac.uk *Subject:* Re: [ccp4bb] How high a B factor is too high to assume

Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

It will have > more physical meaning if we can separate those contributions into separate > bins. > > > > Vaheh > > > > > > > > *From:* Pavel Afonine > *Sent:* Tuesday, July 30, 2024 1:51 PM > *To:* Oganesyan, Vaheh > *Cc:* CCP4BB@jiscmail.ac.uk

Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

Yes, it is and I like the definition of shared “trash bin”. It will have more physical meaning if we can separate those contributions into separate bins. Vaheh From: Pavel Afonine Sent: Tuesday, July 30, 2024 1:51 PM To: Oganesyan, Vaheh Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] How

Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

t; > > > Thank you. > > > > *Vaheh Oganesyan, Ph.D.* > > *R&D* *| Biologics Engineering* > > One Medimmune Way, Gaithersburg, MD 20878 > > T: 301-398-5851 > > *vaheh.oganes...@astrazeneca.com * > > > > > > > > *From:* Pavel Afonine

Re: [ccp4bb] Questions about PanDDA modelling and refining

**Question:** After step 11 in my pandda-export folder I have the following files: File name: Remarks: 1 ensemble-model.log 2 ensemble-model.pdb Contains both bound and ground-state 3 ensemble-model-restraints.log 4 ensemble-model-restraints.phenix.params 5 ensemble-model

Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

Vaheh Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era? From this perspective, all refinable atomic model parameters can be viewed as trash bins, with the size of these bins being proportional to the amount

Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

“That which is not restricted will take its liberties” (Wayne Hendrickson) https://www.sciencedirect.com/science/article/pii/S0969212601001873 in turn, apparently from one of the older CCP4 workshops P.A. Machin, J.W. Campbell, M. Elder (Eds) Refinement of Protein Structures, SERC Daresbury Labor

Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

ne Medimmune Way, Gaithersburg, MD 20878 > > T: 301-398-5851 > > *vaheh.oganes...@astrazeneca.com * > > > > > > > > *From:* CCP4 bulletin board * On Behalf Of *James > Holton > *Sent:* Tuesday, July 30, 2024 10:35 AM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* R

Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

UK Subject: Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era? How high B factors can go depends on the refinement program you are using. In fact, my impression is that the division between the "let the B factors blow up" and "de

Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

The reason why phenix.refine allows B factors to grow until they fit the map is that it uses restraints that do not only require the similarity of B factors of covalently bonded atoms, but rather the similarity of B factors of atoms located within a sphere of radius R (around 5Å). This is to accoun

Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

If it hasn't already been mentioned, I would humbly like to remind everyone that a high B-factor on an atom causes it to have a small or negligible contribution to a fourier transform. Therefore, beware that modelling atoms with high B-factors could be introducing model bias by inserting atoms tha

Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

How high B factors can go depends on the refinement program you are using. In fact, my impression is that the division between the "let the B factors blow up" and "delete the unseen" camps is correlated to their preferred refinement program. You see, phenix.refine is relatively aggressive with

Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

Thank you all for your thoughtful answers. I'll stick to the crystallographic data and model as much as I can with reasonable occupancy and B factors, even if the result is a truncated model. I don't believe in the zero occupancy trick either. I just thought the PDB was more flexible these days,

Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

Hello Javier, Placing atoms implies that you know they are present somewhere (possibly with some uncertainty on exactly where), but setting their occupancies to zero implies that you know they are nowhere at all. This is a paradox. I think atoms with zero occupancy make no sense in a final depo

Re: [ccp4bb] How high a B factor is too high to assume a loop is in place, in the AlphaFold era?

Javier, Flexible loops may be better modeled with ensembles of N models, meaning the occupancy of each-one would be 1/N, and the map contours to visualize them should be chosen as 1/N sigma (not 1 sigma). While model prediction tools such as AlphaFold are helpful, they don't suddenly lift the requ

Re: [ccp4bb] Off topic - fluorescence plate reader in cold room or cold box

Dear Markus, I've had to solve this exact issue in the past. Putting a 'simple' (nothing is simple these days, everything has some kind of AI or other evil gnomes in it) spectrofluorimeter into the cold room *should* be OK. Caveat #1: I don't know if this will work with your specific device Cavea

Re: [ccp4bb] Presence of negative density in Sim Omit map

lletin board on behalf of John Bacik <b45abf420e1f-dmarc-requ...@jiscmail.ac.uk> Sent: Friday, July 26, 2024 11:18 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Presence of negative density in Sim Omit map  | | You don't often get email from b45abf420e1f-dmarc-requ...@jis

Re: [ccp4bb] Off topic - fluorescence plate reader in cold room or cold box

I think you are right, in the final equilibrium all the moisture would condense on the (evaporator?) coils, and there should be provision for them to drip into a reservoir outside. However each time the door opens and humid air is admitted, there will be condensation everywhere. If you leave th

Re: [ccp4bb] Presence of negative density in Sim Omit map

AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Presence of negative density in Sim Omit map You don't often get email from b45abf420e1f-dmarc-requ...@jiscmail.ac.uk. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> [EXTERNAL SENDER - PROCEED CAUTIOUSLY] Hi

Re: [ccp4bb] Presence of negative density in Sim Omit map

Green StreetUniversity of GeorgiaAthens, GA 30602Tel: (706) 583 0303From: CCP4 bulletin board on behalf of John Bacik <b45abf420e1f-dmarc-requ...@jiscmail.ac.uk> Sent: Thursday, July 25, 2024 12:21 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Presence of negative density in

Re: [ccp4bb] Presence of negative density in Sim Omit map

nt: 25 July 2024 07:10 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Presence of negative density in Sim Omit map External Sender: Use caution. Hmm - I cant quite understand your map - that density is not for the lysine ? It looks like a well ordered PHE contoured at quite a high level?As

Re: [ccp4bb] Presence of negative density in Sim Omit map

6a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> Sent: 25 July 2024 07:10 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Presence of negative density in Sim Omit map External Sender: Use caution. Hmm - I cant quite understand your map - that density is not for the lysine ? It looks like a well ordered PHE c

Re: [ccp4bb] High clash score in refinement of cryoEM structure

To improve the clashscore you could try increasing the value of the nonbonded_weight parameter, starting at 1000 (which I understand at one time was the default in phenix.refine, but recently for me already gives a huge decrease in clashscore). Since this will be avoiding clashes at the expense

Re: [ccp4bb] Presence of negative density in Sim Omit map

I also noticed one residue looks like a Phe and there is another that may be a Lys but not a very good view of it. When doing simulated annealing its not outside the realm of possibility that it will introduce errors in other parts of the model that could in theory explain the additional red d

Re: [ccp4bb] Presence of negative density in Sim Omit map

Hmm - I cant quite understand your map - that density is not for the lysine ? It looks like a well ordered PHE contoured at quite a high level? As Edward suggests - if you omit a well ordered feature the resultant difference maps often show high positive density and a surrounding complementary "sag

Re: [ccp4bb] Presence of negative density in Sim Omit map

Does your difference map have mean value ~zero (over 1 ASU or cell)? If maps are constructed by Fourier transform without the 0 0 0 reflection, they have mean of zero (because the mean of a sinusoid over one period is zero). That means that any time you add positive (difference) density, which

Re: [ccp4bb] Presence of negative density in Sim Omit map

Hi Renu, you may try using a Polder omit map for the region rather than a simulated annealing map. You may also check if the red density is due to a symmetry related molecule that is not modeled well. Hope it helps. JP On Tuesday, July 23, 2024 at 04:50:00 PM CDT, Renuka Kadirvelraj

Re: [ccp4bb] Off topic: Nobel prize stats

Thank you all for useful links, slides and thoughtful comments. I completely agree with Mark's comment that it is difficult to quote a single number. Precisely for the reasons he mentioned. The link to PDB, https://pdb101.rcsb.org/learn/other-resources/structural-biology-and-nobel-prizes seems the

Re: [ccp4bb] Ccp4i2 execution problem

Dear Maria, Could you please try deleting the file /home/msa/CCP4I2_PROJECTS/TRT84A11C/DATABASE.db.xml ? I think that this file is corrupted (empty) and that this is causing the problems. Best wishes, Stuart McNicholas On Wed, 24 Jul 2024 at 12:22, Marian Oliva wrote: > > Dear all, > > Since

Re: [ccp4bb] Question about micro RNA structures

Hi Careina, This recent publication evaluate several methods, might be a useful resource. https://doi.org/10.1093/nar/gkae541 And a webtool: https://doi.org/10.1093/nar/gkae356 Best regards, Tales On Tue, Jul 23, 2024 at 10:02 AM careinaedgo...@yahoo.com < 02531c126adf-dmarc-requ...@jiscmai

  1   2   3   4   5   6   7   8   9   10   >