Re: [ccp4bb] DSSP and PDB secondary structure assignments

[Tim Gruene]

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Hash: SHA1

Dear Mark,

I was tought to always check the outcome of automated secondary
structure assignment, because it is defined by hydrogren bondings, not
by what some software thinks. DSSP is certainly very good, but always
worth comparing the boundaries with your own experience/ opinion.Maybe
the authors of the mentioned PDB entries did exactly this - and
fortunately, as has already been pointed out, the PDB do not overwrite
the authors' opinion.

Cheers, Tim

On 07/25/12 22:55, Dr. Mark Mayer wrote:
> I've recently noticed that the Helix and Sheet records in PDB
> entries differ from those generated by DSSP and would like to ask
> if anyone can explain how the PDB makes the assignments. Until now
> I'd always assumed that the PDB and DSSP records were the same.
> 
> As an example I've listed a few lines from 2V3U.pdb. There are
> similar difference in both helix lengths and start/stop positions
> that occur in 9 other entries I've looked at.
> 
> 2V3U.pdb HELIX1   1 GLY A   31  GLY A   45 1
> 15 HELIX2   2 ASN A   68  PHE A   76 1
> 9 HELIX3   3 THR A   89  ASN A   94 1
> 6
> 
> and for the same structure the DSSP entry from the CMBI data base 
> http://swift.cmbi.ru.nl/gv/dssp/
> 
> REMARK   1 secondary structure assigned by dssp HELIX1   1 PHE
> A   32  LEU A   44 1  13 HELIX2
> 2 GLY A   69  VAL A   75 1   7 
> HELIX3   3 PRO A   90  GLU A   93 1
> 4
> 
> Its not a big deal, but makes comparing secondary structures a bit
> more difficult.

- -- 
- --
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

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Re: [ccp4bb] interesting alternative to CCP4's superpose tool

[Bosch, Juergen]

Yes indeed and a very powerful tool. I'm just wondering what the difference 
between his old Theseus and Theseus 2.0 is. From the abstract it seemed fairly 
familiar with what I had been using Theseus 1.6 in conjunction with MUSCLE. 
Sometime BRAIN 1.0 works well too.

Jürgen


On Jul 25, 2012, at 10:03 PM, Francois Berenger wrote:

Hello,

Quite interesting article:
http://bioinformatics.oxfordjournals.org/content/28/15/1972.abstract

Regards,
F.

..
Jürgen Bosch
Johns Hopkins University
Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Office: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-2926
http://lupo.jhsph.edu

[ccp4bb] interesting alternative to CCP4's superpose tool

[Francois Berenger]

Hello,

Quite interesting article:
http://bioinformatics.oxfordjournals.org/content/28/15/1972.abstract

Regards,
F.

Re: [ccp4bb] DSSP and PDB secondary structure assignments

[Nadir Mrabet]

OK, but you don't specify that Promotif uses DSSP for that purpose, right?

--

Pr. Nadir T. Mrabet
Structural & Molecular Biochemistry
N-gere - INSERM U-954
Nancy University, School of Medicine
9, Avenue Foret de Haye, BP 184
F-54500 Vandoeuvre-les-Nancy (France)
Tel : +33 (0)3 83 68 32 73
Fax : +33 (0)3 83 68 32 97
Email : Nadir.Mrabet  medecine.uhp-nancy.fr


-original message-
Subject: Re: [ccp4bb] DSSP and PDB secondary structure assignments
From: mark Mayer 
Date: 25/07/2012 11:18 pm

I got the following response from PDB

In PDB, Helix and sheet records are automatically generated by Promotif 
software. Authors who wish to provide their own helix and sheet records 
may do so; a remark will be added to REMARK 650 and REMARK 700 of the 
PDB entry to indicate that the helix and/or sheet records were author 
provided.

Re: [ccp4bb] DSSP and PDB secondary structure assignments

[mark Mayer]

I got the following response from PDB

In PDB, Helix and sheet records are automatically generated by Promotif 
software. Authors who wish to provide their own helix and sheet records 
may do so; a remark will be added to REMARK 650 and REMARK 700 of the 
PDB entry to indicate that the helix and/or sheet records were author 
provided.

[ccp4bb] DSSP and PDB secondary structure assignments

[Dr. Mark Mayer]

I've recently noticed that the Helix and Sheet records in PDB entries 
differ from those generated by DSSP and would like to ask if anyone 
can explain how the PDB makes the assignments. Until now I'd always 
assumed that the PDB and DSSP records were the same.


As an example I've listed a few lines from 2V3U.pdb. There are 
similar difference in both helix lengths and start/stop positions 
that occur in 9 other entries I've looked at.


2V3U.pdb
HELIX1   1 GLY A   31  GLY A   45  1  15
HELIX2   2 ASN A   68  PHE A   76  1   9
HELIX3   3 THR A   89  ASN A   94  1   6

and for the same structure the DSSP entry from the CMBI data base 
http://swift.cmbi.ru.nl/gv/dssp/


REMARK   1 secondary structure assigned by dssp
HELIX1   1 PHE A   32  LEU A   44  1  13
HELIX2   2 GLY A   69  VAL A   75  1   7
HELIX3   3 PRO A   90  GLU A   93  1   4

Its not a big deal, but makes comparing secondary structures a bit 
more difficult.

--

Mark

Re: [ccp4bb] Refmac: ADP is non-positive

[Ethan Merritt]

I can confirm the problem.

If I take a previous successful refmac refinement, remove the initial N atom 
from
the first residue in the input PDB file, and re-run the refinement I get:

 Problem with the ADP of the atom N   A 33 ADP is non-positive  
-94.380859
 Problem with the ADP of the atom N   A 33 ADP is non-positive  
-94.382088

starting already in CGMAT cycle 1.

Deleting instead the C-terminal O atom[s] does not produce an equivalent error.

CCP4 6.3: Refmac_5.7.0029 

Nevertheless, in my test case the refinement ran successfully despite the error
messages.

Ethan



On Tuesday, July 24, 2012 09:54:26 am wtempel wrote:
> There are atom records for C, O and CA (B-factors 42, 43, 40A**2,
> respectively), but not for N, as density tapers off going to the amino
> terminus (well, without the "amino" in this case). Residue 3 is the
> lowest-numbered residue in its chain. B-factors of N, CA of residue 4 are
> 38, 33A**2, respectively. Could refmac just be taking exception to the
> missing N atom?
> 
> -- Forwarded message --
> From: Ethan Merritt 
> Date: Tue, Jul 24, 2012 at 11:27 AM
> Subject: Re: [ccp4bb] Refmac: ADP is non-positive
> To: wtempel 
> Cc: CCP4BB@jiscmail.ac.uk
> 
> 
> On Tuesday, 24 July 2012, wtempel wrote:
> > CCP4ers,
> >
> > a log file from Refmac_5.7.0027 presents me with this line:
> >
> > 
> > Problem with the ADP of the atom N   A  3 ADP is non-positive
> > -1.7740907E+35
> > 
> >
> > I did not explicitely refine ADPs or TLS.
> > Should I modify my model when I encounter such a message? If yes, does the
> > message refer to a specific atom, such as atom N of residue 3 in chain A?
> I
> > should note that that atom is omitted from my model due to lack of
> electron
> > density/disorder.
> 
> What do you mean by "omitted from the model"?
> Are there no ATOM records for that residue in the PDB file?
> What are the B factors for the other atoms in that region?
> 
> Ethan
> 
> >
> > Many thanks in advance,
> > Wolfram Tempel
> >
> 

-- 
Ethan A Merritt
Biomolecular Structure Center,  K-428 Health Sciences Bldg
University of Washington, Seattle 98195-7742

[ccp4bb] Post-doctoral Fellowship University of Michigan

[rudenko]

 
   Postdoctoral Fellow
Macromolecular crystallography, Biophysics and Biochemistry

We are looking for a highly motivated postdoctoral research fellow to  
join our laboratory at the Life Sciences Institute, University of  
Michigan in Ann Arbor, Michigan.


Synapses mediate communication between neurons, producing neural  
circuitry that enables us to think, move and feel. We are interested  
in the complex protein networks at synapses. We study proteins that  
mediate the formation, maintenance and plasticity of synapses, in  
particular synaptic organizers. Research projects involve protein  
over-expression, purification, crystallization, x-ray crystallography,  
biochemical and biophysical techniques (funded by NIH).  
State-of-the-art equipment is available in a modern research setting.  
Synchrotron radiation is available within driving distance or remotely  
at the Advanced Photon Source (APS) and the University of Michigan is  
a member of LS-CAT at APS.


Qualifications:
Applicants should have received a Ph.D. degree in a field relevant to  
structural biology within the past 3 years and have a strong  
publication record. Applicants with experience in cloning, bacterial  
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proteins, macromolecular crystallization, diffraction data collection  
and structure determination of macromolecules are preferred. However,  
highly motivated recent graduates with a strong background in protein  
over-expression and purification, and an interest in learning  
crystallography are also encouraged to apply. Good written and oral  
communication skills in English are essential as well as the ability  
and desire to work as part of a highly motivated team.


To apply please e-mail the following to rude...@umich.edu:  CV,  
contact information for 3 references (address, phone and e-mail), a  
list of your experimental expertise and skills relevant to this  
position and a research statement describing your past research  
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For questions please contact Dr. Gabrielle Rudenko at rude...@umich.edu

For more information please visit
http://www.lsi.umich.edu/facultyresearch/labs/rudenko

If you are attending the American Crystallographic Association Meeting  
in Boston, come chat on Monday July 30 from 5:30 - 7:30 pm at our  
poster M-75 (abstract #1209).


The University of Michigan is a non-discriminatory, affirmative action  
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--
G. Rudenko PhD
Life Sciences Institute &
Dept. Pharmacology
University of Michigan Medical School 
210 Washtenaw Ave Rm 3163A   
Ann Arbor MI 48109-2216     
tel: (734) 615 - 9323
fax: (734) 763 - 6492
e-mail rude...@umich.edu
http://lsi.umich.edu/facultyresearch/labs/rudenko   

[ccp4bb] Nagoya Symposium: Frontiers in Structural Physiology

[Wang, Da-Neng]

Nagoya Symposium: Frontiers in Structural Physiology
Nagoya University, Nagoya, Japan
January 22 - 24, 2013
Web site: http://symposium.cespi.nagoya-u.ac.jp/
Poster: http://symposium.cespi.nagoya-u.ac.jp/docs/poster.pdf

Topics:
Membrane Proteins
Macromolecular Complexes
Receptors, Channels and Transporters
Cryo-electron Microscopy
X-ray crystallography

Registration fees:
Free

Speakers:
Peter Agre
Wolfgang Baumeister
Yifan Cheng
Wah Chiu
Mari Dezawa
Kenneth Downing
Andreas Engel
Joachim Frank
Yoshinori Fujiyoshi
Eric Gouaux
Stephen Harrison
Hans Hebert
Richard Henderson
Wayne Hendrickson
Masahide Kikkawa
Brian Kobilka
Werner Kühlbrandt
Roderick MacKinnon
Kaoru Mitsuoka
Atsuo Miyazawa
Haruki Nakamura
Keiichi Namba
Osamu Nureki
Douglas Rees
Gebhard Schertler
Ichio Shimada
Christopher Tate
Tomitake Tsukihara
Nigel Unwin
Gunnar von Heijne
Thomas Walz
Da-Neng Wang

Organizers:
Kaoru Mitsuoka
Thomas Walz
Da-Neng Wang


Da-Neng Wang, Ph.D.
Professor
Structural Biology Program
Skirball Institute of Biomolecular Medicine
New York University School of Medicine
540 First Avenue
New York, NY 10016
USA

Phone: (212) 263-8634
Fax: (212) 263-8951
E-mail:w...@saturn.med.nyu.edu
Web:http://saturn.med.nyu.edu/research/sb/wanglab/
Meeting:  http://symposium.cespi.nagoya-u.ac.jp
-

[ccp4bb] modeling thioester bond

[Sebastiano Pasqualato]

No answers yet from the COOTbb (yet), so I'm cross posting this to the ccp4bb.
Sorry for the double post.



Hi there,
I'd like to model a thioester bond, starting from protein A with an exposed 
Cys, and having juxtaposed the carboxyl group of a C-terminal residue of 
protein B.

The way I would like to proceed is by:

1) telling coot that there's a bond between the S atom and the C atom of the 
two groups;
2) regularize that zone in order to have something that makes chemical sense.

Could you advice me on how to proceed for the two steps?
That is, how do I tell coot that the bond exists and it has to be taken into 
account?

Thanks in advance,
ciao,
s



-- 
Sebastiano Pasqualato, PhD
Crystallography Unit
Department of Experimental Oncology
European Institute of Oncology
IFOM-IEO Campus
via Adamello, 16
20139 - Milano
Italy

tel +39 02 9437 5167
fax +39 02 9437 5990

please note the change in email address!
sebastiano.pasqual...@ieo.eu

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

[Colbert, Christopher]

I disagree.  If the primary citation is available in the PDB it should be 
cited.  If we allow reference solely to a database entry, eg. a PDB ID, then 
reference to a wikipedia entry becomes a valid reference and I don't think we 
should go down that road yet.

I agree with Evette's earlier comments that citation of our work has an impact 
on our careers.  Therefore, proper credit needs to be given in the citations.

However, as an increasing number of PDBs do not have primary citations, it is 
logical to cite the PDB ID as the primary reference.

I believe there is a similar issue with program developers.  They were not 
getting proper credit for their efforts until they had a published paper 
detailing the methodology.  Websites helped, but weren't really recognized as a 
valid indication of productivity.

A couple more cents on the fire.

Chris


From: , Thierry 
mailto:thierry.fischm...@merck.com>>
Reply-To: "Fischmann, Thierry" 
mailto:thierry.fischm...@merck.com>>
Date: Wednesday, July 25, 2012 9:15 AM
To: "CCP4BB@JISCMAIL.AC.UK" 
mailto:CCP4BB@JISCMAIL.AC.UK>>
Subject: Re: [ccp4bb] Somewhat OT: question of professional courtesy

I concur with Mike


-  If the paper reproduces at least in part a result already published, 
then the precedent(s) should be referenced (even if the experimental approach 
is different)

-  If the paper discusses a previous experimental result or inference 
from the results of another publication, a reference should be given

-  But a reference other than a PDB code is not required if the paper 
is comparing a structure to another without discussion of the former results. 
Of course there is nothing wrong with giving the reference to the original 
paper.

Thierry

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of R. M. 
Garavito
Sent: Wednesday, July 25, 2012 9:56 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Somewhat OT: question of professional courtesy

Evette,

I think the primary issue is what kind of analysis was being reported on.  That 
is what I look for when I review a manuscript.  If the authors are doing a 
broad structural analysis (homology of TIM barrels, X-ray refinement protocols, 
etc.), I wouldn't expect citations beyond stating the PDB entries used.  
However, if this was a primary structural analysis of a macromolecule, I would 
expect that a discussion of the structural comparison would include references 
to earlier work(s) on related molecules, but I have seen this happen where a 
group reinvents the wheel (sometimes rather badly) because they don't take the 
time to look at the literature, just a DALI run and a PDB search.  It is just 
bad science not to discuss what earlier researchers have done to put your work 
in context.

Just my 2 cents worth,

Michael


R. Michael Garavito, Ph.D.
Professor of Biochemistry & Molecular Biology
603 Wilson Rd., Rm. 513
Michigan State University
East Lansing, MI 48824-1319
Office:  (517) 355-9724 Lab:  (517) 353-9125
FAX:  (517) 353-9334Email:  
rmgarav...@gmail.com





On Jul 25, 2012, at 9:15 AM, Tim Gruene wrote:


-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Evette,

the PDB lists the citation when you enter the PDB-ID in the search
mask of any of the web-interfaces, which is much easier for the reader
than typing the information from the list of references, i.e. all
information is in the article by mentioning the PDB-ID. Why do you
consider it a matter of courtesy to re-cite the structural work?

Cheers,
Tim

On 07/25/12 14:33, Radisky, Evette S., Ph.D. wrote:

Dear bb,

This morning as I scanned an accepted manuscript from a
well-respected-but-not-particularly-glamorous journal that
publishes many macromolecular structures, I came across a brief
mention of homology and rmsd with a published structure listed by
PDB accession number, but no citation of the primary 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 have always thought it a matter of professional courtesy to cite
the appropriate reference when one uses and mentions  a structure
from the PDB, but as I think back, I realize no one explicitly told
me this-- it is just an assumption that I made.  Maybe I am the one
with unrealistic expectations here?  Is there a general consensus
among crystallographers on this practice?

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 Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = 

[ccp4bb] 3rd MX User Workshop at Diamond - September 5th-6th, 2012

[Thomas Sorensen]

Dear All

I quick reminder - last chance to sign up for the 3rd MX User Workshop at 
Diamond - the workshop is part of the Synchrotron User Meeting, September 
5th-6th, 2012. Workshop sessions include presentations from staff and users on 
latest developments, in-situ screening, using fast detectors, kappa goniometry, 
SAXS, and MX software pipelines/developments.

Workshop info: 
http://www.diamond.ac.uk/Home/Events/SR-User-Meeting-2012/MX-Workshop.html
Registration: 
http://www.diamond.ac.uk/Home/Events/SR-User-Meeting-2012/Registration---Delegate-Information.html

Best wishes

Thomas Sorensen
Principal Beamline Scientist
Macromolecular Crystallography
Diamond Light Source

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

[Fischmann, Thierry]

I concur with Mike


-  If the paper reproduces at least in part a result already published, 
then the precedent(s) should be referenced (even if the experimental approach 
is different)

-  If the paper discusses a previous experimental result or inference 
from the results of another publication, a reference should be given

-  But a reference other than a PDB code is not required if the paper 
is comparing a structure to another without discussion of the former results. 
Of course there is nothing wrong with giving the reference to the original 
paper.

Thierry

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of R. M. 
Garavito
Sent: Wednesday, July 25, 2012 9:56 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Somewhat OT: question of professional courtesy

Evette,

I think the primary issue is what kind of analysis was being reported on.  That 
is what I look for when I review a manuscript.  If the authors are doing a 
broad structural analysis (homology of TIM barrels, X-ray refinement protocols, 
etc.), I wouldn't expect citations beyond stating the PDB entries used.  
However, if this was a primary structural analysis of a macromolecule, I would 
expect that a discussion of the structural comparison would include references 
to earlier work(s) on related molecules, but I have seen this happen where a 
group reinvents the wheel (sometimes rather badly) because they don't take the 
time to look at the literature, just a DALI run and a PDB search.  It is just 
bad science not to discuss what earlier researchers have done to put your work 
in context.

Just my 2 cents worth,

Michael


R. Michael Garavito, Ph.D.
Professor of Biochemistry & Molecular Biology
603 Wilson Rd., Rm. 513
Michigan State University
East Lansing, MI 48824-1319
Office:  (517) 355-9724 Lab:  (517) 353-9125
FAX:  (517) 353-9334Email:  
rmgarav...@gmail.com





On Jul 25, 2012, at 9:15 AM, Tim Gruene wrote:


-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Evette,

the PDB lists the citation when you enter the PDB-ID in the search
mask of any of the web-interfaces, which is much easier for the reader
than typing the information from the list of references, i.e. all
information is in the article by mentioning the PDB-ID. Why do you
consider it a matter of courtesy to re-cite the structural work?

Cheers,
Tim

On 07/25/12 14:33, Radisky, Evette S., Ph.D. wrote:

Dear bb,

This morning as I scanned an accepted manuscript from a
well-respected-but-not-particularly-glamorous journal that
publishes many macromolecular structures, I came across a brief
mention of homology and rmsd with a published structure listed by
PDB accession number, but no citation of the primary 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 have always thought it a matter of professional courtesy to cite
the appropriate reference when one uses and mentions  a structure
from the PDB, but as I think back, I realize no one explicitly told
me this-- it is just an assumption that I made.  Maybe I am the one
with unrealistic expectations here?  Is there a general consensus
among crystallographers on this practice?

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 Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen

GPG Key ID = A46BEE1A

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

[Radisky, Evette S., Ph.D.]

Yes, I think this is reasonable.

 

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of R.
M. Garavito
Sent: Wednesday, July 25, 2012 9:56 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Somewhat OT: question of professional courtesy

 

Evette,

 

I think the primary issue is what kind of analysis was being reported
on.  That is what I look for when I review a manuscript.  If the authors
are doing a broad structural analysis (homology of TIM barrels, X-ray
refinement protocols, etc.), I wouldn't expect citations beyond stating
the PDB entries used.  However, if this was a primary structural
analysis of a macromolecule, I would expect that a discussion of the
structural comparison would include references to earlier work(s) on
related molecules, but I have seen this happen where a group reinvents
the wheel (sometimes rather badly) because they don't take the time to
look at the literature, just a DALI run and a PDB search.  It is just
bad science not to discuss what earlier researchers have done to put
your work in context.

 

Just my 2 cents worth,

 

Michael

 

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

[R. M. Garavito]

Evette,

I think the primary issue is what kind of analysis was being reported on.  That 
is what I look for when I review a manuscript.  If the authors are doing a 
broad structural analysis (homology of TIM barrels, X-ray refinement protocols, 
etc.), I wouldn't expect citations beyond stating the PDB entries used.  
However, if this was a primary structural analysis of a macromolecule, I would 
expect that a discussion of the structural comparison would include references 
to earlier work(s) on related molecules, but I have seen this happen where a 
group reinvents the wheel (sometimes rather badly) because they don't take the 
time to look at the literature, just a DALI run and a PDB search.  It is just 
bad science not to discuss what earlier researchers have done to put your work 
in context.

Just my 2 cents worth,

Michael


R. Michael Garavito, Ph.D.
Professor of Biochemistry & Molecular Biology
603 Wilson Rd., Rm. 513   
Michigan State University  
East Lansing, MI 48824-1319
Office:  (517) 355-9724 Lab:  (517) 353-9125
FAX:  (517) 353-9334Email:  rmgarav...@gmail.com





On Jul 25, 2012, at 9:15 AM, Tim Gruene wrote:

> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
> 
> Dear Evette,
> 
> the PDB lists the citation when you enter the PDB-ID in the search
> mask of any of the web-interfaces, which is much easier for the reader
> than typing the information from the list of references, i.e. all
> information is in the article by mentioning the PDB-ID. Why do you
> consider it a matter of courtesy to re-cite the structural work?
> 
> Cheers,
> Tim
> 
> On 07/25/12 14:33, Radisky, Evette S., Ph.D. wrote:
>> Dear bb,
>> 
>> This morning as I scanned an accepted manuscript from a 
>> well-respected-but-not-particularly-glamorous journal that
>> publishes many macromolecular structures, I came across a brief
>> mention of homology and rmsd with a published structure listed by
>> PDB accession number, but no citation of the primary 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 have always thought it a matter of professional courtesy to cite
>> the appropriate reference when one uses and mentions  a structure
>> from the PDB, but as I think back, I realize no one explicitly told
>> me this-- it is just an assumption that I made.  Maybe I am the one
>> with unrealistic expectations here?  Is there a general consensus
>> among crystallographers on this practice?
>> 
>> 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 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/
> 
> iD8DBQFQD/FSUxlJ7aRr7hoRAsCRAKDBB5CprXaR1v2QtA57n+3LmVPbAACfegbW
> I/IlD77jIjoUXgFCiMo9tdI=
> =xqVY
> -END PGP SIGNATURE-

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

[Radisky, Evette S., Ph.D.]

Well, I guess that would be because when my CV and credentials are
reviewed by e.g. study sections of funding agencies, institutional
committees making decisions affecting my promotion and academic
advancement, potential future employers, etc., many will look at metrics
such as h-index and the like, based upon citations of publications
rather than deposited structures.  I am not saying that this is the way
it would be in a perfect universe, but this is the way it is.

Evette

-Original Message-
From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] 
Sent: Wednesday, July 25, 2012 9:15 AM
To: Radisky, Evette S., Ph.D.
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Somewhat OT: question of professional courtesy

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Evette,

the PDB lists the citation when you enter the PDB-ID in the search mask
of any of the web-interfaces, which is much easier for the reader than
typing the information from the list of references, i.e. all information
is in the article by mentioning the PDB-ID. Why do you consider it a
matter of courtesy to re-cite the structural work?

Cheers,
Tim

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

[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
---

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

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear Evette,

the PDB lists the citation when you enter the PDB-ID in the search
mask of any of the web-interfaces, which is much easier for the reader
than typing the information from the list of references, i.e. all
information is in the article by mentioning the PDB-ID. Why do you
consider it a matter of courtesy to re-cite the structural work?

Cheers,
Tim

On 07/25/12 14:33, Radisky, Evette S., Ph.D. wrote:
> Dear bb,
> 
> This morning as I scanned an accepted manuscript from a 
> well-respected-but-not-particularly-glamorous journal that
> publishes many macromolecular structures, I came across a brief
> mention of homology and rmsd with a published structure listed by
> PDB accession number, but no citation of the primary 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 have always thought it a matter of professional courtesy to cite
> the appropriate reference when one uses and mentions  a structure
> from the PDB, but as I think back, I realize no one explicitly told
> me this-- it is just an assumption that I made.  Maybe I am the one
> with unrealistic expectations here?  Is there a general consensus
> among crystallographers on this practice?
> 
> 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 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/

iD8DBQFQD/FSUxlJ7aRr7hoRAsCRAKDBB5CprXaR1v2QtA57n+3LmVPbAACfegbW
I/IlD77jIjoUXgFCiMo9tdI=
=xqVY
-END PGP SIGNATURE-

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

[Bosch, Juergen]

In the least case the PDB DOI number should have been cited.

Jürgen

..
Jürgen Bosch
Johns Hopkins Bloomberg School of Public Health
Department of Biochemistry & Molecular Biology
Johns Hopkins Malaria Research Institute
615 North Wolfe Street, W8708
Baltimore, MD 21205
Phone: +1-410-614-4742
Lab:  +1-410-614-4894
Fax:  +1-410-955-3655
http://lupo.jhsph.edu

On Jul 25, 2012, at 8:33, "Radisky, Evette S., Ph.D." 
mailto:radisky.eve...@mayo.edu>> wrote:


Dear bb,

This morning as I scanned an accepted manuscript from a 
well-respected-but-not-particularly-glamorous journal that publishes many 
macromolecular structures, I came across a brief mention of homology and rmsd 
with a published structure listed by PDB accession number, but no citation of 
the primary 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 have always thought it a matter of professional courtesy to cite the 
appropriate reference when one uses and mentions  a structure from the PDB, but 
as I think back, I realize no one explicitly told me this-- it is just an 
assumption that I made.  Maybe I am the one with unrealistic expectations here? 
 Is there a general consensus among crystallographers on this practice?

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

[ccp4bb] Somewhat OT: question of professional courtesy

[Radisky, Evette S., Ph.D.]

Dear bb,

This morning as I scanned an accepted manuscript from a
well-respected-but-not-particularly-glamorous journal that publishes
many macromolecular structures, I came across a brief mention of
homology and rmsd with a published structure listed by PDB accession
number, but no citation of the primary 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 have always thought it a matter of professional courtesy to cite the
appropriate reference when one uses and mentions  a structure from the
PDB, but as I think back, I realize no one explicitly told me this-- it
is just an assumption that I made.  Maybe I am the one with unrealistic
expectations here?  Is there a general consensus among crystallographers
on this practice?

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

Re: [ccp4bb] How to identify unknown heavy atom??

[Roger Rowlett]

XRF or TXRF would be very quick and definitive. With TXRF you could easily
identify and quantify metals present in 1-10 uL  of a 10 mg/mL solution.
ICP-OES will also work, but will require about 300 ug or so of protein
(depending on MW). ICP-MS is maybe 10x more sensitive than -OES but is more
complex and exotic to use. We've used all these methods to characterize and
quantify metalloenzymes.

Oxidation states may be revealed by visible absorption spectroscopy or
inferred from coordination geometry and bond lengths. For some metal ions,
EPR could be definitive for oxidation state. Atomic spectroscopy methods
won't help here.

Roger Rowlett
On Jul 24, 2012 2:04 PM, "Theresa Hsu"  wrote:

> Does EXAFS requires same amount of samples as ICP-MS/ICP-AES?
>
> Theresa
>
> On Tue, 24 Jul 2012 12:55:31 -0500, Jacob Keller <
> j-kell...@fsm.northwestern.edu> wrote:
>
> >Perhaps also exafs should be mentioned--I believe the various ion species,
> >redox states, and even binding geometry can be determined.
> >
> >JPK
> >
> >
> >
> >
> >--
> >***
> >Jacob Pearson Keller
> >Northwestern University
> >Medical Scientist Training Program
> >email: j-kell...@northwestern.edu
> >***
> >
>

Re: [ccp4bb] Question about weird diffraction map

[Hargreaves, David]

Hi Zhao,



I would try a crystal that has not been treated with any dye. Small
molecules, particularly drug like compounds, crystallise out in soaking
experiments and can give diffraction similar to yours. My worry is that
you have non-diffracting protein crystals coated in some small molecule
crystalsthe question then is whether the addition of the dye has
destroyed your diffraction. Try in-situ or a capillary mount to be more
sure. A crush test might also tell you someting.



Dave



David Hargreaves

Associate Principal Scientist

_

AstraZeneca

DECS, CP&SS

Mereside, 50F49, Alderley Park, Cheshire, SK10 4TF

Tel +44 (0)01625 518521  Fax +44 (0) 1625 232693

David.Hargreaves @astrazeneca.com 



Please consider the environment before printing this e-mail



From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
gengxiang zhao
Sent: 23 July 2012 21:53
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Question about weird diffraction map



Dear CCP4BB,

I have a question about my current diffraction map for one of crystals
which can be found in the attachment. Basically, the crystals were dyed
to initially testify that it belongs to protein. But from this
diffraction, even in the low diffract angle, no diffraction spots
theremeaning-this is not a protein crystal?

Any experienced idea/questions welcomed to discuss here.

Zhao,


--
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Conduct and Policies.

Re: [ccp4bb] Improvement in crystal quality

[Patrick Shaw Stewart]

Niks

Seeding often works very well with needles.  But start with seeding in
RANDOM SCREENS, i.e. "rMMS"


References -

Allan D’Arcy, Frederic Villarda, May Marsh.  'An automated microseed
matrix-screening method for protein crystallization'.  Acta
Crystallographica section D63 (2007) 550–554.  On-line at
http://scripts.iucr.org/cgi-bin/paper?S0907444907007652

**Patrick D. Shaw Stewart, Stefan A. Kolek, Richard A. Briggs, Naomi E.
Chayen and Peter F.M. Baldock. 'Random Microseeding: A Theoretical and
Practical Exploration of Seed Stability and Seeding Techniques for
Successful Protein Crystallization'.  Cryst. Growth Des., 2011, 11 (8), pp
3432–3441. On-line at http://pubs.acs.org/doi/abs/10.1021/cg2001442

*Chatty article that I wrote for SerCat newsletter in 2009*:
http://www.douglas.co.uk/SER-CAT09_1.html

*A bit of theory*:  http://www.douglas.co.uk/mms.htm

*Procedure*:  http://www.douglas.co.uk/MMS_proc.htm

A. G. Villaseñor, A. Wong, A. Shao, A. Garg, A. Kuglstatter and S. F.
Harris. 'Acoustic matrix microseeding: improving protein crystal growth
with minimal chemical bias.' Acta Crystallographica Section D66 (2010)
568-576. On-line at http://scripts.iucr.org/cgi-bin/paper?S0907444910005512

Galina Obmolova,* Thomas J. Malia, Alexey Teplyakov, Raymond Sweet and Gary
L. Gilliland. 'Promoting crystallization of antibody–antigen complexes via
microseed matrix screening.' Acta Crystallographica Section D66 (2010)
927–933.  Open-access at
http://journals.iucr.org/d/issues/2010/08/00/bw5361/bw5361.pdf




On 24 July 2012 14:40, Niks  wrote:
>
> Dear All,
>
> I am trying to crystallize a recombinant dehydrogenase protein. Got five
hits in PEG ION Screen from Hamptons (20% PEG 3350 with 0.2M Sodium
Acetate, 0.2M Potassium acetate, 0.2M ammonium acetate, 0.2M sodium formate
and 0.2M Potassium Chloride) after two days.
> Crystals looks like needles most of time, sometime broader needles
(Pictures attached). UV crystal scanner says those are protein crystals,
but when we tried to pick up one and shoot at room temperature, diffraction
patterns looks like similar like of  powder diffraction (picture attached).
> I have tried 50 of the 96 additives(whichever I can arrange of) mentioned
in the additive screen from Hamptons . I have tried detergent screen from
Hamptons (this time original screen solutions). I have tried incubating the
plate at 28degrees as well as 10degrees, Though waiting for 10degree
results but one drop  showed needles again after normal two days of growth
period.
> I tried to slow down the supersaturation by adding 100ul of 1:1 ratio of
silicon oil and paraffin oil over the 1ml of well solution. This time no
crystals but some precipitation.
>
> If anyone spare any word of wisdom to improve these crystal quality, I
will be very grateful.
> If seeding is the only obvious thing to try, any reference for the
seeding procedure will be highly appreciated.
>
> Thanks very much
> Nishant Varshney
> PhD student,
> National Chemical Laboratory,Pune,India
> --
> "The most difficult phase of  life is not when No one understands you;It
is when you don't understand yourself"




--
 patr...@douglas.co.ukDouglas Instruments Ltd.
 Douglas House, East Garston, Hungerford, Berkshire, RG17 7HD, UK
 Directors: Peter Baldock, Patrick Shaw Stewart

 http://www.douglas.co.uk
 Tel: 44 (0) 148-864-9090US toll-free 1-877-225-2034
 Regd. England 2177994, VAT Reg. GB 480 7371 36

Re: [ccp4bb] How to identify unknow heavy atom??

[Seijo, Jose A. Cuesta]

Shameless self plug:

 

http://scripts.iucr.org/cgi-bin/paper?fw5057

 

That was done with a crappy crystal in a relatively weak beamline. With
a good crystal one can get cleaner data.

 

Cheers.

 

Jose.


Jose Antonio Cuesta-Seijo, PhD
Carlsberg Laboratory
Gamle Carlsberg Vej 10
DK-1799 Copenhagen V
Denmark

Tlf +45 3327 5332
Email josea.cuesta.se...@carlsberglab.dk
 



From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Haytham Wahba
Sent: Tuesday, July 24, 2012 7:14 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] How to identify unknow heavy atom??

 

1- if i have anomalous peak of unknown heavy atom, How can i identify
this heavy atom in general. (different methods)

 

 

2- in my case, i see anomalous peak in heavy atom binding site (without
any soaking). preliminary i did mass spec. i got Zn++ and Cu, How can i
know which one give the anomalous peak in my protein.

 

3- there is way to know if i have Cu+ or Cu++.

 

 

Haytham

UdeM

Biochemistry

Re: [ccp4bb] 2D-bar code scanner to read Hampton pins barcodes

[Johan Turkenburg]

We use a Pepperl+Fuchs Omnitron handheld cabled reader. Our model is a
cr2010_4 but this is now several years old. It looks similar to the
MH200 model that I found after a quick google.

It is used for every synchrotron trip, and works well.

Johan

On 24 July 2012 15:33, Pietro Roversi  wrote:
> Dear all,
>
> I am looking into a 2D-bar code scanner to read Hampton pins barcodes.
> Something we can plug directly to any computer running Windows, Mac or
> Linux,
> via a supplied USB cable, and feed the barcodes into Excel.
>
> Does anybody know a cheaper alternative to the FOCUS MS-1690-38?
>
> Grazie, ciao!
>
> Pietro



-- 
Dr. Johan P. Turkenburg X-ray facilities manager
York Structural Biology Laboratory
University of York   Phone (+) 44 1904 328251
York YO10 5DD   UK  Fax   (+) 44 1904 328266

Note new email address johan.turkenb...@york.ac.uk

Re: [ccp4bb] How to identify unknow heavy atom??

[Murray, James W]

Dear All, 

re identifying metals, 

It's possible to calculate crystallographic element-specific anomalous 
difference maps if you can collect data on either side of the absorption edge. 
I have used this successfully for Sr, Zn and Mn.

http://www.ncbi.nlm.nih.gov/pubmed/15858259

I have a set of scripts to conveniently calculate such a map, which I can send 
off list.

James

--
Dr. James W. Murray
David Phillips Research  Fellow
Division of Molecular Biosciences
Imperial College, LONDON
Tel: +44 (0)20 759 48895

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Frank Murphy 
[frankvmur...@gmail.com]
Sent: Wednesday, July 25, 2012 3:03 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] How to identify unknow heavy atom??

Dear Haytham,

It should be relatively simple (and quick) to determine the metal in your 
sample employing either crystallized sample or solution using X-ray 
fluorescence (http://en.wikipedia.org/wiki/X-ray_fluorescence) at any beamline 
with a silicon drift detector (http://www.amptek.com/drift.html) set up for 
energy dispersive spectrometry (EDS).

We perform these analyses regularly at NE-CAT and I am sure there are a number 
of other beamlines set up for the experiment.

Frank Murphy
Beamline Scientist
NE-CAT / Cornell University
frankvmur...@gmail.com