Re: [ccp4bb] libncurses.so.5 error with imosflm
32 vs 64-bit issue? From your previous image, it appears your MOSFLM is 64-bit, but you’re trying to link it to a 32-bit curses library (check with e.g. "file /usr/lib/libncurses++.so.5.9”). I don’t do Fedora myself, but I could imagine that you’ve got 64-bit libraries in /usr/lib64, in which case $ LD_LIBRARY_PATH=/usr/lib64 imosflm might work. If this does work, I guess the rpath on the MOSFLM binaries does not agree so well with your distribution. // Johan > On May 18, 2018, at 11:14, Murpholino Peligro wrote: > > [murph@localhost ~]$ export LD_LIBRARY_PATH=/usr/lib:$LD_LIBRARY_PATH > [murph@localhost ~]$ ls -1l /usr/lib/libncurses* > lrwxrwxrwx. 1 root root 19 Feb 26 09:24 /usr/lib/libncurses++.so.5 -> > libncurses++.so.5.9 > lrwxrwxrwx. 1 root root 17 Feb 26 09:24 /usr/lib/libncurses.so.5 -> > libncurses.so.5.9 > -rwxr-xr-x. 1 root root 66812 Feb 26 09:24 /usr/lib/libncurses++.so.5.9 > -rwxr-xr-x. 1 root root 189776 Feb 26 09:24 /usr/lib/libncurses.so.5.9 > lrwxrwxrwx. 1 root root 20 Feb 26 09:24 /usr/lib/libncurses++w.so.5 -> > libncurses++w.so.5.9 > lrwxrwxrwx. 1 root root 18 Feb 26 09:24 /usr/lib/libncursesw.so.5 -> > libncursesw.so.5.9 > -rwxr-xr-x. 1 root root 66816 Feb 26 09:24 /usr/lib/libncurses++w.so.5.9 > -rwxr-xr-x. 1 root root 261684 Feb 26 09:24 /usr/lib/libncursesw.so.5.9 > [murph@localhost ~]$ imosflm > Results in some wrong ELFCLASS thing. > > > 2018-05-18 10:55 GMT-06:00 CCP4BB : > Hi Murpholino > > Check your LD_LIBRARY_PATH environment variable and the location of the > libncurses.so.5 file - my guess is that the file is not in the path. If this > is the case, you can set your LD_LIBRARY_PATH env to include the directory > that the file is in. > > Harry > -- > Dr Harry Powell > Chairman of European Crystallographic Association SIG9 (Crystallographic > Computing) > > On 18 May 2018, at 16:23, Murpholino Peligro wrote: > >> hello dear ccp4 users! >> Does anybody know how to solve this issue? >> In a Fedora box, a simple `sudo dnf install libncurses.so.5` installs the >> missing library...but the error still pops up. >> >> > > Research Specialist @ Gonen Lab Janelia Research Campus * 19700 Helix Drive Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376
Re: [ccp4bb] efresol download?
Thanks a lot, Luca, Pavel, and Daniel! I now have sufficiently many copies to last me well into 2020! // Cheers; Johan > On Oct 26, 2017, at 11:58, Bonsor, Daniel wrote: > > Is this not it? > > http://www-ibmc.u-strasbg.fr/spip-arn/rubrique257?lang=en > > At the bottom of the page. > > > Daniel A Bonsor PhD. > Sundberg Lab > Institute of Human Virology > University of Maryland, Baltimore > 725 W Lombard Street N370 > Baltimore > Maryland > MD 21201 > Tel: (410) 706-7457 > > > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Pavel > Afonine > Sent: Thursday, October 26, 2017 11:54 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] efresol download? > > Johan, > > core functionality described in that paper is implemented in cctbx. Re the > stand-alone program -- I'm cc'ing to the author. > > Pavel > > On Thu, Oct 26, 2017 at 8:39 AM, Hattne, Johan > wrote: > Dear all; > > Would anybody know where I can find efresol (as detailed in > http://dx.doi.org/10.1107/S0907444913016673) these days? Googling lead me to > a 2014 post > (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1406&L=ccp4bb&F=&S=&P=155751), > but those links result in 403 Forbidden as of right now. > > // Best wishes; Johan > > > Research Specialist @ Gonen Lab > > Janelia Research Campus * 19700 Helix Drive > Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376 Research Specialist @ Gonen Lab Janelia Research Campus * 19700 Helix Drive Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376
[ccp4bb] efresol download?
Dear all; Would anybody know where I can find efresol (as detailed in http://dx.doi.org/10.1107/S0907444913016673) these days? Googling lead me to a 2014 post (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1406&L=ccp4bb&F=&S=&P=155751), but those links result in 403 Forbidden as of right now. // Best wishes; Johan Research Specialist @ Gonen Lab Janelia Research Campus * 19700 Helix Drive Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376
[ccp4bb] Spring 2016 MicroED workshops at Janelia Research Campus
Due to high demand, two back-to-back MicroED workshops will be held at Janelia Research Campus (Ashburn, VA) in the spring. The workshops are hosted by Tamir Gonen and will have the same content. Accepted participants will be assigned by the organizers to one or the other (not both). May 21-24 and May 24-27, 2017 MicroED is a cryoEM method that uses electron diffraction to facilitate structure determination from sub-micron sized 3D crystals, eliminating the need to grow large crystals. MicroED uses equipment and procedures that are standard on many cryoTEM:s, and because of this the technique can be easily adopted in labs and facilities around the world. To facilitate the widespread use of MicroED, we are offering these workshops to teach microscopists how to perform the technique and adopt it at their own institutions. There is no registration fee for participation, and Janelia will provide on-site housing and meals. Attendees are expected to cover their own travel expenses and must be able to stay for the duration. Applicants must register and submit a brief statement on why they wish to participate, via our online registration system. https://conference.janelia.org Please note that this system is designed to collect abstract information for presentations. Please write your statement of interest in the "abstract" field, put your name in the "author" field, and put "n/a" in the "presentation title" and "keyword" fields. Space in these workshops is limited. The application deadline is February 10, 2017. // Best wishes; Johan, on behalf of the organizers Research Specialist @ Gonen Lab Janelia Research Campus * 19700 Helix Drive Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376
Re: [ccp4bb] Canceled: second installment of the MicroED workshop
> On Aug 23, 2016, at 01:48, Jing Liu wrote: > > The second installment of the MicroED workshop will be held at Janelia > Research Campus (Ashburn, VA) November 13-16, 2016, hosted by Tamir Gonen. Dear all; Just to clarify: the November MicroED workshop is *not* canceled, but will take place at Janelia Research Campus November 13-16, 2016. Applicants were notified a few weeks ago. I’m guessing the message above was sent by Jing’s personal calendar software and was not intended for this list. // Best wishes; Johan Research Specialist @ Gonen Lab Janelia Research Campus * 19700 Helix Drive Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376
Re: [ccp4bb] View Images in Non-Crystallographic Software (ImageJ/FIJI)
> On Jul 14, 2016, at 10:59, Keller, Jacob wrote:
>
> Dear Crystallographers,
>
> I've been trying to view diffraction images in ImageJ. I can read the images
> through a raw import, but the parameters seem a little off. ImageJ asks for
> the following parameters (I just list the questionable ones):
>
> -Image type (8-bit, 32-bit signed, etc.)
> -Width,Height (seems to be, from the header, 1042 x 1042, but this gives four
> images in one; 521 x 521 gives one image, but which is truncated halfway down)
> -Offset to first image (bytes) (seems to be 3584 from the header, but looks
> like wrong offset.)
>
> The header of the images in question is pasted below.
>
> Can anyone point to what is going on here? Is this impossibly complicated, or
> is there an easy way to do this, like I am just missing something? I've
> played around a bit, but cannot get it right.
The image type should be “16-bit Unsigned”; the Data_type item in the header
indicates that this is the case and according to
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/SMV_file_format
this is the data type used by all known SMV images. I would think that this
explains the duplication you see. You may also need to check the
“Little-endian byte order” (see the BYTE_ORDER item in the header).
> Would it be so horrible, btw, to use tif or some other easy universal format?
> I think at least some of these formats can accommodate metadata…
You’re right: TIFF is used by some manufacturers, and the format can
accommodate metadata in different forms. However, the way the metadata is
encoded in the file appears to differ from manufacturer to manufacturer, and I
would think general-purposes software like ImageJ might not have the resources
nor the interest to keep up with all possible variations. If you just want to
look at the image and don’t care what the resolution of the pixels under your
cursor is, this does not matter.
// Cheers; Johan
> All the best,
>
> Jacob Keller
>
>
> {
> HEADER_BYTES= 3584;
> BYTE_ORDER=little_endian;
> BitmapSize=4274;
> BitmapType=BitmapRLE;
> CCD_DETECTOR_DESCRIPTION=Saturn944+ (2x2 bin mode);
> CCD_DETECTOR_DIMENSIONS=1042 1042;
> CCD_DETECTOR_IDENTIFICATION=MSC_REIT_Saturn944+_SN012110304;
> CCD_DETECTOR_OPTIONS=imagekind:2 dezingermode:off dezingertype:average
> subtractclosed:on transform:on simulator:immediate trigger:on;
> CCD_DETECTOR_SERVER_VERSION=MSCServCCDCamera 7.6.2.4;
> CCD_DETECTOR_SIZE=93.7800 93.7800;
> CCD_DETECTOR_TEMPERATURE=-45.0 deg C;
> CCD_DETECTOR_VECTORS=1 0 0 0 1 0;
> CCD_FIELD_OF_VIEW=Square;
> CCD_GONIO_COLLISION_OFFSET=0.0 0 0.0 0.0 0.0 0;
> CCD_GONIO_DESCRIPTION=AFC11 (Right): 2theta arm;
> CCD_GONIO_NAMES=RotAboutBeam 2Theta RotY XShift YShift Distance;
> CCD_GONIO_NUM_VALUES=6;
> CCD_GONIO_UNITS=deg deg deg mm mm mm;
> CCD_GONIO_VALUES=0. 0. 0. 0. 0. 45.;
> CCD_GONIO_VALUES_MAX=0.0 5 0.0 0.0 0.0 300.9;
> CCD_GONIO_VALUES_MIN=0.0 -110 0.0 0.0 0.0 40;
> CCD_GONIO_VECTORS=0. 0. 1. 1. 0. 0. 0. 1.
> 0. 1. 0. 0. 0. 1. 0. 0. 0. -1.;
> CCD_NONUNF_INFO=FirstScanImage;
> CCD_NONUNF_TYPE=Simple_mask;
> CCD_SERIAL_NUMBER=12110304;
> CCD_SPATIAL_BEAM_POSITION=508.0750 522.2700;
> CCD_SPATIAL_DISTORTION_INFO=508.0750 522.2700 0.0900 0.0900;
> CCD_SPATIAL_DISTORTION_TYPE=Simple_spatial;
> CCD_SPATIAL_DISTORTION_VECTORS=0 -1 1 0;
> CCD_TAPER_ORIENTATION=+x+y;
> CCD_UNBINNED_BEAM_POSITION=1016.1500 1044.5400;
> CCD_UNBINNED_DIMENSIONS=2084 2084;
> CCD_VACUUM_PRESSURE=CCD: 2.67 Phosphor: 27.48;
> COLLISION_INFO=C:/Rigaku/MSCServDetCCD/Collision.xml;
> COMPRESSION=None;
> CRYSTAL_GONIO_COLLISION_OFFSET=0 0 0;
> CRYSTAL_GONIO_DESCRIPTION=AFC11 (Right): Eulerian 3 circle;
> CRYSTAL_GONIO_NAMES=Omega Chi Phi;
> CRYSTAL_GONIO_NUM_VALUES=3;
> CRYSTAL_GONIO_SCAN_AXES=Omega Phi ;
> CRYSTAL_GONIO_SERVER_VERSION=MSCServDetCCD 5.5.2.7;
> CRYSTAL_GONIO_UNITS=deg deg deg;
> CRYSTAL_GONIO_VALUES=0. 0. 0.;
> CRYSTAL_GONIO_VALUES_MAX=100 60 3600;
> CRYSTAL_GONIO_VALUES_MIN=-200 0 -3600;
> CRYSTAL_GONIO_VECTORS=1. 0. 0. 0. -1. 0. 1.
> 0. 0.;
> DARK_PEDESTAL=20;
> DETECTOR_NAMES=CCD_;
> DETECTOR_NUMBER=1;
> DIM=2;
> DTDISPLAY_ORIENTATION=+X+Y;
> DTINTEGRATE_OBLIQUE=0;
> DTREK_DATE_TIME=26-Jan-2015 20:49:06;
> DTREK_MODULE=d*TREK;
> DTREK_VERSION=d*TREK version 9.9.9.4 W9RSSI -- Mar 27 2012;
> Data_type=unsigned short int;
> FILENAME=hex_lozAinv_1_0006.img;
> HEADER_VERSION=1.2;
> RAXIS_COMPRESSION_RATIO=128;
> ROTATION=-89.500 -89.400 0.100 5.000 0.000 0.000 0.000 100.000 0.000 0.000;
> ROTATION_AXIS_NAME=Omega;
> ROTATION_LIMITS=0.000 360.000 1000.000;
> ROTATION_VECTOR=1.000 0.000 0.000;
> SATURATED_VALUE=4194176;
> SCAN_CRYS_RELZERO=3.000 0.000 0.000 0.000;
> SCAN_DETECTOR_OPTIONS=None;
> SCAN_DET_RELZERO=2.000 0.000 45.000;
> SCAN_MODE=Scan_Open;
> SCAN_ROTATION=-89.500 -89.400 0.100 5.000 0.000 0.000 0.000 100
Re: [ccp4bb] Coot in MacOSX El Capitan version 10.11.3
> On Feb 3, 2016, at 02:47, Mohit Misra wrote: > > Hello everyone, > > I am unable to open coot in my Mac which is running OSX 10.11.3. When I try > to open coot, it opens the Coot logo and the coot window appears for a > millisecond. Although the coot terminal is running in the background. Has > anyone faced a similar problem and has overcome it? Any suggestions will be > highly appreciated. While I haven’t had any problems specifically with Coot since upgrading, XQuartz under El Capitan is exhibiting a plethora of oddities on my Mac. With the multi-screen setup that I’m using I’ve found that turning display mirroring (System Preferences->Displays) on and off again can recover windows that were lost somewhere off the desktop. Others have suggested temporarily enabling full-screen mode in XQuartz. // Best wishes; Johan Research Specialist @ Gonen Lab Janelia Research Campus * 19700 Helix Drive Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376
Re: [ccp4bb] Off-topic: Transfering data from Diamond
> On Jul 30, 2015, at 18:00, Mohamed Noor wrote:
>
> Dear all
>
> I have about 70 folders of data collected at Diamond. As I only want to keep
> about 50 of them, is there a script that can read in the folder names from a
> text file and download those?
>
> Normally, I use FileZilla but it gets tedious to click so many times after a
> while….
If diamond allows ssh-access, one way is
$ ssh user@host.diamond '( cd your/directory ; tar -cpf - `cat list.txt` )' |
tar -xvpf -
where user is your username, host.diamond is the machine at diamond,
your/directory is the path to where your stuff is stored, and list.txt is a
file in your/directory with the files and directories you want transferred.
> Secondly, some folders have one sweep of data, some others with two or even
> three, is it possible to run a command from terminal that will filter
> different sweeps and output the number of frames?
>
> For example, in a folder with files:
>
> _sweep1_0001.cbf - _sweep1_1800.cbf
> _sweep2_0001.cbf - _sweep2_0900.cbf
>
> I want to get a text file output containing a line saying:
> /folder/name/sweep1 - 1800
> /folder/name/sweep2 - 900
Would
$ ls folder/name/*.cbf | sort | sed -e "s:_\.cbf$::" | awk -vi=0 '{ if
($0 == prev) { i++; } else { print $0 " - " i + 1; i = 0; prev = $0;} }'
do the trick?
> The idea is so that I can feed those lines into XDS.INP without checking how
> many sweeps there are in each folder and how many frames.
>
> I'm pretty sure someone on the BB has a trick for this.
Research Specialist @ Gonen Lab
Janelia Research Campus * 19700 Helix Drive
Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376
Re: [ccp4bb] workable data from PDB sf-cif
Or "Convert to/modify/extend MTZ" in "Reflection Data Utilities”. You can “Import reflection file in mmCIF format and create MTZ file”. // Johan > On Jun 15, 2015, at 13:58, Schubert, Carsten [JRDUS] > wrote: > > Phenix has a menu item for this: Reflection Tools -> Import CIF structure > factors > > HTH > > Carsten > > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of StrBio > Sent: Monday, June 15, 2015 1:53 PM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] workable data from PDB sf-cif > > Hi All, > > How one can convert pdb-sf.cif file downloaded from PDB to a workable format > for further refinement (may be by phenix or Refmac) of the deposited > structure? > > I need help. Research Specialist @ Gonen Lab Janelia Research Campus * 19700 Helix Drive Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376
Re: [ccp4bb] PAD images
We often use ImageJ for looking at electron diffraction images, and do indeed benefit from the plethora of tools it implements. The necessary tools to convert to and from formats that ImageJ understands are quite trivial, but we don’t have a plugin (yet?) nor have have played with anything approaching real-time viewing. // Johan On Apr 28, 2015, at 7:08, Keller, Jacob wrote: > Has anybody tried imageJ/FIJI for looking at diffraction images? There are a > vast amount of processing tools therein, and it could make some things really > easy. I suspect one could look at the data by opening images as “raw” and > then specifying the properties of the image in the resultant menu. An x-ray > data plugin might be really powerful if it could use some of imageJ’s many > image-processing options. > > In this case, one can trivially do a “Gaussian blur” in any of three > dimensions, and one can set the degree of blur whilst seeing a real-time > preview. It’s actually an amazing—and completely free and > open-source—software package. > > JPK > > From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Harry > Powell > Sent: Tuesday, April 28, 2015 5:31 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: Re: [ccp4bb] PAD images > > Hi > > In iMosflm we automatically blur the zoomed out image for Pilatus (not yet > for Eiger or ADSC-PAD) to make it easier to see the spots on these images. > > It's also possible to sum up to 20 images (for viewing) in iMosflm (again, > for Pilatus). We'll add this functionality for the other detectors before the > next release... > > > On 27 Apr 2015, at 23:31, Bernhard Rupp (Hofkristallrat a.D.) wrote: > > > Hi Fellows, > > I wonder whether it's just me and my eyesight failing (or excessive internal > lubrication) > > It seems that the art of looking at diffraction patterns and being able to > tell > a lot about modulation, superstructures, extinctions, etc. becomes kind of > useless > old fart stuff when dealing with PAD images. I can’t for my life see > interpretable patterns on frames where > the beamline autoprocessing delivers actual data sets. The absence of a > point spread function > etc that gave interpretable film-like images on IPs or CCDs, seems to be the > reason. > > A PAD pixel with 100 counts looks like one with 100 when viewed with the > low dynamic range of the displays > compared to the huge dynamic range of the detector. > > Is there somewhere in the process a humanly unusable composite image with a > point spread that > allows visual pre-processing, inspection, and interpretation despite a low > dynamic display range? > > Looking at the hklview or similar after processing is pointless (no pun > intended), because the stuff I might be > interested in is already processed away. > > Some humanly interpretable raw data images would be quite useful... > > Best regards, BR > - > Bernhard Rupp > 001 (925) 209-7429 > +43 (676) 571-0536 > b...@ruppweb.org > http://www.ruppweb.org/ > - > The man who follows the crowd will get > no further than the crowd. > The man who walks alone will find himself > in places where no one has been before. > - > > Harry > -- > Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis Crick Avenue, > Cambridge Biomedical Campus, Cambridge CB2 0QH > Chairman of International Union of Crystallography Commission on > Crystallographic Computing > Chairman of European Crystallographic Association SIG9 (Crystallographic > Computing) Research Specialist @ Gonen Lab Janelia Research Campus * 19700 Helix Drive Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376
Re: [ccp4bb] HKL2000 Display
I’ve seen this when the description in the site file does not actually match the data. // Johan On Dec 3, 2014, at 7:25, David Waterman wrote: > Hi Muhammed, > > It looks a lot to me like denzo thinks your detector has a larger image size > than the actual number of elements in the array. However, I don't use denzo > so I'm not commenting from experience. > > Cheers > > -- David > > On 3 December 2014 at 04:09, Muhammed bashir Khan > wrote: > Hi All; > > Could somebody explain why my Display image in HKL2000 look like that. > Image attached. > Thanks for help in advance. > > Bashir > > > Department of Biochemistry > University of Alberta > Edmonton Canada > > > Research Specialist @ Gonen Lab Janelia Research Campus * 19700 Helix Drive Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376
