Re: [ccp4bb] CCP4Mg problems

2021-09-27 Thread Demetres D. Leonidas

Dear Stuart,

I did try to run is as you suggest "ccp4mg -noredirect" and I got the 
same msg (i.e. "ERROR no status file .CC$MG2/status/last_exit_status.pkl").


The first thing I checked were the write permissions and this was O.K. 
All other ccp4 programs run smoothly.


best

Demetres

On 9/27/2021 3:37 PM, Stuart McNicholas wrote:

Dear Demetres,
   That message is not actually an error, despite it saying ERROR in 
big letters. Apologies we should fix this as soon as possible.


However, I am guessing that the program is not actually opening? Does 
anything else happen after that message?


One way to possibly help is to run it as follows:

ccp4mg -noredirect

This way all messages should be sent to the terminal output and we 
might see something more helpful.


Sorry for your difficulties,
Stuart

On Mon, 27 Sept 2021 at 13:24, Demetres D. Leonidas 
mailto:ddleoni...@bio.uth.gr>> wrote:


Dear all,

we have recently installed ccp4 programs in a new box running ubuntu
21.04. Everything works fine except ccp4mg. When we try to run it
we get
the splash screen and then a message appears at the terminal
"ERROR no
status file .CC$MG2/status/last_exit_status.pkl". I checked and
such a
file does not exist but I thought it will be created automatically
once
you run the program.

Any ideas ?

Demetres

-- 
-------

Dr. Demetres D. Leonidas
Professor in Biochemistry
Department of Biochemistry & Biotechnology
University of Thessaly
Biopolis 41500 Larissa, Greece
-
Tel. +302410 565278
Tel. +302410 565297 (Lab)
Tel. +304210 565263 (X-ray)
Fax. +302410 565290
E-mail: ddleoni...@bio.uth.gr <mailto:ddleoni...@bio.uth.gr>
ORCID ID orcid.org/-0002-3874-2523
<http://orcid.org/-0002-3874-2523>
---


-- 
Αυτό το e-mail ελέγχθηκε για ιούς από το πρόγραμμα Avast antivirus.

https://www.avast.com/antivirus <https://www.avast.com/antivirus>



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1>

This message was issued to members of www.jiscmail.ac.uk/CCP4BB
<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by
www.jiscmail.ac.uk <http://www.jiscmail.ac.uk>, terms & conditions
are available at https://www.jiscmail.ac.uk/policyandsecurity/
<https://www.jiscmail.ac.uk/policyandsecurity/>


--
---
Dr. Demetres D. Leonidas
Professor in Biochemistry
Department of Biochemistry & Biotechnology
University of Thessaly
Biopolis 41500 Larissa, Greece
-
Tel. +302410 565278
Tel. +302410 565297 (Lab)
Tel. +304210 565263 (X-ray)
Fax. +302410 565290
E-mail: ddleoni...@bio.uth.gr
ORCID ID orcid.org/-0002-3874-2523
---




To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/


[ccp4bb] CCP4Mg problems

2021-09-27 Thread Demetres D. Leonidas

Dear all,

we have recently installed ccp4 programs in a new box running ubuntu
21.04. Everything works fine except ccp4mg. When we try to run it we get
the splash screen and then a message appears at the terminal "ERROR no
status file .CC$MG2/status/last_exit_status.pkl". I checked and such a
file does not exist but I thought it will be created automatically once
you run the program.

Any ideas ?

Demetres

--
---
Dr. Demetres D. Leonidas
Professor in Biochemistry
Department of Biochemistry & Biotechnology
University of Thessaly
Biopolis 41500 Larissa, Greece
-
Tel. +302410 565278
Tel. +302410 565297 (Lab)
Tel. +304210 565263 (X-ray)
Fax. +302410 565290
E-mail: ddleoni...@bio.uth.gr
ORCID ID orcid.org/-0002-3874-2523
---


--
Αυτό το e-mail ελέγχθηκε για ιούς από το πρόγραμμα Avast antivirus.
https://www.avast.com/antivirus



To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1

This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list 
hosted by www.jiscmail.ac.uk, terms & conditions are available at 
https://www.jiscmail.ac.uk/policyandsecurity/


[ccp4bb] Postdoctoral research position

2017-11-14 Thread Demetres D. Leonidas

Postdoctoral research position: molecular biologist/bioinformatician
A 2-year Post-Doctoral position is available immediately in the
Laboratory of Molecular Biology and Genomics in the Department of
Biochemistry and Biotechnology of the University of Thessaly, located in
the city of Larissa. The selected candidate will work in the framework
of a national Research Infrastructure program on Synthetic Biology.
Research in the Laboratory of Molecular Biology and Genomics focuses on
various aspects of insect olfaction, reproduction and evolution, aiming
at the development of new approaches for control of insects of
agricultural or medical importance. We are seeking a highly motivated
and creative scientist with a track record of successful research. A
good bioinformatics background is strongly desired. The ideal candidate
should be able to analyze raw sequencing data, perform genome assembly
and annotation and have a good understanding of comparative and
functional genomics. At the same time, he/she should be able to design
and perform experiments in support of the bioinformatics analyses.
Candidates should have a PhD and should have training in one or more of
the following disciplines: bioinformatics, molecular biology,
biochemistry, cell biology, and genome-wide technologies. Familiarity
with insect rearing is desirable but not essential. Curriculum Vitae, a
brief letter describing interests and prior experience and names of
three references should be sent to: kmath...@bio.uth.gr.

Research position: MSc Bioinformatician
A 2-year position for an MSc Bioinformatician is available immediately
in the Laboratory of Molecular Biology and Genomics in the Department of
Biochemistry and Biotechnology of the University of Thessaly, located in
the city of Larissa. The selected candidate will work in the framework
of a national Research Infrastructure program on Synthetic Biology.
Research in the Laboratory of Molecular Biology and Genomics focuses on
various aspects of insect olfaction, reproduction and evolution, aiming
at the development of new approaches for control of insects of
agricultural or medical importance. We are seeking a highly motivated
individual with a BSc in Biology or related science and an MSc in
Bioinformatics. The successful candidate will be involved in raw
sequencing data analysis, genome assembly and annotation and comparative
and functional genomics studies. His/her research could also lead to a
PhD. Curriculum Vitae, a brief letter describing interests and prior
experience and names of three references should be sent to:
kmath...@bio.uth.gr.

--
---
Dr. Demetres D. Leonidas
Professor of Biochemistry
Department of Biochemistry & Biotechnology
University of Thessaly
Biopolis
41500 Larissa, Greece
-
Tel. +302410 565278
Tel. +302410 565297 (Lab)
Fax. +302410 565290
E-mail: ddleoni...@bio.uth.gr
http://www.bio.uth.gr
ORCID ID orcid.org/-0002-3874-2523
---


---
Αυτό το e-mail ελέγχθηκε για ιούς από το πρόγραμμα Avast antivirus.
https://www.avast.com/antivirus


Re: [ccp4bb] X-ray pattern has streaks

2013-10-03 Thread Demetres D. Leonidas

Dear Krithika,

what you probably see is the diffraction pattern of a highly mosaic 
crystal due to probably internal disordering.


cheers

Demetres


On 3/10/2013 3:40 μμ, Krithika GOkulnath wrote:

I introduce myself as Dr.Krithika Gokulnath, CAS in crystallography and 
Biophysics, UNiversity of Madras. I have been working with a cloned protein and 
have been successfully able to crystallise it. However data collection done at 
home source shows a pattern of streaks instead of spots. The crystallization 
set up contained 12% PEG 8000, 10mM Magnesium chloride, 200mM Potassium 
chloride in 50 mM Tris pH 7.0. The protein is an enzyme which is also in the 
buffer containing the above components excepting the precipitant. It is a 
tetramer at native conditions and molecular weight on SDS-PAGE is 54 Kda. 
Kindly share your suggestions and speculations on what might be the reason for 
the streaking. The streaks are many wide spread and there are no high 
resolution spots or streaks as we might expect in salt crystals.


--
---
Dr. Demetres D. Leonidas
Associate Professor of Biochemistry
Department of Biochemistry  Biotechnology
University of Thessaly
26 Ploutonos Str.
41221 Larissa, Greece
-
Tel. +302410 565278
Tel. +302410 565297 (Lab)
Fax. +302410 565290
E-mail: ddleoni...@bio.uth.gr
http://www.bio.uth.gr
---


Re: [ccp4bb] Off topic: Crystallization screening robot

2013-09-04 Thread Demetres D. Leonidas

Hi,

to add my thoughts I believe that what your friend is looking for is the 
OryxNano from Douglas Instruments. We use it for screening, and it is a 
really trouble free machine. The consumables are not expensive (plates 
and sealing tape actually) and the price is rather low. I would think 
that for small crystallization groups (like ours) is the best robot you 
can buy if you have a small budget. I always thought that the posh 
mosquito is for big academic labs or companies that can really afford 
the rather large amount for consumables it requires.


best wishes

Demetres


On 4/9/2013 4:57 ??, Artem Evdokimov wrote:


Hi,

The most rock-solid robotic screening platform in my experience has 
been the Mosquito. It has a supply spend of ~$2000/reel of tape which 
has ~27,000 tips on it so it's roughly 9-9 cents per tip - so per 
plate with thee proteins on it it's about 3 bucks depending on how you 
organize the set up.


Not to say that other machines are bad, no - there are plenty of good 
instruments out there but in my opinion Mosquito has unbeatable 
combination of robust, repeatable set up, disposable tips and 
accuracy. In my career I've tried or owned about 90% of all devices 
out there (I guess that's the advantage of having several industrial 
positions in a row) and so I am fairly confident that this is not a 
biased comparison.


Artem

- Cosmic Cats approve of this message

P.S. naturally I am not affiliated with TTP in any way. Caveat emptor.


On Tue, Sep 3, 2013 at 10:42 AM, Jinyi Zhu jinyi.c...@gmail.com 
mailto:jinyi.c...@gmail.com wrote:


Dear CCP4ers,

Sorry for the off topic question. A friend of mine is considering
purchasing a crystallization screening robot and would like to
know which one would suit his need best. His lab would use the
robot occasionally for screening and have a limited budget. He
also wants minimum supply purchases for the robot. Could you
kindly suggest some models? Thanks!

Btw, I have personally used Douglas OryX, ARI crystal Pheonix,
Mosquito and Hydra II-Edrop systems.

Best,

Jinyi




--
---
Dr. Demetres D. Leonidas
Associate Professor of Biochemistry
Department of Biochemistry  Biotechnology
University of Thessaly
26 Ploutonos Str.
41221 Larissa, Greece
-
Tel. +302410 565278
Tel. +302410 565297 (Lab)
Fax. +302410 565290
E-mail: ddleoni...@bio.uth.gr
http://www.bio.uth.gr
---



Re: [ccp4bb] a challenge

2013-01-13 Thread Demetres D. Leonidas
Since the discussion for crystallographers is fired up. I want to put on 
record that I totally agree with Tassos about the profile of a 
crystallographer. If you take away the crystals, then a crystallographer 
is no long a crystallographer.


Demetres


On 13/1/2013 9:52 μμ, Anastassis Perrakis wrote:

I think the real challenge (and one that makes for an excellent macromolecular 
crystallographer) is how well one can interpret a map with poor phases.

Let me disagree ... An excellent macromolecular crystallographer, is one that 
given some crystals can derive the best strategy to collect data,
process the data optimally, derive phases using all available information, 
build a model and refine it in such a way that it best explains both data
and geometrical expectations, and do these as efficiently as possible.

Efficiency may suggest using one automated suite or another - or indeed may 
best be achieved by manual labor - be it in the map or in data
collection strategy or refinement or another step: and here I am ignoring the 
art of transforming hair-needle-crystalline-like-dingbits to a diffracting 
crystal.

One that can interpret a map with poor phases can be either a genius in 3d 
orientation - or a not necessarily too intelligent nor experienced but 
determined student
that can drink and breathe this map for a few weeks in a row until a solution 
is in place. Neither would make an excellent macromolecular crystallographer by 
necessity.

Tassos


--
---
Dr. Demetres D. Leonidas
Associate Professor of Biochemistry
Department of Biochemistry  Biotechnology
University of Thessaly
26 Ploutonos Str.
41221 Larissa, Greece
-
Tel. +302410 565278
Tel. +302410 565297 (Lab)
Fax. +302410 565290
E-mail: ddleoni...@bio.uth.gr
http://www.bio.uth.gr
---


[ccp4bb] Post-Doctoral position in Molecular Biology

2012-11-25 Thread Demetres D. Leonidas
Dear all, I am posting this on behalf of a colleague, so please do not 
reply to this msg. Instead send any mail to kmath...@bio.uth.gr


many thanks

Demetres

Post-Doctoral position in Molecular Biology

Department: Biochemistry and Biotechnology, University of Thessaly, Greece
Closing date: December 12, 2012
Anticipated start date: January 1, 2013

A postdoctoral position is available at the Laboratory of Molecular 
Biology and Genomics in the Department of Biochemistry and Biotechnology 
of the University of Thessaly, Greece. The Department of Biochemistry 
and Biotechnology is located in the city of Larissa, in the center of 
Greece, 380 km north of Athens and 250 km south of Salonika. The DBB 
offers high level training for biochemists, molecular biologists and 
biotechnologists. The three main directions of Department’s research 
activities are: (i) Functional genomics, (ii) Bioactive molecules and 
(iii) Biodiversity.
The main focus of the Laboratory of Molecular Biology and Genomics 
regards crucial questions of the biology, ecology and sex 
differentiation of the major olive pest, the olive fly, in an effort to 
develop novel, environmentally friendly methods to control this insect. 
The post-doctoral position concerns the analysis of the olfactory system 
of the olive fly. The entire transcriptome of the olfactory system will 
be sequenced and olfactory and gustatory genes will be identified. 
Subsequently, functional analysis of selected loci will be performed via 
RNAi-mediated transient inhibition in adult flies. Finally, efforts 
should be initiated for generation of transgenic lines in which selected 
loci are stably inhibited or impaired.


The length of the appointment will be until August 31, 2015. Candidates 
are expected to have a PhD in molecular biology, biochemistry, 
biotechnology or related areas. Experience in insect rearing and 
insectary maintenance will be an asset. Good knowledge of English 
language is expected (CAE or equivalent certificate is an advantage). 
He/she is contributing to research and teaching activities performed by 
given workplace. Postdoc is responsible for self-educating and for 
sharing the obtained knowledge with other team members. The salary is 
1800€/month.


Required documents (to be sent to kmath...@bio.uth.gr) are: full CV 
including list of publications, motivation letter / research statement 
(no more than 2 pages), names of 2 experts in the field who can provide 
recommendation letters. Electronic applications are strongly preferred.
This position is financed by the European Union and the Greek Ministry 
of Education (project OLFLY SMELL  SEX / 2002).


--
---
Dr. Demetres D. Leonidas
Associate Professor of Biochemistry
Department of Biochemistry  Biotechnology
University of Thessaly
26 Ploutonos Str.
41221 Larissa, Greece
-
Tel. +302410 565278
Tel. +302410 565297 (Lab)
Fax. +302410 565290
E-mail: ddleoni...@bio.uth.gr
http://www.bio.uth.gr
---


[ccp4bb] Unusually low B factors with phenix

2012-11-02 Thread Demetres D. Leonidas

Hello,

I am experiencing a weird problem with B factor refinement (individual, 
isotropic) in phenix.refine (1.8.1.-1168) and  a structure at 1.9 A 
resolution. The ADP values after the refinement are very very low, less 
than 2 and sometimes 0. I am getting the same result with and without 
optimization of the X-ray/ADP weight. Has anyone else noticed that and 
is there a workaround ?


Demetres

--
---
Dr. Demetres D. Leonidas
Associate Professor of Biochemistry
Department of Biochemistry  Biotechnology
University of Thessaly
26 Ploutonos Str.
41221 Larissa, Greece
-
Tel. +302410 565278
Tel. +302410 565297 (Lab)
Fax. +302410 565290
E-mail: ddleoni...@bio.uth.gr
http://www.bio.uth.gr
---


Re: [ccp4bb] Unusually low B factors with phenix

2012-11-02 Thread Demetres D. Leonidas

Dear Tim,

this affects all atoms and yes I did reset the B-factors to 20.00 prior 
to refinement. I have not tried REFMAC but now I will give it a try 
since phenix does not seem to do the job.


best

Demetres


On 2/11/2012 1:34 μμ, Tim Gruene wrote:

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Demetres,

does this affect all atoms, or only a few selected ones?

Did you compare with refmac5 (for e.g. input script errors), or did
you reset the B-factors to a reasonable value (e.g. 20-30) prior to
refinement? pdbset can do this conveniently.

Best,
Tim

On 11/02/2012 11:06 AM, Demetres D. Leonidas wrote:

Hello,

I am experiencing a weird problem with B factor refinement
(individual, isotropic) in phenix.refine (1.8.1.-1168) and  a
structure at 1.9 A resolution. The ADP values after the refinement
are very very low, less than 2 and sometimes 0. I am getting the
same result with and without optimization of the X-ray/ADP weight.
Has anyone else noticed that and is there a workaround ?

Demetres

- -- 
Dr Tim Gruene

Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.12 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/

iD8DBQFQk6+vUxlJ7aRr7hoRAvCZAKDxzmLYV74HKanTuoNiqLEu6AmlRwCgkVQs
Q+SZVN6ISb0X38ZekG119/s=
=xKhB
-END PGP SIGNATURE-


--
---
Dr. Demetres D. Leonidas
Associate Professor of Biochemistry
Department of Biochemistry  Biotechnology
University of Thessaly
26 Ploutonos Str.
41221 Larissa, Greece
-
Tel. +302410 565278
Tel. +302410 565297 (Lab)
Fax. +302410 565290
E-mail: ddleoni...@bio.uth.gr
http://www.bio.uth.gr
---


Re: [ccp4bb] Somewhat OT: question of professional courtesy

2012-07-25 Thread Demetres D. Leonidas
I think that people who do this are not really crystallographers (at 
least to me) since they do not give credit to the effort that produces a 
structure. That is why that I always insist on proper refereeing when I 
review a manuscript. Maybe it is time for this community to ask journals 
to put it on their requirement rules for publishing. Otherwise only the 
PDB takes credit (I think is like mentioning just the journal but not 
the authors when reference to a paper).


Demetres





On 25/7/2012 3:33 ??, Radisky, Evette S., Ph.D. wrote:

Somewhat OT: question of professional courtesy

Dear bb,

This morning as I scanned an accepted manuscript from a 
well-respected-but-not-particularly-glamorous journalthat publishes 
manymacromolecularstructures, I came across a briefmention of 
homologyand rmsdwith a published structure listed by PDB accession 
number, but no citation of theprimary reference for this structure. 
(OK, so I wouldn't have noticed or cared had it not been one of 
mine.)  The paper did not have a lot of references, so it was not due 
to limitation in the number of refs permitted.


I havealwaysthoughtit a matter of professional courtesyto cite the 
appropriate reference when one uses and mentionsastructure from the 
PDB, but as I think back, I realize no oneexplicitly told me this--it 
is just an assumption that I made.  Maybe I am the one with 
unrealistic expectations here? Is there ageneralconsensusamong 
crystallographerson thispractice?


Thanks!
Evette

Evette S. Radisky, Ph.D.

Assistant Professor

Mayo Clinic Cancer Center

Griffin Cancer Research Building, Rm 310

4500 San Pablo Road

Jacksonville, FL 32224

(904) 953-6372



--
---
Dr. Demetres D. Leonidas
Associate Professor of Biochemistry
Department of Biochemistry  Biotechnology
University of Thessaly
26 Ploutonos Str.
41221 Larissa, Greece
-
Tel. +302410 565278
Tel. +302410 565297 (Lab)
Fax. +302410 565290
E-mail: ddleoni...@bio.uth.gr
http://www.bio.uth.gr
---



[ccp4bb] Postdoctoral Position in synthesis of glucopyranonucleosides

2012-06-21 Thread Demetres D. Leonidas

Dear all,

please follow the link

http://www.hecra.gr/vacancies/21_6.pdf

for a posdoctoral position in Organic Synthesis at the Department of 
Biochemistry and Biotechnology, University of Thessaly.



Demetres

--
---
Dr. Demetres D. Leonidas
Associate Professor of Biochemistry
Department of Biochemistry  Biotechnology
University of Thessaly
26 Ploutonos Str.
41221 Larissa, Greece
-
Tel. +302410 565278
Tel. +302410 565297 (Lab)
Fax. +302410 565290
E-mail: ddleoni...@bio.uth.gr
http://www.bio.uth.gr
---


Re: [ccp4bb] Devices Suitable to Concentrate Protein Solutions in Liter Scale

2009-09-03 Thread Demetres D. Leonidas

Dear Xuan Yang,

for such large volumes we use a Pellicon type system. The one we have in 
the lab is a polyethersulfone PTJK prep/Scale TFF 2.5 FT2 High flux 10 k 
from Millipore.


good luck

Demetres


Xuan Yang wrote:

Dear All,
 
I am working on protein refolding via dialysis in large volumn 
(typically 2~4 litters). It was problematic when I wanted to 
concentrate the solution to at least less than 500ml. If you know any 
device appropriate for such task, please help me out:)
 
Thanks in advance!
 
Sincerely,
 
Xuan Yang 


--
Demetres D. Leonidas, Ph.D.
Senior Researcher
Structural Biology  Chemistry Group
Institute of Organic and Pharmaceutical Chemistry
The National Hellenic Research Foundation
48, Vassileos Constantinou Avenue
Athens 116 35, Greece
==
Tel. +30 210 7273841 (office)
+30 210 7273895 (lab) 
Fax. +30 210 7273831

E-mail: d...@eie.gr
URL: http://athena.eie.gr
==


[ccp4bb] Marie Curie Fellowship

2009-02-06 Thread Demetres D. Leonidas
Please find attached an advert for a short Marie-Curie fellowship at the 
National Hellenic Research Foundation, Athens, Greece.


We seek to recruit a biology/biochemistry graduate, with not more than 4 
years of research experience at post-graduate or equivalent level, who 
will be trained by research in the Molecular Endocrinology Laboratory of 
the National Hellenic Research Foundation: 
http://www.eie.gr/nhrf/institutes/ibrb/programmes/molendocrinology-en.html


in the context of the EURODESY project:

http://www.eie.gr/nhrf/institutes/iopc/eu-projects/eurodesy/index-en.html

Familiarity with cell culture and molecular cell biology and 
pharmacology methodologies will be considered an asset. The position 
will be available from March 2009. The duration of the fellowship will 
be 6 months. Eligibility criteria and reimbursement rates for Marie 
Curie Fellows are described in the handbook at: 
http://ec.europa.eu/research/fp6/mariecurie-actions/action/stage_en.html


Applications should be e-mailed to Dr. MN Alexis (mnale...@eie.gr) till 
1st of March 2009 and should include a full CV and the names and 
addresses of 1-2 referees.


--
Demetres D. Leonidas, Ph.D.
Senior Researcher
Structural Biology  Chemistry Group
Institute of Organic and Pharmaceutical Chemistry
The National Hellenic Research Foundation
48, Vassileos Constantinou Avenue
Athens 116 35, Greece
==
Tel. +30 210 7273841 (office)
+30 210 7273895 (lab) 
Fax. +30 210 7273831

E-mail: d...@eie.gr
URL: http://athena.eie.gr
==


[ccp4bb] Nikos Oikonomakos

2008-08-31 Thread Demetres D. Leonidas

Dear all,

it is with great sadness that  we announce the passing of  Nikos 
Oikonomakos yesterday. Nikos was a dear friend, a passionate researcher 
and an innovative teacher.

We will all miss him .

--

Dr. Demetres D. Leonidas
Senior Researcher
Structural Biology and Chemistry Group
Institute of Organic  Pharmaceutical Chemistry
National Hellenic Research Foundation
48, Vassileos Constantinou Avenue
Athens 116 35, Greece

Tel. +30210-7273841 (Office)
 +30210-7273895 (Lab)
Fax. +30210-7273831
E-mail: [EMAIL PROTECTED]
URL: http://athena.eie.gr



[ccp4bb] ccp4mg doesn't start in windows error in startup script

2008-07-21 Thread Demetres D. Leonidas

Dear CCP4rs

This morning we encountered a problem with ccp4mg in windows. It does 
not start and a window entitled error in startup script pops in with 
several lines referring to the code. Uninstalling and reinstallation of 
the program did not help. Has anyone else encountered this ?


Demetres



--
Demetres D. Leonidas, Ph.D.
Structural Biology  Chemistry Group
Institute of Organic and Pharmaceutical Chemistry
The National Hellenic Research Foundation
48, Vassileos Constantinou Avenue
Athens 116 35, Greece
==
Tel. +30 210 7273841 (office)
+30 210 7273895 (lab) 
Fax. +30 210 7273831

E-mail: [EMAIL PROTECTED]
URL: http://athena.eie.gr
==


Re: [ccp4bb] crystallization incubators

2008-06-23 Thread Demetres D. Leonidas

Dear Alexandra,

we are using the VELP FOC incubators 
(http://www.velp.com/en/product/5/Environment_line/101/Refrigerated_incubators/143/FOC_225I/) 
around 2000 Euros.


Demetres

Alexandra Deaconescu wrote:

Hello everyone:

I know this question has been posted before, but what models of 
crystal growth incubators do you recommend? I was thinking of a 
smaller benchtop incubator. I have found this from Torrey Pines 
Scientific,
EchoTherm Chilling Incubator, Digital, Bench Top, Programmable, 
115VAC, 50/60 Hz, 2 amp. 55 liter capacity. 4 racks provided. 
Positions for 6. UL, CSA and CE approved.


*Price: $3380.00*



I was wondering if anyone else knows of something better...

Many thanks,
Alex



Alexandra M. Deaconescu
Postdoctoral Fellow
Grigorieff Laboratory
Brandeis University
Rosenstiel Center MS 029
415 South St.
Waltham, MA 02454
USA

For deliveries:
Brandeis University
Kalman Dock
415 South St.
Waltham, MA 02454
USA





--
Demetres D. Leonidas, Ph.D.
Structural Biology  Chemistry Group
Institute of Organic and Pharmaceutical Chemistry
The National Hellenic Research Foundation
48, Vassileos Constantinou Avenue
Athens 116 35, Greece
==
Tel. +30 210 7273841 (office)
+30 210 7273895 (lab) 
Fax. +30 210 7273831

E-mail: [EMAIL PROTECTED]
URL: http://athena.eie.gr
==


Re: [ccp4bb] crystallisation robot

2008-01-16 Thread Demetres D. Leonidas

Oryxnano 50+50 nL

Demetres


David Briggs wrote:

I'll defend the honour of the phoenix... (again)

Bernhard Rupp 100+100 nl
Dave Briggs (and all users at Univ of Manchester, UK) 100+100nl   


Others..

Only time we have ANY problems is when the nano dispensing tip gets 
clogged. Often a good wash whilst still on the machine will clear the 
blockage.


Dave




--

David C. Briggs PhD
Father  Crystallographer
http://www.dbriggs.talktalk.net http://www.dbriggs.talktalk.net
AIM ID: dbassophile
 


--
Demetres D. Leonidas, Ph.D.
Structural Biology  Chemistry Group
Institute of Organic and Pharmaceutical Chemistry
The National Hellenic Research Foundation
48, Vassileos Constantinou Avenue
Athens 116 35, Greece
==
Tel. +30 210 7273841 (office)
+30 210 7273895 (lab) 
Fax. +30 210 7273831

E-mail: [EMAIL PROTECTED]
URL: http://athena.eie.gr
==


[ccp4bb] Postdoc protein crystallographer in Greece

2007-08-30 Thread Demetres D. Leonidas

Dear all,

the following is been sent on behalf of Prof. Tzartos and all inquiries 
should be send to him.


Postdoc protein crystallographer in Greece
A postdoctoral position for a protein crystallographer is immediately 
available at the Laboratory of Molecular Neurobiology and Immunology, 
Department of Biochemistry of the Hellenic Pasteur Institute, Athens, 
Greece (www.pasteur.gr). The major part of the activities of the lab 
involves the expression of extracellular domains (210-220 amino acids 
long) of several subunits of human nicotinic acetylcholine receptors in 
eukaryotic expression systems, construction of mutant forms, 
purification and, recently, crystallization and co-crystallization 
efforts. The lab has some past expertise in protein crystallography (2 
Fab fragments) but the new post-doc will be now the main 
crystallographer of the group.
The new post-doc should have extensive expertise in protein 
crystallization and considerable expertise in crystallographic analysis. 
Expertise in molecular biology approaches is useful but not necessary.
S/he will collaborate closely with members of the lab (mostly with 
expertise in molecular biology  biochemistry) who currently produce 
sufficient amounts of wt and mutant forms of the AChR domains in various 
expression systems, and with collaborating excellent crystallographers 
in neighbouring labs. The main task of the post-doc will be to obtain 
diffraction quality crystals of these domains and their subsequent 
structure determination (of fundamental importance for subsequent drug 
design). S/he may also be involved with new expressions.
The lab is supported by several international grants (3 EC grants, 2 
MDA, 1 AFM etc) and has (or has access to) all needed equipment. The 
post will be supported by an EC grant.
Please send a preliminary request with a CV and a summary of research 
experience and interests to Prof. Socrates Tzartos, emails: 
[EMAIL PROTECTED] and [EMAIL PROTECTED]


--
Demetres D. Leonidas, Ph.D.
Structural Biology  Chemistry Group
Institute of Organic and Pharmaceutical Chemistry
The National Hellenic Research Foundation
48, Vassileos Constantinou Avenue
Athens 116 35, Greece
==
Tel. +30 210 7273841 (office)
+30 210 7273895 (lab) 
Fax. +30 210 7273831

E-mail: [EMAIL PROTECTED]
URL: http://athena.eie.gr
==


[ccp4bb] Postdoc protein crystallographer in Greece

2007-08-30 Thread Demetres D. Leonidas

Dear all,

the following is been sent on behalf of Prof. Tzartos and all inquiries 
should be send to him.


Postdoc protein crystallographer in Greece
A postdoctoral position for a protein crystallographer is immediately 
available at the Laboratory of Molecular Neurobiology and Immunology, 
Department of Biochemistry of the Hellenic Pasteur Institute, Athens, 
Greece (www.pasteur.gr). The major part of the activities of the lab 
involves the expression of extracellular domains (210-220 amino acids 
long) of several subunits of human nicotinic acetylcholine receptors in 
eukaryotic expression systems, construction of mutant forms, 
purification and, recently, crystallization and co-crystallization 
efforts. The lab has some past expertise in protein crystallography (2 
Fab fragments) but the new post-doc will be now the main 
crystallographer of the group.
The new post-doc should have extensive expertise in protein 
crystallization and considerable expertise in crystallographic analysis. 
Expertise in molecular biology approaches is useful but not necessary.
S/he will collaborate closely with members of the lab (mostly with 
expertise in molecular biology  biochemistry) who currently produce 
sufficient amounts of wt and mutant forms of the AChR domains in various 
expression systems, and with collaborating excellent crystallographers 
in neighbouring labs. The main task of the post-doc will be to obtain 
diffraction quality crystals of these domains and their subsequent 
structure determination (of fundamental importance for subsequent drug 
design). S/he may also be involved with new expressions.
The lab is supported by several international grants (3 EC grants, 2 
MDA, 1 AFM etc) and has (or has access to) all needed equipment. The 
post will be supported by an EC grant.
Please send a preliminary request with a CV and a summary of research 
experience and interests to Prof. Socrates Tzartos, emails: 
[EMAIL PROTECTED] and [EMAIL PROTECTED]



--
Demetres D. Leonidas, Ph.D.
Structural Biology  Chemistry Group
Institute of Organic and Pharmaceutical Chemistry
The National Hellenic Research Foundation
48, Vassileos Constantinou Avenue
Athens 116 35, Greece
==
Tel. +30 210 7273841 (office)
+30 210 7273895 (lab) 
Fax. +30 210 7273831

E-mail: [EMAIL PROTECTED]
URL: http://athena.eie.gr
==


Re: [ccp4bb] Twinning in C2 ?

2007-07-18 Thread Demetres D. Leonidas

Dear Eleanor,

many thanks for all your help and suggestions. We finally have solved 
the mutant structure. The trick was to use the pseudo translation (there 
was not any 2 fold axis in the self rotation) with MOLREP which found 
two molecules and then applied the pseudo translation to provide us with 
the other two molecules yielding a tetramer. I think that initially the 
programs and also ourselves  missed  the pseudo translation because it 
is very close to the  crystallographic one  (0.49 0 0.48).  Many thanks  
to  Peter  Zwart who also advised us to follow the same procedure.


Demetres


Eleanor Dodson wrote:

Oh dear - this is tricky!
You could have a dimer in the asymmetric unit, or two monomers in the 
asymm unit which generate dimers using the crystallographic 2 folds.


Things worth checking -
What does the self rotation show? Is there a clear 2 fold axis which 
is different from the crystallographic one?
If so you can use all of MOLREPs cleverness to use the self rotation 
definition and the pseudo translation.
(Under search parameters you can give the self rotation list of 
solutions - just use self rotation with 1 or 2 solutions and edit out 
the top one which will be the crystallographic 2 fold)


It will find the pseudo trans vector automatically.

If the only 2 fold is the cryst one then you need to search for 2 
molecules with the pseudo translation.


Eleanor

What is the solvent content of the native - the mutant has a smaller 
volume so less solvent - is that feasible?





I think I would generate P1 data Demetres D. Leonidas wrote:

Dear Eleanor,

Yes the native is a dimer and we did the search using the dimer as a 
model but we had similar results (i.e. all programs find one 
molecule). The graphs from TRUNCATE show rather normal and I am 
attaching a gif file with the plot for the cumulative intensity.


As for pseudo-translation running the Analyse Data for MR option in 
ccp4 in the patterson map we are getting a significant peak at 
fractional coordinates 0.4897 0.0 0.4767. How this can help ? Do we 
need to apply this pseudo translation to the solution we are getting 
from molrep ?


many thanks

Demetres

P.S. I will summarize for the members of the list all the suggestions 
I will get at the end



Eleanor Dodson wrote:
You dont say whether the molecules in the native cell form a dimer - 
if so I would search with that (you may need to turn off the packing 
search)


Or whether there is a pseudo translation vector in the mutant form..

Or what the data analysis graphs from TRUNCATE show - are they 
normal?


Eleanor

Demetres D. Leonidas wrote:

Dear all,

we have encountered a problem in solving one mutant structure. The 
mutant protein crystallizes in the same space group as the native 
(C2) but the unit cell dimensions are different. These for the 
native structure are 101.2 33.1 73.4 90 90.3 90 and for the mutant 
160.4 32.3 107.0 90 125.7 90. As a result the mutant structure has  
four molecules in the asymmetric unit while the native had two. 
When we run molecular replacement all programs (CNS, molrep, and 
amore) find only two molecules. Phaser finds four but when we try 
to refine the Rfree does not drop below 0.44 if we use four 
molecules and 0.53 if we only use two no matter how well we built 
the molecule and regardless of any addition of water molecules (the 
resolution of the data is 2.1). The interesting thing is that in 
the electron density map we can clearly see density for a substrate 
analog that was included in the crystallization media. Do you 
thing  that we have a case of twinning here ? We have to mention 
that Tod Yates served did not indicate any perfect merohedral 
twinning (partial merohedral twinning for this space group is not 
possible).


We would appreciate any comments

Many thanks

Demetres














--
Demetres D. Leonidas, Ph.D.
Structural Biology  Chemistry Group
Institute of Organic and Pharmaceutical Chemistry
The National Hellenic Research Foundation
48, Vassileos Constantinou Avenue
Athens 116 35, Greece
==
Tel. +30 210 7273841 (office)
+30 210 7273895 (lab) 
Fax. +30 210 7273831

E-mail: [EMAIL PROTECTED]
URL: http://athena.eie.gr
==


Re: [ccp4bb] Twinning in C2 ?

2007-07-13 Thread Demetres D. Leonidas

Dear Eleanor,

Yes the native is a dimer and we did the search using the dimer as a 
model but we had similar results (i.e. all programs find one molecule). 
The graphs from TRUNCATE show rather normal and I am attaching a gif 
file with the plot for the cumulative intensity.


As for pseudo-translation running the Analyse Data for MR option in 
ccp4 in the patterson map we are getting a significant peak at 
fractional coordinates 0.4897 0.0 0.4767. How this can help ? Do we need 
to apply this pseudo translation to the solution we are getting from 
molrep ?


many thanks

Demetres

P.S. I will summarize for the members of the list all the suggestions I 
will get at the end



Eleanor Dodson wrote:
You dont say whether the molecules in the native cell form a dimer - 
if so I would search with that (you may need to turn off the packing 
search)


Or whether there is a pseudo translation vector in the mutant form..

Or what the data analysis graphs from TRUNCATE show - are they normal?

Eleanor

Demetres D. Leonidas wrote:

Dear all,

we have encountered a problem in solving one mutant structure. The 
mutant protein crystallizes in the same space group as the native 
(C2) but the unit cell dimensions are different. These for the native 
structure are 101.2 33.1 73.4 90 90.3 90 and for the mutant 160.4 
32.3 107.0 90 125.7 90. As a result the mutant structure has  four 
molecules in the asymmetric unit while the native had two. When we 
run molecular replacement all programs (CNS, molrep, and amore) find 
only two molecules. Phaser finds four but when we try to refine the 
Rfree does not drop below 0.44 if we use four molecules and 0.53 if 
we only use two no matter how well we built the molecule and 
regardless of any addition of water molecules (the resolution of the 
data is 2.1). The interesting thing is that in the electron density 
map we can clearly see density for a substrate analog that was 
included in the crystallization media. Do you thing  that we have a 
case of twinning here ? We have to mention that Tod Yates served did 
not indicate any perfect merohedral twinning (partial merohedral 
twinning for this space group is not possible).


We would appreciate any comments

Many thanks

Demetres






--
Demetres D. Leonidas, Ph.D.
Structural Biology  Chemistry Group
Institute of Organic and Pharmaceutical Chemistry
The National Hellenic Research Foundation
48, Vassileos Constantinou Avenue
Athens 116 35, Greece
==
Tel. +30 210 7273841 (office)
+30 210 7273895 (lab) 
Fax. +30 210 7273831

E-mail: [EMAIL PROTECTED]
URL: http://athena.eie.gr
==

inline: cumulative.gif