[ccp4bb] How to compare the same protein crystallized in different conditions?

Hi... Let's say I want to compare the same protein crystallized in different conditions. Same space group, almost same resolution. The global RMSD will be pretty small (around 0.3 Angstroms). There will be some changes in rotamers in some residues and some extra waters here and there... Besides

[ccp4bb] hydrogens?

Hi What is the best way to add hydrogens to a pdb file for a, probably, last round of refinement? Can hydrogens be added in a pH/pka-dependent manner? Something like this ( https://server.poissonboltzmann.org/) but get a pdb file ready for phenix.refine/buster/refmac? Thanks

Re: [ccp4bb] How to install ccp4 in text mode?

Found the instructions at the end of https://www.ccp4.ac.uk/download/installation.html ... sorry. previous email had a typo it was 'never' instead of 'ever' El jue, 22 sept 2022 a la(s) 06:30, Murpholino Peligro ( murpholi...@gmail.com) escribió: > Hi > I want to install ccp4 to a co

[ccp4bb] How to install ccp4 in text mode?

Hi I want to install ccp4 to a computer where I have access only through ssh. ... I have ever done it before... Thanks Computer is running ubuntu 20.04 To unsubscribe from the CCP4BB list, click the following link:

Re: [ccp4bb] what would be the best metric to asses the quality of a mtz file?

murshudov/content/refmac/refmac_keywords.html >> >> If you're looking for a ligand you probably want isomorphism, and in that >> case refining with a reference structure looking for low Rwork is not a bad >> strategy. This will tend to select for crystals containing a molecu

Re: [ccp4bb] what would be the best metric to asses the quality of a mtz file?

de oct. de 2021 a la(s) 10:52, vincent Chaptal ( vincent.chap...@ibcp.fr) escribió: > Hi, > > It's hard to find a single metric... > Ultimately, the quality of electron density maps, lower noise in fo-fc? > > Best > Vincent > > Le 27/10/2021 à 17:44, Murpholino Peli

[ccp4bb] what would be the best metric to asses the quality of a mtz file?

Let's say I ran autoproc with different combinations of options for a specific dataset, producing dozens of different (but not so different) mtz files... Then I ran phenix.refine with the same options for the same structure but with all my mtz zoo What would be the best metric to say "hey this

[ccp4bb] catalog number for bovine trypsin?

Dear all... I want to crystallize trypsin, lots of pdb entries, but so far I have not been able to found the catalog number from which it was crystallized... I see many papers with something like: "Lyophilized bovine pancreas trypsin powder (MW 23 460 Da) was used as purchased (Sigma Chemicals)

Re: [ccp4bb] Generate adx code

If the only problem remaining is the extension of the adx files you can use `rename` to change the extension of all your files (look here https://www.howtogeek.com/423214/how-to-use-the-rename-command-on-linux/). But I think in linux we don't need file extensions. El mar, 20 de jul. de 2021

Re: [ccp4bb] Generate adx code

1) Are you using the latest beta version of adxv? 2) Load the adx file (yes it is an ASCII text file...one for every diffraction image in your working directory) and load also the diffraction image. I also saw the white background after loading the adx file, but after loading the image I got the

Re: [ccp4bb] Generate adx code

Dear Doo Nam Kim, I just followed the instructions at the link provided ! gfortran -O -C generate_adx.f90 -o generate_adx ! Then move the resulting binary to /usr/local/bin or ~/bin ! Usage: go to the directory which has XDS_ASCII.HKL and run generate_adx So you run it, and then open adxv,

[ccp4bb] How to process two datasets 45 degrees apart?

Hi... I have a couple of datasets: A: From 0 to 45 B: From 90 to 135 Can I process them as a unique data set? (with XDS or maybe Mosflm) or should I process them apart and then merge them? Thanks To unsubscribe from the

Re: [ccp4bb] Does anyone know of a "CHARMM bulletin board" ?

Hi Fred.. As an alternative, not mentioned yet, you can use NAMD ( https://www.ks.uiuc.edu/Research/namd/). If I remember correctly it accepts the charmm force fields. I think the documentation is way better... they also have a mailing list ... As a plus... you can download a 'full' version

Re: [ccp4bb] The BDP and the CCPD

n of the BDP, > but you would need to inquire with them. > Best of luck, tom > > Tom Peat, PhD > Proteins Group > Biomedical Program, CSIRO > 343 Royal Parade > Parkville, VIC, 3052 > +613 9662 7304 > +614 57 539 419 > tom.p...@csiro.au > > ---

[ccp4bb] The BDP and the CCPD

Do you know if the BDP ( https://journals.iucr.org/d/issues/2005/12/00/en5128/index.html) and/or the CCPD (https://journals.iucr.org/d/issues/2006/06/00/cy5030/) are still available? Thanks To unsubscribe from the CCP4BB

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 >

Re: [ccp4bb] I cannot download xds

> > > > On June 28, 2020 2:39:56 AM GMT+02:00, Murpholino Peligro < > murpholi...@gmail.com> wrote: >> >> ``` >> ~/Downloads$ aria2c >> ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-INTEL64_Linux_x86_64.tar.gz >> >> 06/27 19:36:10 [NOTICE] Do

[ccp4bb] I cannot download xds

``` ~/Downloads$ aria2c ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-INTEL64_Linux_x86_64.tar.gz 06/27 19:36:10 [NOTICE] Downloading 1 item(s) [#3065b2 0B/10MiB(0%) CN:1 DL:0B] ``` It stays there forever. Is there an alternative download url? Thanks

Re: [ccp4bb] How many microfocus beamlines are in the world?

Scientist > > On 6/24/2020 9:18 AM, Murpholino Peligro wrote: > > I would like to know how many MX beamlines are micro focus? > > > Thanks. > > -- > > To unsubscribe from the CCP4BB list, click the following link: > http

[ccp4bb] How many microfocus beamlines are in the world?

I would like to know how many MX beamlines are micro focus? Thanks. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to

[ccp4bb] number of frames to get a full dataset?

Hi. Quick question... I have seen *somewhere* that to get a 'full dataset we need to collect n frames': at least 180 frames if symmetry is X at least 90 frames if symmetry is Y at least 45 frames if symmetry is Z Can somebody point where is *somewhere*? ...also... what other factors can change

[ccp4bb] How to compare between electron density maps?

I want to compare electron density features of map A from protein A and map B from protein B... Because each map has a different rmsd level... ...what is the best way to compare electron density between maps? Is there a way to normalize maps or something like that? Thanks

[ccp4bb] Dose in diffraction patterns?

Do diffraction patterns publicly accessible contain information about the x-ray absorbed dose? Thanks To unsubscribe from the CCP4BB list, click the following link:

[ccp4bb] Fusion proteins to solubilize your protein

I was wondering how many proteins that help to crystallize the protein of interest are out there... and how effective is the phase extension method (i.e. use MR to get the structure of the fusion protein into its density and the density of the protein of interest...) Is there a way to get this

Re: [ccp4bb] space group "P 21 21 2 A"?

Nov 2019 at 18:16, Murpholino Peligro > wrote: > >> Entry 1gzx has space group P 21 21 2 A ( >> https://www.rcsb.org/structure/1gzx) >> I am lost! >> This is the first time that I see a letter at the end of a (protein) >> space group.

[ccp4bb] space group "P 21 21 2 A"?

Entry 1gzx has space group P 21 21 2 A (https://www.rcsb.org/structure/1gzx) I am lost! This is the first time that I see a letter at the end of a (protein) space group. Can somebody explain this? Please. Thanks To

Re: [ccp4bb] 2Fo-Fc maps in Coot vs. Pymol

I think this is part of the problem. https://pymolwiki.org/index.php/Normalize_ccp4_maps El lun., 30 de sep. de 2019 a la(s) 10:09, Chris Fage (fage...@gmail.com) escribió: > Hi Paul, > > After exporting the maps from Coot, they are directly comparable in Pymol. > That's quite a convenient

Re: [ccp4bb] Are there any proteins capable of crystallizing at a wide range of pH having the same space group?

t; > archive.org suggests the database existed up to December 2018, but > appears to be no more. > > > > What to do when scientific resources associated with published papers > disappear like this? It seems to be a problem that is not very well > addressed. > > > > C

Re: [ccp4bb] What OS do you use?

ce the answers are open, the analysis will involve a lot of curation. > I'm interested in the final results. > > Cheers, > Robbie > > On 22 Sep 2019 04:45, Murpholino Peligro wrote: > > I want to know what operating system you use. > For that I made a poll, it is anonymous, quite sim

[ccp4bb] What OS do you use?

I want to know what operating system you use. For that I made a poll, it is anonymous, quite simple and plus you get to see the results. (link https://forms.gle/7VT4pgbHQQmeAvpp8) I hope you contribute. Thanks To

Re: [ccp4bb] Are there any proteins capable of crystallizing at a wide range of pH having the same space group?

3235 P 43 21 2 17 2.9 6.0 8.7 5.8 Cathepsin K > P00698 P 43 21 2 461 3.0 4.6 8.5 5.5 Lysozyme C > P00772 P 21 21 21 33 4.6 5.9 10.0 5.4 Elastase-1 > please let me know if this helps or if there's any questions about what or > how I did it > > best regards > Michael > --

Re: [ccp4bb] Are there any proteins capable of crystallizing at a wide range of pH having the same space group?

on't know if the crystals will grow > over that range. > >There are a fair number of phage T4 lysozymes variants in the PDB. I > don't think this is considered "overpopulation" but a valuable > contribution to humanity. ;-) > > Dale Tronrud > > On 9/19/2019

[ccp4bb] Are there any proteins capable of crystallizing at a wide range of pH having the same space group?

A quick glance at the entries of hen egg white lysozyme in the PDB show that it can be crystallized at different pH values, but the space group is not always the same. I still have to refine the analysis but I was wondering that maybe there are a few proteins that can crystallize at a wide range

[ccp4bb] change in unit cell volume

Let's say I have a protein crystal from which I collected 30 datasets. If I plot the unit cell volume per dataset the volume rises. My question is: Is there a rule of thumb of some sort* to consider the initial/final datasets isomorphous still? * Something like if the unit cell volume changes

[ccp4bb] Search by name on the PDB fails

Hi all. I was searching for ligands/molecules at www.rcsb.org/pdb/ligand/chemAdvSearch.do (middle tab in blue). If I try to search with the third option, i.e. "name" of the ligand/molecule, it never works. I tried tetraethylene glycol, nitric oxide, cisplatin and even the example provided biotin.

Re: [ccp4bb] How big are my solvent channels in my protein crystal?

t; > > > So, my advice: Stop thinking and just do the experiment. > > > > Ditlev > > > > --- > > > > Ditlev E. Brodersen > > Lektor, Associate Professor > > Department of Molecular Biology and Genetics, Aarhus University > > Gu

[ccp4bb] How big are my solvent channels in my protein crystal?

Dear all. I wonder If any of you know how to calculate the radius along a distance for a bulk solvent channel in a protein crystal. I can see there is a plethora of programs* to find channels, pores, clefts and all the related holes within a protein, but how can I take a look at this for the

[ccp4bb] D37

I just found a paper* where this metric, D37, is used. Third page, line #8: D37 (the radiation dose which reduces the activity to 37% of the control value" * http://www.jbc.org/content/257/22/13297.full.pdf The question is why 37? why not 50 or something else? Thank you.

Re: [ccp4bb] data processing with split/bad crystals

Link provided not working. Need the http prefix, like this http://www.crystal.chem.uu.nl/distr/eval/ El mar., 17 de jul. de 2018 a la(s) 11:24, Kroon-Batenburg, L.M.J. (Louise) (l.m.j.kroon-batenb...@uu.nl) escribió: > Dear Tommi, > You may want to try EVAL: www. cryst.chem.uu.nl/distr/eval >

[ccp4bb] how much red my idxref should show?

As the wiki says "The right side of the tab shows the indexed (black) and not-indexed (red) reflections of SPOT.XDS ." I have a few data sets to contrast this.

Re: [ccp4bb] what's the difference between ccp4's coot and a normal coot?

ot set this, the shifting can get very slow with > some graphics cards, in case an atom label is displayed. > > Best, > Tim > > On 06/06/2018 08:25 PM, Murpholino Peligro wrote: > >> @MW: `bzr checkout bzr+http://oisin.rc-harwell.ac.uk/bzr/series-70/trunk >> <

[ccp4bb] what's the difference between ccp4's coot and a normal coot?

I installed coot from here ( https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/devel/build-info.html). After installing a few libraries with `sudo dnf whatprovides missinglib` got coot working. But it does not feel the same as ccp4's coot. It feels a little bit slow. I am asking if there

Re: [ccp4bb] libncurses.so.5 error with imosflm

ommand > dnf provides libncurses.so.5 > tells you that ncurses-compat-libs is the name of the package? Is that > correct? > > best, > Kay > > > > On Sat, 19 May 2018 00:16:24 -0600, Murpholino Peligro < > murpholi...@gmail.com> wrote: > > >Thanks. Some

Re: [ccp4bb] libncurses.so.5 error with imosflm

Thanks. Somehow I do not have version 5 of the 64 library in /usr/lib64 [murph@localhost d01]$ ls -1l /usr/lib64/libncurses* -rw-r--r--. 1 root root 137936 Feb 26 09:24 /usr/lib64/libncurses++.a -rw-r--r--. 1 root root 409554 Feb 26 09:24 /usr/lib64/libncurses.a -rw-r--r--. 1 root root 137936 Feb

Re: [ccp4bb] libncurses.so.5 error with imosflm

ctory that the file is in. > > Harry > -- > Dr Harry Powell > Chairman of European Crystallographic Association SIG9 (Crystallographic > Computing) > > On 18 May 2018, at 16:23, Murpholino Peligro <murpholi...@gmail.com> > wrote: > > hello dear ccp4 users! > Do

[ccp4bb] libncurses.so.5 error with imosflm

hello dear ccp4 users! Does anybody know how to solve this issue? In a Fedora box, a simple `sudo dnf install libncurses.so.5` installs the missing library...but the error still pops up.

Re: [ccp4bb] Problem with installation in Fedora 25

I guess it was a problem with the directories name. (Changed the locale when downloading... Did it all over again and it works). 2017-05-09 16:21 GMT-05:00 Murpholino Peligro <murpholi...@gmail.com>: > The installation process remains here > ...(attached image) > > Is

Re: [ccp4bb] radiation damage-induced phasing (RIP) tutorial

ey can send you the files on request. > > Cheers > > Christian > > > > Am 28.04.2017 um 17:12 schrieb Murpholino Peligro: > > Hi lads... > Do you know if there is a good tutorial for doing RIP somewhere on the > internet? > What programs can do RIP? > -SHELX > -AutoRickShaw > -? > > Thanks > > >

[ccp4bb] radiation damage-induced phasing (RIP) tutorial

Hi lads... Do you know if there is a good tutorial for doing RIP somewhere on the internet? What programs can do RIP? -SHELX -AutoRickShaw -? Thanks

[ccp4bb] X-rays and matter (the particle-wave picture)

Hello Everybody! I was trying to make some sense from Bernhard Rupp's book page 251. I will copy the relevant part... When photons travel through a crystal, either of two things can happen: (i) nothing, which happens over 99% of the time; (ii) the electric field vector induces oscillations in

Re: [ccp4bb] Equation Editor woes with Office 2011 for Mac

Certainly LyX is very nice for beginners, and yes you can start typing without reading the manual (Although I do recommend reading the manual). But there are lots of problems with compatibility (like Lyx 2.X cannot open Lyx 1.6.x files or something like that). And sometimes if you do

Re: [ccp4bb] Equation Editor woes with Office 2011 for Mac

sharelatex makes them learn latex, because they can see the output and the input... also they can play with lots of examples 2015-05-18 9:57 GMT-05:00 Thomas, Jens jens.tho...@liverpool.ac.uk: Hi Randy, It's not ideal, but until the bug gets fixed or there's a more elegant solution,

Re: [ccp4bb] how to properly remove balbes from ccp4i installation?

thanks. :-] 2015-05-15 12:20 GMT-05:00 Marcin Wojdyr marcin.woj...@diamond.ac.uk: Hi Murpholino On Wed, May 13, 2015 at 07:30:06PM -0500, Murpholino Peligro wrote: and ubuntu/windows7 dual setup). So B and I were trying to make some space...by deleting the 3GB Balbes folder (sudo rm -rf

[ccp4bb] how to properly remove balbes from ccp4i installation?

Hello! Friend B installed linux on the laptop of friend A. Then I installed ccp4i/arpwarp/balbes in the laptop of friend A. Now the problem is that / is running short on space (some weird thing with respect to the ssd ~15Gb and ubuntu/windows7 dual setup). So B and I were trying to make some