[ccp4bb] Transcription start site

[syed ibrahim]

Hi All

I am trying to code gene prediction. I am looking for the consensus pattern for 
transcription start site, pribnov bow, ribosomal binding site and so on. I am 
looking some pattern which are variable and I could not make any conclusion. If 
anyone can provide all consensus pattern for eukaryote and bacterial system, 
that would be of great help.

Thank you in advance

Syed



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[ccp4bb] Wanted: Research Computing Engineer in Structural Biology (+ other fields) in New York City

[Daniel Keedy]

Hello computational crystallography folks,

My institution, the new CUNY Advanced Science Research Center ( 
asrc.cuny.edu ) in New York City, is looking for a 
Research Computing Engineer.  This is a nice opportunity for someone with broad 
interests in computational research to interact with scientists across a 
spectrum of exciting fields here at the ASRC, including Structural Biology ( 
structbio.asrc.cuny.edu ) and also Nanoscience, 
Photonics, Neuroscience, and Environmental Science.  Their role would include 
administering our computing infrastructure, including an incoming CPU- and 
GPU-based high-performance computing cluster, and liaising with ASRC scientists 
to solve computational research problems.

You can apply by following this link to the official ad (I suggest you scroll 
down to “The ASRC invites applications...”):

https://cuny.jobs/new-york-ny/research-computing-engineerit-senior-associate-level-3-provisional-advanced-science-research-center/a1f762c9053842738d4c09f3cb17c169/job/

Please forward this message to anyone who may be interested.

Thank you for your time,

~Daniel

—
Daniel A. Keedy, Ph.D.
Assistant Professor
Structural Biology Initiative, CUNY Advanced Science Research Center
Department of Chemistry and Biochemistry, City College of New York
Biochemistry and Chemistry Ph.D. Programs, CUNY Graduate Center
www.keedylab.org   |  
daniel.ke...@asrc.cuny.edu  |  212-413-3246




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Re: [ccp4bb] Clear Linux

[Jim Fairman]

David,

Luckily, phoronix has also benchmarked 10 different linux OSes on a Ryzen 7
1800X and a Threadripper 1950X chip:
https://www.phoronix.com/scan.php?page=article=ryzen-linux-10way=3

--
Jim Fairman
C: 1-240-479-6575


On Thu, Feb 7, 2019 at 8:16 AM David Schuller  wrote:

> I would be wary of an OS developed and promoted by a hardware
> manufacturer (Intel). The Phoronix benchmarks you linked were conducted
> on an Intel Xeon chip. I wonder how Clear OS performs with AMD chips,
> which are featuring very attractive performance and price recently.
>
>
>
> On 2/7/19 10:38 AM, Karthik Paithankar wrote:
> > Dear Program devs and enthusiasts,
> >
> > After seeing James' email (on dismal CPU performance), I was searching
> > for various ideas and found the so-called "Clear Linux Project". Seems
> > " function multi-version patch" leads to significant improvements.
> > Though I could install the precompiled binary of CCP4 and phenix
> > without any issues but there are no improvements to runtime as FMV
> > needs 'patching' and compiling.
> >
> > Could DIALS, CCP4 or Phenix programmers see if this is
> > useful/possible? Has anyone tried it?
> >
> > https://clearlinux.org/documentation/clear-linux/tutorials/fmv
> >
> https://www.phoronix.com/scan.php?page=article=clear-faster-blas=1
> >
> > Best regards,
> > Karthik Paithankar
> >
> >
> >
> > On 30/11/2018, James Holton < > wrote:
> >> I have a dissenting opinion about computers "moving on a bit".  At least
> >> when it comes to most crystallography software.
> >>
> >> Back in the late 20th century I defined some benchmarks for common
> >> crystallographic programs with the aim of deciding which hardware to
> >> buy.  By about 2003 the champion of my refmac benchmark
> >> (https://bl831.als.lbl.gov/~jamesh/benchmarks/index.html#refmac) was
> the
> >> new (at the time) AMD "Opteron" at 1.4 GHz.  That ran in 74 seconds.
> >>
> >> Last year, I bought a rather expensive 4-socket Intel Xeon E7-8870 v3
> >> (turbos to 3.0 GHz), which is the current champion of my XDS benchmark.
> >> The same old refmac benchmark on this new machine, however, runs in 68.6
> >> seconds.  Only a smidge faster than that old Opteron (which I threw away
> >> years ago).
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>
>
> --
> ===
> All Things Serve the Beam
> ===
> David J. Schuller
> modern man in a post-modern world
> MacCHESS, Cornell University
> schul...@cornell.edu
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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[ccp4bb] Position opening at RCSB PDB/Rutgers University- BIOCHEMICAL INFORMATION & ANNOTATION SPECIALIST

[Jasmine Young]

The RCSB Protein Data Bank (RCSB PDB, rcsb.org ) is a 
publicly accessible information portal for researchers and students 
interested in structural biology. At its center is the PDB Core Archive 
– the single global repository for the 3-dimensional structure data of 
biological macromolecules. These structures hold significant promise for 
the pharmaceutical and biotechnology industries in the search for new 
drugs and in efforts to understand human disease.


The primary mission of the RCSB PDB is to provide accurate, 
well-annotated data in the most timely and efficient way to facilitate 
new discoveries and scientific advances. The RCSB PDB processes, stores, 
and disseminates these important data, and develops the software tools 
needed to assist users in depositing (in collaboration with worldwide 
PDB partners) and accessing structural information.


The RCSB PDB at Rutgers University in Piscataway, NJ has an opening for 
a Biochemical Information & Annotation Specialist (Biocurator) to 
curate, validate, and standardize macromolecular structures for 
distribution in the PDB Core Archive. Data curation is critical for 
these resources. In the case of PDB, data


are carefully reviewed and annotated by wwPDB curators before 
publicrelease. Expert curation of data coming into PDB is critical for 
ensuring findability, accessibility, interoperability, and reusability 
(FAIR). Biocurators communicate daily with members of the deposition 
community, and annotate, publicly release, and update entries in the PDB 
Core Archive.


The position is an academic position with state benefit. The salary is 
compatible with faculty level.


A background in cryo-electron microscopy or small molecule 
crystallography or macromolecular crystallography is a strong advantage. 
Biological chemistry in PhD is required. Experience with metalloprotein, 
small molecules, linux computer systems, biological databases is 
preferred. The successful candidate should be self-motivated, pay close 
attention to detail, possess strong interpersonal, communication, and 
writing skills with the ability to handle multiple projects, shift 
priority, and meet deadlines.


This position offers the opportunity to participate in exciting projects 
with significant impact on the scientific community.


Please apply this job at http://jobs.rutgers.edu/postings/84303. 








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Re: [ccp4bb] Clear Linux

[David Schuller]

I would be wary of an OS developed and promoted by a hardware 
manufacturer (Intel). The Phoronix benchmarks you linked were conducted 
on an Intel Xeon chip. I wonder how Clear OS performs with AMD chips, 
which are featuring very attractive performance and price recently.




On 2/7/19 10:38 AM, Karthik Paithankar wrote:

Dear Program devs and enthusiasts,

After seeing James' email (on dismal CPU performance), I was searching
for various ideas and found the so-called "Clear Linux Project". Seems
" function multi-version patch" leads to significant improvements.
Though I could install the precompiled binary of CCP4 and phenix
without any issues but there are no improvements to runtime as FMV
needs 'patching' and compiling.

Could DIALS, CCP4 or Phenix programmers see if this is
useful/possible? Has anyone tried it?

https://clearlinux.org/documentation/clear-linux/tutorials/fmv
https://www.phoronix.com/scan.php?page=article=clear-faster-blas=1

Best regards,
Karthik Paithankar



On 30/11/2018, James Holton < > wrote:

I have a dissenting opinion about computers "moving on a bit".  At least
when it comes to most crystallography software.

Back in the late 20th century I defined some benchmarks for common
crystallographic programs with the aim of deciding which hardware to
buy.  By about 2003 the champion of my refmac benchmark
(https://bl831.als.lbl.gov/~jamesh/benchmarks/index.html#refmac) was the
new (at the time) AMD "Opteron" at 1.4 GHz.  That ran in 74 seconds.

Last year, I bought a rather expensive 4-socket Intel Xeon E7-8870 v3
(turbos to 3.0 GHz), which is the current champion of my XDS benchmark.
The same old refmac benchmark on this new machine, however, runs in 68.6
seconds.  Only a smidge faster than that old Opteron (which I threw away
years ago).



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--
===
All Things Serve the Beam
===
   David J. Schuller
   modern man in a post-modern world
   MacCHESS, Cornell University
   schul...@cornell.edu



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[ccp4bb] Clear Linux

[Karthik Paithankar]

Dear Program devs and enthusiasts,

After seeing James' email (on dismal CPU performance), I was searching
for various ideas and found the so-called "Clear Linux Project". Seems
" function multi-version patch" leads to significant improvements.
Though I could install the precompiled binary of CCP4 and phenix
without any issues but there are no improvements to runtime as FMV
needs 'patching' and compiling.

Could DIALS, CCP4 or Phenix programmers see if this is
useful/possible? Has anyone tried it?

https://clearlinux.org/documentation/clear-linux/tutorials/fmv
https://www.phoronix.com/scan.php?page=article=clear-faster-blas=1

Best regards,
Karthik Paithankar



On 30/11/2018, James Holton < > wrote:
> I have a dissenting opinion about computers "moving on a bit".  At least
> when it comes to most crystallography software.
>
> Back in the late 20th century I defined some benchmarks for common
> crystallographic programs with the aim of deciding which hardware to
> buy.  By about 2003 the champion of my refmac benchmark
> (https://bl831.als.lbl.gov/~jamesh/benchmarks/index.html#refmac) was the
> new (at the time) AMD "Opteron" at 1.4 GHz.  That ran in 74 seconds.
>
> Last year, I bought a rather expensive 4-socket Intel Xeon E7-8870 v3
> (turbos to 3.0 GHz), which is the current champion of my XDS benchmark.
> The same old refmac benchmark on this new machine, however, runs in 68.6
> seconds.  Only a smidge faster than that old Opteron (which I threw away
> years ago).



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[ccp4bb] Call open for beamtime at DESY beamline P11, PETRA III, Deadline: 1 March 2019

[Anja Burkhardt]

Dear all,

Hereby I would like to invite the submission of regular proposals for DESY 
beamline P11 at the PETRA III synchrotron in Hamburg.

The call is open until Friday March 1, 2019 (inclusive; UTC+1) and is for 
experiments to be performed in the second half of 2019 (5.7.19 – 20.12.19). 

Please note that in in the frame of the proposal harmonization efforts between 
European lightsources we have modified our proposal templates!
Preparation guidelines for the proposals and new templates can be found here: 
https://photon-science.desy.de/users_area/user_guide/write_a_proposal/

Beamline P11 is dedicated to structural investigations of biological samples 
and currently provides two experimental endstations: an X-ray microscope (under 
construction) and a crystallography experiment which is in user operation since 
2013.

Specific features of the P11 crystallography endstation:
• High photon flux (1.3 × 1013 ph/s at 12 keV) at the sample position 
• Broad energy range from 5.5 - 26 keV
• Full SAD/MAD capability
• High-precision single axis goniostat
• Fast data collection via Pilatus 6M detector (25 Hz frame rate, 154 – 
2000 mm sample-to-detector distance)
• Fast automatic sample changer (20 s) with uni-puck compatibility and 368 
sample storage capacity
• Cryo-shutter for crystal annealing
• Beam size tunability from 4 × 9 µm² to 300 × 300 µm² within a minute
• Microbeam capability (4 × 9 µm² focal spot with 1.3 × 1013 ph/s photon 
flux and 1 × 1 µm² with 2 × 1011 ph/s)
• Serial synchrotron crystallography using liquid sample delivery and fixed 
targets
• Parallel beam option for large unit cell systems
• Data collection via Python-based GUI 
• Automated data processing with XDSAPP 
• 40 core workgroup server for fast data processing
• S2 level laboratory for sample preparation

For detailed information about our experimental setup please visit our homepage 
http://photon-science.desy.de/facilities/petra_iii/beamlines/p11_bio_imaging_and_diffraction

On behalf of the P11 team,
Anja Burkhardt



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[ccp4bb] AW: [EXTERNAL] [ccp4bb] refmac same residue different names

[Herman . Schreuder]

Ed,

I did understand your question correctly and (at least for ligands) the 
procedure I and also Diana Tomchick described, worked. However, I just did a 
test with both Refmac and Buster and it seems that these programs have now so 
far been perfected that “errors” like this cannot occur anymore.

So it seems that the poor crystallographers who have crystallized proteins 
which are heterogeneous at certain positions, will have to switch to Phenix.

Best,
Herman


Von: Edwin Pozharski [mailto:pozharsk...@gmail.com]
Gesendet: Mittwoch, 6. Februar 2019 18:19
An: Schreuder, Herman /DE
Cc: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [EXTERNAL] [ccp4bb] refmac same residue different names

Herman,

thanks - however, it seems like I have poorly worded my question.  I do know 
how to generate alternate conformers, what the PDB ATOM record format is etc.  
The point was that when I have alternate conformers that carry the same residue 
ID but different residue types, Refmac exits with the error.  The question was 
whether there is a "native" solution to this that does not include some pdb 
file acrobatics (i.e. separating the alternative type into a separate residue 
and enforcing connectivity using elaborate LINK records).   Based on what I see 
so far, there likely isn't any such native option.  Whether these situations 
are common enough to warrant (possibly elaborate) software changes is a 
separate question.

Cheers,

Ed.

---
I don't know why the sacrifice didn't work. The science seemed so solid.
Julien XIII, Lord of the Lemurs

On Wed, Feb 6, 2019 at 2:36 AM 
mailto:herman.schreu...@sanofi.com>> wrote:
Dear Edwin,

I do not know whether your question has been answered already, but the answer 
is simple: you have to define alternative conformations. Easiest is to generate 
them in coot with the “add alternate conformation” option in the right panel. 
You may have to delete the original unlabeled alternative conformation first 
though.
Alternatively, if you want to keep the original coordinates, or if the 
alternative residue is different: say a Leu versus a Phe you can open the pdb 
file with an editor and generate the alternative conformation yourself:
One of the residues gets an “A” in front of the residue name, e.g. ALEU, and 
the alternative residue a “B”, say BLEU. You also have to reset the occupancies 
to 0.5 for both conformations (or different fractions which add up to one).

Good luck!
Herman

Von: CCP4 bulletin board 
[mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von 
Edwin Pozharski
Gesendet: Montag, 4. Februar 2019 22:35
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] refmac same residue different names

Belated happy 2019, everyone.

For whatever obscure reason, I need to refine a model that has two different 
residue types as alternate conformers with the same residue ID.  Presented with 
a pdb file that has such feature, Refmac fails saying this

 ERROR: in chain A residue: 443
different residues have the same number

There is an error in the input coordinate file
At least one the chains has 2 residues with the same number
Check above to see error
===> Error: Problem with coordinate file

There are several ways of getting around this I can think of.  Perhaps 
duplicate chain with strict NCS for all but the residue in question could work. 
 Perhaps adding this residue as two separate chains and then adding enough LINK 
records to keep things in place could.  Either solution here is inelegant and 
requires reformating pdb file back to sanity prior to deposition.

Is there some way to allow different geometries for alternate conformers that 
is native to Refmac?

Cheers,

Ed.

PS.  I know that phenix.refine takes the mixed name pdb file straight up.  I 
still want to be able to refine such structure with refmac (and buster, 
actually, but that's a question I already asked in the appropriate forum.


Edwin Pozharski, PhD, Assistant Professor
University of Maryland, Baltimore
--
When the Way is forgotten duty and justice appear;
Then knowledge and wisdom are born along with hypocrisy.
When harmonious relationships dissolve then respect and devotion arise;
When a nation falls to chaos then loyalty and patriotism are born.
-- / Lao Tse /



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