Re: [ccp4bb] Automated refinement convergence

, January 19, 2024 2:10:42 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Automated refinement convergence I, too, love the smell of cooking (or cooked?) jobs in the morning. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National

Re: [ccp4bb] Automated refinement convergence

I, too, love the smell of cooking (or cooked?) jobs in the morning. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : nwmoria...@lbl.gov Web : CCI.LBL.gov ORCID :

Re: [ccp4bb] Automated refinement convergence

Hey there Robert, Refmac has a keyword called "kill" that I think is what you are looking for.  It is documented here: https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/refmac/refmac_keywords.html   You can specify a conditional exit based on R factor, etc. Or you can just create a

Re: [ccp4bb] Automated refinement convergence

Hi Robert, I see your point but extending the number of cycles to reach convergence has a big risk of going into infinite loops (which you point out). In the case of Refmac stopping early is not really needed as it is very fast anyway; a few unnecessary cycles won't take that long. Generally

Re: [ccp4bb] Phenix version 1.21 released

For anyone who is confused: Unfortunately, the link given here (https://phenix-online.org/download/) says that the latest release is 1.19.2-4158! That’s very odd because the same URL without the trailing slash (https://phenix-online.org/download) gets to a different page with the right

Re: [ccp4bb] Resolution Discrepancy in Data Set

Hi Liliana, a few things to consider: 0) There is a Phenix mailing list for Phenix specific questions (phenixbb); 1) Bin completeness depends on (obviously) how binning is done (number of reflections per bin or number of bins or binning in d^2 or d^3 spacing or log-binning etc etc etc) -- all

Re: [ccp4bb] Resolution Discrepancy in Data Set

Hi Liliana, Two things leap out at me when I look at your data summary. (1) Your data probably do not go to 1.77Å. The CC1/2 in your outer shell is below any of the usual thresholds. There are discussions to be had about what the threshold is, but normally CC1/2 values of 0.5 or sometimes 0.3

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

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

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

2024 4:51 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [EXTERNAL] 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<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac

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

rminal domains is not just low, but > essentially zero. And as Basil points out, a map-model FSC of 22.3A at 0.5. > So I think you need to look again at the initial fitting. > > > > HTH > > Martyn > > > > > > *From:* CCP4 bulletin board *On Behalf Of *Basil

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

is not just low, but essentially zero. And as Basil points out, a map-model FSC of 22.3A at 0.5. So I think you need to look again at the initial fitting. HTH Martyn From: CCP4 bulletin board On Behalf Of Basil Greber Sent: 10 January 2024 08:12 To: ccp4bb Subject: Re: [ccp4bb] Poor

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

is not just low, but essentially zero. And as Basil points out, a map-model FSC of 22.3A at 0.5. So I think you need to look again at the initial fitting. HTH Martyn From: CCP4 bulletin board On Behalf Of Basil Greber Sent: 10 January 2024 08:12 To: ccp4bb Subject: Re: [ccp4bb] Poor

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

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

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

mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Andrew Gnann mailto:adgn...@gmail.com>> Sent: Thursday, January 4, 2024 8:29 AM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> mailto:CCP4BB@JISCMAIL.AC.UK>> Subject: [External] Re: [ccp4bb] alternatives to Consurf

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?

board on behalf of Pavel Afonine Sent: Sunday, January 7, 2024 11:28 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group? You don't often get email from pafon...@gmail.com. Learn why this is important<https://aka

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

frequently. > Thanks again for the stats and description. > cheers, tom > > ---------- > *From:* Robbie Joosten > *Sent:* Sunday, January 7, 2024 8:24 AM > *To:* Tom Peat ; CCP4BB@JISCMAIL.AC.UK < > CCP4BB@JISCMAIL.AC.UK> >

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

, January 7, 2024 8:24 AM To: Tom Peat ; CCP4BB@JISCMAIL.AC.UK Subject: RE: [ccp4bb] Can Refmac5 refine temperature factor residue by group?   [You don't often get email from robbie_joos...@hotmail.com. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] Hi Tom

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

ent starting points for most. Cheers, Robbie > -Original Message- > From: Tom Peat > Sent: Saturday, January 6, 2024 21:42 > To: CCP4BB@JISCMAIL.AC.UK; Robbie Joosten > > Subject: Re: [ccp4bb] Can Refmac5 refine temperature factor residue by > group? > > It appear

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

gt; >> -Original Message----- >> From: Tom Peat >> Sent: Saturday, January 6, 2024 21:42 >> To: CCP4BB@JISCMAIL.AC.UK; Robbie Joosten >> >> Subject: Re: [ccp4bb] Can Refmac5 refine temperature factor residue by >> group? >> >> It app

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

eeded. I won't claim that this is the best protocol for each of the cases, but I guess they are decent starting points for most. Cheers, Robbie > -Original Message- > From: Tom Peat > Sent: Saturday, January 6, 2024 21:42 > To: CCP4BB@JISCMAIL.AC.UK; Robbie Joosten > > Su

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

as that should reduce the number of parameters being refined. Best regards, tom From: CCP4 bulletin board on behalf of Robbie Joosten Sent: Saturday, January 6, 2024 8:13 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Can Refmac5 refine temperature factor

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

milar functions like one_adp_group_per_residue or two_adp_groups_per_residue in Phenix?    Any help would be highly appreciated!   chenzhonghao...@163.com  From: Eleanor DodsonDate: 2024-01-05 23:48To: CCP4BBSubject: Re: [ccp4bb] Can Refmac5 refine temperature factor residue by group?Hmmm -  I am not

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

:48 To: CCP4BB Subject: 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

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

MAIL.AC.UK Subject: 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 a

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 ?

. ND10.214A Dallas, TX 75390-8816 diana.tomch...@utsouthwestern.edu (214) 645-6383 (phone) (214) 645-6353 (fax) From: CCP4 bulletin board on behalf of Dr. Kevin M Jude Sent: Friday, January 5, 2024 1:51 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] How to make

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: [ccp4bb

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

logy & Biophysics University of Iowa 51 Newton Rd, 4-611 BSB Iowa City, IA 52242 319-335-7671 From: CCP4 bulletin board on behalf of Andrew Gnann Sent: Thursday, January 4, 2024 8:29 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [External] Re: [ccp4bb] alternatives to Consurf se

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¶

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

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

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

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! |

Re: [ccp4bb] what is isomorphous?

ame dehydration state, the data merged with 'typical' statistics of lysozyme (like 3-4%). James will have the details that I do not. cheers, tom *From:* CCP4 bulletin board on behalf of Randy John Read *Sent:* Thursday, December 21, 2023 10:53 PM *To:* CCP4BB@JISCMAIL.

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

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

nd corrected and there is likely to be some hydrogen on > phosphate ions found in crystal structures. > Happy holidays to all, tom > -- > *From:* Dale Tronrud > *Sent:* Monday, December 25, 2023 8:52 PM > *To:* Tom Peat ; CCP4BB@JISCMAIL.AC.UK <

Re: [ccp4bb] Query on density fitting to phosphate

d there is likely to be some hydrogen on > phosphate ions found in crystal structures. > Happy holidays to all, tom > -- > *From:* Dale Tronrud > *Sent:* Monday, December 25, 2023 8:52 PM > *To:* Tom Peat ; CCP4BB@JISCMAIL.AC.UK < > CCP4BB@JISCMAIL.AC.U

Re: [ccp4bb] Query on density fitting to phosphate

From: Dale Tronrud Sent: Monday, December 25, 2023 8:52 PM To: Tom Peat ; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Query on density fitting to phosphate [You don't often get email from de...@daletronrud.com. Learn why this is important at https://aka.ms

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

lion which are failing. Cryosparc is not a problem either. > Thanks > Dhiraj > From: Takanori Nakane > Sent: Friday, December 22, 2023 5:35 PM > To: Srivastava, Dhiraj > Cc: CCP4BB@JISCMAIL.AC.UK > Subject: [External] Re: [ccp4bb] Relion issue with MPI > > Hi, > >

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

, December 22, 2023 5:35 PM To: Srivastava, Dhiraj Cc: CCP4BB@JISCMAIL.AC.UK Subject: [External] 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

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

Re: [ccp4bb] what is isomorphous?

, 2023 10:53 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] what is isomorphous? [You don't often get email from rj...@cam.ac.uk. Learn why this is important at https://aka.ms/LearnAboutSenderIdentification ] I think we’ve strayed a bit from Doeke’s original question involving crystals A, B

Re: [ccp4bb] what is isomorphous?

o be similar. Best wishes to all. Doeke -Original Message- From: CCP4 bulletin board On Behalf Of Randy John Read Sent: Thursday, December 21, 2023 6:53 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] what is isomorphous? I think we’ve strayed a bit from Doeke’s original question invo

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?

From: CCP4 bulletin board On Behalf Of Marius Schmidt Sent: Wednesday, December 20, 2023 14:36 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] what is isomorphous? According to Jon, Isomorphous Replacement ALWAYS works, because it is only supposed to be isomorphous. Isomorphous difference

Re: [ccp4bb] what is isomorphous?

10-dmarc-requ...@jiscmail.ac.uk> Sent: Wednesday, December 20, 2023 4:21 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] what is isomorphous? Unless you have a degree in maths, the IUCr's "Little Dictionary of Crystallography" by A. Authier and G. Chapuis (2014) defies comprehension

Re: [ccp4bb] what is isomorphous?

My apologies my second paragraph was badly wrong. What Ian Tickle said in 2008 (and to save him writing it all again ;-) is: "In general crystallographic usage 'isomorphous' refers to the similarity of crystal structures, i.e. same arrangement of atoms in the a.u. and the same symmetry. So

Re: [ccp4bb] what is isomorphous?

Unless you have a degree in maths, the IUCr's "Little Dictionary of Crystallography" by A. Authier and G. Chapuis (2014) defies comprehension on this matter (it's all to do with set / group theory, I think, and there are many more morphisms covered in about 6 pages: homo, epi, mono, endo,

Re: [ccp4bb] Query on density fitting to phosphate

etin board on behalf of Arpita Goswami Sent: Wednesday, December 20, 2023 3:53 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Query on density fitting to phosphate You don't often get email from bt.arp...@gmail.com. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> Hi

Re: [ccp4bb] Query on density fitting to phosphate

Hi, Thank you all for the replies. As suggested, this is the residual positive difference density after putting water and refinement in coot-refmac: https://i.postimg.cc/DfbrbDZm/Screenshot-from-2023-12-19-16-39-38.png Does this look like any of the three phosphate ions? Two sides are similar,

Re: [ccp4bb] contrast missing issue

os7 logfiles in the attachment. Your Best, Zhihong xin From: Kay Diederichs Date: 2023-12-19 02:35:50 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] contrast missing issue>Dear Zhihong Xin, am I understanding correctly that you get very different output, using CentOS7 versus us

Re: [ccp4bb] extra Fo-Fc density in two Cysteines

We have seen quite a few of these. Oxidation of S. Mostly in our case a result if reaction with beta-mercaptoethanol.. Jan On Mon, Dec 18, 2023 at 6:14 PM Liliana Margent < lmarg...@gradcenter.cuny.edu> wrote: > Hi there, We’ve been having an issue in trying to clear regions of Fo-Fc > density

Re: [ccp4bb] contrast missing issue

Dear Kay, Thank you for your responses. Please find the window10 and Centos7 logfiles in the attachment. Your Best, Zhihong xin From: Kay Diederichs Date: 2023-12-19 02:35:50 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] contrast missing issue>Dear Zhihong Xin, > >am I unde

Re: [ccp4bb] solvent mask for partial ligands, addendum

Hi Gottfried, I was wondering what happens if you make a Polder omit map for the HEPES? I am also curious, if the extra positive density is for missing bulk solvent with ligand of occupany 0.5, do you observe the density with ligand present at 0.5 occupancy to be more diffuse than with no

Re: [ccp4bb] contrast missing issue

Dear Zhihong Xin, am I understanding correctly that you get very different output, using CentOS7 versus using Windows10, for the exact same calculation? In that case, it seems surprising (to me at least) that it is only the contrast value that is affected. There is not much to work on, from

Re: [ccp4bb] extra Fo-Fc density in two Cysteines

Hello, you seem to have positive difference density for the Cys sulphur/sulfur atom. It would be worth checking it's occupancy. Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent from Proton Mail mobile Original Message On 18 Dec 2023, 17:03, Liliana Margent wrote: >

Re: [ccp4bb] extra Fo-Fc density in two Cysteines

Hello, this looks like beta-mercaptoethanol adduct through a S-S bond. See [ https://pubmed-ncbi-nlm-nih-gov.insb.bib.cnrs.fr/12421561/ | The crystal structure of the Epstein-Barr virus protease shows rearrangement of the processed C terminus. ] Buisson M, Hernandez JF, Lascoux D, Schoehn

Re: [ccp4bb] extra Fo-Fc density in two Cysteines

Difficult to be sure from a single angle pic but I would suggest Cys oxidation. There is an important 20 years old paper (see below) on Cys oxidation in a tyrosine phosphatase (like yours) Best Roberti] Nature *

Re: [ccp4bb] extra Fo-Fc density in two Cysteines

Hi Liliana, May be it would be good to know if this adduct was formed during crystallization or protein was modified prior to crystallization. One could consider performing a protease digestion, followed by LC-MS/MS to determine the molecular weight of the adduct and then work backwards to

Re: [ccp4bb] Query on density fitting to phosphate

Have you tried sodium? From: CCP4 bulletin board On Behalf Of Arpita Goswami Sent: Sunday, December 17, 2023 11:47 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Query on density fitting to phosphate Dear All, Hope you all are doing well. The density in the image (in link below) is fitted

Re: [ccp4bb] Query on density fitting to phosphate

Dear Arpita, The hydrogens on phosphate, just like sodium and potassium, will come off the oxygens in water. To be more explicit, you don't have mono- or di-hydrogen phosphate in water (except transiently), you just have phosphate, depending somewhat on the pH of course. At 2.5 Angstrom

Re: [ccp4bb] Query on density fitting to phosphate

Hello, it doesn't look like a phosphate very much, to be honest, and being so close to the carboxylate suggests it isn't. Is there any chance that it is an alternative conformation of the Arg side chain? If you model it as water, is there residual positive difference density? Best wishes, Jon

Re: [ccp4bb] [EXTERNAL] [ccp4bb] Viewing samples under liquid nitrogen

Clear Pyrex beaker/dish/bowl filled with liquid nitrogen on the microscope stand. Place pin on a wand and hold at an angle in the bath. Probably best to do when the safety-officer is not around. Can you mount on a home source with the cryo-stream on? Best, Dan From: CCP4 bulletin board on

Re: [ccp4bb] [pe...@leadszone.live: CCP4 Study Weekend-2024] (fwd)

Well - are any of our names worth pricing?! Very very suspect.. Eleanor On Fri, 15 Dec 2023 at 14:41, Robbie Joosten wrote: > Hotel booking scammers for instance. > > Cheers, > Robbie > > On 15 Dec 2023 15:34, Frank von Delft wrote: > > I mean, who'd actually want that list anyway?! > > On

Re: [ccp4bb] [pe...@leadszone.live: CCP4 Study Weekend-2024] (fwd)

Hotel booking scammers for instance. Cheers,RobbieOn 15 Dec 2023 15:34, Frank von Delft wrote:I mean, who'd actually want that list anyway?! On 15/12/2023 13:23, Gerard Bricogne wrote: > Dear all, > >   I just received this a moment ago, and it looks most suspicious. Can > any action

Re: [ccp4bb] [pe...@leadszone.live: CCP4 Study Weekend-2024] (fwd)

I mean, who'd actually want that list anyway?! On 15/12/2023 13:23, Gerard Bricogne wrote: Dear all, I just received this a moment ago, and it looks most suspicious. Can any action be taken, other than warn people not to follow up? Best wishes, Gerard - Forwarded

Re: [ccp4bb] RMSF calculation in pymol

Dear Dhiraj, What is the script? What is the error? Please send them to us. We may be able to fix the script - it is not easy to help without knowing the script and error. Cheers, Martin On Thu, 2023-12-14 at 21:41 +, Srivastava, Dhiraj wrote: > Hi All >     sorry for off topic

Re: [ccp4bb] RMSF calculation in pymol

Hi Not PyMol, but relevant to the ccp4BB - why not try “gesamt” for this? e.g. for the nmr structure 1q01 - > gesamt pdb1q01.ent -s '/1/A' pdb1q01.ent -s '/2/A' pdb1q01.ent -s '/3/A' > -r0=1.5 -sigma=1.0 -o 1q01_cluster.cif -o-cf -a align.seq gives me an alignment of the first three models

Re: [ccp4bb] RMSF calculation in pymol

I don’t have one for pymol, but there is a function in prody for it. Best wishes James On 14 Dec 2023, at 21:41, Srivastava, Dhiraj wrote:  Hi All sorry for off topic question. does anyone have script for rmsf calculation of multistate pdb file in pymol? There used to be a

Re: [ccp4bb] solvent mask for partial ligands, addendum

You guessed right.  Bulk solvent does not get a localized "occupancy". It is set to "0" anywhere near modeled atoms, even if those atoms have an occupancy of 0.01.  Yes, it might seem sensible to do "occupancy" for the bulk, but in practice it is tricky.  I tried my hand at a "fuzzy" bulk

Re: [ccp4bb] solvent mask for partial ligands

Dear Gottfried Assuming your modelling is correct you can always try occupancy refinement of your ligand (or simply test alternative values). Maybe that will help. You can also play with bulk solvent mask parameters. Keywords (both occupancy and mask parameters) can be found in

Re: [ccp4bb] Can ALF3OH mimic the transition state?

There is also discussion about this for chaperonins such as CCT and GroEL. It may be that beryllium fluoride works better. Best wishes James > On 12 Dec 2023, at 05:30, Matthew BOWLER wrote: > > Dear Jinyu, > we observed exactly this in PGK - see https://doi.org/10.1021/ja100974t where > we

Re: [ccp4bb] Can ALF3OH mimic the transition state?

Dear Jinyu, we observed exactly this in PGK - see https://doi.org/10.1021/ja100974t where we confirmed it by both crystallography and 19F NMR In fact ALF3 does not exist as a trigonal bipyramid - all cases where this geometry is observed are likely MgF3 that does adopt this geometry and will

Re: [ccp4bb] Alternatives to X

Are there any structural biology (or similiar) discord servers out there? Natalie *Dr. Natalie J. Tatum* Research Associate Lead Academic in Structural Computational Chemistry Cancer Research Horizons Newcastle Drug Discovery Unit Newcastle University On Wed, 6 Dec 2023 at 19:33, Stéphane

Re: [ccp4bb] Alternatives to X

Why not give Researchgate a chance?BestStephane BetziPhDCNRS researcher CRCM, Marseille FranceLe 6 déc. 2023 19:47, John Gross a écrit :Below are Bluesky codes for those that want to create an account and experiment with that platform.NB-once a code

Re: [ccp4bb] Alternatives to X

Below are Bluesky codes for those that want to create an account and experiment with that platform. NB-once a code is used it will no longer work, so forgive me if someone takes the code(s) before you can get to it. I agree with what has been said and am still trying to find the right platform

Re: [ccp4bb] The experiment is still very much needed (though AlphaFold helps a lot)

Dear Tim, I remain enthusiastic about the value to my work, research and service to the crystallographic community, in what I learn using twitter ie X. I also appreciate the learned feedback I get to what I share in my tweets. I do not use X to share my opinions on “wider issues”. I have tried

Re: [ccp4bb] Alternatives to X

9793-7339> | Google Scholar <https://scholar.google.co.uk/citations?user=DRKG5KwJ> From: Robbie Joosten Sent: 06 December 2023 07:56 To: David Briggs ; CCP4BB@JISCMAIL.AC.UK Subject: RE: [ccp4bb] Alternatives to X External Sender: Use cau

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