Re: [ccp4bb] Help crystalizing protein

Hello Marco, I know you said you would prefer keeping the full-length protein. But have you looked at an AlphaFold2 prediction? Ideally of the monomer and homo- and hetero-dimers you mentioned. It’s often a good guide for construct design. If you see a lot of “spaghetti” with low pLDDT, that mi

Re: [ccp4bb] Help crystalizing protein

Adding to the excellent advice offered by others: 1. Try to purify a unique oligomeric state: mixtures of homodimers, heterodimers etc are less likely to crystallize. Collect a narrow peak off a size exclusion column. 2. Try adding mono- or dinucleotides during crystallization, with or without d

Re: [ccp4bb] Help please

ARES PRIVATE This is terrific. Many thanks Derek. Yes indeed this is what we are looking for chandra From: Derek Logan Sent: Monday, January 13, 2025 4:36 AM To: Chandra Verma Cc: CCP4BB@jiscmail.ac.uk Subject: Re: [ccp4bb] Help please CAUTION: External

Re: [ccp4bb] Help please

Hi Chandra, If I understand correctly, you are looking for structures in which two ATP molecules have been seen to interact directly with each other. This has been observed several times in the ATP-cone domains of the enzyme ribonucleotide reductase (RNR) and its associated transcription factor

Re: [ccp4bb] Help crystalizing protein

I'll second limited proteolysis with chymotrypsin. Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Sent from Proton Mail Android Original Message On 10/01/2025 07:02, Jeroen Mesters wrote: > Hi, > > three things come to mind besides what has been mentioned already > > - m

Re: [ccp4bb] Help crystalizing protein

stabilising your protein (if this is an issue). Cheers, Sara From: CCP4 bulletin board on behalf of Marco Bravo <d0eb7bee83ae-dmarc-requ...@jiscmail.ac.uk> Sent: 10 January 2025 01:00 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Help crystalizing protein C

Re: [ccp4bb] Help crystalizing protein

Hi, three things come to mind besides what has been mentioned already - many proteins that have an affinity for nucleic acids actually love sulfates or phosphates… And yes, phosphates may lead to salt crystals at higher pH values but this should not stop you a priori from screening with the sam

Re: [ccp4bb] Help crystalizing protein

Hi Marco, I wonder what is the highest concentration of the protein you've tried. Once I worked with a protein which would crystallize only if it was concentrated into a jell... Good luck! Nukri On Thu, Jan 9, 2025 at 7:01 PM Marco Bravo < d0eb7bee83ae-dmarc-requ...@jiscmail.ac.uk> wrote: > H

Re: [ccp4bb] Help crystalizing protein

Hello and you are welcome. - You can add things after you purify, or buffer exchange on a concentrator - sometimes one residue change makes a difference, removing 20 is almost certainly going to change things, maybe for the better - fusion of guest domains was mentioned with the intent of crysta

Re: [ccp4bb] Help please

https://pmc.ncbi.nlm.nih.gov/articles/PMC3901029/ One that comes to mind... not sure if this is what you are looking for. Artem On Thu, Jan 9, 2025, 20:23 Chandra Verma < 64fcc5b1f9c3-dmarc-requ...@jiscmail.ac.uk> wrote: > ARES PRIVATE > > Are there examples where anyone has seen two ATP mo

Re: [ccp4bb] Help crystalizing protein

Hello Marco This is a classic case of protein that just won't behave :) Nil desperandum! Without rewriting several large ish chapters on protein crystallization, let's review your options from a bird's eye view: 0. Modify crystallization setup This is something that you already have explored co

Re: [ccp4bb] Help crystalizing protein

hey! I would like some more information... which buffers have you used and at what pH? Em qui., 9 de jan. de 2025, 22:01, Marco Bravo < d0eb7bee83ae-dmarc-requ...@jiscmail.ac.uk> escreveu: > Hello all, > I am seeking some advice or ideas to crystalize a nuclease protein. It > exists within a

Re: [ccp4bb] help with wwPDB validation warning

This old message claims that / = "weighted" by s. If counting error is significant, s will be larger for stronger reflections, which are likely to have small I/s, so in general / > unweighted . As Werten points out. However this seems to be the opposite of the OP's situation, if both measur

Re: [ccp4bb] help with wwPDB validation warning

Dear Gerard, I disagree in two points with what you write: On Mon, 10 Jun 2024 19:15:43 +0100, Gerard Bricogne wrote: ... > Much worse, in fact: that quantity (I_avg/sigI_avg) makes no sense >whatsoever in statistical terms. It must be a relic of a quantity that may >have seemed like a good

Re: [ccp4bb] help with wwPDB validation warning

Ok - I have tracked down where it is coming from. The value being reported is sum(I)/sum(sigma_I).   This is not the same as Mean(I/sigmaI) - as I interpret the later as (Sum(I/sigma))/n. Where I comes from is the intensity_meas, intensity_meas_au, or intensity column - whichever is present (

Re: [ccp4bb] help with wwPDB validation warning

Dear Aline, This is an intriguing message: by what exact piece of software was it produced? The notation I_avg/sigI_avg does not appear in the definition of the closest item in the mmCIF dictionary, which would be _reflns_shell.meanI_over_sigI_obs that can be f

Re: [ccp4bb] help with wwPDB validation warning

Hi Aline, I see nothing wrong with / being 0.83 Mean((I)/sd(I)) is , which is not the same as / so you cannot expect the numerical values to be the same (even in case the resolution shell definition is identical), although the two values usually do not differ much. Take for example two reflect

Re: [ccp4bb] help with wwPDB validation warning

Hmm - no idea but perhapd=s interesting that 0.83 ~ 1.7/2 Eleanor On Fri, 7 Jun 2024 at 15:13, Aline Dias da Purificação < d5ed37c6eb7b-dmarc-requ...@jiscmail.ac.uk> wrote: > Dear all, > > I am currently validating a structure for deposition in the wwPDB and > encountered the following warnin

[ccp4bb] help with wwPDB validation warning

Dear all, I am currently validating a structure for deposition in the wwPDB and encountered the following warning in the validation system: Warning: Value of (I_avg/sigI_avg = 0.83) is out of range (check Io or SigIo in SF file). The Mean((I)/sd(I)) in the aimless log is 1.7 in the OuterShel

Re: [ccp4bb] Help with isomer ligand from PDB database

On 17/09/2022 15:48, Marion Schuller wrote: > >   > > Dear CCP4bb community, > >   > > I am writing regarding a problem with the refinement of an isomer > ligand. I try to refine a structure which has the ligand “Carba-NAD” > (as beta isomer) bound. This ligand is already in the pdb database as >

[ccp4bb] Help with isomer ligand from PDB database

Dear CCP4bb community, I am writing regarding a problem with the refinement of an isomer ligand. I try to refine a structure which has the ligand "Carba-NAD" (as beta isomer) bound. This ligand is already in the pdb database as "CNA". Although the ligand is in its beta-Carba-NAD form in the da

Re: [ccp4bb] help for motion correction

Hi, Please check the X and Y of your gain reference file using the e2iminfo.py command. It is possible that those values do not match those of the micrographs. If it is indeed that case, you can use the relion_image_handler options (for example --flipXY) to flip the gain reference file. Hope this

Re: [ccp4bb] help for motion correction

Might be better posted to cc...@jiscmail.ac.uk m -Original Message- From: CCP4 bulletin board On Behalf Of Jing Sent: 16 July 2022 20:56 To: ccp4bb Subject: [ccp4bb] help for motion correction Hello All, I have a question about gain reference file. When I try to work on Motion

Re: [ccp4bb] Help with One dimensional electron density calculation

For some perhaps relevant discussion please see Appendix B here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6096492/pdf/d-74-00531.pdf Pavel On Sat, Jul 16, 2022 at 6:17 AM Marcin Wojdyr wrote: > On Thu, Jul 14, 2022 at 3:15 AM Pavel Afonine wrote: > > > Map values are calculated using tric

[ccp4bb] help for motion correction

Hello All, I have a question about gain reference file. When I try to work on Motion Correction on relion 3.1.3, it always reports an error message said "the size of image and the size of the gain reference do not match." Because of that error, I could not proceed motion correction of my da

Re: [ccp4bb] Help with One dimensional electron density calculation

On Thu, Jul 14, 2022 at 3:15 AM Pavel Afonine wrote: > Map values are calculated using tricubic interpolation. Optionally you can > choose a less accurate eight-point interpolation (use interpolation keyword > for this). > I've been wondering which one is better. Tri-cubic is more accurate for

Re: [ccp4bb] Help with One dimensional electron density calculation

On 13/07/2022 19:18, Ravikumar wrote: I would like to calculate One-dimension electron density profiles of the different number of ions bound to an ion channel. Are there any programs in CCP4/ Phenix which can do the same job as the MAPMAN (UPPSALA electron density server) program to extract

Re: [ccp4bb] Help with One dimensional electron density calculation

will also read in maps and manipulate. It understands crystal symmetry, if that is what you have. It also has functions for interpolation. HTH Martyn From: CCP4 bulletin board On Behalf Of Ravikumar Sent: 13 July 2022 19:18 To: ccp4bb Subject: [ccp4bb] Help with One dimensional electron

Re: [ccp4bb] Help with One dimensional electron density calculation

Hi Ravikumar, next nightly build of Phenix (dev-4661 and up, likely becomes available tomorrow) found in the usual place https://phenix-online.org/download/nightly_builds.cgi?show_all=1 will contain the new command line program called phenix.map_values_along_line. The program inputs the map (rea

Re: [ccp4bb] Help with One dimensional electron density calculation

Dear Pavel, I guess you know that Billy made cctbx "available" on colab. So installing cctbx and python is not needed any more. https://github.com/phenix-project/Colabs/blob/main/Start_cctbx.ipynb There are also some descriptions of some modifications to the installation so that everything w

Re: [ccp4bb] Help with One dimensional electron density calculation

Hi Ravikumar, this can be easily done in CCTBX, but requires knowing CCTBX and Python scripting. I can write a script-example for you, if interested, or feel free to give it a try yourself and let me know if you need any help. Pavel On Wed, Jul 13, 2022 at 11:19 AM Ravikumar wrote: > > Dear all,

Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed

Dear CCP4 Users, Thank you very much for all suggestions. Special thanks to Oliver for the ready-to-use files. Great job :) Hopefully it will solve my problems... Best wishes, Rafal -- |--| |Rafal Dolot, Ph.D.| |

Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed

Dear Rafal, Apologies my email client rather scrambled the text from my previous message, so I will send again here Please find attached (in the previous message!) a restraint CIF file and a corresponding PDB file for your FESAN ligand. Details: Your ligand FESAN is a difficult test case for

Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed

Dear Rafal, Acedrg could not handle with ligands containing metal elements at the moment. When your input file was a mol file, acedrg gave that information. For other kind of input format, acedrg should give the same information. We are checking why it produced those confusing info. The developme

Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed

Dear all, Thank you very much for all your messages. Unfortunately, I'm still on the same place, as yesterday... First of all, I prepared a pdb/cif file of the ligand based on CCDC entry 1176355 containing FESAN molecule. Also, I prepared SMILES file based on SMILES of CB5 ligand (COSAN) ava

Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed

Hi, as previously suggested you can use AceDRG to generate a cif file for your ligand by input different type of files (SMILES, mmCIF, SDF/MOL, and SYBYL MOL2 files). You can use the AceDRG command line: https://www2.mrc-lmb.cam.ac.uk/groups/murshudov/content/acedrg/acedrg.html or via ccp4i2, 'L

Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed

Although it may not be apparent, there has been a lot of work going on in Acedrg development regarding Boron. One cannot say the same for Coot though and I can reproduce the behaviour reported by Rafa Dolot. If/when I can fix it, it will be available in 0.9.8.4. Paul. On 06/06/2022 13:24

Re: [ccp4bb] Help with preparation of the ligand coordinates/restraints needed

Hi, In case you don't have a cif file for the ligand, I would load the SMILES expression into acedrg (or use any other input option) to create a cif file which you can then read into Coot. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University Beer Sheva, Israel On Jun 6,

[ccp4bb] Help with preparation of the ligand coordinates/restraints needed

Dear CCP4 Users, I am working with data containing a possible complex of protein with FESAN (iron bis(1,2-dicarbollide)). Unfortunately, to my knowledge, this ligand is not available in PDB. The closest molecule is COSAN (cobalt bis(1,2-dicarbollide)), which is labelled as CB5 and is available

Re: [ccp4bb] help request (synchrotron schedules)

If you'd be interested in historical synchrotron schedules, they can be approximately guessed from pdb data, from data collection dates. Unfortunately, in many entries the dates are random, so there is significant noise there. Here is how it looks: https://project-gemmi.github.io/pdb-stats/calendar

[ccp4bb] help request (synchrotron schedules)

Dear CCP4-ers :) I used to have a handy chart where major synchrotron schedules were all drawn out as lines (across an entire year) with shutdowns and other blackout dates marked such that it was pretty easy to find what synchrotron is open for business at what week/month. This schedule took me a

Re: [ccp4bb] Help with interpreting Tyrosine modification

ionate? >>>> The carboxylate group could make H-bonds to both the Arginine sidechain >>>> and the the tyrosine OH group. Propionate should show no anomalous signal. >>>> >>>> Just my 2-bits worth. >>>> >>>> Cheers, >>>

Re: [ccp4bb] Help with interpreting Tyrosine modification

AIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Sent: Saturday, 29 January, 2022 18:34:26 Subject: Re: [ccp4bb] Help with interpreting Tyrosine modification Dear Misba, Thank you for your reply and for the very clear picture. I hope you will be able to share the result once the mystery is solved.

Re: [ccp4bb] Help with interpreting Tyrosine modification

> >> - Original Message - >> From: "Gerard Bricogne" >> To: CCP4BB@JISCMAIL.AC.UK >> Sent: Saturday, 29 January, 2022 18:34:26 >> Subject: Re: [ccp4bb] Help with interpreting Tyrosine modification >> >> Dear Misba, >> >> Thank

Re: [ccp4bb] Help with interpreting Tyrosine modification

the the tyrosine OH group. Propionate should show no anomalous signal. > > Just my 2-bits worth. > > Cheers, > Bill > > > - Original Message - > From: "Gerard Bricogne" > To: CCP4BB@JISCMAIL.AC.UK > Sent: Saturday, 29 January, 2022 18:34:26 > Sub

Re: [ccp4bb] Help with interpreting Tyrosine modification

ginal Message - From: "Gerard Bricogne" To: CCP4BB@JISCMAIL.AC.UK Sent: Saturday, 29 January, 2022 18:34:26 Subject: Re: [ccp4bb] Help with interpreting Tyrosine modification Dear Misba, Thank you for your reply and for the very clear picture. I hope you will be able to share the

Re: [ccp4bb] Help with interpreting Tyrosine modification

in Structural Biology > > > > > > > > > > > > School of Biosciences > > > > LES CollegeEmail: > > > > k.futte...@bham.ac.uk > > > > University of Birmingham Phone: +44 - 121 - 414 > > > > 5895 > >

Re: [ccp4bb] Help with interpreting Tyrosine modification

5895 > > Birmingham, B15 2TT, UK(voice mail messages > > will forward to my email inbox) > > > > My normal working hours are Mon - Fri 8.30 - 5.30 pm. > > > > > > === > > -

Re: [ccp4bb] help needed with link description

he Francis Crick Institute >> London, UK >> == >> about.me/david_briggs >> >> From: CCP4 bulletin board >> <mailto:CCP4BB@JISCMAIL.AC.UK> on behalf of Gerlind Sulzenbacher >> <mailto:gerlind.sulzenbac...@univ-amu.fr> >> Sent: Thur

Re: [ccp4bb] help needed with link description

avid_briggs *From:* CCP4 bulletin board on behalf of Gerlind Sulzenbacher *Sent:* Thursday, June 3, 2021 7:10:12 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] help needed with link description External Sender: Use caution. Dear all, I am going litteraly mad (or just old). I would lik

Re: [ccp4bb] help needed with link description

Dear Gerlind, Where did you get your mad_monlib.cif file? It shouldn't be neccesary for you to be manually modifying such restraint dictionaries (any more). You can generate these using AceDRG, either via CCP4i2 or Coot. Shameless plug: https://journals.iucr.org/d/issues/2021/06/00/ir5021/index

Re: [ccp4bb] help needed with link description

: Thursday, June 3, 2021 7:10:12 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] help needed with link description External Sender: Use caution. Dear all, I am going litteraly mad (or just old). I would like to make a covalent link between a carbohydrate moiety and and ASP of my well-cheered protein

[ccp4bb] help needed with link description

Dear all, I am going litteraly mad (or just old). I would like to make a covalent link between a carbohydrate moiety and and ASP of my well-cheered protein. The identifier for the carbohydrate moiety is MAD, chain C, res number 1. The link is established between C5 of MAD and OD2 of ASP 518,

[ccp4bb] Help EMBL-EBI maintain its services: articulating the value of open data

Dear colleagues, As a community of structural molecular (and, increasingly, cellular) biologists we are fortunate to have a large collection of well-established, well-managed and open data resources at our disposal. (Physicists are often impressed when they learn that a protein structure depos

Re: [ccp4bb] Help for Twin Refinement in Refmac5 / CCP4i2

I fell into the same trap this week. Apparently if in the first screen you tick the box Crystal is twinned” the interface resets the input data to FMEAN (or IMEAN if you have asked to use intensitirs) and you don’t need to say TWIN . Semi logical I guess but easy to miss. Eleanor On Tue, 26 Jan 20

Re: [ccp4bb] Help for Twin Refinement in Refmac5 / CCP4i2

Dear All, Please you may ignore my previous email. TWIN refinement in Refmac5 / CCP4i2 worked well once used "HKLOUT_0-observed_data_asIMEAN.mtz" from the data-reduction job. I am slowly getting used to the finer-aspects of CCP4i2. Previously, I used to have both Intensities and Amplitudes in a si

[ccp4bb] Help for Twin Refinement in Refmac5 / CCP4i2

Dear All, I have not had much experience in refining structure using data from twinned crystals and has started using CCP4i2 very recently only. Here is a background: antigen-Fab crystal structure determined by MR first in P4(3)2(1)2 space group with 1-complex molecule in the asymmetric unit (ASU

[ccp4bb] Help us help you: write support for Ultra-XChem beamline in Diamond-II

Dear all - please *help us help you*: * Some of you have used and even liked Diamond's XChem facility for crystal-based fragments screening. * Some of you have wanted to use it but didn't know how or didn't get time. * Lots and lots of you hope your crystallography will turn into ch

Re: [ccp4bb] Help needed (input files)

Hi Fred, Have you tried http://www.charmm-gui.org/ ? I think this is the easiest way to walk through setting up input files, and you can have it generate input files for several different programs. Cheers, Alex On Tue, Aug 4, 2020 at 4:07 AM Fred Vellieux wrote: > Hello, > > I need to perform so

Re: [ccp4bb] Help needed (input files)

Hi. You can try namd (https://www.ks.uiuc.edu/Research/namd/) It Is free and there are good tutorials available. HiH El mar., 4 de agosto de 2020 3:07, Fred Vellieux < frederic.velli...@lf1.cuni.cz> escribió: > Hello, > > I need to perform some MD calculations and then trajectories of some > smal

Re: [ccp4bb] Help needed (input files)

Fred, you could use the Academic version of Desmond freely available here: https://www.deshawresearch.com/resources_desmond.html The only difference from the commercial version is absence of OPLS3e force field but you still could use GPU. вт, 4 авг. 2020 г. в 10:08, Fred Vellieux : > Hello, > >

[ccp4bb] Help needed (input files)

Hello, I need to perform some MD calculations and then trajectories of some small molecules analyzed. What I have is 1. protein 2. cofactor (FAD) 3. small molecule (either single O2 atom or single Chlorine atom) 4. crystallographic waters The software I can access is either Gromacs (with yum

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

same. Thank you. *From:*CCP4 bulletin board <mailto:CCP4BB@JISCMAIL.AC.UK>>*On Behalf Of*Marian Oliva *Sent:*Thursday, July 30, 2020 8:46 AM *To:*CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> *Subject:*[ccp4bb] Help With Setting up a Stereo view system Dear colleagues. I woul

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

to do the same. > > Thank you. > > From: CCP4 bulletin board <mailto:CCP4BB@JISCMAIL.AC.UK>> On Behalf Of Marian Oliva > Sent: Thursday, July 30, 2020 8:46 AM > To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> > Subject: [ccp4bb] Help With Setting up

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

Dear all. Issue solved. It was a matter of installing the MATE desktop environment. Now everything is up and kicking Thanks a lot for all the help Marian Oliva CSIC-Centro de Investigaciones Biológicas Margarita Salas 9, Ramiro de Maeztu 28040-Madrid (Spain) phone: 0034 91 8373112 (x4380) e-

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

Dear Marian Oliva, in my experience, MATE, XFCE and Plasma 5/KDE work well with 3D stereo if the compositor is disabled. You don't even have to disable COMPOSITE in the xorg.conf - for those desktops, it is sufficient to disable composite in the respective desktop/compositor/window manager set

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

h this card? >>> >>> best, matthias >>> >>> >>> >>> Dr. Matthias Barone >>> >>> AG Kuehne, Rational Drug Design >>> >>> Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) >>> Robert-Rössle

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

rasse 10 >>> 13125 Berlin >>> >>> Germany >>> Phone: +49 (0)30 94793-284 >>> >>> >>> *From:* CCP4 bulletin board >> <mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of

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

t; >> Dr. Matthias Barone >> >> AG Kuehne, Rational Drug Design >> >> Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP) >> Robert-Rössle-Strasse 10 >> 13125 Berlin >> >> Germany >> Phone: +49 (0)30 94793-284 >> >> From:

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

tut für Molekulare Pharmakologie (FMP) > Robert-Rössle-Strasse 10 > 13125 Berlin > > Germany > Phone: +49 (0)30 94793-284 > > From: CCP4 bulletin board on behalf of Marian Oliva > > Sent: Thursday, July 30, 2020 2:46:07 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject:

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

: [ccp4bb] Help With Setting up a Stereo view system Dear colleagues. I would like to check if some one can help me with the setup of my hardware stereo system in Coot under Ubuntu 14 With the help of a friend I collect a bunch of second hand stuff. 1 NVIDIA 3D Video 2 system. 1 Monitor ASUS VG248

[ccp4bb] Help With Setting up a Stereo view system

Dear colleagues. I would like to check if some one can help me with the setup of my hardware stereo system in Coot under Ubuntu 14 With the help of a friend I collect a bunch of second hand stuff. 1 NVIDIA 3D Video 2 system. 1 Monitor ASUS VG248 conectes through the display port 1 NVIDIA QUADRO

[ccp4bb] Help to fight COVID-19

Dear Structure Biologists, We have some significant expertise in stabilizing the membrane proteins and domains in different kinds of membranous environments such as liposomes (small and giant vesicles suitable for biochemical and electrophysiological analysis), nanodiscs and malic acid based p

[ccp4bb] Help us design PDBe-KB's aggregated views of small molecules

PDBe-KB is a community-driven resource managed by the Protein Data Bank in Europe (PDBe) team, integrating functional annotations and structure data in the PDB archive. Recently, we started providingaggregated views of available structure data and annotations for ind

Re: [ccp4bb] Help please, COOT destroys PDB

Awesome. Thank you. Just changing the "," to "." did the trick. Thing is, this setting hadn't been changed before and used to work perfectly. Thanks again. Ale Paul Emsley escribió: On 03/07/2019 05:20, ALEJANDRA ANGELA CARRILES LINARES wrote: I am currently having problems with COOT (runni

Re: [ccp4bb] Help please, COOT destroys PDB

On 03/07/2019 05:20, ALEJANDRA ANGELA CARRILES LINARES wrote: I am currently having problems with COOT (running on a Windows 10 environment). Thing is, whenever I write a PDB file (save new coordinates), next time I open them (whether it is on a Windows or Mac computer), bonds are unexistant. I

[ccp4bb] Help please, COOT destroys PDB

Hi there! I am currently having problems with COOT (running on a Windows 10 environment). Thing is, whenever I write a PDB file (save new coordinates), next time I open them (whether it is on a Windows or Mac computer), bonds are unexistant. I reckon something is wrong when the file is writt

[ccp4bb] Help for BALBES Results

Hi All, I want to get the phases from balbes. have submitted my data to BALBES (online ccp4i). I am getting the results in txt file only. I am not getting the mtz and model result files. I would be very thankful for suggestions. Thanks & Regards, [image: Mailtrack]

Re: [ccp4bb] help with TNCS + MR

Dear Randy, thank you very much, I had a look at it and it seems that fortunately it was one of the "straighforward" cases. Best, Almudena El jue., 14 mar. 2019 a las 14:48, Randy Read () escribió: > Dear Almu, > > We have a discussion on the Phaser Wiki about some of the possibilities > for t

Re: [ccp4bb] help with TNCS + MR

Sorry to plug MOLREP to a Phaser Q, but it does have some simple tNCS functions which work well for straightforward cases. Something to consider: tNCS can make spacegroup determination based on axial reflection absences tricky so set a flag to test all SGS in the pointgroup. For example: (A transl

Re: [ccp4bb] help with TNCS + MR

Dear Almu, We have a discussion on the Phaser Wiki about some of the possibilities for tNCS, what you should look for, and what Phaser can handle: http://www.phaser.cimr.cam.ac.uk/index.php/Molecular_Replacement#Translational_Non-crystallographic_Symmetry. As it explains, if you have one major

[ccp4bb] help with TNCS + MR

Dear all, I have a dataset with strong TNCS and I would like to know if there are a "series of steps" that I could follow in order to find out whether I can solve my structure or not. I see on the Phaser wiki that structure determination in the presence of TNCS is not fully automated. which steps

Re: [ccp4bb] help needed with a rabbit-head-shaped blob

Hello, it looks if the density is located around a 2-fold axis. It cannot be the superposition of a bis-tris methane molecule bound asymmetrically and its symmetry mate ? Best Wim De: "Deborah Harrus" À: "CCP4BB" Envoyé: Vendredi 2 Novembre 2018 22:14:32 Objet:

Re: [ccp4bb] help needed with a rabbit-head-shaped blob

0) To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] help needed with a rabbit-head-shaped blob Dear all, I came across an unidentified rabbit-head-shaped blob and would need help for its identification. There are 2 molecules of protein per asymmetric unit but there are some differences betwee

Re: [ccp4bb] help needed with a rabbit-head-shaped blob

In all seriousness, it looks like it may be some form of hexose sugar? Tristan Croll Research Fellow Cambridge Institute for Medical Research University of Cambridge CB2 0XY > On 2 Nov 2018, at 21:14, Deborah Harrus wrote: > > Dear all, > > I came across an unidentified rabbit-head-sh

Re: [ccp4bb] help needed with a rabbit-head-shaped blob

Or dumbo the elephant. [Image] Get Outlook for iOS<https://aka.ms/o0ukef> From: CCP4 bulletin board on behalf of Frank Von Delft Sent: Saturday, November 3, 2018 7:41:46 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] help needed with a rabbit-head-

Re: [ccp4bb] help needed with a rabbit-head-shaped blob

It's more a Pacman ghost, innit?? Sent from Nine<http://www.9folders.com/> From: Deborah Harrus Sent: Friday, 2 November 2018 21:25 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] help needed with a rabbit-head-shaped blob Dear all, I came across an u

Re: [ccp4bb] help needed with a rabbit-head-shaped blob

Fig. 2.13 in Gale Rhodes’ “Crystallography Made Crystal Clear” touches on rabbit heads and diffraction, and is one of my favorite cartoons (sadly it doesn’t directly address your problem). > On 2 Nov 2018, at 5:14 PM, Deborah Harrus wrote: > > Dear all, > > I came across an unidentified rabbi

[ccp4bb] Help PDBe to enrich structure data with functional annotations

Dear All, We would be grateful if you could spend a moment of your time filling out this short survey on PDBe-KB [https://goo.gl/forms/6jcmDZNXIQm6IZFj2], to help us understand what types of additional structure annotations would be useful to you. PDBe-KB (Protein Data Bank in Europe - Knowl

Re: [ccp4bb] Help with omit map

As others suggested, you can use Polder map: - how-to video tutorial can be found here: http://www.phenix-online.org/documentation/reference/tutorial_channel.html - background is described here: http://journals.iucr.org/d/issues/2017/02/00/ba5254/ba5254.pdf Pavel On Tue, Jul 24, 2018 at 3:26

Re: [ccp4bb] Help with omit map

Vikram, you can use phenix.polder program. 2018-07-24 22:26 GMT+03:00 Vikram Dalal : > Hi everyone, > > > I have to generate the omit map of metal and coordinating residues of > protein structure for the figure. > > Which program can be used to generate the omit map for my requirement. > > > > Th

[ccp4bb] Help with omit map

Hi everyone, I have to generate the omit map of metal and coordinating residues of protein structure for the figure. Which program can be used to generate the omit map for my requirement. Thanks & Regards, To unsubscri

Re: [ccp4bb] help

Llok at this paper: Does NMR Mean “Not for Molecular Replacement”? Using NMR-Based Search Models to Solve Protein Crystal Structures The references there clainm to give the first instance of success... And Hi Eleanor On 5 March 2018 at 13:51, Chandra wrote: > Hello all > > Does anyone know

[ccp4bb] help

Hello all Does anyone knows of a review that highlights the first examples of the use of NMR combined with X-ray crystallography to solve the structures of proteins thanks chandra

Re: [ccp4bb] Help with assigning density

shape. > Cheers, > Mirella > > Get Outlook for Android <https://aka.ms/ghei36> > > -- > *From:* CCP4 bulletin board on behalf of Tristan > Croll > *Sent:* Friday, January 26, 2018 6:09:01 PM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subje

Re: [ccp4bb] Help with assigning density

ct: Re: [ccp4bb] Help with assigning density Yes it can. See 5x49 (residue 603) for a wonderful example. On 2018-01-26 16:46, Michal Boniecki wrote: > I have positive density around lysine residue (image). This density is > found in all crystals, and only with this lysine. It is solvent >

Re: [ccp4bb] Help with assigning density

Yes it can. See 5x49 (residue 603) for a wonderful example. On 2018-01-26 16:46, Michal Boniecki wrote: I have positive density around lysine residue (image). This density is found in all crystals, and only with this lysine. It is solvent accessible but again not only this one is surface K resid

Re: [ccp4bb] Help needed to make a clue about ligand

Shankar, It looks like Acetyl coA to me. Best wishes, - Allister > On 10 Jan 2018, at 04:09, Shankar Prasad Kanaujia > wrote: > > Dear All, > > Wishing you all a very happy and prosperous new year 2018 > > We have recently solved a structure which contains a huge density in the > ac

Re: [ccp4bb] Help needed to make a clue about ligand

Looks like it could be a G-C dinucleotide? Tristan Croll Research Fellow Cambridge Institute for Medical Research University of Cambridge CB2 0XY > On 10 Jan 2018, at 04:09, Shankar Prasad Kanaujia > wrote: > > Dear All, > > Wishing you all a very happy and prosperous new year 2018..

Re: [ccp4bb] help identifying unknown density

- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Stephen Cusack Sent: Monday, October 09, 2017 5:40 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] help identifying unknown density Dear All, I am refining the crystal structure of an E. coli expressed protein at

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