Re: [ccp4bb] Win-coot: replace residue

2013-09-11 Thread Paul Emsley 

On 11/09/13 22:03, Uma Ratu wrote:

Hi, Bernhard and Yury:
I did change Cys to CSX or CSO with older version of Coot. And the 
program replace the residue inner the chain.

With present Coot-0.7, it seems to be complicated to replace a residue.
Thank you for your suggestions.

Uma



On Wed, Sep 11, 2013 at 4:40 PM, Bernhard Lechtenberg 
> wrote:


Hi Uma,

when I do the same procedure (in OSX, but the problem seems to be
the same), the new residue is stored in a new chain with residue
number 1. So you would need to renumber the residue and change the
chain ID back to the original chain ID. It's annoyingly
complicated, but it works for me.

Hope that helps,
Bernhard



On Sep 11, 2013, at 12:56 PM, Uma Ratu mailto:rosiso2...@gmail.com>> wrote:


Hello,
I try to replace one of cysteine residue to CSX using Win-coot.
Here is how I did:
Extensions > Modelling > Replace Residue... and enter the three
letter code.
The program place the CSX residue, but with break bond. The new
residue is no longer linked with other residue and not in the chain.
I then try to replace with other residues, such as ALA. The
results are the same: the new residues all with break bond.
How could I put the replaced residue back to the main-chain?
I use Win-coot-0.7.
Thank you
Uma





What is the group of CSX? If you tell coot that it is not an "L-peptide" 
(or in modern coots, simply "peptide" will do) , it will believe you 
(and thus not create peptide bonds).


Edit -> Restraints -> CSX -> Info -> Group

I just tried with Coot-0.8-pre and the latest Refmac Monomer Library and 
it seemed to work.


Paul.

Re: [ccp4bb] Win-coot: replace residue

2013-09-11 Thread Uma Ratu 
Hi, Bernhard and Yury:

I did change Cys to CSX or CSO with older version of Coot. And the program
replace the residue inner the chain.

With present Coot-0.7, it seems to be complicated to replace a residue.

Thank you for your suggestions.

Uma


On Wed, Sep 11, 2013 at 4:40 PM, Bernhard Lechtenberg <
blechtenb...@sanfordburnham.org> wrote:

> Hi Uma,
>
> when I do the same procedure (in OSX, but the problem seems to be the
> same), the new residue is stored in a new chain with residue number 1. So
> you would need to renumber the residue and change the chain ID back to the
> original chain ID. It's annoyingly complicated, but it works for me.
>
> Hope that helps,
> Bernhard
>
>
>
>  On Sep 11, 2013, at 12:56 PM, Uma Ratu  wrote:
>
>  Hello,
>
> I try to replace one of cysteine residue to CSX using Win-coot.
>
> Here is how I did:
> Extensions > Modelling > Replace Residue... and enter the three letter
> code.
>
> The program place the CSX residue, but with break bond. The new residue is
> no longer linked with other residue and not in the chain.
>
> I then try to replace with other residues, such as ALA. The results are
> the same: the new residues all with break bond.
> How could I put the replaced residue back to the main-chain?
>
> I use Win-coot-0.7.
>
> Thank you
>
> Uma
>
>
>
>

Re: [ccp4bb] Win-coot: replace residue

2013-09-11 Thread Bernhard Lechtenberg 
Hi Uma,

when I do the same procedure (in OSX, but the problem seems to be the same), 
the new residue is stored in a new chain with residue number 1. So you would 
need to renumber the residue and change the chain ID back to the original chain 
ID. It's annoyingly complicated, but it works for me.

Hope that helps,
Bernhard



On Sep 11, 2013, at 12:56 PM, Uma Ratu 
mailto:rosiso2...@gmail.com>> wrote:

Hello,

I try to replace one of cysteine residue to CSX using Win-coot.

Here is how I did:
Extensions > Modelling > Replace Residue... and enter the three letter code.

The program place the CSX residue, but with break bond. The new residue is no 
longer linked with other residue and not in the chain.

I then try to replace with other residues, such as ALA. The results are the 
same: the new residues all with break bond.
How could I put the replaced residue back to the main-chain?

I use Win-coot-0.7.

Thank you

Uma

[ccp4bb] Win-coot: replace residue

2013-09-11 Thread Uma Ratu 
Hello,

I try to replace one of cysteine residue to CSX using Win-coot.

Here is how I did:
Extensions > Modelling > Replace Residue... and enter the three letter code.

The program place the CSX residue, but with break bond. The new residue is
no longer linked with other residue and not in the chain.

I then try to replace with other residues, such as ALA. The results are the
same: the new residues all with break bond.
How could I put the replaced residue back to the main-chain?

I use Win-coot-0.7.

Thank you

Uma

Re: [ccp4bb] MRBUMP - PHASER ?

2013-09-11 Thread Ronan Keegan 


Hi Douglas,

Have you applied all of the automatic updates to your installed version 
of CCP4? There was a bug relating to this that I fixed at one point and 
it was pushed out using our update system. However, if you've installed 
from source code you won't have this option.


Best wishes,

Ronan


On 10/09/13 15:44, Bailey, Douglas (NIH/NCI) [E] wrote:


Hello Everyone,

PHASER is returning the following error "Input Error: No Mode Set" 
when called from MRBUMP.


CCP4-6.3.0 running on Centos5-x64.

Any help , ideas, comment would be greatly appreciated.

Thanks,

  Doug

#

### CCP4 PROGRAM SUITE: 
Phaser  2.5.1 ###


#

User: jacek

Run time: Tue Sep 10 10:02:53 2013

Version:  2.5.1

OS type:  linux

Release Date: Fri Jul  6 07:21:42 2012 (svn )

If you use this software please cite:

$TEXT:Reference1: $$ $$

"Phaser Crystallographic Software"

A.J. McCoy, R.W. Grosse-Kunstleve, P.D. Adams, M.D. Winn, L.C. Storoni 
& R.J. Read


J. Appl. Cryst. (2007). 40, 658-674

$$

*

*** Phaser Module: 
PREPROCESSOR 2.5.1 ***


*

END



$TEXT:Warning: $$ Baubles Markup $$

-

INPUT ERROR: No MODE set

-

$$

Douglas Bailey

NCI-Frederick

1050 Boyles Street

Frederick, Maryland 21702

301-846-5328




--
Scanned by iCritical.

Re: [ccp4bb] Please Delete: FW: Departmental License for Pymol

2013-09-11 Thread Jason Vertrees 
Hi Phoebe,

We all accidentally mis-forward an email at one time or another, so no
worries. Schrödinger has reissued new credentials to your department.

Cheers,

-- Jason

On Wed, Sep 11, 2013 at 9:54 AM, Phoebe A. Rice  wrote:
> MANY APOLOGIES the wrong address got auto-filled when I tried to forward
> this to my lab.
> Please delete.
>
> ++
>
> Phoebe A. Rice
> Dept. of Biochemistry & Molecular Biology
> The University of Chicago
>
> 773 834 1723; pr...@uchicago.edu
> http://bmb.bsd.uchicago.edu/Faculty_and_Research/
>
> http://www.rsc.org/shop/books/2008/9780854042722.asp
>
> 
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Phoebe A.
> Rice [pr...@uchicago.edu]
> Sent: Wednesday, September 11, 2013 9:50 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] FW: Departmental License for Pymol
>
> This may get us a more advanced version than the one embedded in phenix?
>
> 
> From: Erin Adams [ejad...@uchicago.edu]
> Sent: Wednesday, September 11, 2013 9:32 AM
> To: Shohei Koide; Herbert C Friedmann; Andrzej Joachimiak; Godfrey Getz;
> James Shapiro; Ronald S. Rock; Robert Haselkorn; Geoffrey L. Greene; Sean
> Crosson; Nancy Schwartz; Joe Piccirilli; Tao Pan; Keith Moffat; David R.
> Kovar; Tobin R. Sosnick; Stephen C. Meredith M.D., Ph.D.; Phoebe A. Rice;
> Francisco Bezanilla; Marvin W. Makinen; Stephen Kent; Donald F. Steiner Md.;
> Benoit Roux; D Allan Drummond; Glyn Dawson; Erin Adams; Robert Keenan;
> Theodore L. Steck; Tony Kossiakoff; Eduardo Perozo
> Subject: Departmental License for Pymol
>
> Dear colleagues,
>
> Tobin has generously agreed to fund another three year departmental
> licensing for Pymol.  The information is below, please distribute this to
> your labs.
>
> Thanks,
>
> Erin
>
>
> Begin forwarded message:
>
> From: Schrodinger Licensing 
> Subject: PyMOL Invoice #13348
> Date: September 10, 2013 5:24:01 PM CDT
> To: 
>
>
> Dear Erin J. Adams,
>
> Thank you for your recent purchase of PyMOL.
> Here is the information you need for downloading the software:
>
> Invoice number: 13348
> Download & documentation URL: http://pymol.org/dsc
> USER: 16sep10
> PASSWORD: xoeklc4y
>
> The following links should be helpful to you while using the software:
>
> PyMOL-Users mailing list. Please consider joining the community mailing
> list if you haven't done so already.
> http://lists.sourceforge.net/lists/listinfo/pymol-users
>
> For technical support issues, please email:
> licens...@schrodinger.com
>
> The community-maintained Wiki documentation server:
> http://pymolwiki.org
>
> Additional PyMOL-related links:
> http://pymol.sourceforge.net/links.html
>
> We hope you enjoy PyMOL.
>
> Sincerely,
>
> Schrodinger PyMOL licensing team
>
> 
> Schrodinger Licensing | licens...@schrodinger.com
> http://www.schrodinger.com | 503-299-1150 | 503-299-4532 (fax)
> 101 SW Main St. Suite 1300, Portland OR 97204
> 
>
>
> 
> Erin J. Adams Ph.D.
> Associate Professor
> Department of Biochemistry and Molecular Biology
> University of Chicago
> 929 E. 57th Street
> Chicago, IL  60637
> office:  CIS W236
> lab:  CIS W229
> website: http://ejadamslab.bsd.uchicago.edu
> Office phone: 773-834-9816
> Lab phone: 773-834-0660
> Department Fax: 773-702-0439
> 
>



-- 
Jason Vertrees, PhD
Director of Core Modeling Products
Schrödinger, Inc.

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

[ccp4bb] Research Assistant Position in Structural Biology of Macromolecular Complexes

2013-09-11 Thread Sebastian Klinge 
*Research Assistant Position in Structural Biology of Macromolecular 
Complexes*


The Rockefeller University, a premier biomedical research institute, 
seeks a Research Assistant to join our Laboratory of Protein and Nucleic 
Acid Chemistry.


The successful applicant will be part of a creative and highly motivated 
team of biochemists and structural biologists, which are interested in 
the structure and function of multi-protein complexes involved in key 
steps of the Central Dogma of Molecular Biology. The laboratory houses a 
state of the art large scale fermenter, tissue culture and 
crystallization rooms and has access to the Rockefeller Structural 
Biology Resource Center with liquid handling and crystallization robots 
(Formulator by Formulatrix and Phoenix by Art Robbins respectively) and 
a Rigaku/MSC microMax 007 HF X-ray generator.


B.S. or M.S. degree with a strong background in biochemistry or 
molecular biology is required. Experience with protein production in 
insect cells (preferably MultiBac) and familiarity with molecular 
biology techniques is essential.


The ideal candidate will interact well with other members of the 
laboratory, be well organized and interested in working in a high 
quality research environment and collaborate closely with the principal 
investigator in running the laboratory. Responsibilities will include 
setting up an insect cell facility as well as general laboratory duties 
such as inventory, organization and pick-up of supplies and cataloging 
the laboratory's clone stocks.


We offer a competitive salary, comprehensive benefits, and a beautiful 
working environment. To apply to this job, click the following URL, 
click on 'staff opportunities' and enter keyword 'IRC14241':


http://www.rockefeller.edu/hr/career

/The Rockefeller University is an Affirmative Action/Equal Employment 
Opportunity/VEVRAA employer./

[ccp4bb] Please Delete: FW: Departmental License for Pymol

2013-09-11 Thread Phoebe A. Rice 
MANY APOLOGIES the wrong address got auto-filled when I tried to forward this 
to my lab.
Please delete.


++

Phoebe A. Rice
Dept. of Biochemistry & Molecular Biology
The University of Chicago

773 834 1723; pr...@uchicago.edu
http://bmb.bsd.uchicago.edu/Faculty_and_Research/

http://www.rsc.org/shop/books/2008/9780854042722.asp


From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Phoebe A. Rice 
[pr...@uchicago.edu]
Sent: Wednesday, September 11, 2013 9:50 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] FW: Departmental License for Pymol

This may get us a more advanced version than the one embedded in phenix?


From: Erin Adams [ejad...@uchicago.edu]
Sent: Wednesday, September 11, 2013 9:32 AM
To: Shohei Koide; Herbert C Friedmann; Andrzej Joachimiak; Godfrey Getz; James 
Shapiro; Ronald S. Rock; Robert Haselkorn; Geoffrey L. Greene; Sean Crosson; 
Nancy Schwartz; Joe Piccirilli; Tao Pan; Keith Moffat; David R. Kovar; Tobin R. 
Sosnick; Stephen C. Meredith M.D., Ph.D.; Phoebe A. Rice; Francisco Bezanilla; 
Marvin W. Makinen; Stephen Kent; Donald F. Steiner Md.; Benoit Roux; D Allan 
Drummond; Glyn Dawson; Erin Adams; Robert Keenan; Theodore L. Steck; Tony 
Kossiakoff; Eduardo Perozo
Subject: Departmental License for Pymol

Dear colleagues,

Tobin has generously agreed to fund another three year departmental licensing 
for Pymol.  The information is below, please distribute this to your labs.

Thanks,

Erin


Begin forwarded message:

From: Schrodinger Licensing 
mailto:licens...@schrodinger.com>>
Subject: PyMOL Invoice #13348
Date: September 10, 2013 5:24:01 PM CDT
To: mailto:ejad...@uchicago.edu>>


Dear Erin J. Adams,

Thank you for your recent purchase of PyMOL.
Here is the information you need for downloading the software:

Invoice number: 13348
Download & documentation URL: http://pymol.org/dsc
USER: 16sep10
PASSWORD: xoeklc4y

The following links should be helpful to you while using the software:

PyMOL-Users mailing list. Please consider joining the community mailing
list if you haven't done so already.
http://lists.sourceforge.net/lists/listinfo/pymol-users

For technical support issues, please email:
licens...@schrodinger.com

The community-maintained Wiki documentation server:
http://pymolwiki.org

Additional PyMOL-related links:
http://pymol.sourceforge.net/links.html

We hope you enjoy PyMOL.

Sincerely,

Schrodinger PyMOL licensing team


Schrodinger Licensing | licens...@schrodinger.com
http://www.schrodinger.com | 503-299-1150 | 503-299-4532 (fax)
101 SW Main St. Suite 1300, Portland OR 97204



Erin J. Adams Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
University of Chicago
929 E. 57th Street
Chicago, IL  60637
office:  CIS W236
lab:  CIS W229
website: http://ejadamslab.bsd.uchicago.edu
Office phone: 773-834-9816
Lab phone: 773-834-0660
Department Fax: 773-702-0439

[ccp4bb] FW: Departmental License for Pymol

2013-09-11 Thread Phoebe A. Rice 
This may get us a more advanced version than the one embedded in phenix?


From: Erin Adams [ejad...@uchicago.edu]
Sent: Wednesday, September 11, 2013 9:32 AM
To: Shohei Koide; Herbert C Friedmann; Andrzej Joachimiak; Godfrey Getz; James 
Shapiro; Ronald S. Rock; Robert Haselkorn; Geoffrey L. Greene; Sean Crosson; 
Nancy Schwartz; Joe Piccirilli; Tao Pan; Keith Moffat; David R. Kovar; Tobin R. 
Sosnick; Stephen C. Meredith M.D., Ph.D.; Phoebe A. Rice; Francisco Bezanilla; 
Marvin W. Makinen; Stephen Kent; Donald F. Steiner Md.; Benoit Roux; D Allan 
Drummond; Glyn Dawson; Erin Adams; Robert Keenan; Theodore L. Steck; Tony 
Kossiakoff; Eduardo Perozo
Subject: Departmental License for Pymol

Dear colleagues,

Tobin has generously agreed to fund another three year departmental licensing 
for Pymol.  The information is below, please distribute this to your labs.

Thanks,

Erin


Begin forwarded message:

From: Schrodinger Licensing 
mailto:licens...@schrodinger.com>>
Subject: PyMOL Invoice #13348
Date: September 10, 2013 5:24:01 PM CDT
To: mailto:ejad...@uchicago.edu>>


Dear Erin J. Adams,

Thank you for your recent purchase of PyMOL.
Here is the information you need for downloading the software:

Invoice number: 13348
Download & documentation URL: http://pymol.org/dsc
USER: 16sep10
PASSWORD: xoeklc4y

The following links should be helpful to you while using the software:

PyMOL-Users mailing list. Please consider joining the community mailing
list if you haven't done so already.
http://lists.sourceforge.net/lists/listinfo/pymol-users

For technical support issues, please email:
licens...@schrodinger.com

The community-maintained Wiki documentation server:
http://pymolwiki.org

Additional PyMOL-related links:
http://pymol.sourceforge.net/links.html

We hope you enjoy PyMOL.

Sincerely,

Schrodinger PyMOL licensing team


Schrodinger Licensing | licens...@schrodinger.com
http://www.schrodinger.com | 503-299-1150 | 503-299-4532 (fax)
101 SW Main St. Suite 1300, Portland OR 97204



Erin J. Adams Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
University of Chicago
929 E. 57th Street
Chicago, IL  60637
office:  CIS W236
lab:  CIS W229
website: http://ejadamslab.bsd.uchicago.edu
Office phone: 773-834-9816
Lab phone: 773-834-0660
Department Fax: 773-702-0439

[ccp4bb] Fluidigm TOPAZ system looking for new home

2013-09-11 Thread Chris Richardson 
We have a Fluidigm TOPAZ free interface diffusion crystallisation system that 
we no longer use.  If it can't find a new home it will be disposed of.  We're 
offering it free of charge to any interested UK organisation on the condition 
that the recipient pays for its transport.  It's currently in central London.

The TOPAZ system automates nanoscale crystallisation trials.  We have the FID 
Crystallizer and associated laptop (assuming we can unchain it from the lab 
bench).  The system also requires TOPAZ Screening Chips and associated 
reagents.  Although Fluidigm has ended new system sales for the Topaz, it 
continues to manufacture and supply consumables.

For further information, look at:

  http://www.fluidigm.com/topaz-system.html 

Note that this is *not* the system we are offering.  We have the previous 
model, which can be seen on this page from the Internet Archive:

  
http://web.archive.org/web/20060326075010/http://www.fluidigm.com/topazinstruments.htm

If you're interested, please email nora.cro...@icr.ac.uk.

Chris
--
Dr Chris Richardson :: Sysadmin, structural biology, icr.ac.uk

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
Limited by Guarantee, Registered in England under Company No. 534147 with its 
Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the addressee only.  If the 
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[ccp4bb] principle beamline scientist for SAXS/BioSAXS beamline at Diamond -Closingdate 6th October 2013

2013-09-11 Thread Martin Walsh 
Dear all B21 is a tuneable bending magnet beamline dedicated to small angle 
X-ray scattering (SAXS) which will come online in 2014 at Diamond. There is now 
an exciting opportunity to take the scientific and operation lead of the 
beamline. As there is an increased need for SAXS in the biological sciences and 
the beamline aims to deliver an automated facility for BioSAXS experiments, 
this opportunity may be of strong interest to readers of this BB

Full details and how to apply can be found here:
http://www.diamond.ac.uk/Home/Jobs/Current/DIA0870_SB.html

Don't hesitate to contact me directly for informal discussions
thanks
Martin


Martin A. Walsh
Diamond Light Source Ltd.,
Harwell Science & Innovation Campus,
Didcot OX11 0DE
UK
t: +44-1235-778518
f: +44-1235-778448
e: martin.wa...@diamond.ac.uk




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