Re: [ccp4bb] Problems with refinement of nucleic acid structure

Dear Rafal, with such a small molecule, and if you really have 1.0A resolution, you should be able to solve the structure by direct methods with shelxt. By default, shelxt searches all space groups in the Laue group. The output will not be very practical to assign residue, etc. but at least it mig

[ccp4bb] Brookhaven Lab’s Cryo-EM facility now open for COVID-19-related research

Dear Community: On July 29, Brookhaven National Laboratory opened its new cryo-electron microscopy center , the Laboratory for BioMolecular Structure (LBMS) , with an initial focus on COVID-19-related research through an

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

Hi Marian, If you need to change the desktop the best option is to install that Linux flavor from scratch using a live image. I personally prefer LXDE and it works fine with stereo and I don't have the composite extension enabled in my xorg.conf. Look at the /var/log/Xorg.0.log file and see if y

[ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] Problems with refinement of nucleic acid structure

Dear Rafal, Another few comments from my side: 1) I guess you tried to fit alternative positions for the bases but this did not work? 2) I also guess you refined already anisotropic B-factors? 3) from the figure you send, the absolute value of the difference density looks very low (maybe 10% of

Re: [ccp4bb] AW: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement

To paraphrase from our 2018 Acta Cryst D74(6) paper: “There has been debate as to whether refinement should be performed in real space or reciprocal space; both approaches have advantages and disadvantages. In real space, refinement can be performed locally, which has advantages for computation

Re: [ccp4bb] CCP4 tutorials (files)

Hi Rafael, CCP4 ships with lots of tutorial data. If you launch CCP4i2, then there is a Help/Tutorials menu which will introduce those techniques through CCP4i2, and help you identify file locations if you want to have a crack at command line structure determination. Best wishes Martin On 30

Re: [ccp4bb] CCP4 tutorials (files)

Hello, it should be possible to get the example data, at least for SAD, thru the i2 interface. It worked last week... Best wishes, Jon Cooper. jon.b.coo...@protonmail.com Original Message On 30 Jul 2020, 15:10, Rafael Marques wrote: > Hello folks. > > During the quarantine I a

Re: [ccp4bb] CCP4 tutorials (files)

Hi Rafael, http://legacy.ccp4.ac.uk/docs.php -> tutorials Looks like there’s something very broken with the style sheets or something but the information does appear to be available The links to tar files of data appear to work Best wishes Graeme On 30 Jul 2020, at 15:10, Rafael Marques mai

[ccp4bb] CCP4 tutorials (files)

Hello folks. During the quarantine I am trying to use some softwares on CCP4 that I have never used before and also to learn how to solve structures differently than the usual MR (for me). However, the ccp4 tutorial website is down and error 404 is everywhere. Does anybody know a link where I c

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

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 all the system are recognized, but I am still stuck and it seems to be the composite extension of the desktop manager I am using lightdm and I trie

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

This may be a problem with the cable, but normally you need to use a DVI connection between the graphics card and the monitor. > No dia 30/07/2020, às 14:41, Barone, Matthias escreveu: > >  > Hi Marian > > I used the quadro 4000 myself and had two Acer monitors connected to it, one > with di

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

Hi Marian I used the quadro 4000 myself and had two Acer monitors connected to it, one with display port, one with VGA connector. Only the VGA showed 3D, the other would not. Have you tried going analog with this card? best, matthias Dr. Matthias Barone AG Kuehne, Rational Drug Design Leibn

[ccp4bb] Help With Setting up a Stereo view system

Dear colleagues. I would like to check if some one can help me with the setup of my hardware stereo system in Coot under Ubuntu 14 With the help of a friend I collect a bunch of second hand stuff. 1 NVIDIA 3D Video 2 system. 1 Monitor ASUS VG248 conectes through the display port 1 NVIDIA QUADRO

[ccp4bb] AW: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement

Thank you. I think I will then first try to optimize the weight and then increase the cycles. Herman -Ursprüngliche Nachricht- Von: Tom Burnley - UKRI STFC Gesendet: Donnerstag, 30. Juli 2020 14:35 An: ccp4bb@jiscmail.ac.uk; Schreuder, Herman /DE Betreff: Re: [ccp4bb] AW: [EXTERNAL] Re

Re: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement

Hi Herman, Just a couple of tips for Refmac... 1) increase number of cycles - we find some cases require a lot of cycles, more than you may be used from MX refinement. 2) optimise weight - this is important and at present the autoweighting option is not as reliable for EM refinement as MX.

[ccp4bb] AW: [ccp4bb] AW: [EXTERNAL] Re: [ccp4bb] real real-space-refinement

Hi everybody, Thank you very much for the many tips! I discovered that in Coot by clicking on the N- and C-terminus of a protein chain, one can indeed run a real-space refinement on the complete chain and the same is true for a rigid body fit. However, subsequent refinement with Refmac did not

Re: [ccp4bb] Problems with refinement of nucleic acid structure

Dear all, Thank you for the response. I will try to explain it more precisely. The molecule of interest is a duplex with 9 nt length, but is paired on the length of eight bases, with overhangs at ends. Molecules form a parallel strings across the crystal lattice, parallel to C-axis, because o

[ccp4bb] Senior Postdoctoral Researcher in Artificial Intelligence-led drug discovery

Dear all, the Oxford/Diamond XChem initiative lead by Frank von Delft in partnership with the Oxford Protein Informatics group (headed by Professor Charlotte Deane) is recruiting for a senior postdoctoral fellow who will have responsibility for establishing a research project in Artificial In