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

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

Re: [ccp4bb] replacement for Scientific Linux

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

Re: [ccp4bb] Request for assistance with structure solution

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

Re: [ccp4bb] Request for assistance with structure solution

, Genetics, and Microbiology Structural Biology Group, Room 3-7, Agricultural Sciences Building, University of Pretoria c/o University & Lynnwood Roads Hatfield Pretoria 0083 Cell: +27638643131 South Africa -- Kay Diederichshttp://strucbio.biologie.uni-konstanz.de email: kay.die

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

Hi Venkat, so what I suggested is not the real problem. To get to the bottom of this, I suggest you show the logfiles from REFMAC5 and phenix.refine, and the output of the following command: mtzdmp experimental_data.mtz >& mtzdmp.log run on the command line. Please upload the files to some

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

Hi Venkatareddy Dadireddy, do the unit cell parameters of your MTZ file and PDB file agree exactly ? Take for example a cell of (100,110,120,90,90,90) in the header of the MTZ file, and (97,110,120,90,90,90) in the CRYST1 line of the PDB file. In this example, the (50,0,0) reflection would be

Re: [ccp4bb] twinning or not?

Hi Len, a possible theory: your crystals may be macroscopically twinned, i.e. consisting of single crystals attached to each other in the way that the twin operation describes. At your home source, you employ a rather big beam that hits more than one single crystal. So the data appear twinned.

Re: [ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography

Fred, nobody would be offended if you'd just post your SHELXL .ins file here; there are enough experienced crystallographers to spot the mistake. Best would be if you could pare it down to small size, but such that it is still reproducible (my own experience is that this almost always makes me

Re: [ccp4bb] RES: [ccp4bb] Rwork and Rfree the same?

Hi Rafael, I guess that you ask for a number to be used as a "cutoff", but there is no such number. Completeness is measured on a continuous scale, typically from 0 to 100%. Higher is better, of course. Resolution shells with low completeness just carry proportionally less information about

Re: [ccp4bb] Difficult Molecular replacement

Hi Vaheh, for this purpose, I use pointless hklin refmacXY.mtz < wrote: ... >This might be a silly question, but I do not know the answer: After refinement >in P1 how do I distinguish which axis is crystallographic and which one in >non-crystallographic? > >Vaheh

Re: [ccp4bb] Difficult Molecular replacement

Hi Marco: short comments (I sent you also a private mail): - the stats in CORRECT.LP look ok, but I'd like to know what ISa is, and what the number of outliers is ("misfits"). Seeing the delta-CC1/2 stats as a function of frame number is also useful for judging e.g. the radiation damage - this

Re: [ccp4bb] Difficult Molecular replacement

Hello Marco, this sounds to me like there is space group confusion in the sense that if you use the output model from Phaser, it may say space group P22121 (with a wrote: >Hello Todd, I get the best solution for p22121 space group after MR with an >LLG score of 640 from phaser. and the Rfree

Re: [ccp4bb] Which version of ccp4 introduced i2run and/or where does it live?

Hi Maggie, I have CCP4 version 8.0 on my Mac and it does have the file /Applications/ccp4-8.0/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/ccp4i2/bin/i2run If I run it without arguments, it says CCP4 /Applications/ccp4-8.0 ccp4i2 version 1.1.0 ccp4i2 source revision 6539

Re: [ccp4bb] About Staraniso

Dear readers of CCP4BB, for various reasons I don't feel inclined to reply to this. I'm really sorry, Kay On Tue, 13 Feb 2024 15:25:03 +, Gerard Bricogne wrote: >Dear Kay, > ... To unsubscribe from the CCP4BB

Re: [ccp4bb] About Staraniso

Dear Arpita, I'll try to answer below - On Mon, 12 Feb 2024 13:57:28 +0530, Arpita Goswami wrote: >Dear all, > >Greetings to all! Apologies if the below query seems very naive! > >This is to query on the consensus to use Staraniso for pdb submission. We >have solved a structure previously at

Re: [ccp4bb] mtz/cif file for depostion

Dear Gottfried, after cad, you need to uniqueify -f FREER Hope this helps! Best wishes, Kay On Fri, 9 Feb 2024 18:54:25 +0100, Palm, Gottfried wrote: >Dear all, >  I have problems preparing my experimental data (XRD) for >deposition. I have two mtz files, which work well for refmac5,

Re: [ccp4bb] nearestcell

e to http://www.strubi.ox.ac.uk/nearest-cell/nearest-cell.cgi does not respond - "othercell" is also useful but for other purposes, and it is in CCP4 thanks to all who responded so quickly! Kay On Wed, 27 Dec 2023 18:38:15 +, Kay Diederichs wrote: >Dear all, > >I seem to rememb

[ccp4bb] nearestcell

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 anyone point me to it or give alternatives, please? (I did try the PDB's advanced

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] 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] Multi-lattice crystal data processing strategy for structure solution

Hello Devbrat, your project is difficult and there is no magic bullet to solve its problems. Your approach is good because it always pays off to process the data carefully. In this respect, let me make a few comments. 1) you don't say why you call the diffraction patterns "multi-lattice". What

Re: [ccp4bb] About model building

Hi Sam, What you write does not sound good to me. Did you have Phaser check "all possible [spacegroups] in same pointgroup" (this is how it is called in ccp4i)? P321 is quite rare, compared to P3121 and P3221. If you miss a screw axis, you will not find a solution. An R-factor of 50% does not

Re: [ccp4bb] how to increase b factor for water in protein- ligand crystal structure

Hi Mandar Bhutkar, ok now that new table shows that your data are at least reasonable. Nevertheless it pays off to optimize the data processing, and the high resolution cutoff ... Is it publishable? Not possible to say from your table. If I were a reviewer, I'd want to see the raw data and

Re: [ccp4bb] how to increase b factor for water in protein- ligand crystal structure

Hi Mandar Bhutkar, the data statistics (Rmerge, I/sigma, CC1/2) appear to be poor. So you may want to check the data processing; try with different programs, and perhaps with help from experienced people in your group. You could ask for help here, but you should give more details - what

Re: [ccp4bb] radiation damage and image discard

Dear Jorge, the plots available from XDSGUI in the "statistics" tab are helpful in this respect (see https://journals.iucr.org/j/issues/2023/05/00/yr5110/index.html and in particular Fig 4). In particular, delta-CC1/2 and R_d are sensitive to radiation damage. Pls note that sometimes a few

Re: [ccp4bb] Database for submitting unprocessed diffraction data

There is one more - https://mxrdr.icm.edu.pl/ HTH, Kay On Wed, 18 Oct 2023 19:23:06 +0300, JEROME JOHNSON wrote: >Hello all, > >As the subject says, I am looking for an open online database to store >unprocessed diffraction data. Does such a database exist? Essentially we >would like our

Re: [ccp4bb] Issues in diffraction image export compatible to iMosflm

If you export the images in XDS format, then you get .pck files that MOSFLM certainly can read, plus a XDS.INP with the geometry parameters. Hope this helps, Kay On Tue, 10 Oct 2023 10:47:51 +0530, Vyankatesh Rajmane wrote: >Dear all, >We have collected diffraction data on a Rigaku FR-X

Re: [ccp4bb] Error in xdsgui: you have to install generate_XDS.INP in your path

Dear Zhen Gong, Installation of XDS and associated programs is documented in the "Installation" article in XDSwiki. If I google "XDSwiki installation article", it is the first hit. Your PATH is probably different when you double-click XDSGUI to start it, compared to what it is on the command

Re: [ccp4bb] problem with typing characters into ccp4interface 8.0.011

Hi Alex, What is your operating system? Linux or Mac? Version? Best, Kay On Thu, 18 May 2023 23:21:47 +, Alex Aleshin wrote: >This morning I've discovered that I cannot type any character (numbers are >fine) into CCP4I command windows. I've upgraded the package to a 8.0.011 >version,

Re: [ccp4bb] Structural alignment and classification

Dear Armando, besides THESEUS, you could use SUPERPOSE (in CCP4) or USalign (https://zhanggroup.org/US-align/). In my tests, THESEUS sometimes crashed in different ways. USalign is very robust; SUPERPOSE is fast. HTH, Kay On Mon, 6 Mar 2023 08:35:20 +0100, Armando Albert wrote: >Dear all,

Re: [ccp4bb] Careless and negative Wilson B-factor

Dear Gyuhyeok, I have no first-hand experience with CARELESS. But my understanding is that CARELESS gives you normalized structure factor amplitudes; this "normalization" roughly corresponds to a removal (subtraction) of the Wilson B-factor from conventionally processed structure factor

Re: [ccp4bb] Regarding RNA simulation through Gromacs

Hallo Abhilasha Thakur, (I am not a Gromacs user, but I'll nevertheless try to answer) You'll have to identify the Amber99 forcefield topology file, and read it to find out the naming of RNA atoms in that file. The error message asks you to change (e.g. using an editor) the atom names in your

Re: [ccp4bb] xds crashes

2022 10:25:17 +0200, Demetres D. Leonidas wrote: >Dear Kay, > >you are right and I do apologize for the misunderstanding. Point 1 and 2 >are sufficient. > >best > >Demetres > >On 11/29/2022 10:00 AM, Kay Diederichs wrote: >> Dear Demetres, >> >> sou

Re: [ccp4bb] xds crashes

s the memory.  It was fulling rapidly. The workaround was to: > >1. unzip the cbf files prior to processing > >2. use maximum number of jobs 1 > >3. use number of processors 4 > >4. run xds_par > >Many thanks for all your help > >Demetres > >On 11/29/2022 9:

Re: [ccp4bb] xds crashes

Dear Demetres, I agree with what James says: this is the operating system trying to to prevent, in an over-zealous way, the forking of too many or too big (in terms of memory) processes. In other words, XDS hasn't changed, but the operating system changed - it applies different limits to its

Re: [ccp4bb] outliers

On Tue, 8 Nov 2022 15:25:03 -0800, James Holton wrote: >Thank you Ian for your quick response! > >I suppose what I'm really trying to do is put a p-value on the >"geometry" of a given PDB file.  As in: what are the odds the deviations >from ideality of this model are due to chance? > >I am

Re: [ccp4bb] PAIREF, Anisotropy and STARANISO

Dear Gerard, I'm not going to comment on what others said in this (new) thread; just trying to make a few remarks about what you write below - On Tue, 4 Oct 2022 17:01:10 +0100, Gerard Bricogne wrote: >Dear all, > > First of all, apologies for breaking the threads entitled "PAIREF -

Re: [ccp4bb] PAIREF - Warning - not enough free reflections in resolution bin

Hi Matt, you cite the message "WARNING: There are only 40 < 50 free reflections ..." but in the next sentence you write "This error ...". Being a program developer myself, I'd like to point out that there is a difference between a warning and an error. An error typically makes the program

Re: [ccp4bb] Problems running CCP4 sc

I believe you need to establish the "environment" before running certain CCP4 programs. Something like source /where/ever/ccp4-8.0/bin/ccp4.setup-sh HTH, Kay On Mon, 26 Sep 2022 21:32:42 +0100, Zhen Gong wrote: >Dear CCP4 developers and users, > >I am trying to run CCP4 sc but encountered an

Re: [ccp4bb] ccp4 installation problem

Hi Robert, you are welcome. It seems that you own (rgampe.rgampe) the directory /software/ccp4-8.0 . You should revert the ownerships in /software/ccp4-8.0 from root.root with sudo chown -R rgampe.rgampe /software/ccp4-8.0 so that in the future you don't need sudo for updates. Your real

Re: [ccp4bb] ccp4 installation problem

Hi Robert, hmm, more ideas: a) check if CCP4 directory is writable, and who the owner is: mount | grep software sudo touch /software/ccp4-8.0/deleteme ls -ld /software/ccp4-8.0 ls -l /software/ccp4-8.0/deleteme sudo rm /software/ccp4-8.0/deleteme b) try sudo su ccp4um c) try sudo -i

Re: [ccp4bb] ccp4 installation problem

Hi Robert, two points - a) before you tried to update, did you source /where/ever/ccp4/bin/ccp4.setup-sh ? The above applies to bash; for (t)csh you need to source /where/ever/ccp4/bin/ccp4.setup-csh That sets the PATH environment variable such that you don't always have to specify the

Re: [ccp4bb] ccp4 installation problem

Hi Robert, Concerning PROBLEM 1: have you tried sudo ccp4um or sudo ccp4i ? HTH, Kay P.S. didn't find Andrey Lebedev's reply on August 30 that you refer to On Fri, 16 Sep 2022 14:11:34 +, Robert Gampe wrote: >Hello Marcin Pedro and the CCP4 community, > > > >PROBLEM 1: I have the same

Re: [ccp4bb] suggestions on refinement of a protein-ligand complex

Dear Deepak, I guess that the spacegroup in the MTZ file that you use for refinement is wrong. I think you should carefully check the output of PHASER, and in particular the PDB file that it wrote. The correct spacegroup is given there (and it may also be P4122 or P4222 or P4322, because

Re: [ccp4bb] ISO model with large groups of atoms in alternative conformations

Dear Pavel, I have seen this in very high-resolution models of triclinic lysozyme but I don't remember the PDB ids. Best wishes, Kay On Tue, 23 Aug 2022 15:02:07 -0700, Pavel Afonine wrote: >Dear community, > > > >I’m looking for an example of a crystal structure where a large group of

Re: [ccp4bb] Regarding the correct space group identification

Dear Sayan, On Thu, 28 Jul 2022 15:12:30 +0530, Sayan Saha wrote: >Dear Sir, > >1. There are no ice-rings. However, diffraction spots seem to be >overlapping. This can be seen during the data processing, as the space >group (C2 or P222) varies even in the consecutive frames. spot overlap

Re: [ccp4bb] Determining space group

indexing ambiguity. Best wishes, Kay On Fri, 22 Jul 2022 19:02:19 +0100, Eleanor Dodson wrote: >Surely once you have indexed one crystal, you can use the facility to check >the next ones indexing against the reference - aka pointless? > >On Fri, 22 Jul 2022 at 16:20, Kay Diederichs >

Re: [ccp4bb] Determining space group

Hi Monika, in June we had a summer school at MaxIV, and one of the topics was serial crystallography - with lectures and tutorials. Maybe you can talk to the people who attended the course, and the organizers, Ana Gonzalez and Thomas Ursby, and ask them for help. It is more difficult to

Re: [ccp4bb] symmetry possibilities

Dear Jorge, what you write makes sense to me, and I cannot answer your questions. This is just to say that the situation you encounter is not completely uncommon, although most crystallographers would abandon such a crystal form, I guess. The technical term that describes this 4-fold twinning

Re: [ccp4bb] find clashes

Hi Henrike, I use CCP4's "contact" program: #!/bin/bash # find bad contacts: list all CA-CA distances < 3.8A between non-adjacent residues # in a well-folded protein, these should be very rare (1 contact in 1000 residues) # KD 20.12.21 grep CA $1 > /tmp/temp.pdb contact xyzin /tmp/temp.pdb <

Re: [ccp4bb] Eiger images and XDS

Hi Patrick, I have not seen similar reports. The 2nd error message has ~/Desktop/dectris-neggia.so, 258): image not found so maybe the ~ is not understood; try to specify more explicitly LIB=/Users/ploll/Desktop/dectris-neggia.so or whatever the name of your $HOME is. Could you try

Re: [ccp4bb] sftools

Dear Eleanor, there appears to be a bug. See the sourcecode of sftools near line 11700: do l=1,ndatasets if (xname(l)(1:lenstr(xname(l))).eq.tmp_xname .and. $ dname(l)(1:lenstr(xname(l))).eq.tmp_dname) then dwavel(l) = tmp_dwave endif

Re: [ccp4bb] Anomalous maps from twinned crystal

Dear Petr, a map needs amplitudes and phases. In the case of the usual maps (2Fobs-Fcalc and Fobs-Fcalc) calculated for twinned data, one can either detwin the amplitudes, or take twinning into account in the Fcalc term. When calculating the anomalous map, I believe that detwinning of

Re: [ccp4bb] Unable to reduce the values of R-work and R-free

Hello Mudassar ali Khan, these R-values after refinement rather indicate a failure of Molecular Replacement. Did you see in aimless.pdf: "WARNING: the L-test suggests that the data may be twinned so the indicated Laue symmetry may be too high Rough estimated twin fraction alpha from

Re: [ccp4bb] Why there are two solutions about heavy atoms in SHELXD

On Wed, 2 Mar 2022 22:56:28 +0800, fu wrote: >Dear Colleagues, > I get two solutions after running SHELX C/D. In both results, the > coordinates of the heavy atoms are centrosymmetric. Why there are two > solutions? > >Best wishes, >Fu Xingke >Institute of Physics CAS Hello Fu, SHELXD

Re: [ccp4bb] Why there are two solutions about heavy atoms in SHELXD

On Wed, 2 Mar 2022 22:56:28 +0800, fu wrote: >Dear Colleagues, > I get two solutions after running SHELX C/D. In both results, the > coordinates of the heavy atoms are centrosymmetric. Why there are two > solutions? > >Best wishes, >Fu Xingke >Institute of Physics CAS Hello Fu, SHELXD

Re: [ccp4bb] SHELXD for help

On Tue, 1 Mar 2022 18:06:34 +0800, fu wrote: >Dear Colleagues, >I have two question. >The first question is, in SHELXD, they use XPREP to calculate the > correlation coefficient(CCano) between the signed anomalous differences at > different wavelengths? What’s the meaning? And how to

Re: [ccp4bb] Updating Ubuntu 18 LTS to 20?

I have updated Ubuntu on notebooks a couple of times from one LTS release to the next. This works well (and is tested) for those packages that are part of the old release, but it does not necessarily work well for packages outside the distribution. apt-mark showmanual should show those manually

Re: [ccp4bb] any issues getting through to the CCP4 servers?

I have the same problem - https://www.ccp4.ac.uk/download/ is not accessible. Kay On Fri, 28 Jan 2022 09:46:17 +0100, Julian Nomme wrote: >Hi, > >I'm still facing the same issue today. >I just can't get access to the download section, the rest of the website >being accessible. >I'm getting the

[ccp4bb] XDS package: new version and support for Apple M1

Dear academic users of XDS, there is an updated version available at https://xds.mr.mpg.de/ . Since the old (current) version will expire in March, it is advisable to download and test the updated version before that. The biggest change is the availability of binaries for the Apple M1

Re: [ccp4bb] Validation of structure prediction

Hi Reza, the term "validation" as used by e.g. crystallographers - namely by checking geometric parameters of a structure derived from experiment(s) - is euphemistic since realistic geometry is a required but not sufficient property of a model - it can be completely wrong even if it has good

Re: [ccp4bb] am I doing this right?

of the >problem, but this sounds worrying. > >I think you're trying to say the same thing here, Kay. Is that right? > >Best wishes, > >Randy > >On 21 Oct 2021, at 08:51, Kay Diederichs >mailto:kay.diederi...@uni-konstanz.de>> wrote: > >Hi Ian, > >it is

Re: [ccp4bb] am I doing this right?

pond to the hardware pixels, they can be any arbitrary subdivision of >the detector surface. > >Best wishes > >-- Ian > > >On Tue, 19 Oct 2021 at 12:39, Kay Diederichs >wrote: > >> James, >> >> I am saying that my answer to "what is the expectation a

Re: [ccp4bb] am I doing this right?

on is NOT Gaussian, but rather >exponential. And that means adding variances may not be the way to >propagate error. > >Is that right? > >-James Holton >MAD Scientist > > > >On 10/18/2021 7:00 AM, Kay Diederichs wrote: >> Hi James, >> >> I'm a bi

Re: [ccp4bb] am I doing this right?

Hi James, I'm a bit behind ... My answer about the basic question ("a patch of 100 pixels each with zero counts - what is the variance?") you ask is the following: 1) we all know the Poisson PDF (Probability Distribution Function) P(k|l) = l^k*e^(-l)/k! (where k stands for for an integer

Re: [ccp4bb] am I doing this right?

If you write/analyze/improve a data-reduction program in crystallography, then these questions are important: how to estimate the intensity of a Bragg spot by evaluating the counts in the pixels of the signal area, and those of the background area? When calculating mean and standard deviation

Re: [ccp4bb] am I doing this right?

Biology, University of Gothenburg >Box 462, 40530 Göteborg, Sweden >Tel: +46-31-786-3959 / M: +46-70-912-3309 / Fax: +46-31-786-3910 >Web: http://katonalab.eu, Email: gergely.kat...@gu.se > >From: CCP4 bulletin board On Behalf Of James Holton >Sent: 15 October, 2021 18:06 >

Re: [ccp4bb] COOT running on Macbook Pro M1 chip

Dear Wim, on my M1 Macbook Air, coot 0.9.6 (latest from CCP4) works smoothly/fast. What is your XQuartz version? I have 2.8.1 . HTH, Kay On Thu, 16 Sep 2021 15:40:53 +0800, WENHE ZHONG wrote: >Dear CCP4 community, > >The COOT is not running smoothly on my M1 chip Macbook. For example, when

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

Dear Eleanor, Thanks for pointing out that CCP4 FreeRflag selects the test set in the highest possible symmetry for the crystal class! I didn't know that. The following sentences (which are somewhat difficult to understand for me) in https://www.ccp4.ac.uk/html/freerflag.html appear to

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

;did you have something else in mind Kay? > >Cheers, > >Andrew > >> On 30 Aug 2021, at 13:59, Kay Diederichs >> wrote: >> >> Hi Jon, >> >> generally I agree that the accuracy of the data is inversely related to the >> danger of ove

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

Hi Jon, generally I agree that the accuracy of the data is inversely related to the danger of overfitting, and that selection in shells is not necessary. But if twinning is suspected, as here, and/or a choice between high and low symmetry spacegroup has to be made, one has to make sure that

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

Hi Jeffrey, good question. Both twinning and NCS may couple reflections across free and working sets, and this should be avoided by proper selection - otherwise Rfree is biased towards Rwork. Selecting thin shells should be a good option, and can be done in SFTOOLS (or DATAMAN, or SHELXPRO).

Re: [ccp4bb] AW: [ccp4bb] Antwort: Re: [ccp4bb] chain on 2-fold axis?

tes one (and just on!) orientation for >> the 5th chain. Thank you all for your suggestions. >> >> Have a nice evening, >> Peer >> >> -"CCP4 bulletin board" <mailto:CCP4BB@JISCMAIL.AC.UK%0b>> <mailto:CCP4BB@JISCMAIL.AC.UK>> schrieb:

Re: [ccp4bb] chain on 2-fold axis?

Dear Peer, I suspect that the true spacegroup has lower symmetry than P3221, and that there may be twinning masked by tNCS. Subgroups of P3221 are C2 and P32 (

Re: [ccp4bb] Entries pointed out on pubpeer

Proteopedia (https://proteopedia.org/wiki/index.php/Main_Page) can be used for commenting individual PDB entries. See also https://proteopedia.org/wiki/index.php/Retractions_and_Fraud and https://proteopedia.org/wiki/index.php/Proteopedia:Comments_on_Published_Structures best wishes, Kay On

Re: [ccp4bb] Generate adx code

as of 093757merged_9) When I used your compiled generate_adx (that you provided kindly via personal email), I don't see newly generated files. Best, Doo Nam -- Kay Diederichshttp://strucbio.biologie.uni-konstanz.de email: kay.diederi...@uni-konstanz.de Tel +49 7531 88 4049

Re: [ccp4bb] Generate adx code

Hi Doo Nam, it seems that your frames do not have an extension (like .cbf or .img or.xyz). Maybe this is related to the fact that the program does not properly add the extension .adx ? It is puzzling for me since I made an attempt to take this possibility into account: if

Re: [ccp4bb] pdb2ins "cannot open self"

Hi James, have never seen this ... could you try the solution at https://community.snowflake.com/s/article/Snowsql-installed-via-RPM-fails-with-Cannot-open-self-usr-lib64-snowflake-snowsql-snowsql i.e. exclude from prelink? HTH, Kay On Mon, 28 Jun 2021 11:51:19 -0700, James Holton wrote:

Re: [ccp4bb] TWIN?

Hi Almudena, if it is a packing problem, you need to find the correct subgroup of P6522 (179). Take a look at https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Space_group_determination#Subgroup_and_supergroup_relations_of_these_space_groups . Subgroups of 179 are 20, 153, 154, 170,

Re: [ccp4bb] Coot crashes on CentOS 7.9

try to use NVidia driver from ELRepo. Time being I will use the one bundled with CCP4-7.1. Once again thanks for the help. With regards Karthik On 22-04-2021 02:18 pm, Kay Diederichs wrote: Dear Karthikeyan Subramanian, which processor does your computer have? Look at the output of e.g.

Re: [ccp4bb] Coot crashes on CentOS 7.9

Dear Karthikeyan Subramanian, which processor does your computer have? Look at the output of e.g. "head -20 /proc/cpuinfo". What is "model name"? To my understanding, the main problem is > >*./coot: line 264:  5365 Illegal instruction (core dumped) $coot_bin This means that the compiler,

Re: [ccp4bb] academic users of XDS: time to update the old version

Sorry, I mistyped the old XDS site address. Correct is http://xds.mpimf-heidelberg.mpg.de/ . best, Kay On Tue, 23 Mar 2021 17:12:33 +, Kay Diederichs wrote: >Dear academic users of XDS, > >the latest version of XDS has its release notes now at https://xds.mr.mpg.de >(the o

[ccp4bb] academic users of XDS: time to update the old version

Dear academic users of XDS, the latest version of XDS has its release notes now at https://xds.mr.mpg.de (the old xds.mpimf-heidelberg.de can still be used but is redirected). The download location can also be found there. If your current (academic license) version of XDS is from last year,

Re: [ccp4bb] Linux Distro for setting up workstations - Is CentOS still a good choice?

completely agree! There are actually several potential CentOS replacements, if needed. Kay On Fri, 19 Feb 2021 13:47:25 -0800, Dale Tronrud wrote: >For what it's worth, CentOS 7 will continue to be supported to the >middle of 2024. That will give you time to see how all this shakes

Re: [ccp4bb] Anomalous signal to noise details

Hi David, On Fri, 18 Dec 2020 11:53:08 +, David Waterman wrote: >Hi folks > >The paper "Substructure solution with SHELXD >" >(Schneider & Sheldrick, 2002) describes how > >data can be truncated at the resolution at which [ΔF

Re: [ccp4bb] autoPROC question

Hello Almudena, XDS_ASCII.HKL _has_ all the information. Whether the HKL values of a given record of that file refer to I(+) or I(-) is worked out by the scaling program. HTH, Kay On Sat, 7 Nov 2020 19:07:59 +0100, Almudena Ponce Salvatierra wrote: >Hello everyone, > >I am using autoPROC in

Re: [ccp4bb] CCwork/CCfree

Hi Patrick, the main point is that the values of CCwork and CCfree should be lower than those of CC*, but by as little as possible. Thus they are expected to decrease from about 0.95 at low resolution, to low values at high resolution - how low they decrease, depends on the high resolution

Re: [ccp4bb] [xds] how to specify measuring angle

Dear Doo Nam Kim, actually the results of XDS processing are deterministic for all practical purposes (to be nitpicking, the multi-processor version xds_par may result in slighly different output each time it is run, because for a few calculations the order of operations is influenced by the

Re: [ccp4bb] [xds] how to specify measuring angle

I agree with Tim that Doo Nam Kim's question appears to be directed towards the rotation per frame, which is specified in XDS.INP using OSCILLATION_RANGE= ! (not OSCILLATION_WIDTH!) please see the documentation at

Re: [ccp4bb] font issues in imosflm under xubuntu 18

hmm, should have looked more carefully! Now I see the letters that should be greek (e.g. phi) and look like a strike-through epsilon. Maybe somebody else has xubuntu 18 without this problem? Do you use non-standard repositories? Kay On Tue, 29 Sep 2020 14:34:07 +0100, Kay Diederichs wrote

Re: [ccp4bb] font issues in imosflm under xubuntu 18

Wim, I can see your message and the attachment on the CCP4BB mailing list's website at https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=ind2009=CCP4BB=D=145319 . If the attachment is deleted in emails, it may be a local problem (I can't check this now because I only receive the daily

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

we use the Mate desktop; this interacts well with the composite extension. HTH Kay On Thu, 30 Jul 2020 16:01:20 +0200, Marian Oliva wrote: >Thanks Matthias & Pedro, > >Yes, this was the initial point. I needed to connect the monitor through a DVI >port and not through the display port. > >Now

Re: [ccp4bb] AW: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 >>>> >>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1=DwMFaQ=Dbf9zoswcQ-CRvvI7VX5j3HvibIuT3ZiarcKl5qtMPo=HK-CY_tL8CLLA93vdywyu3qI70R4

Re: [ccp4bb] AW: [ccp4bb] [EXTERNAL] Re: [ccp4bb] number of frames to get a full dataset?

Dear Dirk, XDS_ASCII.HKL (and equivalent files from other processing software) gives you all the information that you're after, since every reflection is stored individually. However when you analyze that, you will find that in a data set that comprises less than 360 degrees of rotation, there

Re: [ccp4bb] I cannot download xds

The problem could be that your current network / firewall does not allow FTP transfer, whereas it does allow HTTP. HTH Kay On Sun, 28 Jun 2020 13:56:34 -0500, Murpholino Peligro wrote: >Dear Gianluca and bogbasic, the provided link will send to a page where if >you click on

Re: [ccp4bb] Space group/Unit cell

Dear Maria, maybe a case of underpredicted/overlooked reflections? It could then be P2x2x2x instead of I222/I212121. Have you checked the predictions? best, Kay On Fri, 22 May 2020 10:08:40 +, Demou, Maria wrote: >Dear all, >I have a question that may have a straight forward answer,

Re: [ccp4bb] linux issue- Ubuntu specific?

Hello Tom, I have Ubuntu 18.04.4 and ccp4-7.0 is fully updated. ccp4i works without problems. I never installed tcl on this machine, and when I 'locate tcl', I see /usr/local/ccp4-7.0/ccp4-7.0/bin/tclsh /usr/local/ccp4-7.0/ccp4-7.0/bin/tclsh8.4 /usr/local/ccp4-7.0/ccp4-7.0/lib/itcl3.4

Re: [ccp4bb] Coot 0.9 Released

has anybody tried to run coot-0.9 on Windows under WSL2 ( https://pureinfotech.com/install-windows-subsystem-linux-2-windows-10/ ) ? WSL2 is supposed to provide good compatibility between Windows and Linux. To try this, one needs to become participant of the Windows Insider Program (

Re: [ccp4bb] [3dem] Which resolution?

I'd say that it depends on your state of knowledge, and on their I and sigma. - if you know the space group for sure before you do the measurement of the systematic absences, their I and sigma don't matter to you (because they don't influence your mental model of the experiment), so their

Re: [ccp4bb] [3dem] Which resolution?

we can use model B factors to validate structures - see Analysis and validation of macromolecular B values R. C. Masmaliyeva and G. N. Murshudov Acta Cryst. (2019). D75, 505-518 https://doi.org/10.1107/S2059798319004807 HTH Kay On Sun, 8 Mar 2020 09:08:32 +, Rangana Warshamanage wrote:

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