Von Samsung Mobile gesendet
-------- Ursprüngliche Nachricht --------
Von: CCP4BB automatic digest system <[log in to unmask]>
Datum: 31.07.2015 1:02 (GMT+01:00)
An: [log in to unmask]
Betreff: CCP4BB Digest - 29 Jul 2015 to 30 Jul 2015 (#2015-31)
There are 11 messages totaling 1584 lines in this issue.znx
Topics of the day:
L
1. puzzled (6)
2. Xorg Settings for three Monitors: Planar Stereo + 1 normal Monitor
3. Postdoc and technician positions at University of Warsaw
4. Opening for a Structural Biologist with an emphasis X-ray Crystallography
at Monsanto Company in St. Louis
5. Berkeley Server Downtime
6. Off-topic: Transfering data from Diamond
----------------------------------------------------------------------
Date: Thu, 30 Jul 2015 11:31:55 +0200
From: Almudena Ponce Salvatierra <[log in to unmask]>
Subject: puzzled
Dear all,
I would like to ask your opinion on something (I was actually not expecting
to work...but it did!!).
I am now solving a protein of 135 kDa. I did SIRAS within SHELX and the
poly ala trace I discarded, but I kept the density modified map.
I gave the map and the sequence to buccaneer and it gave back 1532 residues
built in 133 fragments. This looked more like a spaghetti dish (excuse me,
I'm used not NA rather than proteins), with lots of small fragments... but
I wanted to give it a try and gave it to Phaser for molecular replacement
(here is where I was having the most doubts). I gave it along with a native
data set collected at 2.9 Angstroms and phaser gives a TFZ score of 90.6
plus an LLG of 4512.88. So, it looks like it is a correct solution!!
Now the question is, this is mostly a poly-ala thing, with lots of
fragments... can I think that actually this is a solution? I want to,
actually, I mean, at the end these short pieces are oriented respect to
each other in a specific manner, even if they're not connected, and phaser
could place it. But now my question is, how or from where do I start to
make it continuous? Or to complete the structure...
Any comments on this are more than welcome!!
Best wishes,
Almu
--
Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11 37077 Göttingen
Germany
------------------------------
Date: Thu, 30 Jul 2015 10:48:06 +0100
From: David Briggs <[log in to unmask]>
Subject: Re: puzzled
1) Is it a solution?
Not sure - Seems plausible - but it would be nice to have longer continuous
stretches of chain traced (what is your single longest continuous
stretch?). Have you put your spaghetti into REFMAC/Phenix.refine to see if
you can refine/improve the maps?
2) Assuming it is a solution:
When faced with similar problems, I tend to look at my amino acid sequence
and try and pick out little motifs that will have obvious features in the
electron density - typically runs of aromatic residues, but also metal ion
binding sites or disulphide bonds if you have them.
Then I walk through my poly-ala trace looking for density that might fit,
and work my way out from that. It is a time consuming trial-and-error
procedure.
If you have good-enough data, you can always give your sequence to <insert
favourite autobuilding software here> and see if it can do it for you.
If you have related domains (I'm guessing not, since you went with SIRAS
phasing) you can try to align them on your 'spaghetti' to figure out where
you are in the sequence.
HTH
Dave
[image: David Briggs on about.me]
David Briggs
about.me/david_briggs
<http://about.me/david_briggs>
On 30 July 2015 at 10:31, Almudena Ponce Salvatierra <[log in to unmask]>
wrote:
> Dear all,
>
> I would like to ask your opinion on something (I was actually not
> expecting to work...but it did!!).
>
> I am now solving a protein of 135 kDa. I did SIRAS within SHELX and the
> poly ala trace I discarded, but I kept the density modified map.
>
> I gave the map and the sequence to buccaneer and it gave back 1532
> residues built in 133 fragments. This looked more like a spaghetti dish
> (excuse me, I'm used not NA rather than proteins), with lots of small
> fragments... but I wanted to give it a try and gave it to Phaser for
> molecular replacement (here is where I was having the most doubts). I gave
> it along with a native data set collected at 2.9 Angstroms and phaser gives
> a TFZ score of 90.6 plus an LLG of 4512.88. So, it looks like it is a
> correct solution!!
>
> Now the question is, this is mostly a poly-ala thing, with lots of
> fragments... can I think that actually this is a solution? I want to,
> actually, I mean, at the end these short pieces are oriented respect to
> each other in a specific manner, even if they're not connected, and phaser
> could place it. But now my question is, how or from where do I start to
> make it continuous? Or to complete the structure...
>
> Any comments on this are more than welcome!!
>
> Best wishes,
>
> Almu
>
> --
> Almudena Ponce-Salvatierra
> Macromolecular crystallography and Nucleic acid chemistry
> Max Planck Institute for Biophysical Chemistry
> Am Fassberg 11 37077 Göttingen
> Germany
>
>
------------------------------
Date: Thu, 30 Jul 2015 10:10:13 +0000
From: Bert Van-Den-Berg <[log in to unmask]>
Subject: Re: puzzled
If you have NCS, give the model to Autobuild within phenix. You can try either model building with resolve or resolve/buccaneer. The building itself won't be great probably (like you have now) due to the low resolution but the density modified maps produced by Resolve can be great even at lo-res (but you'd need to have NCS so that averaging produces better maps). This has worked great for me in the past.
Maps obtained from refinement at this stage probably won't be useful; my experience is that Rfree needs to be below 40% or so. You probably will need to build by hand first to get Rfree to those kind of values.
good luck, bert
________________________________
From: CCP4 bulletin board [[log in to unmask]] on behalf of Almudena Ponce Salvatierra [[log in to unmask]]
Sent: Thursday, July 30, 2015 10:31 AM
To: [log in to unmask]
Subject: [ccp4bb] puzzled
Dear all,
I would like to ask your opinion on something (I was actually not expecting to work...but it did!!).
I am now solving a protein of 135 kDa. I did SIRAS within SHELX and the poly ala trace I discarded, but I kept the density modified map.
I gave the map and the sequence to buccaneer and it gave back 1532 residues built in 133 fragments. This looked more like a spaghetti dish (excuse me, I'm used not NA rather than proteins), with lots of small fragments... but I wanted to give it a try and gave it to Phaser for molecular replacement (here is where I was having the most doubts). I gave it along with a native data set collected at 2.9 Angstroms and phaser gives a TFZ score of 90.6 plus an LLG of 4512.88. So, it looks like it is a correct solution!!
Now the question is, this is mostly a poly-ala thing, with lots of fragments... can I think that actually this is a solution? I want to, actually, I mean, at the end these short pieces are oriented respect to each other in a specific manner, even if they're not connected, and phaser could place it. But now my question is, how or from where do I start to make it continuous? Or to complete the structure...
Any comments on this are more than welcome!!
Best wishes,
Almu
--
Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11 37077 Göttingen
Germany
------------------------------
Date: Thu, 30 Jul 2015 12:36:26 +0200
From: Almudena Ponce Salvatierra <[log in to unmask]>
Subject: Re: puzzled
Hi David, Hi Bert,
thanks for getting back so quickly. So, the longest stretches of autotraced
protein that I have are around 100 residues. I am now running a refinement
and also autobuild. In any case I will try resolve too, I have 4 copies of
my protein in the ASU so the NCS averaging should work well there.
Thanks a lot!! hopefully I will have some happy news soon!
Best wishes,
Almudena
2015-07-30 12:10 GMT+02:00 Bert Van-Den-Berg <
[log in to unmask]>:
> If you have NCS, give the model to Autobuild within phenix. You can try
> either model building with resolve or resolve/buccaneer. The building
> itself won't be great probably (like you have now) due to the low
> resolution but the density modified maps produced by Resolve can be great
> even at lo-res (but you'd need to have NCS so that averaging produces
> better maps). This has worked great for me in the past.
>
> Maps obtained from refinement at this stage probably won't be useful; my
> experience is that Rfree needs to be below 40% or so. You probably will
> need to build by hand first to get Rfree to those kind of values.
>
> good luck, bert
> ------------------------------
> *From:* CCP4 bulletin board [[log in to unmask]] on behalf of Almudena
> Ponce Salvatierra [[log in to unmask]]
> *Sent:* Thursday, July 30, 2015 10:31 AM
> *To:* [log in to unmask]
> *Subject:* [ccp4bb] puzzled
>
> Dear all,
>
> I would like to ask your opinion on something (I was actually not
> expecting to work...but it did!!).
>
> I am now solving a protein of 135 kDa. I did SIRAS within SHELX and the
> poly ala trace I discarded, but I kept the density modified map.
>
> I gave the map and the sequence to buccaneer and it gave back 1532
> residues built in 133 fragments. This looked more like a spaghetti dish
> (excuse me, I'm used not NA rather than proteins), with lots of small
> fragments... but I wanted to give it a try and gave it to Phaser for
> molecular replacement (here is where I was having the most doubts). I gave
> it along with a native data set collected at 2.9 Angstroms and phaser gives
> a TFZ score of 90.6 plus an LLG of 4512.88. So, it looks like it is a
> correct solution!!
>
> Now the question is, this is mostly a poly-ala thing, with lots of
> fragments... can I think that actually this is a solution? I want to,
> actually, I mean, at the end these short pieces are oriented respect to
> each other in a specific manner, even if they're not connected, and phaser
> could place it. But now my question is, how or from where do I start to
> make it continuous? Or to complete the structure...
>
> Any comments on this are more than welcome!!
>
> Best wishes,
>
> Almu
>
> --
> Almudena Ponce-Salvatierra
> Macromolecular crystallography and Nucleic acid chemistry
> Max Planck Institute for Biophysical Chemistry
> Am Fassberg 11 37077 Göttingen
> Germany
>
>
--
Almudena Ponce-Salvatierra
Macromolecular crystallography and Nucleic acid chemistry
Max Planck Institute for Biophysical Chemistry
Am Fassberg 11 37077 Göttingen
Germany
------------------------------
Date: Thu, 30 Jul 2015 12:10:57 +0100
From: Randy Read <[log in to unmask]>
Subject: Re: puzzled
Dear Almudena,
I hope you have indeed solved the structure, but any model that has been fit and refined to the diffraction data will give a very strong signal in Phaser. I’m afraid that running molecular replacement in Phaser is not an independent check for the validity of the model — unless of course you have a second crystal form, in which case overfitting of the data in the first crystal form wouldn’t affect the fit to the data for the second form.
Best wishes,
Randy
-----
Randy J. Read
Department of Haematology, University of Cambridge
Cambridge Institute for Medical Research Tel: +44 1223 336500
Wellcome Trust/MRC Building Fax: +44 1223 336827
Hills Road E-mail: [log in to unmask]
Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk
> On 30 Jul 2015, at 11:36, Almudena Ponce Salvatierra <[log in to unmask]> wrote:
>
> Hi David, Hi Bert,
>
> thanks for getting back so quickly. So, the longest stretches of autotraced protein that I have are around 100 residues. I am now running a refinement and also autobuild. In any case I will try resolve too, I have 4 copies of my protein in the ASU so the NCS averaging should work well there.
>
> Thanks a lot!! hopefully I will have some happy news soon!
>
> Best wishes,
>
> Almudena
>
> 2015-07-30 12:10 GMT+02:00 Bert Van-Den-Berg <[log in to unmask]>:
> If you have NCS, give the model to Autobuild within phenix. You can try either model building with resolve or resolve/buccaneer. The building itself won't be great probably (like you have now) due to the low resolution but the density modified maps produced by Resolve can be great even at lo-res (but you'd need to have NCS so that averaging produces better maps). This has worked great for me in the past.
>
> Maps obtained from refinement at this stage probably won't be useful; my experience is that Rfree needs to be below 40% or so. You probably will need to build by hand first to get Rfree to those kind of values.
>
> good luck, bert
> From: CCP4 bulletin board [[log in to unmask]] on behalf of Almudena Ponce Salvatierra [[log in to unmask]]
> Sent: Thursday, July 30, 2015 10:31 AM
> To: [log in to unmask]
> Subject: [ccp4bb] puzzled
>
> Dear all,
>
> I would like to ask your opinion on something (I was actually not expecting to work...but it did!!).
>
> I am now solving a protein of 135 kDa. I did SIRAS within SHELX and the poly ala trace I discarded, but I kept the density modified map.
>
> I gave the map and the sequence to buccaneer and it gave back 1532 residues built in 133 fragments. This looked more like a spaghetti dish (excuse me, I'm used not NA rather than proteins), with lots of small fragments... but I wanted to give it a try and gave it to Phaser for molecular replacement (here is where I was having the most doubts). I gave it along with a native data set collected at 2.9 Angstroms and phaser gives a TFZ score of 90.6 plus an LLG of 4512.88. So, it looks like it is a correct solution!!
>
> Now the question is, this is mostly a poly-ala thing, with lots of fragments... can I think that actually this is a solution? I want to, actually, I mean, at the end these short pieces are oriented respect to each other in a specific manner, even if they're not connected, and phaser could place it. But now my question is, how or from where do I start to make it continuous? Or to complete the structure...
>
> Any comments on this are more than welcome!!
>
> Best wishes,
>
> Almu
>
> --
> Almudena Ponce-Salvatierra
> Macromolecular crystallography and Nucleic acid chemistry
> Max Planck Institute for Biophysical Chemistry
> Am Fassberg 11 37077 Göttingen
> Germany
>
>
>
>
> --
> Almudena Ponce-Salvatierra
> Macromolecular crystallography and Nucleic acid chemistry
> Max Planck Institute for Biophysical Chemistry
> Am Fassberg 11 37077 Göttingen
> Germany
>
------------------------------
Date: Thu, 30 Jul 2015 15:00:13 +0200
From: George Sheldrick <[log in to unmask]>
Subject: Re: puzzled
Dear Almudena,
You can actually pass on both the phases and the poly-Ala trace from
SHELXE to BUCCANEER followed by REFMAC. The new CCP4 pipelines CCP4i2
and CCP4 Online do this (this is after all the CCP4bb!). The R-factors
from REFMAC will then give a good indication as to whether the structure
is solved.
If the resolution of your native data is good enough (better than about
2.5A) the CC against the native data that SHELXE outputs each
autotracing cycle will give you a rather reliable indication as to
whether the structure is solved. A value greater than 25% indicates that
the structure is 'solved'. This criterion has been very thoroughly
tested by AMPLE (in the current CCP4) and ARCIMBOLDO (included in the
next version of CCP4). See the papers about these programs.
Best wishes, George
On 30.07.2015 11:31, Almudena Ponce Salvatierra wrote:
> Dear all,
>
> I would like to ask your opinion on something (I was actually not
> expecting to work...but it did!!).
>
> I am now solving a protein of 135 kDa. I did SIRAS within SHELX and
> the poly ala trace I discarded, but I kept the density modified map.
>
> I gave the map and the sequence to buccaneer and it gave back 1532
> residues built in 133 fragments. This looked more like a spaghetti
> dish (excuse me, I'm used not NA rather than proteins), with lots of
> small fragments... but I wanted to give it a try and gave it to Phaser
> for molecular replacement (here is where I was having the most
> doubts). I gave it along with a native data set collected at 2.9
> Angstroms and phaser gives a TFZ score of 90.6 plus an LLG of
> 4512.88. So, it looks like it is a correct solution!!
>
> Now the question is, this is mostly a poly-ala thing, with lots of
> fragments... can I think that actually this is a solution? I want to,
> actually, I mean, at the end these short pieces are oriented respect
> to each other in a specific manner, even if they're not connected, and
> phaser could place it. But now my question is, how or from where do I
> start to make it continuous? Or to complete the structure...
>
> Any comments on this are more than welcome!!
>
> Best wishes,
>
> Almu
>
> --
> Almudena Ponce-Salvatierra
> Macromolecular crystallography and Nucleic acid chemistry
> Max Planck Institute for Biophysical Chemistry
> Am Fassberg 11 37077 Göttingen
> Germany
>
--
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-33021 or -33068
Fax. +49-551-39-22582
------------------------------
Date: Thu, 30 Jul 2015 18:42:00 +0200
From: Sabine Schneider <[log in to unmask]>
Subject: Xorg Settings for three Monitors: Planar Stereo + 1 normal Monitor
Hello everyone,
I am trying to add a Planar 3D-Monitor to my computer.
What I want is to have the two monitors side by side and have the stereo
in the second one enabled.
I can easily have all three next to each other (mouse wise) (the planar
system consists of two monitors)
Or just have the Planar monitor with stereo by adding the following (see
below) to xorg.conf; runs perfectly fine.
However I am struggling to add my normal monitor at the side as the main
monitor. I am loosing stereo than or have other funny effects.
DFP-1 and DFP-2 are the two monitors of the planar system; graphics
card: Nvidia Quadro K2200 and I am on Centos 6
I tried adding: "DP-0: nvidia-auto-select +0+0" for the main non-stereo
monitor and moving the two stereo monitors to the right by changing:
DP-1: nvidia-auto-select +0+0 -> DP-1: nvidia-auto-select +1920+0
Can anyone give me a hint where I am going wrong?
Thanks a lot!
Sabine
Section "ServerLayout"
Option "Xinerama" "0"
Section "Screen"
Identifier "Screen0"
Device "Device0"
Monitor "Monitor0"
DefaultDepth 24
Option "TwinView" "1"
Option "TwinViewXineramaInfoOrder" "DFP-1, DFP-2"
Option "EnablePageFlip" "ON"
Option "Stereo" "4"
Option "nvidiaXineramaInfoOrder" "DFP-2"
Option "metamodes" "DP-1: nvidia-auto-select +0+0
{stereo=PassiveLeft}, DP-2: nvidia-auto-select +0+0{stereo=PassiveRight}"
Option "SLI" "Off"
Option "MultiGPU" "Off"
Option "BaseMosaic" "off"
SubSection "Display"
Depth 24
EndSubSection
EndSection
Section "Extensions"
Option "Composite" "Disable"
EndSection
--
------------------------------------------
Dr. Sabine Schneider
Junior Research Group Leader
Technische Universität Munich
Department of Chemistry
Chair of Biochemistry
Lichtenbergstr. 4
85748 Garching
Germany
Tel.: +49 (0) 89 289 13336
Fax: +49 (0) 89 289 13363
http://www.biochemie.ch.tum.de/index.php?id=919
------------------------------
Date: Thu, 30 Jul 2015 19:18:51 +0200
From: Maria Górna <[log in to unmask]>
Subject: Postdoc and technician positions at University of Warsaw
Dear Colleagues,
Two postdoc positions and one research technician post are available for 3
years in the group of Maria Gorna at the University of Warsaw, Poland.
The project aims to study the structure of human RNA-binding proteins
involved in post-transcriptional regulation in the mitochondria.
This is an opportunity to join a young, dynamic team at a launch of a new
research institute (http://www.cent3.uw.edu.pl). The Biological and
Chemical Research Centre is a brand new building which hosts also NMR and
computational groups and provides excellent opportunities for
interdisciplinary research. We also offer international collaborations and
support for attendance at conferences. The laboratory has the latest
equipment and facilities for protein expression and purification, SEC-MALS,
DLS, MST, as well as crystallization robots (Mosquito, Dragonfly...), a
plate hotel with UV imaging, home X-ray sources.
To apply, please send your cover letter, CV and reference letters to:
[log in to unmask] (with a reference in the topic either
Sonata-Postdoc or Sonata-Tech) by August 31st.
For more details see: http://crystal.chem.uw.edu.pl/staff/gorna.html
Best regards,
Maria Gorna
--
----------------
Maria Gorna, Ph.D.
Faculty of Chemistry
University of Warsaw
Pasteura 1
02-093 Warsaw
Poland
tel.: +48 22 822 0211 ext. 543
email: [log in to unmask]
------------------------------
Date: Thu, 30 Jul 2015 13:44:56 -0500
From: Tim Panosian <[log in to unmask]>
Subject: Opening for a Structural Biologist with an emphasis X-ray Crystallography at Monsanto Company in St. Louis
Hi Everyone,
We have an opening ad Monsanto on the Protein Structure and Design Team
within the Biotechnology Organization. The position is located at our
Chesterfield Missouri research campus, just outside of Saint Louis. We are
looking for a Ph.D. level scientist with X-ray Crystallography experience
who is interested in being part of a collaborative team that contributes to
many diverse projects in the Biotech pipeline.
I am the hiring manager, so please feel free to reach out at my work email (
[log in to unmask]) if you have any questions, but please note
that only applications submitted through our online system will be
considered.
If you are interested or know someone who many be, apply through our
careers page:
https://monsanto.taleo.net/careersection/jobdetail.ftl?job=013UK&lang=en
The full job description is below.
Regards,
Tim
#########
Scientist - Structural Biology-013UK
The Monsanto Protein Structure and Design team is interested in receiving
applications for the position of a *Protein Structural Biology Scientist*
in St. Louis, Missouri. The ideal candidate is a practicing structural
biologist with hands-on, current expertise in modern techniques used to
determine structures of challenging macromolecules and macromolecular
complexes using X-ray crystallography via both molecular replacement and
experimental phasing. Expertise in both robotic and manual screening of
crystals, follow-up, and condition optimization is a must as is expertise
with data collection (both at a home source and remotely at a synchrotron),
processing and refinement. The ideal candidate has a broad interest in
utilizing structural biology as a collaborative tool to advance a broad
array of scientific projects. Top candidate will have demonstrated the
artful use of protein chemistry, rational mutagenesis and other sample
modification techniques to accomplish the ultimate goal of producing useful
crystals of the target molecule, will have demonstrated collaborative
project management, and will have had experience creatively utilizing
molecular biology, protein purification, bioinformatics, database mining
and/or utilizing scripting languages to accomplish goals.
*Responsibilities include:*
· Collaboration with diverse project teams to design and execute
experiments that enable product development decisions to be informed with
relevant protein structure information
· Sustained efforts on parallel crystallization and structure
determination projects for multiple novel proteins, protein complexes, and
other macromolecular entities
· Development and testing of new approaches to successful and
speedy crystallization and structure determination of macromolecules
· Support of diverse crystallization and imaging robotics
· Active participation in structure driven protein discovery and
protein engineering projects
· Gene to structure ownership of select structural projects
· Record keeping, publication, and other IP associated activities
The Protein Structure and Design group at Monsanto is an inter-disciplinary
nexus in a highly collaborative team-based environment. We interact with
numerous project teams in areas spanning the entire spectrum of Discovery
activities, from gene discovery through regulatory review. Together we
catalyze the discovery and optimization of protein leads for novel
agronomic traits and the development of innovative biotechnologies. Our
expression, purification, automated crystallization/imaging, data
collection and structure solution facilities are state of the art and are
updated on a regular basis.
*Required Education and Skills:*
· Minimum of a Ph.D. in a relevant discipline (biochemistry,
biophysics, chemistry, etc.)
· Minimum of four or more years of experience with demonstrated and
sustained practical expertise in crystallization of macromolecules with
several years practicing crystallization in a multi-project environment
· Demonstrated experience working on multidisciplinary
collaborative teams
· Highly effective written and oral communication and interpersonal
skills
· Diverse basic science background: molecular structure, protein
crystallization/crystallography, biochemistry, pharmacology, molecular
biology, biophysics, etc.
*Desired Education and Skills:*
· Demonstrated team and/or project leadership and experience
carrying a project to completion
· Demonstrated gene to structure skill set
· Successfully solved at least 20 protein structures (utilizing
both molecular replacement and experimental phasing)
· Experience with membrane proteins
· Experience with scripting languages Perl or Python
· Demonstrated interest in developing and or improving protein
crystallization techniques
------------------------------
Date: Thu, 30 Jul 2015 17:53:04 -0400
From: Paul Adams <[log in to unmask]>
Subject: Berkeley Server Downtime
Dear Colleagues,
as part of final commissioning of our new building there will be a power outage to the Computational Crystallography Initiative server room. As a result several structural biology web services will be offline for a short while. These include:
- The Phenix web site (http://phenix-online.org/)
- The DIALS West web site (http://dials.lbl.gov/)
- The CCI web site (http://cci.lbl.gov/)
- The Structural Biology Technology Portal (http://technology.sbkb.org/)
The servers will be shutdown at 5pm Pacific time on Thursday 30th (i.e. tonight). Services should resume by the morning of Friday August 31st. During the downtime bug reports and emails requesting help should be queued and received by us once the servers are back online. We greatly appreciate your understanding, and hope that this doesn’t present too much of an inconvenience.
Cheers,
Paul
--
Paul Adams
Deputy Division Director, Physical Biosciences Division, Lawrence Berkeley Lab
Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab
Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Vice President for Technology, the Joint BioEnergy Institute
Laboratory Research Manager, ENIGMA Science Focus Area
Building 33, Room 347
Building 80, Room 247
Building 978, Room 4126
Tel: 1-510-486-4225, Fax: 1-510-486-5909
http://cci.lbl.gov/paul
Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 33R0345
Berkeley, CA 94720, USA.
Executive Assistant: Louise Benvenue [ [log in to unmask] ][ 1-510-495-2506 ]
--
------------------------------
Date: Thu, 30 Jul 2015 23:00:53 +0100
From: Mohamed Noor <[log in to unmask]>
Subject: Off-topic: Transfering data from Diamond
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....
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:
xxxx_sweep1_0001.cbf - xxxx_sweep1_1800.cbf
xxxx_sweep2_0001.cbf - xxxx_sweep2_0900.cbf
I want to get a text file output containing a line saying:
/folder/name/sweep1 - 1800
/folder/name/sweep2 - 900
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.
Thanks.
------------------------------
End of CCP4BB Digest - 29 Jul 2015 to 30 Jul 2015 (#2015-31)
************************************************************