Re: [ccp4bb] atom names for beta-D-xylopyranose

Hi Andrew, I can only make a guess: As the atom that actually should be "O1" is called "O4A", and all the other atom names look fine apart from a "B" added to the them, it looks as if this residue was derived from a disaccharide, where the XYP part was linked to O4 of another residue. But I agr

[ccp4bb] Workshop on Advanced Topics in EM Structure Determination November 9-14, 2014

Please note that the ap plication deadline is approaching for the Workshop on Advanced Topics in EM Structure Determination, hosted by the The National Resource for Automated Molecular Microscopy, to be held November 9-14, 2014. If you would like to attend the workshop, please make sure to get y

[ccp4bb] possible twinning issue in P4212 / I422

Dear All, I have a strange potential twinning issue that I cannot understand. I've searched high and low on all the internets to find an answer but have come up empty-handed, so I look to the wisdom of The Board to enlighten me. I have a 4'ish Å dataset that processes nicely in P 4 21 2 (#90).

Re: [ccp4bb] Observations-to-parameter ratio in Refmac

Ethan is right. I also have compiled a few estimates how to get to this number pp638 ff 'Estimating the restraint count' in BMC Best, BR -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Ethan A Merritt Sent: Tuesday, June 03, 2014 11:44 AM To: CCP

Re: [ccp4bb] Observations-to-parameter ratio in Refmac

On Tuesday, 03 June, 2014 17:02:56 Klaus Fütterer wrote: > Does someone know whether Refmac outputs the observations-to-parameters ratio > or, failing that, the number of refined parameters in the log file? > > Klaus This turns out to be much more complex than you might think. See: "To B or

Re: [ccp4bb] Searching for DNA structures in the PDB

The rscb has/had a nucleic acid database which included protein dan information. Have you checked that? Eleanor On 3 Jun 2014, at 16:51, Raji Edayathumangalam wrote: > Hi Sophie, > > The crystal structure of winged helix protein/transcription factor HNF-3gamma > bound to DNA comes to mind. Als

[ccp4bb] Observations-to-parameter ratio in Refmac

Hi CCP4BB readers, Does someone know whether Refmac outputs the observations-to-parameters ratio or, failing that, the number of refined parameters in the log file? Klaus === Dr. Klaus Fütterer Deputy Head of School Undergr

Re: [ccp4bb] negative density around disulfide bond

Hi Eze - I’m glad to see you solved your problem. On Jun 2, 2014, at 9:07 PM, Eze Chivi mailto:ezech...@outlook.com.ar>> wrote: Thanks to everyone for the useful information. I refined my structure in the reduced form (using the method suggested by Pavel). Negative density disappeared, and als

Re: [ccp4bb] Searching for DNA structures in the PDB

Hi Sophie, The crystal structure of winged helix protein/transcription factor HNF-3gamma bound to DNA comes to mind. Also, other transcription factors of that ilk would be worth looking at. Also, if you are looking for proteins that bend DNA in a sequence-independent manner, one of the best examp

Re: [ccp4bb] baverage: no tables were found in this file

Thank you guys! Fix it already! It is the problem that a space was put into my file paths. When I move the files to other place as you guys said, it works! Bing From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Eugene Krissinel [eugene.krissi

[ccp4bb] atom names for beta-D-xylopyranose

Does anyone out there have some insight into, or a credible explanation for, why PDB ligand id XYP (beta-D-xylopyranose) has what seems like non-standard atom notation, at least compared to other sugars! The standard atom naming convention for nearly all monosaccharides, including XYS (alpha-

Re: [ccp4bb] baverage: no tables were found in this file

Positive I'd imagine -- Eugene On 3 Jun 2014, at 13:48, Ed Pozharski wrote: Would a no-space symlink resolve this? Sent on a Sprint Samsung Galaxy S® III Original message From: Mark J van Raaij Date:06/03/2014 8:03 AM (GMT-05:00) To: CCP4BB@JISCMAIL.AC.UK

[ccp4bb] Searching for DNA structures in the PDB

Hello, I was wondering if anyone knows of a method that can be used to search the PDB for DNA/RNA structures (essentially a Dali search for DNA/RNA)? I have recently obtained a 2.3 A protein structure bound in complex with DNA. X3DNA has shown the DNA to be B-form generally but the 3DNA output a

[ccp4bb] HERCULES HSC16: Non-atomic resolution scattering for biology "New deadline: 15th June"

Dear all, A HERCULES special course on non-crystallographic X-ray and neutron scattering techniques for structural biology is organised by the ESRF, ILL and EMBL-Grenoble from the 14th to the 19th of September. New dead line for registration: 15th of June. Objective of the course: This HERCU

Re: [ccp4bb] baverage: no tables were found in this file

Would a no-space symlink resolve this? Sent on a Sprint Samsung Galaxy S® III Original message From: Mark J van Raaij Date:06/03/2014 8:03 AM (GMT-05:00) To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] baverage: no tables were found in this file completely agree with avoi

[ccp4bb] How to grow crystals for serial crystallography, neutron diffraction and other exciting techniques

Students, postdocs and scientists interested in the latest crystal-growth methodologies and advances regarding serial crystallography, neutron diffraction and other exciting techniques may wish to *join ICCBM15* (Sep. 17 - 20, Hamburg, www.iccbm15.org). Early bird registrations deadline is July

Re: [ccp4bb] baverage: no tables were found in this file

This may not work if a program implements its own algorithm for parsing command line parameters Sent on a Sprint Samsung Galaxy S® III Original message From: Tim Gruene Date:06/03/2014 8:27 AM (GMT-05:00) To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] baverage: no tables

Re: [ccp4bb] baverage: no tables were found in this file

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Eleanor, yes, it does. At least on Linux and OpenBSD (i.e. 'real' UNIX) typing #> mkdir "dir with spaces" #> cd dir\ with\ spaces/ #> touch "file with spaces" #> echo "Some text" > file\ with\ spaces causes no problems at all. Changing code reliabl

Re: [ccp4bb] baverage: no tables were found in this file

I thought the addition of " ..." around file names got round this problem eg "This_is_Mine.pdb" and "That is Yours.pdb" Eleanor On 3 June 2014 13:15, Eugene Krissinel wrote: > I am afraid that it is us who will need to conform eventually :), same to > say about "Program Files (x86)" and the

Re: [ccp4bb] experimental phasing at low resolution

Dear Vijay, I managed success on a large, 4.5 Ang SeMet phasing years ago. I strongly recommend trying to get a heavy atom derivative - even a crappy one - that allows you to use difference Fouriers to find your Seleniums. For me this was the only approach that worked, and it required bootst

Re: [ccp4bb] baverage: no tables were found in this file

I am afraid that it is us who will need to conform eventually :), same to say about "Program Files (x86)" and the overall culture in Windows, the system where some 40% () of CCP4 users have chosen to work. Eugene On 3 Jun 2014, at 13:03, Mark J van Raaij wrote: > completely agree with avo

Re: [ccp4bb] baverage: no tables were found in this file

Dear Felix, I, too, do not use spaces and file names in Russian :) However, these things are coming nearly for free and automatic with today's development tools, so little effort, if any, is required to adopt them, while the benefits in terms of user friendliness and convenience are not exactly

Re: [ccp4bb] baverage: no tables were found in this file

I'm wondering if GUI2 will cope with accents as well as spaces (e.g. in the Spanish "carpeta sin título" which is the default new folder on Macs)? Discipline. That's what we need... On 3 Jun 2014, at 13:03, Mark J van Raaij wrote: > completely agree with avoiding spaces in paths and file names,

Re: [ccp4bb] baverage: no tables were found in this file

Hi Felix Couldn't agree more, particularly when non-native anglophones have to contend with limiting themselves to ASCII characters in their filenames anyway (e.g. Spanish users have to carefully rename the OSX unnamed folder (carpeta sin título) to something without an accent...) On 3 Jun 20

Re: [ccp4bb] baverage: no tables were found in this file

completely agree with avoiding spaces in paths and file names, but Google Drive is very handy for sharing files, so every once in a while I forget to move a file someone shares with me before running Unix programs on it and get strange errors. Depending on how awake one is at the time finding ou

Re: [ccp4bb] baverage: no tables were found in this file

Possibility to have file names with the spaces is a curse put on the community by Microsoft, and it will be a big mistake to introduce this to CCP4 (my opinion). I guess there are much more important things new CCP4 GUI should deal with. If CCP4 GUI will start to go this way, file names with spa

Re: [ccp4bb] baverage: no tables were found in this file

I take this chance to to confirm once more, as publicly as possible, that file paths with spaces are discouraged in today's CCP4. This inconvenience originates from ancient times in computing when good half of CCP4 was written and when spaces were disallowed on file system nodes. Please take a

Re: [ccp4bb] experimental phasing at low resolution

Don't forget that your SeMet has real differences from your native - the S to Se brings in 18 extra electrons (less obviously if there is lower incorporation). But that mean if your native is isomorphous enough (you didn't say) then you possibly have 'ordinary' isomorphous differences to work wi

Re: [ccp4bb] experimental phasing at low resolution

First, I wouldn't worry about the extent of SeMet incorporation. If you have followed an established protocol (either using an auxotroph or regular strain) the incorporation should be fine. For your SeMet data, what is the redundancy and resolution? In my experience it is often very hard to fi

Re: [ccp4bb] experimental phasing at low resolution

Dear Kay , I have used SG P6322 for run and P3 is the typo error. regards  Vijay On Tuesday, 3 June 2014 3:53 PM, Kay Diederichs wrote: Hi Vijay, I think your data may be good enough to solve the substructure and get phases, but 1) you should be using the latest versions of SHELXC SHEL

Re: [ccp4bb] experimental phasing at low resolution

Hi Vijay, I think your data may be good enough to solve the substructure and get phases, but 1) you should be using the latest versions of SHELXC SHELXD SHELXE - it seems you are using SHELXD-2006/3 . 2) you could try more cycles (100 is on the low side) 3) you might want to try searching for le

Re: [ccp4bb] [ccp4bb] phaser issue MR

Dear Almudena, We actually have a tutorial that goes through the process of defining a solution step by step: http://www.phaser.cimr.cam.ac.uk/index.php/MR_using_keyword_input. The .sol file is a small text file that just contains the description of how a defined ensemble should be rotated and

Re: [ccp4bb] R-merge,R-meas > 1 in outermost resolution shell

Dear sreetama, I have published data with Rmerge > 5 in the outer resolution shell and could reason this the way Phil Evans explained to you yesterday. Best regards, Tim On 06/03/2014 11:19 AM, sreetama das wrote: > Dear All, > What are reasonable values of Rmerge in the outermost

[ccp4bb] R-merge,R-meas > 1 in outermost resolution shell

Dear All,   What are reasonable values of Rmerge in the outermost resolution shell? Some of the recent discussions suggest using data up to those shells where ~2 and CC1/2 = 0.5. But I am getting Rmerge & Rmeas > 1 in the outermost shell for those values of and CC1/2. Reducing t

[ccp4bb] Fwd: [ccp4bb] phaser issue MR

Dear all, thank you for your suggestions, I finally fix the problem as follows. I'll write a summary here for future reference. 1) Phaser run 1# - I provide different ensembles - I get a solution in which some of them have been placed 2) Phaser run 2# ERROR - I provide the ensembles that were

[ccp4bb] Publishing raw data

Hi Folks, Colleague of mine here at Diamond just pointed out a neat EU funded way of publishing raw data which generates a digital object identifier as part of the process: http://zenodo.org Worked through it myself to see if it "works" and apparently it does: doi:10.5281/zenodo.10271 Thought

Re: [ccp4bb] baverage: no tables were found in this file

This also occurred to me once where the file path had a space,(/Google Drive/), when I moved the file somewhere else it worked. I was using baverage from the CCP4i GUI. Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid

Re: [ccp4bb] baverage: no tables were found in this file

Dear Bing, can you post the exact command you were using, please? Also please check with a different PDB file. In case you are using baverage from the command line, can you make sure you are actually using the program from ccp4 by typing 'which baverage' at the command prompt? Regards. Tim On 06