[ccp4bb] Calculating over all bend in a DNA

[Sasha Pausch]

Hello CCP4bb,

May I know how can we calculate or use any server which can calculate the
overall bend in a DNA (crystal structure)?

[ccp4bb] Position available: Software Release Engineer - SBGrid

[Michelle Ottaviano]

Apply at the Harvard

Auto req ID34021BRBusiness TitleSoftware Release EngineerSchool/UnitHarvard
Medical SchoolLocationUSA - MA - Boston


Job FunctionInformation TechnologyTime StatusFull-time

Duties & ResponsibilitiesThe SBGrid Consortium has an immediate opening for
a Software Release Engineer. The primary responsibilities of the position
will be installing, configuring and testing biomedical software on Linux
and OS X for use in the Harvard Medical School laboratories as well as
providing first level technical support for software users. The majority of
user support occurs over email, so the ability to communicate clear English
instructions is critical. Additional responsibilities include working with
scientific software developers to integrate new applications into the
software collection.

The scientific software is written in a polyglot of languages (Fortran, C,
C++, Python, Java, Perl, Tcl/Tk and many sh/csh scripts) and built with any
one of a number of different build systems (autotools, cmake, scons,
homebrew shell scripts/makefiles, setuptools, etc). This is a hybrid type
position where some software development experience is useful, but it is
not a traditional developer job in any sense. This individual will work as
a member of a multidisciplinary research and computing environment that
integrates a software consortium, research computing support, research
laboratories, and teaching initiatives.Basic QualificationsBachelor’s
degree in computer science, computer engineering or technology-related
discipline; or PhD in biological sciences; or equivalent combination of
education plus relevant experience. 5-7 years of research computing or
related experience.Additional QualificationsRequires working knowledge of
at least one programming or scripting language; sh or csh shell scripting
experience. Knowledge of how to drive a compiler and linker as well as an
understanding of shared libraries. Autodidact with strong attention to
detail and enthusiasm for hard problems. Familiarity with Python or other
programming languages; familiarity with biomedical software applications
and structure determination/analysis workflows; strong knowledge of Linux
and OS X operating systems. The successful candidate will have excellent
organizational skills and particular ability to work independently and
prioritize work. Proven project and/or program management skills. Excellent
interpersonal and communications skills. Ability to work with
discretion.Additional
InformationThis is a 12 month term appointment with the possibility of
extension.

[ccp4bb] 10 DAYS REMAIN to apply for the DLS/CCP4 data analysis workshop

[David Waterman]

Dear all,

Please be aware that the application period for the first DLS/CCP4 data
analysis workshop closes on the 31st October. Successful applicants will be
notified shortly after that date.

As a reminder, the workshop is intended for PhD students, postdocs and
early career scientists who are *currently working on a project in MX, and
who are able to bring crystals or data with them*. The workshop will
consist of a mixture of lectures and tutorials, plus hands-on practical
sessions, in which the students will work alongside the leading software
developers and scientists on their own data. Applicants please note that
you must provide the e-mail address of a supervisor who will write a letter
in support of your application.

More details may be found here:
http://www.ccp4.ac.uk/schools/DLS-2014/index.php

The online application form is at Diamond's Events site:
http://www.diamond.ac.uk/Home/Events/2014/Diamond-CCP4-Data-Collection-and-Analysis-workshop.html

Many thanks for your interest

David Waterman, on behalf of the organisers.

Re: [ccp4bb] Normal mode refinement

[Ethan Merritt]

On Tuesday, 21 October 2014 07:39:53 AM Appu kumar wrote:
> Dear All,
> Thank you very much for valuable suggestions and educating me on the normal
> mode refinement. Actually, I am trying to refine a protein (cytosolic
> domain and trans-membrane domain). I found a solution through PHASER and
> density looks really good in both domain but as i proceeds with refinement
> density remain great in both domain till Rfree around 38%. Interestingly,
> with further refinement cycle, Rfree reduced to  30% but the density in the
> trans-membrane domain becomes very weak. That is why i am wondering whether
> it is possible to improve the density in the trans-membrane domain by using
> Normal mode refinement. Conservatively speaking, it could be possible that
> trans-membrane is highly flexible or disordered and after much cerebration,
> i am thinking to incorporate the normal mode refinement to monitor if there
> is any improvement in electron density trans-membrane domain.

Please keep in mind that if the density is poor because the protein really
is disordered, a perfect description of those disordered cell contents will
perfectly reproduce that poor density.   So "improved description" does not
necessarily imply "improved map quality".

This is quite different from the case of a poor model for a well-ordered
structure.  Here also you will see a low quality map, but in this case it
will improve as your description of the cell contents improves.


Ethan



> I would follow suggestions of Dr, Mande and Dr. Ethan.  Also, would give a
> try to what Arpita has suggested.  I further, warmly welcome any suggestion
> on refinement procedure to improve electron density in flexible or
> disordered trans-membrane domain.
> Appu
> 
> On 20 October 2014 23:41, Arpita Goswami  wrote:
> 
> > Hello,
> >
> > You can also contact elNemo or NOMAD-Ref server developers about getting
> > covariance/correlation matrices from normal mode analysis outputs to know
> > the correctly coordinated mobile atoms. In this way you can compare with
> > biological data also. In Shekhar's said paper K. Suhre (one of the
> > developer of el-Nemo server) has done the same very correctly.
> >
> > best wishes,
> > Arpita
> >
> > On Tue, Oct 21, 2014 at 5:40 AM, Appu kumar  wrote:
> >
> >> Dear CCP4 Users,
> >> I seek your valuable advice and suggestion in carrying out the normal
> >> mode structure refinement which manifest the dynamics of protein as linear
> >> combination of harmonic modes, used to describe the motion of protein
> >> structure in collective fashion. Studies suggest that it is highly useful
> >> in refining the protein structure which harbors a considerable magnitude of
> >> flexibility in atomic position owing to high thermal factors.
> >> Therefor I want to know is there any software/script available to execute
> >> the normal mode of refinement. Thanks a lot in advance for your imperative
> >> suggestions
> >>
> >> Appu
> >>
> >
> >
> >
> > --
> > Arpita
> >
> > --
> > Arpita Goswami
> > Senior Research Fellow
> > Structural Biology Laboratory
> > Centre for DNA Fingerprinting and Diagnostics (CDFD)
> > Tuljaguda (Opp MJ Market),
> > Nampally, Hyderabad 500 001
> > INDIA
> > Phone: +91- 40- 24749401/404
> > Mobile: 9390923667, 9502389184
> > Email: arp...@cdfd.org.in
> >

-- 
mail:   Biomolecular Structure Center,  K-428 Health Sciences Bldg
MS 357742,   University of Washington, Seattle 98195-7742

Re: [ccp4bb] Normal mode refinement

[Appu kumar]

Dear All,
Thank you very much for valuable suggestions and educating me on the normal
mode refinement. Actually, I am trying to refine a protein (cytosolic
domain and trans-membrane domain). I found a solution through PHASER and
density looks really good in both domain but as i proceeds with refinement
density remain great in both domain till Rfree around 38%. Interestingly,
with further refinement cycle, Rfree reduced to  30% but the density in the
trans-membrane domain becomes very weak. That is why i am wondering whether
it is possible to improve the density in the trans-membrane domain by using
Normal mode refinement. Conservatively speaking, it could be possible that
trans-membrane is highly flexible or disordered and after much cerebration,
i am thinking to incorporate the normal mode refinement to monitor if there
is any improvement in electron density trans-membrane domain.
I would follow suggestions of Dr, Mande and Dr. Ethan. Also, would give a
try to what Arpita has suggested. I further, warmly welcome any suggestion
on refinement procedure to improve electron density in flexible or
disordered trans-membrane domain.
Appu

On 21 October 2014 07:39, Appu kumar  wrote:

> Dear All,
> Thank you very much for valuable suggestions and educating me on the
> normal mode refinement. Actually, I am trying to refine a protein
> (cytosolic domain and trans-membrane domain). I found a solution through
> PHASER and density looks really good in both domain but as i proceeds with
> refinement density remain great in both domain till Rfree around 38%.
> Interestingly, with further refinement cycle, Rfree reduced to  30% but the
> density in the trans-membrane domain becomes very weak. That is why i am
> wondering whether it is possible to improve the density in the
> trans-membrane domain by using Normal mode refinement. Conservatively
> speaking, it could be possible that trans-membrane is highly flexible or
> disordered and after much cerebration, i am thinking to incorporate the
> normal mode refinement to monitor if there is any improvement in electron
> density trans-membrane domain.
> I would follow suggestions of Dr, Mande and Dr. Ethan. Also, would give a
> try to what Arpita has suggested. I further, warmly welcome any suggestion
> on refinement procedure to improve electron density in flexible or
> disordered trans-membrane domain.
> Appu
>
> On 20 October 2014 23:41, Arpita Goswami  wrote:
>
>> Hello,
>>
>> You can also contact elNemo or NOMAD-Ref server developers about getting
>> covariance/correlation matrices from normal mode analysis outputs to know
>> the correctly coordinated mobile atoms. In this way you can compare with
>> biological data also. In Shekhar's said paper K. Suhre (one of the
>> developer of el-Nemo server) has done the same very correctly.
>>
>> best wishes,
>> Arpita
>>
>> On Tue, Oct 21, 2014 at 5:40 AM, Appu kumar 
>> wrote:
>>
>>> Dear CCP4 Users,
>>> I seek your valuable advice and suggestion in carrying out the normal
>>> mode structure refinement which manifest the dynamics of protein as linear
>>> combination of harmonic modes, used to describe the motion of protein
>>> structure in collective fashion. Studies suggest that it is highly useful
>>> in refining the protein structure which harbors a considerable magnitude of
>>> flexibility in atomic position owing to high thermal factors.
>>> Therefor I want to know is there any software/script available to
>>> execute the normal mode of refinement. Thanks a lot in advance for your
>>> imperative suggestions
>>>
>>> Appu
>>>
>>
>>
>>
>> --
>> Arpita
>>
>> --
>> Arpita Goswami
>> Senior Research Fellow
>> Structural Biology Laboratory
>> Centre for DNA Fingerprinting and Diagnostics (CDFD)
>> Tuljaguda (Opp MJ Market),
>> Nampally, Hyderabad 500 001
>> INDIA
>> Phone: +91- 40- 24749401/404
>> Mobile: 9390923667, 9502389184
>> Email: arp...@cdfd.org.in
>>
>
>

Re: [ccp4bb] Normal mode refinement

[Appu kumar]

Dear All,
Thank you very much for valuable suggestions and educating me on the normal
mode refinement. Actually, I am trying to refine a protein (cytosolic
domain and trans-membrane domain). I found a solution through PHASER and
density looks really good in both domain but as i proceeds with refinement
density remain great in both domain till Rfree around 38%. Interestingly,
with further refinement cycle, Rfree reduced to  30% but the density in the
trans-membrane domain becomes very weak. That is why i am wondering whether
it is possible to improve the density in the trans-membrane domain by using
Normal mode refinement. Conservatively speaking, it could be possible that
trans-membrane is highly flexible or disordered and after much cerebration,
i am thinking to incorporate the normal mode refinement to monitor if there
is any improvement in electron density trans-membrane domain.
I would follow suggestions of Dr, Mande and Dr. Ethan. Also, would give a
try to what Arpita has suggested. I further, warmly welcome any suggestion
on refinement procedure to improve electron density in flexible or
disordered trans-membrane domain.
Appu

On 20 October 2014 23:41, Arpita Goswami  wrote:

> Hello,
>
> You can also contact elNemo or NOMAD-Ref server developers about getting
> covariance/correlation matrices from normal mode analysis outputs to know
> the correctly coordinated mobile atoms. In this way you can compare with
> biological data also. In Shekhar's said paper K. Suhre (one of the
> developer of el-Nemo server) has done the same very correctly.
>
> best wishes,
> Arpita
>
> On Tue, Oct 21, 2014 at 5:40 AM, Appu kumar  wrote:
>
>> Dear CCP4 Users,
>> I seek your valuable advice and suggestion in carrying out the normal
>> mode structure refinement which manifest the dynamics of protein as linear
>> combination of harmonic modes, used to describe the motion of protein
>> structure in collective fashion. Studies suggest that it is highly useful
>> in refining the protein structure which harbors a considerable magnitude of
>> flexibility in atomic position owing to high thermal factors.
>> Therefor I want to know is there any software/script available to execute
>> the normal mode of refinement. Thanks a lot in advance for your imperative
>> suggestions
>>
>> Appu
>>
>
>
>
> --
> Arpita
>
> --
> Arpita Goswami
> Senior Research Fellow
> Structural Biology Laboratory
> Centre for DNA Fingerprinting and Diagnostics (CDFD)
> Tuljaguda (Opp MJ Market),
> Nampally, Hyderabad 500 001
> INDIA
> Phone: +91- 40- 24749401/404
> Mobile: 9390923667, 9502389184
> Email: arp...@cdfd.org.in
>

[ccp4bb] Probleme with D-peptide cif dictionary with refmac5.8

[LEGRAND Pierre]

Dear all,

A quick note to report the problems I have experienced (and a solution) with 
the refinement of a peptide containing both D- and L-amino-acids with refmac5.8 
(Refmac_5.8.0073).
This refinement was done with high resolution data, with hydrogens included in 
the model (important to remember !).

When using the standard dictionary for D-TRYPTOPHAN: $CLIBD_MON/d/DTR.cif, most 
of the geometrical definitions were altered after the inserted D-amino-acid. 
The geometrical Rms deviations are strongly increased already at the first 
cycle (see differences of two runs at the end of my message). 

The first solution was to generate a new cif dictionary from the standard 
TRP.cif file in the following way:

sed -e 's/negativ/positiv/'  -e 's/TRP/DTR/g' -e 's/L-peptide/D-peptide/' 
$CLIBD_MON/t/TRP.cif  > DTRP.cif

Running again refmac5 with this cif file using the LIBIN DTRP.cif instruction 
produced the more sensible results. 

It looked to me that the TRP and DTR cif definitions have diverged at some 
point. Looking more closely at the differences in this two files, pointed me to 
this:
Hydrogen on the indole NE1 is named HE1 in TRP and HNE1 for DRT...
Using a pdb file with HE1 renamed as HNE1 worked with the current DRT file, but 
with slightly worst results.

The DTR.cif file probably needs to be updated (and maybe the other 
D-amino-acids cifs also revisited).

Best regards,
Pierre

PS1. I can send the log and pdb files to developers if they are interested.
PS2. I haven't checked with other D-amino-acids, since I have only this one in 
my structure.

With modified TRP as DTRP.cif:
<  InitialFinal
  InitialFinal
>R factor0.0865   0.1916
>  R free0.0913   0.2006
>  Rms BondLength2.4522   1.7415
>   Rms BondAngle   33.3672  32.1460
>  Rms ChirVolume1.1972   1.0767

With DRT.cif and renamed HE1 as HNE1:
>  InitialFinal
>   R factor0.0865   0.0848
> R free0.0913   0.0901
> Rms BondLength0.0207   0.0200
>  Rms BondAngle2.4024   2.3884
> Rms ChirVolume0.1122   0.1140