[ccp4bb] Fwd: divulgacao bolsa, obrigada

Dear all I'd like to draw your attention to the postdoc position in protein crystallography, currently open in my group at UCIBIO-NOVA (Faculty of Science and Technology, NOVA University of Lisbon, Portugal). I am a young PI interested in protein-ligand interactions for structural-based drug

[ccp4bb] Fwd: Postdoc in Cryo-EM of Membrane Proteins at the Max Planck Institute for Biophysics

Forwarded Message > Dear colleagues,  > > My group is looking for a postdoc interested in doing subtomogram averaging > on membrane proteins.  > > Naturejob post:  > https://www.nature.com/naturejobs/science/jobs/626553-postdoc-in-cryo-em-of-membrane-proteins-in-situ > > Inform

[ccp4bb] Fwd: Granada Crystallization Boxes?

Dear friends, I am resending this post just in case any of you have Granada Crystallation Boxes (GCBs) in your lab supplies that you do not need. The NASA protein crystal growth community could really use them. Please see my message below. Thank you, Gloria -- Forwarded message ---

[ccp4bb] Fwd: Please register - 7th Annual SBMB Workshop - July 13 - Omaha, NE

You are invited to attend this year's Structural Biology and Molecular Biophysics workshop and below is a link where you can register to attend. The meeting is free with breakfast, lunch and afternoon snacks provided. We need you to register to know how many are attending and to make name tags, etc

[ccp4bb] Fwd: biotech opportunity

From: Steven McKnight mailto:steven.mckni...@utsouthwestern.edu>> Subject: favor Date: June 2, 2017 at 3:21:39 PM CDT To: Michael Rosen mailto:michael.ro...@utsouthwestern.edu>> Cc: Joseph Ready mailto:joseph.re...@utsouthwestern.edu>> Mike – could you share this e-mail message with late-stage

Re: [ccp4bb] Fwd: [ccp4bb] shadow at the edge

Depends on the geometry of the goniometer/pin relative to the X-ray beam. If the pin is too close, it will possibly cast a shadow. If the pin is aligned at a shallow angle relative to the X-ray source beam, the pin or the goniometer may get in the way regardless of how far away the crystal is from

[ccp4bb] Fwd: [ccp4bb] Contouring 2Fo-Fc map, large blobs in Fo-Fc

I searched for 4 copies, but Phaser only found 3. It's possible there is an additional copy of the molecule in the ASU On Wed, Apr 26, 2017 at 2:40 AM, Randy Read wrote: > Dear Roger, > > You didn’t mention this, but did you search for 2 copies (or an even > number of copies) and, if so, did Pha

[ccp4bb] Fwd: Structural Bioinformatics Training Workshop & Hackathon 2017 - Application of Big Data Technology and 3D Visualization

*Structural Bioinformatics Training Workshop & Hackathon 2017 - Application of Big Data Technology and 3D Visualization* San Diego Supercomputer Center/University of California, San Diego, June 26 - 28, 2017 *Application deadline: April 30, 2017.* https://www.etouches.com/mmtf2017 This 3-day ha

[ccp4bb] Fwd: Re: [ccp4bb] Glycoprotein expression question

Hi Savvas, Thank you for kindly pointing to our review. Bernhard, in my experience your case is a rare exception rather than the rule, so indeed lucky. Adrian summarised very nicely the wide impact glycans may have on folding, trafficking and/or function. To keep things simple, there is no need to

Re: [ccp4bb] Fwd: Re: [ccp4bb] Structure comparison

Gert, There is nothing wrong with suggesting 45 softwares, as one of those may do exactly what a person needs and save loads of time. Besides, comparing protein structures locally need not involve any superposition method. I would say comparing torsion angles/distances between atoms is a mor

[ccp4bb] Fwd: Re: [ccp4bb] Structure comparison

Rather then now start mentioning yet 45 other 3D superposition softwares, I think a pointer to the Wikipedia should suffice: https://en.wikipedia.org/wiki/Structural_alignment The Russian Doll effect (if you align more residues the comparison stats get worse) is best explained (my opinion) by th

[ccp4bb] Fwd: [ccp4bb] No improvement in R-factor after Refmac.

-- Forwarded message -- From: Polisetty Satya Dev Date: Mon, Mar 20, 2017 at 1:35 PM Subject: Re: [ccp4bb] No improvement in R-factor after Refmac. To: Sudipta Bhattacharyya Hi, I had tried running xtriage but it does not show any sign of NCS. But pointles is showing the followi

Re: [ccp4bb] Fwd: how to calculate a difference map between two heterodimers in heterotetrameric protein

Tricky - perhaps this could be viewed as "anti-averaging" methodologically. Use USF programs MAMA, IMP to generate a mask and optimize the NCS operator (or skip this step if you feel you know yours accurately) Use CCP4's MAPROT to rotate the map of one monomer onto the other Conceivably use U

Re: [ccp4bb] Fwd: how to calculate a difference map between two heterodimers in heterotetrameric protein

This would be pretty difficult, but you know in COOT you can overlap the maps for related chains / hetero dimers/ etc. ( Ask for NCS difference maps in the DRAW menu ] The matrix which converts one set of coordinates to the other is then applied to the electron density so you see the NCS relatd ma

[ccp4bb] Fwd: how to calculate a difference map between two heterodimers in heterotetrameric protein

Dear All, We are working on a tetrameric protein containing 2 heterodimers which are related to each other by 2 fold symmetry. There are difference at the active site between the two heterodimers in the crystals, and we would like to make a difference map to compare one heterodimer to the other.

[ccp4bb] Fwd: CANES MSc/PhD Applications Reminder: Deadline approaching

Applications are now open for the CANES Programme (September 2017 entry) Download our poster here

[ccp4bb] Fwd: Re: [ccp4bb] comparison of different protein states

Dear all, just a side comment to Guillermo's and Debanu´s discussion, which deals with the term "apo". I got the text below from a reviewer, who—as an exception ;-)—was absolutely right: In enzymology, enzymes that require the aid of cofactors such as metal ions or prosthetic groups (e.g.

[ccp4bb] Fwd: [ccp4bb] Calculation of generalised R-factor?

Dear CCP4ers, many thanks to all of you who replied to my request! I wish you a Merry Christmas and a Happy New Year! Dirk. Forwarded Message Subject:[ccp4bb] Calculation of generalised R-factor? Date: Tue, 20 Dec 2016 14:47:00 +0100 From: Dirk Kostrewa Reply-To

Re: [ccp4bb] Fwd: [ccp4bb] Remittance advice - Invitation to edit

P4 bulletin board mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Anindito Sen mailto:andysen.to...@gmail.com>> Sent: Sunday, December 11, 2016 12:45:16 PM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] Fwd: [ccp4bb] Remittance advice - Invitation to edit G

Re: [ccp4bb] Fwd: [ccp4bb] Remittance advice - Invitation to edit

Phishing spam. Don't click. T Tristan Croll Research Fellow Cambridge Institute for Medical Research University of Cambridge CB2 0XY > On 11 Dec 2016, at 17:45, Anindito Sen wrote: > > Guys > > are you all receiving the same??? What on earth is this ? > > Andy > > > >> Begin for

Re: [ccp4bb] Fwd: [ccp4bb] Remittance advice - Invitation to edit

The Nigerian Prince wants your money. Get Outlook for Android<https://aka.ms/ghei36> From: CCP4 bulletin board on behalf of Anindito Sen Sent: Sunday, December 11, 2016 12:45:16 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Fwd: [ccp4bb] Remittance

[ccp4bb] Fwd: Please read, and sign

Begin forwarded message: From: Myron Liptzin mailto:mbli...@me.com>> Subject: Please read, and sign Date: November 15, 2016 at 12:37:50 PM EST To: Raymond Dooley mailto:rdoo...@email.unc.edu>>, Myron Liptzin mailto:mbli...@mac.com>>, Richard Wolfenden mailto:wa...@med.unc.edu>>, White Jim mai

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

From the Washington Post (https://www.washingtonpost.com/news/speaking-of-science/wp/2016/11/09/what-will-president-trump-mean-for-science/): Last year, Trumptold conservative radio host Michael Savage, “I hear

Re: [ccp4bb] [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

Sorry - didn't realise that was going out to the whole list, and just made a liar out of myself. Will bow out now. On 2016-11-10 10:20, Tristan Croll wrote: Hi Elton, I certainly didn't say I agreed with their choice or thought it was a good one. But as someone who grew up in a low-income, low

Re: [ccp4bb] [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

Hi Elton, I certainly didn't say I agreed with their choice or thought it was a good one. But as someone who grew up in a low-income, low-employment environment myself this has the ring of truth to it. I totally agree with you (and worry just as much) regarding the proliferation of anti-exper

Re: [ccp4bb] [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

Hi Tristan, I’m afraid I don’t get the logic in the article you sent. In this case the farmers who are crying for the attention of the people in shiny palaces have voted for one who lives in golden mansions. For me the really worrying thing here is how can so many people be misled by a false

Re: [ccp4bb] [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

From letters in yesterday’s Guardian:- today is 9/11 Make America grate again > On 10 Nov 2016, at 08:00, Marjolein Thunnissen > wrote: > > Dear Bill, > > I fully agree with you, awareness has to be spread and one should not ignore > politics completely, especially when there are so stron

Re: [ccp4bb] [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

In the interests of promoting understanding... the link below is to an article on what is ostensibly a comedy website and contains a bit of coarse language, but nevertheless is quite possibly the most insightful exposition of the situation I've come across. The two-sentence synopsis: don't thin

Re: [ccp4bb] [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

Dear Bill, I fully agree with you, awareness has to be spread and one should not ignore politics completely, especially when there are so strong anti-intellectual (anti-science) statements out there. best regards Marjolein On 10 Nov 2016, at 04:17, William G. Scott mailto:wgsc...@ucsc.edu>>

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

It is better to light a candle than curse the darkness... Enviado desde mi iPhone > El 10/11/2016, a las 01:17, William G. Scott escribió: > > Dear Edward et al: > > I agree we shouldn’t engage in partisan arguments on the CCP4bb. However, I > think it is a mistake, and perhaps a missed oppo

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

Dear Edward et al: I agree we shouldn’t engage in partisan arguments on the CCP4bb. However, I think it is a mistake, and perhaps a missed opportunity, to ignore politics completely. For example, Newt Gingrich is currently in the running for Sec HHS. He has previously written editorials in t

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

We got 4K0F! From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Radu Aricescu Sent: Thursday, 10 November 2016 12:33 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ... Hi JPK, Not sure about them, but I was

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

PDBID of 5HIT. I wonder what the authors thought when they got this ID back from RCSB! > >   > > JPK > >   > > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Robbie Joosten > Sent: Wednesday, November 09, 2016 4:18 PM > To: CCP4BB@JISCMAIL.AC.UK >

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ... There is nothing wrong with discussing sex at work, either theorethical http://www.rcsb.org/pdb/search/structidSearch.do?structureId=1sex or experimental http://www.rcsb.org/pdb

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

edu> Verzonden: woensdag 9 november 2016 21:43 Aan: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Onderwerp: Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ... I Agree with Edward. No discussion of politics, religion, or sex at work. Best wishes,

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

: Wednesday, November 9, 2016 1:24 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ... Eddie Snell for President On Wed, Nov 9, 2016 at 11:02 AM, Edward Snell mailto:esn...@hwi.buffalo.edu>> wrote: As a Brexit and Trumpet af

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

Eddie Snell for President On Wed, Nov 9, 2016 at 11:02 AM, Edward Snell wrote: > As a Brexit and Trumpet affected person having a foot in both countries > ,this topic is too far off the normal discussion on CCP4 and probably > better taken up privately. CCP4 is not a political discussion site.

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

I would concur with Ed. I can understand the emotions, but political shouting should be done elsewhere. Let’s remain civil. Klaus === Dr. Klaus Fütterer Deputy Head of School Undergraduate Admissions Room 717, Biosciences

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; } I totally agree with you, Edward! James Sent from Yahoo Mail for iPhone On Wednesday, November 9, 2016, 5:02 pm, Edward Snell

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

As a Brexit and Trumpet affected person having a foot in both countries ,this topic is too far off the normal discussion on CCP4 and probably better taken up privately. CCP4 is not a political discussion site. With CCP4 the signal is unusually high and the noise low when compared to any discuss

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

You are kidding right? Artem On Nov 9, 2016 11:53 AM, "John Hardin" wrote: > Greetings, > > I fully understand that I will be labeled as ignorant and that I will > likely be hated because of my views, > but I am thrilled that Hillary lost this election. > > The United States has embarked on a p

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

Moral? Donald Trump? Really? On Wed, Nov 9, 2016, 17:53 John Hardin wrote: > Greetings, > > I fully understand that I will be labeled as ignorant and that I will > likely be hated because of my views, > but I am thrilled that Hillary lost this election. > > The United States has embarked on a pa

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

Greetings, I fully understand that I will be labeled as ignorant and that I will likely be hated because of my views, but I am thrilled that Hillary lost this election. The United States has embarked on a path of immorality, and I am excited by the possibility of restoring the moral character a

[ccp4bb] Fw: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

6, 12:25 Subject: Re: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ... Abraham Lincoln was right, or at least this famous quote was attributed to him in a speech he gave in Clinton (yes!), Illinois: "You can fool all of the people some of the time, and some of the people a

Re: [ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

rom:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *Ian > Tickle > *Sent:* Wednesday, November 9, 2016 2:25 PM > *To:* CCP4BB@JISCMAIL.AC.UK > *Subject:* Re: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity > ... > > > > > > Abraham Lincoln wa

[ccp4bb] FW: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

@JISCMAIL.AC.UK] On Behalf Of Ian Tickle Sent: Wednesday, November 9, 2016 2:25 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ... Abraham Lincoln was right, or at least this famous quote was attributed to him in a speech he gave in Clinton (yes

Re: [ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

Abraham Lincoln was right, or at least this famous quote was attributed to him in a speech he gave in Clinton (yes!), Illinois: "You can fool all of the people some of the time, and some of the people all of the time, but you cannot fool all the people all the time." https://www.academia.edu/2506

[ccp4bb] Fwd: [ccp4bb] just out of totally idle curiosity ...

A note of optimism ... in Italy we could survive to Berlusconi ... Best, Roberto. Inizio messaggio inoltrato: > Da: "William G. Scott" > Data: 09 novembre 2016 06.37.30 GMT+01.00 > A: CCP4BB@JISCMAIL.AC.UK > Oggetto: [ccp4bb] just out of totally idle curiosity ... > Rispondi a: "William G. Scot

[ccp4bb] Fwd: [ccpem] Postdoctoral position in cryo-EM of membrane protein complexes at PSI

Prof. Gebhard F.X. Schertler Head of Biology and Chemistry Paul Scherrer Institut Laboratory of Biomolecular Research, BMR OFLC 109 CH-5232 Villigen PSI gebhard.schert...@psi.ch phone +41 56 310 4265 Anfang der weitergeleiteten E‑Mail: Von: "Korkhov Volodymyr (

Re: [ccp4bb] [Fwd: Re: [ccp4bb] FW: New ligand 3-letter code (help-7071)]

> > > > > -Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On > Behalf Of Martyn Symmons > Sent: 22 June 2015 23:39 > To: CCP4BB@JISCMAIL.AC.UK > Subj

Re: [ccp4bb] [Fwd: Re: [ccp4bb] FW: New ligand 3-letter code (help-7071)]

smithkline> > > > > > > > > > > > -Original Message----- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK > ] On Behalf Of Martyn Symmons > Sent: 22 June 2015 23:39 > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] [Fwd: Re: [ccp4bb] FW:

Re: [ccp4bb] [Fwd: Re: [ccp4bb] FW: New ligand 3-letter code (help-7071)]

board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Martyn Symmons Sent: 22 June 2015 23:39 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] [Fwd: Re: [ccp4bb] FW: New ligand 3-letter code (help-7071)] Well the problem is there is a lot more to a ligand than PDB coordinates - little things li

Re: [ccp4bb] [Fwd: Re: [ccp4bb] FW: New ligand 3-letter code (help-7071)]

Well the problem is there is a lot more to a ligand than PDB coordinates - little things like bond orders... In addition people can publish ligands with atoms for which they have no density - so zero-occupancy is allowed too. So who should get priority - the group who publishes a ligand first, or t

Re: [ccp4bb] [Fwd: Re: [ccp4bb] FW: New ligand 3-letter code (help-7071)]

I can't imagine a journal doing that can you? When I work on my supplementary material in a paper I don't expect that the journal will take a bit out and publish it separately to support the work of my competitors. Not out of spite that I was beaten - but because I don't want to take the respon

Re: [ccp4bb] [Fwd: Re: [ccp4bb] FW: New ligand 3-letter code (help-7071)]

Miri raises important points about issues in the PDB Chemical Component Dictionary - I think part of the problem is that this is published completely separately from the actual PDB - so for example I don't think we have an archive of the CCD for comparison alongside the PDB snapshots? This makes it

Re: [ccp4bb] [Fwd: Re: [ccp4bb] FW: New ligand 3-letter code (help-7071)]

Sun., June 21st 2015 Good evening, adding several general points to the thread. (1) Fundamentally PDB unlike other chemical databases insists that all equal structures should have the same 3-letter code and the same atom names - obviously for amino acids and say ATP. (1.1) Needless to say t

Re: [ccp4bb] Fwd: HETATM (.pdb) vs. ATOM (cif) records for modified nucleotides

Dear Xiang-Jun Lu, the part of the mmCIF file comes from a loop "_atom_site.group_PDB". According to the mmCIF dictionary, " The group of atoms to which the atom site belongs. This data item is provided for compatibility with the original Protein Data Bank format, and only for that purpose." I r

[ccp4bb] Fwd: HETATM (.pdb) vs. ATOM (cif) records for modified nucleotides

Recently, I came across and was a bit surprised by the different assignment of HETATM vs. ATOM records for modified nucleotides in PDB vs. PDBx/mmCIF format. Using PDB entry 1ehz (the crystal structure of yeast phenylalanine tRNA at 1.93 Å resolution) as an example, 1MA58 in .pdb has atomic coordin

Re: [ccp4bb] Fwd: Re: [ccp4bb] coot space bar translate rather slow at host machine but not in virtual machine

Dear Marcin, Yes, it worked pretty fine. As for the "side effect" , I could not, for while, observe any degradation. Thank you very much. Jorge On 05/18/2015 03:00 PM, Marcin Wojdyr wrote: That problem has been discussed several times on the coot mailing list. Currently a workaro

Re: [ccp4bb] Fwd: Re: [ccp4bb] coot space bar translate rather slow at host machine but not in virtual machine

Thanks Marcin, I thought I'd patched this already some time ago (shortly after you mentioned it to me), but now that I try to find it in the logs, it seems to have been missed/lost. Paul. On 18/05/15 19:00, Marcin Wojdyr wrote: That problem has been discussed several times on the coot maili

Re: [ccp4bb] Fwd: Re: [ccp4bb] coot space bar translate rather slow at host machine but not in virtual machine

That problem has been discussed several times on the coot mailing list. Currently a workaround is to type: (set-use-stroke-characters 1) in scheme console (Calculate > Scripting > Scheme). (You can also add it to coot settings). As a side effect fonts will look worse. I've just tested a better

Re: [ccp4bb] Fwd: Re: [ccp4bb] coot space bar translate rather slow at host machine but not in virtual machine

Dear Jorge, A virtual machine simulates a physical machine based on the host OS. Almost all the hardware resources is simulated by the virtual machine, BIOS,CPU,RAM Of course, all these instruction will finally be carried out by the really hardware. Your action on the guest OS will fir

Re: [ccp4bb] Fwd: Re: [ccp4bb] coot space bar translate rather slow at host machine but not in virtual machine

Hi Jorge May I suggest you try opensuse 13.1 or 13.2 where vendor graphic card drivers are now part of the kernel. I'm just testing now 13.1 with the latest version of Coot and Pymol work well with the native graphic driver. Also you already have some (not the latest ones) coot and pymol ver

[ccp4bb] Fwd: Re: [ccp4bb] coot space bar translate rather slow at host machine but not in virtual machine

Thanks Carlos Contreras-Martel and Lu Zuokun for pointing me to check graphic driver problems (or update them from the vendor, by the way, controller model Intel HD 4000). Taking some time with this today, I still feel I will have to study further before making changes. This poses me yet other q

[ccp4bb] Fwd: Re: [ccp4bb] coot space bar translate rather slow at host machine but not in virtual machine

Hi Jorge I have several opensuse (11.1, 11.4, 13.1) machines running all of them coot and pymol with out any problem. By sure, your problem come from the graphic driver. If you want to obtain the best from your graphic card you will need to install the vendor graphic card drivers in order to e

Re: [ccp4bb] Fwd: [ccp4bb] XDS Rmeas in space group determination

Dear Chen, On Thu, May 14, 2015 at 10:05:05AM -0400, Chen Zhao wrote: > Thanks a lot for your reply! I am a little surprised to learn that the > centrosymmetry is always considered as a point groups symmetry component. > That might explain why all the anomalous data I have seen have higher Rmeas >

[ccp4bb] Fwd: [ccp4bb] XDS Rmeas in space group determination

From: Chen Zhao Date: Thu, May 14, 2015 at 10:04 AM Subject: Re: [ccp4bb] XDS Rmeas in space group determination To: Kay Diederichs Hi Kay, Thanks a lot for your reply! I am a little surprised to learn that the centrosymmetry is always considered as a point groups symmetry component. That migh

[ccp4bb] Fwd: [ccp4bb] XDS INP

Dear Lu you can freely download the tutorial from here: http://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Main_Page You can check if your detector is supported here: http://xds.mpimf-heidelberg.mpg.de/html_doc/detectors.htm Best Fulvio > Il giorno 07/mag/2015, alle ore 10:33, luzu

[ccp4bb] Fwd: [ccp4bb] Structural classification

Dear Deepa, When classifying structures you need to first ask "why?". For example, if you want to get an idea about evolutionary relations, you must try to find their DNA sequences and analyse those in the light of a multiple sequence alignment (MSA) that follows the protein alignment. In phar

Re: [ccp4bb] Fwd: Structure with high B-factor

On Tuesday, 17 March, 2015 17:34:24 Manish Shah wrote: > Hi All, > > I solved a structure using molecular replacement (Phaser) and the current > R-factor and R-free is 0.2 and 0.25. The electron density looks great for > residues and the ligand, however, the issue is with the B-values. The > avera

[ccp4bb] Fwd: Structure with high B-factor

Hi All, I solved a structure using molecular replacement (Phaser) and the current R-factor and R-free is 0.2 and 0.25. The electron density looks great for residues and the ligand, however, the issue is with the B-values. The average B-value is 110 at this stage of refinement and I could not bring

[ccp4bb] Fwd: CCP4-6.5 Update 005

Dear CCP4 Users An update for the CCP4-6.5 series has just been released, consisting of the following changes * ccp4mg (all platforms) - update to 2.10.4. - improved SMILES parser. - Get monomer from library correctly bonds H atoms. - Badly-named ligands no longer generate bad bonding schemes. -

[ccp4bb] Fwd: [ccp4bb] how to recover my data

Inizio messaggio inoltrato: > Da: "Fulvio Saccoccia, Sapienza" > Oggetto: Re: [ccp4bb] how to recover my data > Data: 05 marzo 2015 13:48:34 CET > A: Smith Lee > > Dear Smith, >It is curious; I am not sure about what I am going to suggest since I > never had that problem but the simplest

Re: [ccp4bb] Fwd: [ccp4bb] adjusting bad Ramachandran angles

Jeremy, apparently I was unclear (and possibly moving off-topic) since I got other emails off list about this. I did not mean to imply that I would use Ramachandran restraints to fix a register error since this obviously needs to be addressed in real space. Rather, inspection of the Ramachandran

[ccp4bb] Fwd: [ccp4bb] adjusting bad Ramachandran angles

Dear Kevin Please re-read my earlier email paying particular attention to the words "explicitly" and "expressly". To my mind, the notion of moving a Ramachandran outlier by moving a dot across a graph (which you feel is a danger) is identical to expressly forcing that residue into a favoured Ra

Re: [ccp4bb] Fwd: Re: coot file names with spaces not readable in ccp4

Dear kas, I just noticed your email was not in response to my previous mail, but a forward, so I may have misinterpreted these few words in their intention when I replied. Cheers, Tim On 01/24/2015 08:10 PM, Kenneth A. Satyshur wrote: > Spaces are not friendly to linux. > kas > > -- > Kenneth A

Re: [ccp4bb] Fwd: Re: coot file names with spaces not readable in ccp4

Dear kas, I don't understand why you say that. Spaces may require a little more typing (the quotes), althouh e.g. the bash automatically inserts them when you expand a file / directory name with the TAB-key, but linux has no personal issues with spaces. Best, Tim On 01/24/2015 08:10 PM, Kenneth

[ccp4bb] Fwd: Re: coot file names with spaces not readable in ccp4

Spaces are not friendly to linux. kas -- Kenneth A. Satyshur, M.S.,Ph.D. Senior Scientist University of Wisconsin Madison, Wisconsin 53706 608-215-5207 --- Begin Message --- Dear Kas, that's probably a bug in CCP4, in that file names ought to be enclosed in single quotes when passed to a program.

Re: [ccp4bb] Fwd: question about calculating electrostatic potentials

cjeff...@uic.edu] Envoyé : dimanche 30 novembre 2014 21:26 À : CCP4BB@JISCMAIL.AC.UK Objet : [ccp4bb] Fwd: question about calculating electrostatic potentials Dear CCP4 users, I have a question about protein electrostatic surfaces. We used Pymol to calculate electrostatic surfaces of several pr

Re: [ccp4bb] Fwd: question about calculating electrostatic potentials

Dear Connie, pymol uses the APBS program to calculate the ESP, which in turn needs a 'pqr'-file as input. This pqr-file contains all atoms with the entries for the B-value replaced with partial charges. It is probably better to compare these partial charges than the redness of the surfaces. Best,

[ccp4bb] Fwd: question about calculating electrostatic potentials

Dear CCP4 users, I have a question about protein electrostatic surfaces. We used Pymol to calculate electrostatic surfaces of several protein structures. Is there a way to calculate the percent of surface that is red, or the area of surface that is red, so that we can quantitatively compare th

Re: [ccp4bb] Fwd: [ccp4bb]

And what is the NC translation vector (in fractional coordinates)? If it is x, 1/2, z then your SG could be P2 - the NC translation will generate absences along the 0k0 diffraction vector. Eleanor On 28 November 2014 at 14:01, rohit kumar wrote: > yes...right know its monoclinic (p21) space g

Re: [ccp4bb] Fwd: [ccp4bb]

yes...right know its monoclinic (p21) space gp. On Fri, Nov 28, 2014 at 7:24 PM, Eleanor Dodson wrote: > Are you testing all SGs? for your known point group? > > Eleanor > > On 28 November 2014 at 13:34, rohit kumar wrote: > >> >> >> Dear all, >> >> i am solving a structure of 2.5 A resolution

Re: [ccp4bb] Fwd: [ccp4bb]

Are you testing all SGs? for your known point group? Eleanor On 28 November 2014 at 13:34, rohit kumar wrote: > > > Dear all, > > i am solving a structure of 2.5 A resolution by PHASER but every time i > got this following warning. > > $TEXT:Warning: $$ Baubles Markup $$ > > ---

[ccp4bb] Fwd: [ccp4bb]

Dear all, i am solving a structure of 2.5 A resolution by PHASER but every time i got this following warning. $TEXT:Warning: $$ Baubles Markup $$ - Large non-origin Patterson peak indicates that translational NC

Re: [ccp4bb] Fwd: [ccp4bb] B-factor blurring

Dear Mike, I am not sure what you mean by 'reference'. When you multiply your data with exp(-Bs^2) with B > 0 you weight your reflections depending on resolution so that high resolution data (probably including noise) are supressed while low resolution data a underlined. Using the term 'B' with it

[ccp4bb] Fwd: [ccp4bb] B-factor blurring

My sincere thanks to all who are responding to my request below. To be explicit, my question relates to B-factor blurring (+B correction), not to B-factor sharpening (-B correction). thanks Mike Begin forwarded message: > From: Mike Lawrence > Subject: [ccp4bb] B-factor blurring > Date: 18

[ccp4bb] Fwd: Re: [ccp4bb] molprobity clashscore, symmetry-related molecules?

This brings me a related issue with COOT: the spherical refinement does not consider symeqs either or does it? Xavier Original Message Subject:Re: [ccp4bb] molprobity clashscore, symmetry-related molecules? Date: Thu, 23 Oct 2014 14:53:53 +0200 From: Jose Manuel Du

[ccp4bb] Fwd: Re: [ccp4bb] Calculating over all bend in a DNA

Dear Sasha, dear all, I meant 'two _sets_ of three atoms each'. Thanks to Mark for pointing this out to me. Best, Tim Forwarded Message Subject: Re: [ccp4bb] Calculating over all bend in a DNA Date: Wed, 22 Oct 2014 10:50:10 +0200 From: Tim Gruene Reply-To: Tim Gruene To: C

Re: [ccp4bb] Fwd: mapsig errors

Hi Scott, it's complaining that the input files are not in the standard CCP4 map format. Since they have the extension 'pdb' and not 'map' could they by any chance be PDB format files? If so then this won't work! Cheers -- Ian On 20 October 2014 14:47, Scott Horowitz wrote: > Hi all, > > I t

[ccp4bb] Fwd: mapsig errors

Hi all, I tried using mapsig for the first time, and I got multiple errors (text pasted at bottom). This is on mac os x 10.8.5, and the CCP4 install is 6.4.0. I followed these instructions to be able to use CCP4 programs at the command line: http://plested.wordpress.com/2012/10/31/run-ccp4-progra

Re: [ccp4bb] Fwd: ipmosflm from ccp4-6.4.0 read image 0 error

hi That's odd. Can you send me the script that you are using (off-bulletin-board), and maybe access to the image and I'll do what I can to help. Harry -- ** note change of address ** Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambrid

[ccp4bb] Fwd: ipmosflm from ccp4-6.4.0 read image 0 error

Hello, I’m forwarding this error on behalf of Jürgen since he seems to have lost the ability to send messages to the bb, saving all of our inboxes some space :) And yes, we do realize that imosflm is more preferred, but would like the participants to be able to use the older version, too. Tha

Re: [ccp4bb] Fwd:

> How we can define NCS in phenix.refine. > phenix.refine uses torsion ncs and top-out restraints target, which all in all means no need to do anything special apart from enabling using ncs in refinement. Details: http://journals.iucr.org/d/issues/2014/05/00/rr5054/index.html Acta Cryst. (2014)

[ccp4bb] Fwd: Re: [ccp4bb] Shelxc failure

Dear Roberto, If you are using shelxc/d/e, it is best to read the XDS.ASCII.HKL file DIRECTLY into shelxc. This is what hkl2map does. When you run shelxe (from the command line or hkl2map), you usually need to try both hands of the heavy atom substructure. If the 'contrast' for one hand is

[ccp4bb] Fwd: [ccp4bb] : MTZ for a protein fragment and R factors, Masking and Maps

George, Remember that scattering from every point in the cell contributes to every reflection; the R-value is a global metric of agreement between the model and the data. Hence, calculating the R-value for a few selected residues is not a sensible thing to do, unless you want to ask how well yo

[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] Fwd: Crystallize proteins with liposomes

My name is Silvina Salinas and I doing my post doctoral research at Universidad Nacional de Córdoba, Argentina. We are studing a protein of 15 kDa with a known crystallography structure. This is a soluble protein, but interact with membranes peripherically. We observed that in the presence of phos

[ccp4bb] Fwd: [ibs.tous] Les Houches SUMMER SCHOOL LAST CALL

Dear all, Find enclosed the last call for the Summer School on Integrated Biology to be held next July in the French Alps. Best regards, Isabel Début du message réexpédié : > De : Eva Pebay-Peyroula > Objet : [ibs.tous] Les Houches SUMMER SCHOOL LAST CALL > Date : 14 mars 2014 08:10:17 HNEC >

Re: [ccp4bb] Fwd: Akta Service

May the gods smile upon you all. My Akta's are in tip top condition, thanks. However, I have a dear friend who is the son of a recently deceased general in Nigeria who has 250 000 000 TWO HUNDRED AND FIFTY MILLION of Aktas that need servicing. Just send post your bank account details, pin number,

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