Re: [ccp4bb] Question about Phaser rotation and translation search parameters

Look at this presentation by Airlie McCoy - it answers some of your questions. https://www.ccp4.ac.uk/schools/DLS-2014/course_material/day07/Airlie_McCoy_Phaser_MR.pdf The crystal symmetry is taken into account when choosing the range of angles to search. If you run MOLREP - another more limited

[ccp4bb] Question about Phaser rotation and translation search parameters

Dear All, I hope this email finds you well. I would like to clarify how the Phaser program determines the search range and step size for both the rotation and translation searches. Specifically, I am wondering: 1. Rotation search range: What are the typical angular ranges for α, β, and γ? Fo

Re: [ccp4bb] question

ning Shelx-C and >this is what is causing the failure. >Cheers, tom > >From: CCP4 bulletin board on behalf of Tom Peat ><b7e4a7a8af49-dmarc-requ...@jiscmail.ac.uk> >Sent: Thursday, October 17, 2024 11:36 AM >To: CCP4BB@JISCMAIL.AC.U

Re: [ccp4bb] question

Shelx-C and >this is what is causing the failure. >Cheers, tom > >From: CCP4 bulletin board on behalf of Tom Peat ><b7e4a7a8af49-dmarc-requ...@jiscmail.ac.uk> >Sent: Thursday, October 17, 2024 11:36 AM >To: CCP4BB@JISCMAIL.AC.UK >Subject: [ccp4bb] q

Re: [ccp4bb] question

<b7e4a7a8af49-dmarc-requ...@jiscmail.ac.uk> Sent: Thursday, October 17, 2024 11:36 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] question Hello all, I just have a quick question regarding the latest CCP4 version (9.03) on Apple Sequoia- has anyone had issues? I'm sitting at the Cold Sp

Re: [ccp4bb] question

, tom From: CCP4 bulletin board on behalf of Tom Peat <b7e4a7a8af49-dmarc-requ...@jiscmail.ac.uk> Sent: Thursday, October 17, 2024 11:36 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] question Hello all, I just have a quick question regarding the lates

[ccp4bb] question

Hello all, I just have a quick question regarding the latest CCP4 version (9.03) on Apple Sequoia- has anyone had issues? I'm sitting at the Cold Spring Harbor course and have certain things hanging when I try to start them (Crank2 for example- I get the wheel of death with CCP4i2 and just a ha

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

Re: [ccp4bb] Question about micro RNA structures

lf of careinaedgo...@yahoo.com <02531c126adf-dmarc-requ...@jiscmail.ac.uk> Sent: 23 July 2024 09:02 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Question about micro RNA structures CAUTION: This email originated from outside of the ICR. Do not click links or open attachments unless you re

[ccp4bb] Question about micro RNA structures

Hello Everyone.I am working with miRNA for the first time. I would like to start of doing some docking studies to protein. Are there any suggestions on good tools to use to generate the miRNA structure from it's sequence?Kind regardsCareina  Yahoo Mail: Search, Organize, Conquer ##

Re: [ccp4bb] Question about BIOVIA DiscoveryStudio 2021

onday, July 3, 2023 10:10 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Question about BIOVIA DiscoveryStudio 2021 Folks, apologies for the non-CCP4 software question. I have tried to contact the BIOVIA DiscoveryStudio support team, somehow my browser does not allow me to open their "contact fo

[ccp4bb] Question about BIOVIA DiscoveryStudio 2021

Folks, apologies for the non-CCP4 software question. I have tried to contact the BIOVIA DiscoveryStudio support team, somehow my browser does not allow me to open their "contact form". I am trying to visualize and perform an analysis on a protein:smaller molecule complex. The smaller molecule

Re: [ccp4bb] Question about CCP4 monomer dictionaries

az Shaanan mailto:bshaa...@bgu.ac.il>> > Sent: 28 November 2022 23:33 > To: Carr, Stephen (MRC,RAL,RCAH) <mailto:stephen.c...@rc-harwell.ac.uk>> > Subject: Re: [ccp4bb] Question about CCP4 monomer dictionaries > > Hi stephen, > > I obviously don't have the ful

Re: [ccp4bb] Question about CCP4 monomer dictionaries

01235 567717 From: Boaz Shaanan Sent: 28 November 2022 23:33 To: Carr, Stephen (MRC,RAL,RCAH) Subject: Re: [ccp4bb] Question about CCP4 monomer dictionaries Hi stephen, I obviously don't have the full context of your case, but I am not sure why you invoke

Re: [ccp4bb] Question about CCP4 monomer dictionaries

x at Harwell (RCaH) > Rutherford Appleton Laboratory > Harwell Oxford > Didcot > Oxon OX11 0FA > United Kingdom > Email stephen.c...@rc-harwell.ac.uk > tel 01235 567717 > -- > *From:* Paul Emsley > *Sent:* 28 November 2022 19:20 > *To:* C

Re: [ccp4bb] Question about CCP4 monomer dictionaries

: [ccp4bb] Question about CCP4 monomer dictionaries On 28/11/2022 17:29, stephen.c...@rc-harwell.ac.uk<mailto:stephen.c...@rc-harwell.ac.uk> wrote: Dear CCPBB, I have a question regarding the origin of the monomer libraries in CCP4. I ask because I have quoted the bond length listed in the m

Re: [ccp4bb] Question about CCP4 monomer dictionaries

Dear Stephen, The current monomer library is, for the most part, generated by running AceDRG - for non-metal containing entries at least. AceDRG [1,2] derives atom types using the cif files in the Crystallography Open Database [3], not the CSD. You can see which version of Acedrg has been using

Re: [ccp4bb] Question about CCP4 monomer dictionaries

Hi Stephen, On top of Roberto's reply I was wondering whether the resolution of your structure and the ensuing s.d. of the bond length was taken into account by the refree. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University Beer Sheva, Israel On Nov 28, 2022 19:29, "s

Re: [ccp4bb] Question about CCP4 monomer dictionaries

u...@jiscmail.ac.uk> Reply to: "stephen.c...@rc-harwell.ac.uk" Date: Monday, 28 November 2022 at 18:29 To: "CCP4BB@JISCMAIL.AC.UK" Subject: [ccp4bb] Question about CCP4 monomer dictionaries You don't often get email from 8f3604def7f0-dmarc-requ...@jiscmail.ac.uk.

[ccp4bb] Question about CCP4 monomer dictionaries

Dear CCPBB, I have a question regarding the origin of the monomer libraries in CCP4. I ask because I have quoted the bond length listed in the monomer library describing peroxide in a manuscript and a referee has asked for a reference since they seem to disagree with the quoted value of ~1.48

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] question using a model from a multiple model PDB file using Phaser

Cc: CCP4BB@JISCMAIL.AC.UK Subject: [EXTERNAL] Re: [ccp4bb] question using a model from a multiple model PDB file using Phaser EXTERNAL EMAIL: Use caution before replying, clicking links, and opening attachments. Hi Yong, Sorry, this is a scripting feature I haven’t actually used before! It turns

Re: [ccp4bb] [EXTERNAL] [ccp4bb] question using a model from a multiple model PDB file using Phaser

half Of Randy John Read > Sent: Thursday, December 9, 2021 4:18 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [EXTERNAL] Re: [ccp4bb] question using a model from a multiple model > PDB file using Phaser > > EXTERNAL EMAIL: Use caution before replying, clicking links, and opening >

[ccp4bb] AW: [ccp4bb] [EXTERNAL] Re: [ccp4bb] question using a model from a multiple model PDB file using Phaser

o write a small script to do this. Best, Herman Von: CCP4 bulletin board Im Auftrag von Yong Wang Gesendet: Donnerstag, 9. Dezember 2021 22:28 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] question using a model from a multiple model PDB file using Phaser Hi Randy, I

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] question using a model from a multiple model PDB file using Phaser

Behalf Of Randy John Read Sent: Thursday, December 9, 2021 4:18 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [EXTERNAL] Re: [ccp4bb] question using a model from a multiple model PDB file using Phaser EXTERNAL EMAIL: Use caution before replying, clicking links, and opening attachments. Hi Yong, If you make an

Re: [ccp4bb] question using a model from a multiple model PDB file using Phaser

script it is “MODEL 1”. > I will try “MODEL 0” in the script to see how it goes. > > > > Thanks, > > > > Yong > > > > From: Boaz Shaanan > Sent: Wednesday, December 8, 2021 7:37 AM > To: Yong Wang > Cc: CCP4BB@JISCMAIL.AC.UK > Sub

Re: [ccp4bb] question using a model from a multiple model PDB file using Phaser

Hi, The first model number in the pdb file is 1. In the script it is "MODEL 1". I will try "MODEL 0" in the script to see how it goes. Thanks, Yong From: Boaz Shaanan Sent: Wednesday, December 8, 2021 7:37 AM To: Yong Wang Cc: CCP4BB@JISCMAIL.AC.UK Subject: [E

Re: [ccp4bb] question using a model from a multiple model PDB file using Phaser

Hi, Did you try to edit 'Model 1' to 'Model 0'? I seem to recall that it was reported on this bb as the solution to this problem. Cheers, Boaz Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben Gurion University Beer Sheva, Israel On 7 Dec 2021 22:56, Yong Wang <3c4fc05cc53b-dmarc-requ...@jiscma

[ccp4bb] question using a model from a multiple model PDB file using Phaser

Hi All, I am interested in using individual models from a PDB file containing multiple models with MODEL/ENDMDL records as a template for use in Phaser. The usage in the manual "ENSEMBLE [PDB|CIF] [RMS 1 | ID 2 | CARD ON3] CHAIN ""4 MODEL 5 " seems to support this. However, I am getting a

Re: [ccp4bb] Question about tncs and SAD phasing

On top of what Eleanor mentioned, looking for about 160 S atoms with anomalous signal to 3.9A will be VERY hard. If you manage actually find those sites (or a good subset of them), the next density modification step can also be very hard: jumping over that 3.5-4A hurdle to get interpretable density

Re: [ccp4bb] Question about tncs and SAD phasing

Well - I would start with a self rotation analysis. That non-cryst twofold and three folds would suggest something with 3-2 symmetry. I vaguely remember an insulin structure with the hexamer 3-fold in similar orientation.. And this paterson peak "one major off origin peak at 0.5 0.5 0.173" might

Re: [ccp4bb] Question about P3, H3 and R3 space groups

** >>> Dr Jeremy Karl Cockcroft >>> Department of Chemistry >>> (University College London) >>> Christopher Ingold Laboratories >>> 20 Gordon Street >>> London WC1H 0AJ >>> +44 (0) 20

Re: [ccp4bb] Question about P3, H3 and R3 space groups

*** 6 Wellington Road Horsham West Sussex RH12 1DD +44 (0) 1403 256946 (home) *** On Wed, 22 Jul 2020 at 14:51, Nicholas Keep mailto:n.k...@mail.cryst.bbk.ac

Re: [ccp4bb] Question about P3, H3 and R3 space groups

>> 6 Wellington Road >> Horsham >> West Sussex >> RH12 1DD >> +44 (0) 1403 256946 (home) >> *** >> >> >> On Wed, 22 Jul 2020 at 14:51, Nicholas Ke

Re: [ccp4bb] Question about P3, H3 and R3 space groups

** > > > On Wed, 22 Jul 2020 at 14:51, Nicholas Keep > wrote: > >> >> >> >> Forwarded Message >> Subject: Re: [ccp4bb] Question about P3, H3 and R3 space groups >> Date: Wed, 22 Jul 2020 14:41:27 +0100 >> From: Eleanor D

Re: [ccp4bb] Question about P3, H3 and R3 space groups

; -- > *From:* CCP4 bulletin board on behalf of David > Vizarraga Revuelto > *Sent:* 22 July 2020 12:20 > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* [ccp4bb] Question about P3, H3 and R3 space groups > > Dear all, > > Let me ask a questi

Re: [ccp4bb] Question about P3, H3 and R3 space groups

ond Light Source Ltd. > Diamond House > Harwell Science & Innovation Campus > Didcot > Oxfordshire > OX11 0DE > From: CCP4 bulletin board on behalf of David > Vizarraga Revuelto > Sent: 22 July 2020 12:20 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Question about

Re: [ccp4bb] Question about P3, H3 and R3 space groups

Hi Eleanor H3 #143 is (and always has been) a triply-primitive cell setting of P3. http://img.chem.ucl.ac.uk/sgp/large/143bz1.htm Cheers -- Ian On Wed, 22 Jul 2020 at 14:42, Eleanor Dodson < 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote: > But surely P3 symmetry ' cell ( a,a,c 90 90 1

Re: [ccp4bb] Question about P3, H3 and R3 space groups

But surely P3 symmetry ' cell ( a,a,c 90 90 120) with origin shifts (⅓,⅔,0), +(⅔,⅓,0) can just be indexed as P3 with cell (a/sqrt(3), a/sqrt(3), c, 90 90 120) ?? Eleanor On Wed, 22 Jul 2020 at 14:32, Nicholas Keep wrote: > I have an answer from Jeremy Cockcroft the author of the 'Birkbeck' > Tab

Re: [ccp4bb] Question about P3, H3 and R3 space groups

o: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Question about P3, H3 and R3 space groups Dear all, Let me ask a question about the P3,H3, R3 space group annotations. I had the idea that H3 was the recommended annotation for the hexagonal representation of R3 (space group number 146). However, in the Birb

[ccp4bb] Question about P3, H3 and R3 space groups

I have an answer from Jeremy Cockcroft the author of the 'Birkbeck' Tables. Actually Jeremy has been at UCL for a decade or so and they are hosted from their Nick In answer to the question regarding the use of R and H for trigonal space groups, the letters refer to two distinct types of latti

Re: [ccp4bb] Question about P3, H3 and R3 space groups

This is precisely why SHELX always used the coordinates of the general position (LATT+SYMM) to define the space group rather than a name or number. George On 22/07/20 14:15, Ian Tickle wrote: Hi David The problem is that the PDB incorrectly used the H lattice symbol (without consulting any

Re: [ccp4bb] Question about P3, H3 and R3 space groups

Hi David The problem is that the PDB incorrectly used the H lattice symbol (without consulting any crystallographers AFAIK) for the hexagonal R-centred cell when it had already been in use for many years for the triply-primitive setting of P3, so now we have this confusion between MX & XRD/powder

Re: [ccp4bb] Question about P3, H3 and R3 space groups

This does seem confusing! Maybe the International tables have changed, but in my copy spacegroup 143 is labelled P3 Spacegroup 146 is equivalent to P3 with translations 1/3,2/3.2/3 and 2/3,1/3,1/3 is called rhombehedral This can be indexed with. "a=b=c in the rhombehedral setting" and labelled R

[ccp4bb] Question about P3, H3 and R3 space groups

Dear all, Let me ask a question about the P3,H3, R3 space group annotations. I had the idea that H3 was the recommended annotation for the hexagonal representation of R3 (space group number 146). However, in the Birbeck space groups web page (attached) H3 is associated with the space group number

Re: [ccp4bb] Question about small molecule crystallography

Correction: It should read "with the detector almost but not quite hitting the source." On 02.07.20 17:13, Navdeep Sidhu wrote: > Alexander Blake wrote a nice chapter on small-molecule crystallization > in this book, if you run into problems in the crystallization stage: > > Alexander Blake. Cry

Re: [ccp4bb] Question about small molecule crystallography

Alexander Blake wrote a nice chapter on small-molecule crystallization in this book, if you run into problems in the crystallization stage: Alexander Blake. Crystal growth and evaluation (Chapter 3). In Clegg, William (Ed.) Crystal Structure Analysis: Principles and Practice. 2nd Edition. IUCr/Oxf

Re: [ccp4bb] Question about Refmac

Thank you for cell. For P32 21 2 spacegroup with this cell the only higher Laue symmetry you could generate is P6/mmm, so as Jonathan says I wouldnt worry about the FreeR assignment.. I can look at possible NCS operators if you like - the most informative output is to run MOLREP Self Rotation on yo

Re: [ccp4bb] Question about Refmac

I remember we discussed this a lot about a year ago when Ed Berry revived a thread from 2003! https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=ind1905&L=CCP4BB&O=D&P=72099 I think the upshot of it all was that you do not need to use shells even with quite high NCS since Ian Tickle rightly pers

Re: [ccp4bb] Question about Refmac

Hmm - this finally was rather deprecated - there are some less happy consequences to have all reflections in a particular resolution shell excluded. If your NCS means there is pseudo- symmetry in the diffraction and it would be possible to have a cell with higher point symmetry (an example might be

[ccp4bb] Question about Refmac

Hello, I'm refining protein structure in Refmac and I have NCS greater than 4 ( I've 8 identical subunits in the asymmetric unit). In the "Refinement parameters" section in Refmac, how can I pick Rfree set based on thin resolution shells rather than in the normal random method? I've read abou

Re: [ccp4bb] Question about small molecule crystallography

It's not all that hard to exceed it with a protein crystal too. A 50 um wide lysozyme crystal sitting in a 50x50um beam will scatter into a single spot up to: I = 7e-14*flux*(F/mosaic)^2 Where I is in photons/s flux is incident photons/s mosaic is in deg F is the structure factor of the relev

Re: [ccp4bb] Question about small molecule crystallography

Hi Jon Ambiguous phrasing, perhaps - the detector has a maximum count rate, as events per second, and it is easy to exceed this with a good quality small molecule crystal on an undulator beamline thus under record the intensity of strong reflections Best wishes Graeme On 8 Jun 2020, at 20:55,

Re: [ccp4bb] Question about small molecule crystallography

Re: "it turns out to be very very easy to exceed the count rate where the detector electronics can keep up."Sorry if this is obvious, but I take it you mean "_can't_" keep up?Jon CooperOn 4 Jun 2020 13:06, "Winter, Graeme (DLSLtd,RAL,LSCI)" wrote: Dear All, A small word of caution regarding chem

Re: [ccp4bb] Question about small molecule crystallography

Dear All, A small word of caution regarding chemical crystallography on an MX-like beamline - if you have a bright source, a well diffracting crystal and a pixel array detector it is perfectly possible to lose counts in the strongest reflections without noticing - certainly without going over t

Re: [ccp4bb] Question about small molecule crystallography

Dear Jiyuan, maybe I can add something from the small molecule crystallographer view :-) Crystallization: For crystallization of small molecules you normally use solvents and water or mixtures as mentioned already before. At my lab the most successful way to crystallise is evaporation. Please use

Re: [ccp4bb] Question about small molecule crystallography

Dear Jiyuan, There was a similar question on the bulletin board some 6 years ago; my response then (links below) complements some of the other great suggestions already made in answer to your question: , and

Re: [ccp4bb] Question about small molecule crystallography

Dear Jiyuan, May I make some advertisement for our tutorial, we published some time ago? Our article "Some thoughts about the single crystal growth of small molecules" (https://pubs.rsc.org/en/content/articlelanding/2012/ce/c1ce05624g#!divAbstract) should exactly answer most of your questions. Y

Re: [ccp4bb] Question about small molecule crystallography

Hi Jiyuan, I don't have much to add on the small molecule crystallization advice, but I will put in another plug for electron diffraction (microED). You could first check to see if you already have microcrystal by performing some X-ray powder diffraction or XRPD (many CROs offer this service). If

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] Question about small molecule crystallography

f Tim Gruene Sent: Tuesday, June 2, 2020 4:37 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [EXTERNAL] Re: [ccp4bb] Question about small molecule crystallography Dear Francois, provided you are not restricted to the trademark term 'microED', but open minded to include '3D electron crystal

Re: [ccp4bb] Question about small molecule crystallography

Dear Francois, provided you are not restricted to the trademark term 'microED', but open minded to include '3D electron crystallography', there are plenty of published structures of small compounds, both organic and inorganic. Several of them date back to 2005, and include complex structures like

Re: [ccp4bb] Question about small molecule crystallography

Hi everyone Pr Tamir gonen (UCLA, los Angeles) have solved (not published) few chemical compounds structures with mircoED. And, the more important is that crystals were present in the powder (whatever condtions to get it (preciptation, evaporation ..). I have myself test with 2 powders coming

Re: [ccp4bb] Question about small molecule crystallography

> > From: CCP4 bulletin board on behalf of Artem > Evdokimov > Sent: Tuesday, June 2, 2020 8:07 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] Question about small molecule crystallography > > Hi > > A small organic molecule is typically crystallized

Re: [ccp4bb] Question about small molecule crystallography

bulletin board on behalf of Artem Evdokimov Sent: Tuesday, June 2, 2020 8:07 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Question about small molecule crystallography Hi A small organic molecule is typically crystallized from organic solvents (or water, if soluble) by means of at least

Re: [ccp4bb] Question about small molecule crystallography

Hi A small organic molecule is typically crystallized from organic solvents (or water, if soluble) by means of at least three main techniques: 1. slow evaporation of solvent leading to supersaturation and eventual crystallization 2. supersaturation at higher temperature followed by gradual drop i

[ccp4bb] Question about small molecule crystallography

Hi Everyone, I want to crystallize a small organic molecule. I have very limited experience in small molecule crystallography. I found that the Crystal Screen HT from the Hampton research is good for both small molecule and macromolecule crystallization. Plan to set up a sitting drop screen just l

Re: [ccp4bb] Question about losing reflections when refining in PHENIX

Hi, following Jonathan's reply, unless you specify "no anomalous" in the input file, Phenix will refine by default against the anomalous data in your input mtz, even if the signal is weak. You should also check how you define the type of mtz columns to be used in the refinement. There are sever

Re: [ccp4bb] Question about losing reflections when refining in PHENIX

Hello, it looks as though the No observations that phenix is reporting is exactly twice the number of unique reflections. Perhaps phenix is reporting the merging statistics for the Friedel pairs (i.e. F(+) and F(-)) within your merged dataset. Hence the stats look much better than those for the

[ccp4bb] Question about losing reflections when refining in PHENIX

Dear All, I need a bit of help with an issue I am encountering with one of my datasets when using phenix.refine. After processing data with Mosflm I get the following parameters: Overall InnerShell OuterShell Low resolution limit 65.69 65.69 2.55 High resolutio

Re: [ccp4bb] Question on author provided HELIX/SHEET records and assignment of a continuous helix that changes its helix class.

Re: question 2, for simplicity, I would call it all one helix and regard the 3-10 part as a distortion. Just my opinion.  Sent from Yahoo Mail on Android On Tue, 28 May 2019 at 13:48, Paul Emsley wrote: On 28/05/2019 11:51, Stephan Grunwald wrote: > > I [have] recently solved [my] first

Re: [ccp4bb] Question on author provided HELIX/SHEET records and assignment of a continuous helix that changes its helix class.

On 28/05/2019 11:51, Stephan Grunwald wrote: I [have] recently solved [my] first X-ray structure and I would like to have an opinion on two questions, both dealing with secondary structure assignments. First of all, the wwPDBs says ”We encourage authors to use the calculated helix (or sheet)

[ccp4bb] Question on author provided HELIX/SHEET records and assignment of a continuous helix that changes its helix class.

Dear CCP4BB community, I am PhD student, who has recently solved his first X-ray structure and I would like to have an opinion on two questions, both dealing with secondary structure assignments. 1) Is it advisable to add author provided secondary structure annotations? (in my humble opinion it i

Re: [ccp4bb] Question regarding edstats

Hi John The script runs MTZFIX as a safety check to ensure that the supplied map coefficients are valid (since in some cases they are not), i.e. calculated according to the equations in the literature, as shown here: ftp://ftp.ccp4.ac.uk/ccp4/6.4.0/ccp4-6.4.0/src/edstats/mtzfix.html So it calcul

[ccp4bb] Question regarding edstats

Dear CCP4bb crystallographers, in regards to the CCP4 program EDSTATS using a Phenix refinement output file, I tried running the file through MTZFIX and it gives the error: ERROR: Labels not found - maybe non-standard labels used? So I tried changing all the column labels to the equivalent in R

Re: [ccp4bb] Question about the electron density maps (.ccp4) in PDBe

Thanks for the clarification, Pavel! And the article is very helpful as well. Cheers, Sen On Tue, Mar 5, 2019 at 1:07 PM Pavel Afonine wrote: > P.S.: while on the topic, it might be helpful to you to have a look at > this article ("On the analysis of residual density distributions on an > absol

Re: [ccp4bb] Question about the electron density maps (.ccp4) in PDBe

P.S.: while on the topic, it might be helpful to you to have a look at this article ("On the analysis of residual density distributions on an absolute scale", page 43) available here: http://phenix-online.org/newsletter/CCN_2012_07.pdf Pavel On Tue, Mar 5, 2019 at 10:02 AM Pavel Afonine wrote:

Re: [ccp4bb] Question about the electron density maps (.ccp4) in PDBe

Hi Sen, As Pavel mentioned, phenix.f000 will give you F(0,0,0) value, but I don't > see that information stored and easily calculated from .ccp4 data. > phenix.f000 requires atomic model (PDB or mmCIF file) as input, not a map. If you want bulk-solvent to be added, then you need to give it mean

Re: [ccp4bb] Question about the electron density maps (.ccp4) in PDBe

Dear Sen, Our messages just crossed ... . With best wishes, Gerard. -- On Tue, Mar 05, 2019 at 11:32:01AM -0500, Yao, Sen wrote: > Dear Gerard, > > Thank you for your reply. I totally agree with you. > > The average value of the 2mFo-DFc map should be zero, and from my > ob

Re: [ccp4bb] Question about the electron density maps (.ccp4) in PDBe

Dear Sen On Tue, Mar 05, 2019 at 11:05:26AM -0500, Yao, Sen wrote: > Thank you Ian! The response is really informative. > > I am aware that electron density is a point sample. And multiply it by the > voxel volume is an estimated average. I do have a normalization step in my > calculation that sh

Re: [ccp4bb] Question about the electron density maps (.ccp4) in PDBe

Dear Gerard, Thank you for your reply. I totally agree with you. The average value of the 2mFo-DFc map should be zero, and from my observation, most of them are a very small number (<0.001) that can be viewed as zero practically. As Pavel mentioned, phenix.f000 will give you F(0,0,0) value, but I

Re: [ccp4bb] Question about the electron density maps (.ccp4) in PDBe

Hi, > Unfortunately not all structure > factor programs will give you that F000. > phenix.f000 will give you F(0,0,0) value based on atomic model alone or atomic model plus bulk-solvent. Pavel To unsubscribe from the CCP

Re: [ccp4bb] (EXTERNAL) Re: [ccp4bb] Question about the electron density maps (.ccp4) in PDBe

Also check if the mean value of the map over the ASU is zero. If so, the map was probably calculated without the 0,0,0 term of the Fourier series, so zero does not represent zero density but rather the mean density. On 03/04/2019 12:43 PM, Ian Tickle wrote: Hi Sen If you multiply the electro

Re: [ccp4bb] Question about the electron density maps (.ccp4) in PDBe

Dear Sen, I may be unaware of special features of these maps, but if they are computed in conventional ways, they lack an F000 term. Therefore the average value of the 2mFo-DFc map is zero, just as if it was a difference map. This may explain why you do not find all the electrons you would be

[ccp4bb] Question about the electron density maps (.ccp4) in PDBe

Hi all, I have been using the electron density maps available on the PDBe website to run some analysis. And I run into this question that I hope that I can get some help from the community. In the ccp4 format, the electron density is represented as a 3-d array map, with each number corresponds to

Re: [ccp4bb] question about resolution bins in deposition

See Table 1 and corresponding discussion here: http://journals.iucr.org/d/issues/2013/04/00/dz5273/dz5273.pdf Hope that hints you the answer. If not get back to me with questions. All the best, Pavel On Mon, Nov 6, 2017 at 7:18 PM, Eze Chivi wrote: > Hi, my PDB file lists only 4 resolution b

[ccp4bb] question about resolution bins in deposition

Hi, my PDB file lists only 4 resolution bins (full range: 1.6-19.1A). This is the first time I noted this behavior (It's used to be 20 bins). It is OK for deposition? It is need to rearrange statistics? How I can do that? Thank you very much. (I did my refinements in phenix, oops!, but the ccp4b

Re: [ccp4bb] AW: [ccp4bb] question regarding sequence numbering

*Von:*CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von *Briggs, David C *Gesendet:* Dienstag, 19. September 2017 14:24 *An:* CCP4BB@JISCMAIL.AC.UK *Betreff:* Re: [ccp4bb] question regarding sequence numbering Hi Tony, When I've had similar issues, I've numbered them s

[ccp4bb] AW: [ccp4bb] question regarding sequence numbering

. Best, Herman Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Briggs, David C Gesendet: Dienstag, 19. September 2017 14:24 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] question regarding sequence numbering Hi Tony, When I've had similar issues, I've num

Re: [ccp4bb] question regarding sequence numbering

quentially, then often graphics and refinement software won't treat them as linked. Dave -- Dr David C Briggs Hohenester Lab Department of Life Sciences Imperial College London UK http://about.me/david_briggs From: Antonio Ariza Sent: Tuesday 19 September, 13:15 Subject: [ccp4bb] question reg

[ccp4bb] question regarding sequence numbering

Hi all, Here's a problem I haven't come across before. I'm working on a structure whose expression plasmid was designed to remove the first 9 amino acids from the protein of interest and to which an N-terminal tag was added. After cleaving the tag I am left with 3 amino acids (GPM) followed by

Re: [ccp4bb] Question for those who use AutoSharp via CCP4i on MacOSX Yosemite

I’ll add to this that you should also set the relevant path in launchd.conf as well to access other external programs (SHELXC/D/E) when opening ccp4i via the Finder/Spotlight. setenv PATH /where/ever/shelx Cheers, Aaron -- Dr. Aaron Finke Postdoctoral Fe

Re: [ccp4bb] Question for those who use AutoSharp via CCP4i on MacOSX Yosemite

Dear Mark, Indeed there is a way. You have to set the environment variable so that all Mac apps can access it. This is most easily done via launchd. In the Terminal, type ‘sudo vi /etc/launchd.conf’ and add the following text (the file will likely be blank): setenv SHARP_home /where/ever/SHARP

[ccp4bb] Question for those who use AutoSharp via CCP4i on MacOSX Yosemite

Dear All, when starting CCP4i via the icon, AutoSharp remains greyed out, suggesting it is not installed. However, when I start CCP4i in an XQuartz window (i.e. “ccp4i &”), AutoSharp can be run. I guess this may be because in first way my “.profile” file is not read, any ideas how to fix this?

[ccp4bb] question rosie server, wrong plots? (off topic)

From: conan_...@hotmail.com To: ccp4bb@jiscmail.ac.uk CC: enz...@rice.edu Subject: rosie server, wrong plots? (off topic) Date: Tue, 14 Apr 2015 22:07:21 + Dear All, Any one knows why the Rosie Server for protein docking (docking2) gave two plots that seem not consistent with each othe

Re: [ccp4bb] Question on sca file

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Dear Smith, The sca file most likely does not contain flags. pointless can read the sca file, standardise it to ccp4 standards and freerflag marks random reflections. You should use the maximum of 500 unique reflections or 5% of the unique reflections

[ccp4bb] Question on sca file

Dear All, I have a sca file. Will you please tell me by which software or how I can know whether the sca file contains R-free tags? If not, by which software or how I can add the R-free tags? And how much of the reflections I add the R-free tags? I am looking forward to getting your reply. Smith

Re: [ccp4bb] Question on Refmac5

Dear Dialing, have you any specific reasons to believe that the crated PDB file does not correspond to the refined model ? This could be easily checked by comparing the statistics written in the header of the PDB file and those at the end of the refmac logfile. If they do not differ, then your

Re: [ccp4bb] Question on Refmac5

Dear Dialing, unless this has changed recently, in my experience refmac5 writes the PDB and MTZ file only at the end of refinement, not intermediately. Have you ruled out this is an issue with your operating system or file system setup? Maybe the timestamp is messed up e.g. through an NFS system?

Re: [ccp4bb] Question on Refmac5

I am talking the "creating date". For my situation, once the PDB file and mtz file were created at around 6:00 pm, with the progression of the refinement and completed at 8:00 pm, the date shown in the directory folder is always 6:00 pm. After 8:00 pm when the refinement finished, I check the pr

Re: [ccp4bb] Question on Refmac5

Dear Dialing are you talking about the 'creating date' or the 'modified date'? Leo > On Jan 6, 2015, at 2:55 AM, Dialing Pretty > <03f1d08ed29c-dmarc-requ...@jiscmail.ac.uk> wrote: > > Dear All, > > When I run Refmac, it would produce a refined PDB file and mtz file. My > question is, if

[ccp4bb] Question on Refmac5

Dear All, When I run Refmac, it would produce a refined PDB file and mtz file. My question is, if I started the refinement at 6:00 pm and completed at 8:00 pm, I find the refined PDB file and mtz file were created in the target directory at perhaps 6:30 pm. I think from 6:30 pm the created PDB f

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