[ccp4bb] Has anyone successfully used RoseTTAFold or AF2 to guide crystallization?

[Scott Classen]

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
~~




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Re: [ccp4bb] [phenixbb] comfortable OS X level

[Scott Classen]

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

[Scott Classen]

I think he just did ;-)

Sincerely,
Scott

 On Sep 3, 2014, at 6:05 AM, Keller, Jacob kell...@janelia.hhmi.org 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 avisekmonda...@gmail.com 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

[Scott Classen]

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



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Re: [ccp4bb] Best compounds for heavy atom soaks

[Scott Classen]

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

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Re: [ccp4bb] a problem when using NOMACHINE Player from OSX 10.7.4

[Scott Classen]

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 aales...@sanfordburnham.org 
 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

[Scott Classen]

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

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Re: [ccp4bb] HKL2000 24IDE beam center.

[Scott Classen]

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 



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Re: [ccp4bb] negative difference density around sulphur and oxygen atoms

[Scott Classen]

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

[Scott Classen]

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 ?

[Scott Classen]

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
:~:~:~:~:~:~:~:~:~:~:~:~:~:~:~:~:~:~:~:~:~: