[ccp4bb] Has anyone successfully used RoseTTAFold or AF2 to guide crystallization?
Hello CCP4, Has anyone successfully used the available ML/AI protein folding tools to guide crystallization construct design? Maybe you had a protein or domain that was resistant to crystallization efforts and the folding algorithms predicted some loops or termini that were disordered? Then you trimmed or modified them in some way to aid in crystallization? Or if you haven’t done this yourself, are you aware of anyone who has? Thanks, Scott ~~ Scott Classen, Ph.D. ALS-ENABLE TomAlberTron Beamline 8.3.1 SIBYLS Beamline 12.3.1 Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Rd MS6R2100 Berkeley, CA 94720 mobile 510.206.4418 desk 510.495.2697 beamline 510.495.2134 ~~ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] [phenixbb] comfortable OS X level
10.2 ? That OS is 15 years old. > On Jun 7, 2017, at 8:27 AM, Diana Tomchick > wrote: > > I’ve not had any problems; the current version is 10.2.5, so it’s pretty > stable now. > > Diana > > ** > Diana R. Tomchick > Professor > Departments of Biophysics and Biochemistry > University of Texas Southwestern Medical Center > 5323 Harry Hines Blvd. > Rm. ND10.214A > Dallas, TX 75390-8816 > diana.tomch...@utsouthwestern.edu > (214) 645-6383 (phone) > (214) 645-6353 (fax) > > On Jun 7, 2017, at 10:14 AM, Patrick Loll wrote: > > I’m still running Yosemite on my Macs, both because I’m change-averse and > because folks reported problems with some crystallographic software upon > upgrading the OS. > > These reports have now faded into the haze of the past, and so I ask, have > the issues been resolved? Is it safe to move to Sierra? > > Thanks as always, > > Pat > > --- > Patrick J. Loll, Ph. D. > Professor of Biochemistry & Molecular Biology > Drexel University College of Medicine > Room 10-102 New College Building > 245 N. 15th St., Mailstop 497 > Philadelphia, PA 19102-1192 USA > > (215) 762-7706 > pat.l...@drexelmed.edu > > > ___ > phenixbb mailing list > pheni...@phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-le...@phenix-online.org > > > > > UT Southwestern > > > Medical Center > > > > The future of medicine, today. >
Re: [ccp4bb] paper
I think he just did ;-) Sincerely, Scott > On Sep 3, 2014, at 6:05 AM, "Keller, Jacob" wrote: > > Can you do this for structural biology? > > JPK > > -Original Message- > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of William > G. Scott > Sent: Wednesday, September 03, 2014 2:07 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] paper > >> On Sep 2, 2014, at 9:10 PM, Avisek Mondal wrote: >> >> please can you send me this paper... i can not subscribe it from my lab... >> Acta Cryst. (2014). F70, 1296-1302[ doi:10.1107/S2053230X14014381 ] > > No problem: http://tinyurl.com/n3gurpe
Re: [ccp4bb] fluorescent pedal
Hi Ronnie, We use YAG discs (Yttrium Aluminum Garnet). We buy small 10mm x 100um or 500um thick discs, break them into shards, glue them to various alignment jigs and they provide a very effective X-ray visualization tool. Our latest supplier is Star Tech Instruments (http://www.startechinstruments.com) There are other suppliers, but it does take some calling around because Google doesn't appear to be very helpful… unless you want 5000 lbs from a supplier in China. Good luck, Scott On Feb 14, 2014, at 7:54 AM, Ronnie wrote: > I am trying to find out where I can get the fluorescent material (just a > small flat piece) I can glue to the tip of a pin for aligning the X-ray beam > of our home source. Does anyone know? > > Thanks in advance! > Ronnie smime.p7s Description: S/MIME cryptographic signature
Re: [ccp4bb] Best compounds for heavy atom soaks
On Jan 15, 2014, at 10:27 AM, Jim Pflugrath wrote: > > Quiz time: What wavelength would give iodide a similar signal to that of > selenium? Can one get a better signal than selenium by choosing a different > wavelength for data collection? I'll bite, At ~11,000eV Iodine has about 3.8 anomalous electrons. Going to lower energies will increase the anomalous signal. At 10,000eV Iodine has ~4.6 anomalous electrons. Scott smime.p7s Description: S/MIME cryptographic signature
Re: [ccp4bb] a problem when using NOMACHINE Player from OSX 10.7.4
The keyboard combo to get the settings is control+option+0 Sincerely, Scott > On Sep 18, 2013, at 19:14, Scott Classen wrote: > > I think if you press option + command + 0 a menu will pop up in the middle of > the screen. There should be a display settings icon there. You can choose > full screen or 1:1 pixel ratio etc. Just explore the various options and > something should work for you hopefully. > > > Sincerely, > Scott > >> On Sep 18, 2013, at 19:06, Alexander Aleshin >> wrote: >> >> I've got a question to people using a remote access to synchrotron >> computers. I've got Macbook pro with Mac OSX 10.7.4, which requires the use >> of nxplayer instead of commonly used nxclient. It works, but the size of >> emulated screen gets twice bigger than the size of my computer's screen. As >> a result I can see only a half of it. Does anybody know how to fix this >> problem? >> >> Alexander Aleshin
Re: [ccp4bb] a problem when using NOMACHINE Player from OSX 10.7.4
I think if you press option + command + 0 a menu will pop up in the middle of the screen. There should be a display settings icon there. You can choose full screen or 1:1 pixel ratio etc. Just explore the various options and something should work for you hopefully. Sincerely, Scott > On Sep 18, 2013, at 19:06, Alexander Aleshin > wrote: > > I've got a question to people using a remote access to synchrotron computers. > I've got Macbook pro with Mac OSX 10.7.4, which requires the use of nxplayer > instead of commonly used nxclient. It works, but the size of emulated screen > gets twice bigger than the size of my computer's screen. As a result I can > see only a half of it. Does anybody know how to fix this problem? > > Alexander Aleshin
[ccp4bb] 5D data storage
I stumbled across this interesting abstract today, and though I'd rekindle the perennial data storage debate on ccp4bb. Apparently these researchers have figured out a way to store 360TB of data on a "disc" (not sure of the actual dimensions). The memory crystal should have a thermal stability of 1000ºC and the data should remain readable "forever". Here is the news release: http://www.southampton.ac.uk/mediacentre/news/2013/jul/13_131.shtml and a PDF abstract from the recent Conference on Lasers and Electro-Optics (CLEO’13) in San Jose: http://www.orc.soton.ac.uk/fileadmin/downloads/5D_Data_Storage_by_Ultrafast_Laser_Nanostructuring_in_Glass.pdf smime.p7s Description: S/MIME cryptographic signature
Re: [ccp4bb] HKL2000 24IDE beam center.
Hello Niu, Have you tried adding the following line to appropriate areas in the macro tab (indexing, refinement and integration I believe they're called?): x beam 156 y beam 157 Sincerely, Scott Classen On Jan 17, 2013, at 1:19 PM, Niu Tou wrote: > Hi colleagues, > > We have collected several datasets at APS with detector 24IDE, while > processing date, the beam center is obviously not in position. But no matter > what values we set in "Site Configuration" or "def.site", it remains about > (156, 165). Based on the image, the estimated correct center should be around > (156, 157). Does anyone know how to solve this problem? > > Thanks > Niu smime.p7s Description: S/MIME cryptographic signature
Re: [ccp4bb] refining against weak data and Table I stats
On Dec 13, 2012, at 11:00 AM, Ed Pozharski wrote: > I am not a perfectionist by > any measure, but deliberately not placing water molecules that you can > place because it "does not make biological difference" can hardly be > justified. Hello Ed, As an admitted water adder I couldn't agree more with your sentiment. If something is worth doing then it is worth doing well. I want my model to be the best possible representation of the experimentally measured data... even if that lonely water 16Ang away from the active site will never be looked upon by human eyes. Scott
Re: [ccp4bb] how to ignore spot overlap in imosflm?
Hello Xinghua, I don't think you need to do anything special to ignore overlapping reflections. Mosflm will not integrate them. You biggest concern is that your data will not be complete, which will result in poor density or inability to solve your structure. Have you looked closely at your images to see if the spots really are too close? You can give some keywords (SEPERATION CLOSE) to mosflm/imosflm in order to encourage very close spots to be properly resolved, but this of course will only work if there are a few pixels of non-reflection between reflections. Scott On May 13, 2012, at 7:22 PM, Xinghua Qin wrote: > Dear CCP4ers, > > We collected a diffraction dataset with high percentage of spot overlaps, It > would be so kind to tell me how to ignore spot overlap in imosflm and explain > the hazard of high percentage of spot overlaps. > Thanks in advance. > > Best wishes > > Xinghua Qin > -- > Xinghua Qin > State Key Laboratory of Plant Physiology and biochemistry > College of Biological Sciences > China Agricultural University > No.2, Yuan Ming Yuan West Road > Haidian District, Beijing, China 100193 > Tel: +86-10-62732672 > E-mail: xinghua...@126.com > >
Re: [ccp4bb] negative difference density around sulphur and oxygen atoms
Hello Chris, Are you refining individual atomic B factors or grouped? Perhaps the B factors of the terminal atoms of the side chain are being restrained to too low of a B factor resulting in excessive negative density? Scott On Apr 4, 2012, at 8:16 AM, Chris Meier wrote: > Dear all, > I am refining the X-ray structure of a protein: > Data to ~2A were collected at a latest-generation synchrotron. > The 2fo-Fc maps are crisp, the model of the protein is complete and I am > reasonably happy with the stats (R below 20%, Rfree below 25% in Refmac 5.5). > However, I am seeing a lot of negative difference density, > especially around sulphur atoms (negative density around -9 sigma) > and oxygen atoms (e.g. side-chain oxygens of Glu, Asp, etc. residues with > negative density around -6 sigma). > Has anyone observed this before? > I have found CCP4bb postings discussing radiation damange of suplphur atoms > (e.g. http://www.dl.ac.uk/list-archive-public/ccp4bb/2004-07/msg00532.html ). > Can this also happen with oxygen atoms? > What would be an appropriate way to deal with this issue during refinement? > Suggestions greatly appreciated. > Thanks, > Chris >
Re: [ccp4bb] images
On Mar 19, 2009, at 3:26 AM, Andrew Purkiss-Trew wrote: On Wed, 2009-03-18 at 18:19 +, Frank von Delft wrote: Maybe, but images without experimental context (sequence? ligands? purification? crystallization format? -- PURPOSE OF EXPERIMENT!?!! relationship to the other 15 similar datasets) are as good as no images. And as far as I know, there's no good discussion on the table for that. At least, no-one on the thread mentioned it, so they're probably not thinking about it either. I suppose efforts like PIMS or are a start, and maybe they can even have enough information (my feeling is they currently don't). But that's where the discussion should start: how to index (in sense of annotate) the datasets. The technicalities are just that: technicalities. Or even closer to home: does ANY detector/beamline write even timestamps into the image header...? Never mind ring current, intensity of the beam, size of beam, size of crystal, length of direct beam path, etc etc... As far as I know, most detectors write the current time into the image header. Certainly our in house MAR image plate systems do, as do the detectors at Diamond and ESRF (for those that I've looked at this morning). FYI at my beamline (ALS 12.3.1), in addition to the usual useful metadata, we also put in the beamline ID and the serial number of the detector. In theory anything can be added if you take the time to customize the detector code. HEADER_BYTES= 512; DIM=2; BYTE_ORDER=little_endian; TYPE=unsigned_short; SIZE1=3072; SIZE2=3072; PIXEL_SIZE=0.102592; BIN=2x2; BIN_TYPE=HW; ADC=fast; CREV=1; BEAMLINE=ALS1231; DETECTOR_SN=907; DATE=Tue Feb 3 11:07:38 2009; TIME=10.00; ACC_TIME=11516; DISTANCE=649.80; TWOTHETA=0.00; PHI=191.310; OSC_START=191.310; OSC_RANGE=1.000; WAVELENGTH=1.033184; BEAM_CENTER_X=155.70; BEAM_CENTER_Y=157.40; DENZO_X_BEAM=157.76; DENZO_Y_BEAM=155.70; Scott
Re: [ccp4bb] foam dewar usage ?
I just wanted to pass along a very nice trick I learned this last week for preventing ice build up in and around the foam dewars. This technique was suggested to George Meigs at ALS 8.3.1 by some users from the former SGX. Place a large Kimwipe sheet over the top of the dewar before putting the foam lid on. It just works! I don't know what else to say. Scott :~:~:~:~:~:~:~:~:~:~:~:~:~:~:~:~:~:~:~:~:~: Scott Classen, Ph.D. SIBYLS Beamline 12.3.1 Advanced Light Source Lawrence Berkeley National Laboratory 1 Cyclotron Road, MS6R2100 c) 510.206.4418 o) 510.495.2697 beamline) 510.495.2134 :~:~:~:~:~:~:~:~:~:~:~:~:~:~:~:~:~:~:~:~:~:
