[ccp4bb]

[Chavas Leo]

Dear all --

Just a short reminder that we are looking for talented and motivated  
persons to apply for the following post-doctoral position. The  
deadline is coming closer now !
I would like to add as well that knowledge of Japanese is not a  
requirement (although the successful candidate might enjoy eating  
sushi...).


Kind regards.

-- Leo --

### STARTS HERE ###

Post-doctoral position. Structural Biology Research Center, Tsukuba,  
Japan


[Closing date]
All documents should arrive at the latest on the 29th of January 2010.

[Job description]
The Structural Biology Research Center offers a state of the art  
international and stimulating environment for research in a multi- 
disciplinary framework. Notably, molecular structural biology  
research in the field of intracellular transport and  
posttranslational modification including ubiquitylation is vigorously  
pursued and tightly linked with development and operation of  
synchrotron protein crystallography beamlines at the Photon Factory.  
We are looking for an enthusiastic post-doctoral fellow to work on  
proteins involved in intracellular transport and posttranslational  
modification processes. Some of the recent publications on the  
relevant research areas include:


• Rahighi S, Ikeda F, Kawasaki M et al. (2009) Specific recognition  
of linear ubiquitin chains by NEMO is important for NF-kappaB  
activation. Cell 136:1098-1109


• Dikic I, Wakatsuki S, Walters KJ (2009) Ubiquitin-binding domains -  
from structures to functions. Nat Rev Mol Cell Biol 10:659-671


•  Chavas LM, Ihara K, Kawasaki M et al (2008) Elucidation of Rab27  
recruitment by its effectors: structure of Rab27a bound to Exophilin4/ 
Slp2-a. Structure. 16:1468-77


• Kudo N, Kimagai K, Tomishige N et al. (2008) Structural basis for  
specific lipid recognition by CERT responsible for nonvesicular  
trafficking of ceramide. Proc Natl Acad Sci U S A. 105:488-93


• Hirano S, Suzuki N, Slagsvold T et al. (2006) Structural basis of  
ubiquitin recognition by mammalian Eap45 GLUE domain. Nat Struc Mol  
Biol. 13:1031-2


More information can be obtained on the following website: http:// 
pfweis.kek.jp/eng/index.html.


[Qualifications and Experience]
Motivated applicants should have a Ph.D. in a relevant field. Working  
experience in molecular biology and biochemistry is required.  
Previous experience with large-scale protein expression,  
purification, crystallization, structure determination, and structure  
analysis will be considered advantageous. Experience in the field of  
intracellular transport or posttranslational modifications would be a  
plus.


[Contract]
The contract will be issued on a yearly basis with possible  
extensions. The future employee will benefit from the social  
insurance, travel allowance and assistance with housing in accordance  
with the institute restrictions.


[Start of the contract]
Ideally, the contract will start from April 2010. Nevertheless, the  
exact starting date stays open to discussion with the candidate.


[Applications]
To apply, please send a cover letter, CV (in English) with a summary  
of your previous work and research skills (A4, 1-2 sheets), reprints  
of your key papers, your research aspirations (A4, 1-2 sheets), and  
the contact information of two professional references. When  
possible, the required documents should be submitted by e-mail.


[Inquiries and contact information]
When possible, the candidates should apply by e-mail. Please address  
all communications to Mrs. Ishikawa Gin (gin.ishik...@kek.jp).


Prof. Soichi Wakatsuki
Structural Biology Research Center,
Photon Factory, Institute of Materials Structure Science,
High Energy Accelerator Research Organization (KEK).
1-1 Oho, Tsukuba, Ibaraki, 305-0801, Japan.
Tel: +81-(0)29-879-6178 - Fax: +81-(0)29-879-6179
e-mail: soichi.wakats...@kek.jp

### ENDS HERE ###


Chavas Leonard, Ph.D.
Assistant Professor

Structural Biology Research Center
Photon Factory
High Energy Research Organization (KEK)
305-0801 Tsukuba Oho 1-1
Japan

Tel: +81(0)29-864-5642 (4901)
Fax: +81(0)29-864-2801
e-mail: leonard.cha...@kek.jp

Science Advisory Board (BIT Life Sciences)
Editorial Board (JAA)

http://pfweis.kek.jp/~leo

Re: [ccp4bb] Zalman LCD availability

[Martin Hallberg]

BTW, has anyone tried out the higher resolution 24 inch 3D model from Zalman 
that appears to be available
from this reseller in Japan?:
http://mikimoto-japan.com/beans/products/product_dsp.htm

and this reseller in the UK:
http://www.cleverpc.co.uk/index.php?productID=5338

My guess it that it is the same monitor as this one by another Korean company:
http://www.miracube.net/product/detail_g240s.jsp

Cheers,

Martin


On Jan 15, 2010, at 7:49 AM, Takaaki Fukami wrote:

> Hi, Francois
> 
> We bought it 5 months ago from a supplier in Japan.
> (and it has been put back in a box under a desk.)
> 
> Zalman has its own web site in Japan.  Model name is the same.
> http://www.zalman.com/jpn/product/monitors/ZM-M220W.asp
> 
> You can buy it from many shops through the web.
> Check the most famous comparison site in Japan, kakaku.com:
> http://kakaku.com/item/00854312463/
> 
> HTH
> 
> Takaaki Fukami
> 
> 
> -Original Message-
> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of 
> Francois Berenger
> Sent: Friday, January 15, 2010 1:31 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] Zalman LCD availability
> 
> Hello,
> 
> By the way, does anyone got this LCD in Japan?
> 
> My team is interested to know the model's exact
> reference as well as from where you ordered it.
> 
> Thanks a lot,
> Francois.

Re: [ccp4bb] Zalman LCD availability

[Takaaki Fukami]

Hi, Francois

We bought it 5 months ago from a supplier in Japan.
(and it has been put back in a box under a desk.)

Zalman has its own web site in Japan.  Model name is the same.
http://www.zalman.com/jpn/product/monitors/ZM-M220W.asp

You can buy it from many shops through the web.
Check the most famous comparison site in Japan, kakaku.com:
http://kakaku.com/item/00854312463/

HTH

Takaaki Fukami


-Original Message-
From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Francois 
Berenger
Sent: Friday, January 15, 2010 1:31 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Zalman LCD availability

Hello,

By the way, does anyone got this LCD in Japan?

My team is interested to know the model's exact
reference as well as from where you ordered it.

Thanks a lot,
Francois.

Re: [ccp4bb] Zalman LCD availability

[Francois Berenger]

Hello,

By the way, does anyone got this LCD in Japan?

My team is interested to know the model's exact
reference as well as from where you ordered it.

Thanks a lot,
Francois.

Re: [ccp4bb] Zalman LCD availability

[Jürgen Bosch]

Yes,
contact mark.gar...@asipartner.com and ask for it.
ASI – Fremont, California
48289 Fremont Blvd.
Fremont, California  94538

Jürgen

On Jan 14, 2010, at 10:07 PM, William G. Scott wrote:


Does anyone know how to get extra glasses?


-
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://web.mac.com/bosch_lab/

Re: [ccp4bb] Zalman LCD availability

[William G. Scott]

 Does anyone know how to get extra glasses?

[ccp4bb] Postdoctoral Position in Cryo-Electron Tomography at UT Houston

[jun liu]

Postdoc position in cryo-electron tomography

A postdoctoral fellow position is available beginning in April 2010
in Dr. Liu’s laboratory at UT Houston Medical School
(http://www.uth.tmc.edu/pathology/faculty/faculty-Liu-Jun.html). My
laboratory is studying 3-D structure/function of macromolecular
assemblies in living organisms by using cryo-electron tomography
(cryo-ET). High-throughput cryo-ET with advanced image processing has
the great potential to understand the biomedical important events
within the cell. We have developed the capability to visualize
hundreds of living cells at molecular resolution within a week, by
combining automated data collection and high-throughput image
processing. We expect to expand the utility of cryo-ET through the
development of innovative techniques for increasing throughput and
resolution, and combining genetic approaches for the specific
characterization of pathogenic bacteria and their driving machine:
flagellar motor.

Highly motivated candidates with Ph. D degree in the Natural
Sciences and strong interest in cryo-electron tomography are
encouraged to apply. The appointment is for 2 years with possible
extension and is funded by a new research grant (R01) from National
Institutes of Health. Interested candidates should send a CV including
areas of expertise and interest, publications list, and names and
contact information for 3 references to: Dr. Jun Liu, Department of
Pathology & Laboratory Medicine, University of Texas Medical School at
Houston, 6431 Fannin, MSB 2.228, Houston, TX 77030, Email:
jun.li...@uth.tmc.edu

UT Medical School at Houston is equipped with state-of-the art
cryo-electron microscopy instruments, including a FEI Polara 300kv
electron microscope with helium stage and a 4kx4k CCD camera, one JEOL
1400 and two JEOL 1200 electron microscopes. As part of the Texas
Medical Center, we have the unique opportunity to collaborate and
interact with the other academic and health components including
Baylor College of Medicine, M.D. Anderson Cancer Center, Rice
University, the Texas A&M Institute of Bioscience and Technology, and
UTMB at Galveston.

Jun Liu, Ph.D
Department of Pathology and Laboratory Medicine
Univ of. Texas - Houston Medical School
Houston, Texas 77030
Phone: 713-500-5342
Email: jun.li...@uth.tmc.edu
http://www.uth.tmc.edu/pathology/faculty/faculty-Liu-Jun.html

[ccp4bb] Postdoc position at the University of Oregon

[Brad Nolen]

Postdoc position at the University of Oregon, Institute of Molecular Biology

Eugene, OR

 

We are seeking a highly motivated postdoctoral researcher to join our lab
full time on a flexible start date. Our interest is in understanding the
molecular basis for the regulation of the cytoskeleton. We are currently
focusing on proteins that control the assembly and disassembly of actin
filaments. Using a combination of x-ray crystallography, biochemistry,
biophysics, and cell biology, we seek to understand the structure-function
relationships of these proteins and how their molecular mechanisms relate to
their cellular activities. 

 

Successful candidates will have a Ph.D. in biochemistry, biophysics,
structural biology or a related field, a published record of accomplishment,
and good written and oral communication skills. 

 

For more information, please see:

Nature, 460(7258), 1031-4., J. Mol. Bio.,376, 166-183, Mol. Cell, 11, 449-57

or

 
http://www.molbio.uoregon.edu/facres/nolen.html

 

To apply, please email a cover letter and curriculum vitae to
 bno...@uoregon.edu. Also arrange to have two or
three letters of reference sent to the same email address.

 

Re: [ccp4bb] Zalman LCD availability

[Sabuj Pattanayek]

Hi,

http://www.provantage.com/zalman-tech-trimonzm-m220w~7ZALM03E.htm

As someone mentioned still showing 4 in stock. That's where we got ours from.

HTH,
Sabuj Pattanayek

Re: [ccp4bb] Zalman LCD availability

[Andrew Ring]

Hello All,

Thank you all for the replies.

It appears that the Zalmans are out there, but one may need to check
several of the smaller sites before finding one with them in stock and
one should not be surprised to find that it is back ordered after the
order is placed.

I tried another tactic with Zalman and they suggested quietpcusa.com. 
So at worst, emailing sales@zalmanusa.com will help with supplier
locating.

I had not tried all of the stores with the google shopping, and at least
a couple of them still have them in stock.

Thank you,
Andrew


Ben Eisenbraun wrote:
> Hi Andrew,
>
>   
>> Has anyone else noticed a lack of availability of Zalman 3-D LCD
>> monitors?
>> 
>
> Yes, we noticed the same thing.  Newegg went out of stock around
> Thanksgiving, and various other retailers were either out of stock or had
> "coming soon" sort of notices on the product pages over the last month and
> a half.
>
>   
>> I attempted to contact Zalman, but have not yet had a response.
>> 
>
> I'm curious to hear what they have to say if they get back to you.
>
>   
>> If you know of a retailer with them in stock could you send me a message?
>> 
>
> http://www.google.com/products/catalog?q=zalman+lcd+zm-m220w&oe=utf-8&rls=org.mozilla:en-US:official&client=firefox-a&um=1&ie=UTF-8&cid=15528606820264268025&ei=AopPS_Mt0uqUB5-hrKwK&sa=X&oi=product_catalog_result&ct=result&resnum=3&ved=0CBMQ8wIwAg#ps-sellers
>
> This is nicer: http://bit.ly/5PCj7r
>
> Anyway, a few of those listed retailers have them.  I think we bought our
> last one from Provantage and another lab around the corner got one from
> xPCgear.
>
>
> -ben
>
> --
> | Ben Eisenbraun  | Software Sysadmin  |
> | Structural Biology Grid | http://sbgrid.org  |
> | Harvard Medical School  | http://hms.harvard.edu |
>
>   

-- 
===
Andrew Ring
System Administrator
Kuriyan Laboratory
http://jkweb.qb3.berkeley.edu/
Doudna Laboratory
http://rna.berkeley.edu/
University of California, Berkeley
Office:
542 Stanley Hall
Shipping:
176 Stanley Hall, QB3
Berkeley, CA 94720-3220
tel: (510) 643 0166
fax: (510) 643 2352

Re: [ccp4bb] Zalman LCD availability

[Ben Eisenbraun]

Hi Andrew,

> Has anyone else noticed a lack of availability of Zalman 3-D LCD
> monitors?

Yes, we noticed the same thing.  Newegg went out of stock around
Thanksgiving, and various other retailers were either out of stock or had
"coming soon" sort of notices on the product pages over the last month and
a half.

> I attempted to contact Zalman, but have not yet had a response.

I'm curious to hear what they have to say if they get back to you.

> If you know of a retailer with them in stock could you send me a message?

http://www.google.com/products/catalog?q=zalman+lcd+zm-m220w&oe=utf-8&rls=org.mozilla:en-US:official&client=firefox-a&um=1&ie=UTF-8&cid=15528606820264268025&ei=AopPS_Mt0uqUB5-hrKwK&sa=X&oi=product_catalog_result&ct=result&resnum=3&ved=0CBMQ8wIwAg#ps-sellers

This is nicer: http://bit.ly/5PCj7r

Anyway, a few of those listed retailers have them.  I think we bought our
last one from Provantage and another lab around the corner got one from
xPCgear.


-ben

--
| Ben Eisenbraun  | Software Sysadmin  |
| Structural Biology Grid | http://sbgrid.org  |
| Harvard Medical School  | http://hms.harvard.edu |

Re: [ccp4bb] Zalman LCD availability

[Jason Vertrees]

On Thu, Jan 14, 2010 at 3:57 PM, Andrew Ring  wrote:
> Hello All,
>
> Has anyone else noticed a lack of availability of Zalman 3-D LCD
> monitors?  For at least a few weeks now, NewEgg and Dell are "currently
> out of stock", as is every retailer that lists their inventory.
> I attempted to contact Zalman, but have not yet had a response.
>
> If you know of a retailer with them in stock could you send me a message?
>
> Does anyone have insight into Zalman's situation they can share?
>
> Thank you,
> Andrew
>
> --
> ===
> Andrew Ring
> System Administrator
> Kuriyan Laboratory
> http://jkweb.qb3.berkeley.edu/
> Doudna Laboratory
> http://rna.berkeley.edu/
> University of California, Berkeley
> Office:
> 542 Stanley Hall
> Shipping:
> 176 Stanley Hall, QB3
> Berkeley, CA 94720-3220
> tel: (510) 643 0166
> fax: (510) 643 2352
> 


Andrew,

My Zalman Trimon is in the mail.  It was ordered about a week ago, so
no issues here.  I am discussing 3D PyMOL development with Zalman
support and can ask them about it if you like.

-- Jason

P.S.  First post.  :-)

-- 
Jason Vertrees, PhD
PyMOL Product Manager
Schrodinger, LLC

(e) jason.vertr...@schrodinger.com
(o) +1 (603) 374-7120

[ccp4bb] Zalman LCD availability

[Andrew Ring]

Hello All,

Has anyone else noticed a lack of availability of Zalman 3-D LCD
monitors?  For at least a few weeks now, NewEgg and Dell are "currently
out of stock", as is every retailer that lists their inventory.
I attempted to contact Zalman, but have not yet had a response.

If you know of a retailer with them in stock could you send me a message?

Does anyone have insight into Zalman's situation they can share?

Thank you,
Andrew

-- 
===
Andrew Ring
System Administrator
Kuriyan Laboratory
http://jkweb.qb3.berkeley.edu/
Doudna Laboratory
http://rna.berkeley.edu/
University of California, Berkeley
Office:
542 Stanley Hall
Shipping:
176 Stanley Hall, QB3
Berkeley, CA 94720-3220
tel: (510) 643 0166
fax: (510) 643 2352

[ccp4bb] macromolecular crystallography school

[Pawel Grochulski]

The Canadian Light Source (CLS) is pleased to introduce the fifth annual 
Saskatoon Synchrotron Summer School (S4V) scheduled for June 13 - 18th, 2010 in 
Saskatoon, Saskatchewan. This year's school is for students and researchers 
interested in learning synchrotron techniques for life science research. The 
first day of the school will take participants through the basics of 
synchrotron operations and techniques. The following three days are divided in 
concurrent streams. One stream is a dedicated macromolecular crystallography 
course which will take students through the steps of structure solution 
including sample preparation, data collection, data processing, phase 
determination, refinement and structure validation. The other stream is 
multifaceted and will introduce experimental techniques in the areas of 
diffraction enhanced imaging, x-ray florescence mapping, and mid-infrared 
mapping. After completing the school the participant will have sufficient 
knowledge to conduct synchrotron based research.
http://www.lightsource.ca/education/summerschool/.
The deadline for early application is March 30th. Additional details regarding; 
application, fees and school syllabus can be found at. 
http://www.lightsource.ca/education/summerschool/

Sincerely,

S4V Planning Committee

Questions? Contact the Educational Outreach Coordinator, Tracy Walker 
tracy.wal...@lightsource.ca or 
(306)657-3525. Watch for more details and registration information at 
http://www.lightsource.ca/education/summerschool/

__
Pawel Grochulski, Ph.D., D.Sc.
Canadian Macromolecular Crystallography Facility
Canadian Light Source Inc.,
101 Perimeter Road, Saskatoon,
SK S7N 0X4, Canada.
Phone: 306-657-3538;  Fax: 306-657-3535
http://exshare.lightsource.ca/cmcf/
Adjunct Professor of Pharmacy and of Biochemistry,
University of Saskatchewan,
http://homepage.usask.ca/~pag266
__

[ccp4bb] Experience with experimental phasing in P21 with c cos Beta = - a/2 ?

[Francis E Reyes]

Or know of any references besides Declercq and Evrard, 2001 ? I'd love  
to hear from you. Please PM me.


Cheers

FR

-
Francis Reyes M.Sc.
215 UCB
University of Colorado at Boulder

gpg --keyserver pgp.mit.edu --recv-keys 67BA8D5D

8AE2 F2F4 90F7 9640 28BC  686F 78FD 6669 67BA 8D5D

Re: [ccp4bb] DSSP server

[Nathaniel Echols]

On Thu, Jan 14, 2010 at 7:02 AM, Schubert, Carsten [PRDUS] <
cschu...@its.jnj.com> wrote:

> you could use ksDSSP, which is an OpenSource implementation of DSSP.
> Requires some compiling though and I am not sure if OSX is supported.
> You also need to compile the PDB record I/O libraries.
>

It runs fine on OS X, but I think I had to run 'ranlib' on the PDB library
to get it to compile properly.  However, I've seen at least one structure
(1ywf) for which it produces incorrect results; this may not matter if you
just want to make figures, but it's problematic for any other uses.

I was able to download the DSSP source code from CMBI without signing
anything - but it's still proprietary and only free to academics.  (And I
had no luck compiling it on a Mac, unfortunately.)

-Nat

Re: [ccp4bb] DSSP server

[Guenter Fritz]

Hi,
you can use the nice tool dssp2pdb by James Stroud 
(http://structure.usc.edu/dssp2pdb) to assign the ss of the DSSP output 
to your pdb file. See instructions there.

HTH
Guenter



I am sorry for this off-topic question. I see it has been discussed 
many times, but somehow I got stuck in the very beginning.


I want to assign ss to my pdb file in DSSP, but I could not find a 
server to run it. Does anybody know a webserver where I could run this 
kind of tasks? I use iMAC.


Many thanks!

Jane



--
***

Priv.Doz.Dr. Guenter Fritz
Fachbereich Biologie
Sektion Naturwissenschaften
Universitaet Konstanz
http://www.biologie.uni-konstanz.de/fritz

Universitaetsstrasse 10
Postfach M665
D-78457 Konstanz

e-mail: guenter.fr...@uni-konstanz.de

Phone Office: +49-(0)7531 88 3205 
Phone Lab   : +49-(0)7531 88 3733

Fax:  +49-(0)7531 88 2966

Re: [ccp4bb] Haem-cysteine interactions

[Edward A. Berry]

Thomas Womack wrote:

. . .
There are a number of high-resolution structures deposited recently containing haems near 
cysteines, and in most of them a re-refinement gives substantial positive difference 
density about the CM atoms; there is even occasionally a sign of some kind of longer tail 
coming out from the CMB position.  It seems to be purely positive density, rather than the 
dipole that tends to be diagnostic of anisotropy.


My current thought is that even a 1.4A structure of a haem-containing protein 
(I'm looking at an autoBUSTER re-refinement of the 3fo3 deposition from EMBL 
Hamburg) may well come from a crystal sufficiently well-ordered that we're 
seeing hydrogens - one of these structures has at least one isoleucine with 
green blobs at positions which would be reasonable for every hydrogen on the 
side-chain - but I would be interested to know other peoples' experience and 
interpretation.


In the case of non-covalently bound hemes, this can be indicative of promiscuity with 
respect to orientation around the pseudo-2-fold axis: In a few percent of the heme, CMB is 
really CAC, with CBC coming out of it. But I guess this is impossible for covalently-bound 
heme (which is inserted and ligated by an enzyme) and at that resolution CBC should be 
resolved, so I think your explanation is reasonable.

Ed

Re: [ccp4bb] DSSP server

[Dirk Kostrewa]

Hello Jane,

CMBI (http://swift.cmbi.kun.nl/gv/dssp/) offers the source code after 
signing a licence agreement. I compiled it on my Mac using one of the 
compile-scripts that came with the tar file. You have to install the Mac 
developer package Xcode (free from developer.apple.com) for getting the 
C-compiler.


Best regards,

Dirk.

Am 14.01.10 15:54, schrieb Jane Bailey:

Hello all,

I am sorry for this off-topic question. I see it has been discussed 
many times, but somehow I got stuck in the very beginning.


I want to assign ss to my pdb file in DSSP, but I could not find a 
server to run it. Does anybody know a webserver where I could run this 
kind of tasks? I use iMAC.


Many thanks!

Jane


--

***
Dirk Kostrewa
Gene Center, A 5.07
Ludwig-Maximilians-University
Feodor-Lynen-Str. 25
81377 Munich
Germany
Phone:  +49-89-2180-76845
Fax:+49-89-2180-76999
E-mail: kostr...@genzentrum.lmu.de
WWW:www.genzentrum.lmu.de
***

Re: [ccp4bb] DSSP server

[Schubert, Carsten [PRDUS]]

Jane,

you could use ksDSSP, which is an OpenSource implementation of DSSP.
Requires some compiling though and I am not sure if OSX is supported.
You also need to compile the PDB record I/O libraries.

http://www.cgl.ucsf.edu/Overview/software.html

Cheers,

Carsten




> -Original Message-
> From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of
> Jane Bailey
> Sent: Thursday, January 14, 2010 9:54 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] DSSP server
> 
> Hello all,
> 
> I am sorry for this off-topic question. I see it has been discussed
> many
> times, but somehow I got stuck in the very beginning.
> 
> I want to assign ss to my pdb file in DSSP, but I could not find a
> server to run it. Does anybody know a webserver where I could run this
> kind of tasks? I use iMAC.
> 
> Many thanks!
> 
> Jane

Re: [ccp4bb] DSSP server

[Tim Gruene]

Hello Jane,

if I remember correctly, rasmol uses the dssp algorithm for the secondary 
structure assignment. You can also use pymol or molscript (molauto) for 
the same task. In any case you should always check the boundaries of the 
secondary structure elements manually because no program is perfect ;-)


Tim

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

GPG Key ID = A46BEE1A


On Thu, 14 Jan 2010, Jane Bailey wrote:


Hello all,

I am sorry for this off-topic question. I see it has been discussed many 
times, but somehow I got stuck in the very beginning.


I want to assign ss to my pdb file in DSSP, but I could not find a server to 
run it. Does anybody know a webserver where I could run this kind of tasks? I 
use iMAC.


Many thanks!

Jane

[ccp4bb] DSSP server

[Jane Bailey]

Hello all,

I am sorry for this off-topic question. I see it has been discussed many 
times, but somehow I got stuck in the very beginning.


I want to assign ss to my pdb file in DSSP, but I could not find a 
server to run it. Does anybody know a webserver where I could run this 
kind of tasks? I use iMAC.


Many thanks!

Jane

Re: [ccp4bb] Blob help

[Vin Purp]

Yes, thanks for asking.  Having 6 active sites in my AU, showed that 4 of
them had a single beta-mercaptoethanol molecule, and the other two had the
density I posted here. It turned out to be a single BME in 2 different
conformations. thanks for the help and suggestions!

[ccp4bb] Haem-cysteine interactions

[Thomas Womack]

One of the features that Global Phasing's routine runs of deposited PDB 
structures often pick up is very close contacts between the SG of cysteine 
residues and the CAB and CAC atoms of the propenyl groups on HEM ligands, not 
described by LINK cards in the header of the deposited structure.  There is 
generally a CXXC motif in the protein which provides two cysteines to hold a 
haem in place.

Am I right that, in general, a haem bound to cysteines should be modelled as 
the molecular entity called by the PDB HEC, with the CAB and CAC atoms 
essentially tetrahedral, the CAB-CBB and CAC-CBC bond lengths the same as a 
carbon-carbon single bond, and a link from SG to CAB with angle and bond 
lengths around the SG as in methionine?

There are a number of high-resolution structures deposited recently containing 
haems near cysteines, and in most of them a re-refinement gives substantial 
positive difference density about the CM atoms; there is even occasionally a 
sign of some kind of longer tail coming out from the CMB position.  It seems to 
be purely positive density, rather than the dipole that tends to be diagnostic 
of anisotropy.

My current thought is that even a 1.4A structure of a haem-containing protein 
(I'm looking at an autoBUSTER re-refinement of the 3fo3 deposition from EMBL 
Hamburg) may well come from a crystal sufficiently well-ordered that we're 
seeing hydrogens - one of these structures has at least one isoleucine with 
green blobs at positions which would be reasonable for every hydrogen on the 
side-chain - but I would be interested to know other peoples' experience and 
interpretation.

Tom Womack (Global Phasing)