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

Dear Tom Be aware that python2 is currently not supported. It is end-of-life since 1/1-2020 and is not part of Ubuntu 20.04 This might not be a big concern, bit depends on which software you use. Best regards Folmer lør. 20. feb. 2021 21.50 skrev Peat, Tom (Manufacturing, Parkville) : >

Re: [ccp4bb] coot is drawing the unit cell away from the modelled molecule

Aside from Paul's instructions on how to manually choose a different location from inside *Coot *perhaps using the http://achesym.ibch.poznan.pl/ server would be a good idea for setting a position on the molecule that should be more objective Hope this helps, Folmer man. 1. feb. 2021 14.51

Re: [ccp4bb] how to swap chain IDs

ld be good? Best regards Folmer Fredslund man. 7. dec. 2020 18.49 skrev Christian GALICIA < christian.galicia.diaz.sant...@vub.be>: > Hello, > I'm trying to swap the chain IDs of a structure. I tried changing the IDs > in coot and with PDBset, both change labels of the chains but not

Re: [ccp4bb] Phenix refine distorting a sidechain despite correct density

Dear Igor There's a phenix bulletin board for question like this, which is where you should post the question. ( I crosspost here) I would choose to not do the real space refinement in phenix.refine during the last rounds of refinement of a model, when sidechain positions are essentially

Re: [ccp4bb] I cannot download xds

Dear Murpholino, Perhaps you accidentally came upon a rare server outage? Or perhaps you had a problem locally? Did you try other programs to download or investigate the problem in any other ways? Historically and anecdotally, I've never had issues downloading XDS from the website. I normally

Re: [ccp4bb] Problem with structural alignment

Dear Ishan Would it be possible for you to use a fitting of the atoms of the ligand? I've done that with success before. Hope this helps Folmer man. 16. dec. 2019 07.38 skrev Ishan Rathore : > Hi, > > I am trying to compare multiple homologous structures of a protein, where > I am analysing

Re: [ccp4bb] Coot on Macosx Catalina

Hi Jan If I remember correctly, you need to start the program once by right-clicking, and choosing "Open" from the menu. Then you can choose "trust this program" (or something similar) and you should be able to use it as normal after that small extra step. Hope this helps, Fo

Re: [ccp4bb] Calculating RMSD of a loop

load your already superimposed structures and calculate on the selection you want. Hope this helps, Folmer Fredslund tir. 17. sep. 2019 15.42 skrev Kyle Gregory < 3632e92fcc15-dmarc-requ...@jiscmail.ac.uk>: > Hi all, > > What is the best/easiest way to calculate RMSD of a loo

Re: [ccp4bb] PyMOL now packaged as a snap on Linux

Hi Darren, That's brilliant! I'll give it a spin and see how it works. Best regards Folmer tor. 16. maj 2019 13.02 skrev Darren Hart : > Since yesterday, PyMOL (open source version v2.3) has been packaged as a > distro-independent "snap" that can be installed easily on linux > platforms - no

Re: [ccp4bb] PISA command line

Hi Wolfram, I just tried running pisa 5jju  -analyse 5jju.pdb pisa 5jju -list interfaces with  PISA v.2.1.1 built 05-04-2017   with SSM v.1.4.0, SRS v.1.0.0, MMDB v.2,0.17 on Ubuntu 16.04 and that seems to work as expected. Hope this helps, Folmer On 2018-07-06 19:54, wtempel wrote: Hi,

Re: [ccp4bb] processing hd5 files from Dectris detector

This does depend on knowing the location of the file on the filesystem, and hence not really easily portable. Nonetheless and easy and quick workaround for a local system. Best regards Folmer Fredslund Staff scientist DTU Biosustain fre. 1. jun. 2018 11.04 skrev Harry Powell < 193323b1e6

Re: [ccp4bb] mmCIF and CIF

Dear Oliviero, The suggestion made by Tim Grüne is probably best, you didn't specify exactly what you have in the mmCIF file. Anyway, openbabel should be able to read mmCIF files and write a CIF, (https://openbabel.org/wiki/MmCIF) Best regards, Folmer On 2017-11-14 14:16, Oliviero Carugo

Re: [ccp4bb] RMSD between superposed structures without moving

, but the replies are generally from the developers or very knowledgeable users. Hope this helps, Folmer Fredslund On 2017-08-27 13:09, Johannes Sommerkamp wrote: Hello everybody, I have superposed two structures based on the central beta-sheet CA atoms with the "super" command in Pym

Re: [ccp4bb] Remittance advice - Invitation to edit

Dear all, Just to point out the obvious (I hope) this is spam and points to a scam site trying to acquire your Google account password (in case you have one). Sorry to spam the list, just writing in case anyone stumbles upon it and thinks it's legit. Best regards, Folmer On 2016-12-05

Re: [ccp4bb] Good 3D Monitor for Molecular Modelling

Hi Matt, Have you tried looking at these pages: http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo https://pymolwiki.org/index.php/Stereo_3D_Display_Options HTH, Folmer Fredslund On 2016-10-27 17:20, Matthew Graf wrote: Hello All, I am looking for suggestions on a good

Re: [ccp4bb] completeness drops from conversion from XDS to Fs

Hi Tommi, Could it be the bug that was reported in June? https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1606=ccp4bb===119181 Obviously if you recently updated XDS is can't be that. HTH, Folmer On 2016-10-21 18:00, Kajander, Tommi A wrote: Problem solved, or well, circumvented - for the

Re: [ccp4bb] How many is too many free reflections?

. Hope this helps, Folmer Fredslund 2015-06-02 12:26 GMT+02:00 Graeme Winter graeme.win...@gmail.com: Hi Folks Had a vague comment handed my way that xia2 assigns too many free reflections - I have a feeling that by default it makes a free set of 5% which was OK back in the day (like I/sig(I

Re: [ccp4bb] Cryo-EM

readings related to Cryo-EM.. Thanx in advance -- Regards Faisal School of Life Sciences JNU -- Folmer Fredslund

Re: [ccp4bb] Strange Ancient Diffraction Pattern...

of Biochemistry and Biophysics Stockholm University 106 91 Stockholm Sweden phone: +46-(0)8-162 778 email: gri...@dbb.su.se -- Folmer Fredslund

Re: [ccp4bb] Absence of contact between layers in a crystal

-issues For 2hr0, the Nature letter ( http://www.nature.com/nature/journal/v444/n7116/full/nature05258.html) and the associated structure has not been removed from the archives. Best regards, Folmer Fredslund Disclosure: I published the structure of native bovine C3 (2b39) 2015-02-06 12:08 GMT

Re: [ccp4bb] Absence of contact between layers in a crystal

et al., mention that they actually don't have gaps, but just some low occupancy contaminant that makes crystal contacts. So, even with this structure being fraud, you would not be able to use it as an example of absence of crystal contacts. Best regards, Folmer Fredslund Best regards, Fred

Re: [ccp4bb] rebuild by coot

residues to its sidechain position in the electron density may? In addition, for coot real space refinement, can you tell me how many residues or the length of the fragment one time can process? Dialing -- Folmer Fredslund

Re: [ccp4bb] A Moleman alternative?

Dear Yong, It's easy enough to get it, http://xray.bmc.uu.se/markh/usf/ Even though there's no development or support. Best regards, Folmer Fredslund 2014-11-17 20:55 GMT+01:00 Yong Tang liutan...@gmail.com: Dear all, I have no access to Moleman now but I need to compile a statistics table

Re: [ccp4bb] How to run CCP4 without source command

help you with questions like the one you just asked. Venlig hilsen/Best regards Folmer Fredslund Den 16/11/2014 07.34 skrev 陈昂 angsc...@outlook.com: Dear all: I have installed CCP4 suit on my computer. The OS IS fedora 18. Every time I open the software, I have to use the command source. Does

Re: [ccp4bb] Amino acid side chains without density

for which we are not finding density or people prefer keeping the side chains occupancy zero? Is there any other way to do this? -- Folmer Fredslund

Re: [ccp4bb] R free flag missing after ARP/wARP?

the thought is that the free reflections will be uncoupled during further building and refinement? Best regards, Folmer Fredslund 2014-10-20 4:41 GMT+02:00 luzuok luzuo...@126.com: Dear all, I was using ARP/wARP in ccp4i, the input mtz file certainly has free R flag, but the output mzt

Re: [ccp4bb] how to get a reflection cid file from PDB

wishes! Yamei Yu Sichuan University,Chengdu,610041, P.R.China Tel: 15882013485 Email: ymyux...@gmail.com ymyux...@163.com yamei...@scu.edu.cn -- Folmer Fredslund

Re: [ccp4bb] IUCR bibtex

mail me the iucr.bst file for bibtex. The website hosting this file is not opening. Thank you Regards Kavya -- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- Folmer Fredslund

Re: [ccp4bb] 100.000?

. Then the volume of that pizza is equal to pi*z*z*a ! ** -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -- Folmer Fredslund

Re: [ccp4bb] CCP4 BB email change

, Arnau Casañas, PhD Institute of Molecular Biology and Biophysics ETH Zurich Schafmattstr. 20 HPK H10 8093 Zurich Switzerland +41.44.633845 -- Folmer Fredslund

Re: [ccp4bb] I/sigmaI or I/sigmaI

1-2, 2003 if you browse the CCP4BB archives. Richard Gillilan MacCHESS On Feb 12, 2014, at 6:43 AM, Cai Qixu wrote: Dear all, Does the I/sigmaI in “Table 1” mean for I/sigmaI or I/sigmaI ? Thanks for your answer. Best wishes, Qixu Cai -- Folmer Fredslund

Re: [ccp4bb] resubmission of pdb

accepted? Venlig hilsen Folmer Fredslund On Jan 31, 2014 10:04 PM, Faisal Tarique faisaltari...@gmail.com wrote: Dear all Dear Dr. PDB, Some time back i had submitted a coordinate in PDB but because of unacceptance of the manuscript we had to retract the submission. During this procedure i

Re: [ccp4bb] How to show the ligands (both as sticks and sphere) as shown here in Pymol

like this? Thank you so much! Best, Wei -- Folmer Fredslund

Re: [ccp4bb] OT: Who's Afraid of Peer Review?

, Navdeep --- Navdeep Sidhu University of Goettingen --- -- Folmer Fredslund

Re: [ccp4bb] Docking models into low-res SAD map

/pymol/ To me, that means free. It is also possible to pay for PyMOL http://www.pymol.org/pymol which will give you an easy installer for windows and support amongst other things. Sorry for the OT post, Folmer -- Folmer Fredslund

Re: [ccp4bb] I can not find edstat in ccp4i

of CCP4-6.2 or -6.3. How I can run it under Windows? Thanks -- Folmer Fredslund

Re: [ccp4bb] Off-topic, visualization

/~glasfeld/xsection.jpg Does anyone know of any software that can produce similar images? http://skuld.bmsc.washington.edu/raster3d/raster3d.html Thanks, Arthur Glasfeld Reed College Portland, OR -- Folmer Fredslund

Re: [ccp4bb] a new version of XDS

. best, Kay -- Folmer Fredslund

Re: [ccp4bb] a new version of XDS

, given the short-living license of XDS. ;-) Anyway, I second the request, ciao, s On May 30, 2013, at 8:50 AM, Folmer Fredslund folm...@gmail.commailto: folm...@gmail.com wrote: Hi all, Nice with a new version (I guess that means improvements :-) Before I upgrade, I just have one question

Re: [ccp4bb] Rfree flag

-- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean. -- Folmer Fredslund

[ccp4bb] Building sugars

they are indeed made up of three individual sugars with bonds between them. Thank you for any pointers. Best regards, Folmer -- Folmer Fredslund

Re: [ccp4bb] Building sugars

to the group of the linked protein residue or to have specific groups for your sugar trees. Cheers, Robbie HS. From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Folmer Fredslund Sent: Thursday, February 21, 2013 12:33

Re: [ccp4bb] Boveral in SFCheck

at the discretion of the depositors in question. mvh Folmer Fredslund 2012/12/14 Zhijie Li zhijie...@utoronto.ca ** Hi, Seems not officially retracted from Nature either. On the paper's web page, there was only a line in small font read like this: There is a Brief Communications Arisinghttp

Re: [ccp4bb] manipulation of water molecules in pdb files

-- Folmer Fredslund

Re: [ccp4bb] pymol question

European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990 -- Folmer Fredslund, Post doc The MAX IV laboratory

Re: [ccp4bb] Ubuntu Maverick and coot menus

=== David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu -- Folmer Fredslund Maj Allé 86 2730 Herlev Mobil: (+45

Re: [ccp4bb] Fwd: Installing ccp4-6.0.99e on 64 bit Ubuntu - Bioscreencast Wiki (works for 32-bit also)

, Folmer 2011/10/4 Edward A. Berry ber...@upstate.edu I think I captured most of it in the attached. Hope this doesn't violate anyone's copyright: -- Folmer Fredslund, Ph.D.

Re: [ccp4bb] unusual sighting of a crystal structure

Nice find! ;-) Just in case anyone want to see it IRL http://www.youtube.com/watch?v=4sYSyuuLk5ghd=1t=38s Regards, Folmer 2011/7/16 Artem Evdokimov artem.evdoki...@gmail.com: Fellow structural biologists, I just caught a brief glimpse of a crystal structure (looks like an Fv complex or

Re: [ccp4bb] exploding hydrogens during real space refinement in coot

don't remember which version Coot uses, but here is an old thread on the subject http://www.mail-archive.com/coot@jiscmail.ac.uk/msg00405.html Best regards, -- Folmer Fredslund

Re: [ccp4bb] COOT water retention problem...

Dear Myron, What is wrong with using the Delete Item option from the menu? It's gives you a couple of choices, one of which is waters. Means that you will only delete waters when selecting in the main window. That is the way I do it anyway. Best regards, Folmer Fredslund 2010/11/10 Smith

Re: [ccp4bb] how to superpose density maps?

Hi Mark. This is hidden in the Extensions menu. Extenstions - Maps- Transform map by LSQ model fit Or at least that is what I think you want. Best regards, Folmer Fredslund On 28 January 2010 15:29, Matt Warkentin mattw...@gmail.com wrote: Hi all I have a seemingly simple task that I can't

Re: [ccp4bb] Electron Density Maps

that you want to load you CNS map as a difference map. This section http://www.ysbl.york.ac.uk/~emsley/coot/doc/chapters/user-manual_6.html#SEC160 of the user manual might explain better. Hope this helps, Folmer Fredslund

Re: [ccp4bb] Phaser SAD+MR followed by CNS

Dear Kelly-Anne 2009/3/27 Kelly-Anne Twist wils...@rockefeller.edu: Hello all, I have a structure that has been solved by MR and now have experimental SAD phases that I hope will improve the map. I used Phaser for this from within the CCP4i suite but I would like to take the solution and

Re: [ccp4bb] two identical proteins in one asymmetric unit

Dear Sang They are really different! And I guess you would probably want to use NCS restraints depending on your resolution. Regards, Folmer 2009/3/24 Sang Hoon Joo s...@duke.edu: I am refining my crystal structure in which I have two identical chains in one asymmetric unit. Space group is