Re: [ccp4bb] problem in mtz2various

[Sita Ram Meena]

Thank all for kind suggestion.

it works now, as suggested by the Ian, it was a column label selection
error for the CNS.



On Mon, May 21, 2012 at 2:47 PM, Ian Clifton wrote:

> Sita Ram Meena  writes:
>
> >Hello everyone
> > I Was trying to convert my mtz output of the SCALA to CNS format in
> >mtz2various but its gives some error
> >please look at log file 
>
> [...]
>
> > Data line--- OUTPUT CNS
> > Data line--- labin  FP=F_New SIGFP=SIGF_New FPH=F_New SIGFPH=SIGF_New
> >DP=DANO_New SIGDP=SIGDANO_New FREE=FreeR_flag F(+)=F_New(+)
> >SIGF(+)=SIGF_New(+) F(-)=F_New(+) SIGF(-)=SIGF_New(+)
>
> [...]
>
> >/home/ajay/programs/ccp4/ccp4-6.2.0/lib/data/syminfo.lib
> > MTZ2VARIOUS:   *** You are inputting F(+) AND  FP  - incompatible ***
>
> [...]
>
> This just means you have to choose one of the sets {FP, SIGFP, DP,
> SIGDP} or {F(+), F(-) SIGF(+), SIGF(-)} — you can’t have both.
> --
> Ian Clifton ⚗ Phone: +44 1865 275677
> Chemistry Research Laboratory Fax:   +44 1865 285002
> Oxford University ian.clif...@chem.ox.ac.uk
> Mansfield Road   Oxford OX1 3TA   UK
>



-- 
Sita Ram

Re: [ccp4bb] Propane still?

[Jim Pflugrath]

As with all reagents used in the lab it is best to understand the health 
hazards.  Thanks for note.

Jim


From: Jacob Keller [j-kell...@fsm.northwestern.edu]
Sent: Monday, May 21, 2012 5:22 PM
To: Jim Pflugrath
Cc: CCP4BB@jiscmail.ac.uk
Subject: Re: [ccp4bb] Propane still?

Well, not to be a downer, but wikipedia has some comments on the hazards...

Environmental effects

Tetrafluoromethane is a potent greenhouse 
gas that contributes to the 
greenhouse effect. It is very 
stable, has an atmospheric lifespan of 50,000 years, and a high greenhouse 
warming potential of 
6500 (CO2 has a factor of 1); 
however, the low amount in the atmosphere restricts the overall radiative 
forcing effect.

Although structurally similar to 
chlorofluorocarbons (CFCs), 
tetrafluoromethane does not deplete the ozone 
layer. This is because the 
depletion is caused by the chlorine atoms in CFCs, which dissociate when struck 
by UV radiation. Carbon-fluorine bonds are stronger and less likely to 
dissociate. According to Guinness World 
Records Tetrafluoromethane 
is the most persistent greenhouse gas.

[edit]Health
 risks

Depending on the concentration, inhalation of tetrafluoromethane can cause 
headaches, nausea, dizziness and damage to the cardiovascular 
system (mainly the heart). 
Long-term exposure can cause severe heart damage.

Due to its density, tetrafluoromethane can displace air, creating an 
asphyxiation hazard in inadequately 
ventilated areas.

On Mon, May 21, 2012 at 5:08 PM, Jim Pflugrath 
mailto:jim.pflugr...@rigaku.com>> wrote:
Here is a trick which I will attribute to Cambridge:

Fill balloon with gas.  Put end of balloon over 15 ml Falcon tube.  Put Falcon 
tube in LN2.  No wasted gas.

I would recommend CF4 or carbon tetrafluoride instead of propane though.  CF4 
is cheap and non-dangerous.

Jim



From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] 
on behalf of Prince, D Bryan 
[dbryan.pri...@astrazeneca.com]
Sent: Monday, May 21, 2012 4:15 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Propane still?

Good afternoon fellow ccp4bb’rs,

I was wondering if anyone knows if a still to condense gaseous propane to 
liquid propane using dry ice is commercially available. I want to make sure 
that it is not something I can purchase before I build one fit to purpose. I 
appreciate any advice and knowledge you can share.

Regards,
Bryan Prince



Confidentiality Notice: This message is private and may contain confidential 
and proprietary information. If you have received this message in error, please 
notify us and remove it from your system and note that you must not copy, 
distribute or take any action in reliance on it. Any unauthorized use or 
disclosure of the contents of this message is not permitted and may be unlawful.





--
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

[ccp4bb] Problems installing CCP4 6.2 on Mac OS X 10.7.3

[Terry Lang]

Hey Everyone,

I am having some problems getting CCP4 up and running on a 
laptop with Mac OS X 10.7.3.  I have downloaded the .dmg and run the 
installation with no errors.  However, when I try to set up my Project 
directory, I run into some problems.  It seemingly won't let me access 
my directory tree.  When I click on Users, for example, the Browse 
window does not enter the directory and frequently just closes without 
an error message.  Any ideas?


Thanks,
Terry

--
Paula Therese Lang
Postdoctoral Scholar
Alber Lab
UC Berkeley/QB3

Re: [ccp4bb] Propane still?

[Jacob Keller]

Well, not to be a downer, but wikipedia has some comments on the hazards...
Environmental effects

Tetrafluoromethane is a potent greenhouse
gas that
contributes to the greenhouse
effect.
It is very stable, has an atmospheric lifespan of 50,000 years, and a
high greenhouse
warming potential of
6500 (CO2  has a factor of 1);
however, the low amount in the atmosphere restricts the overall radiative
forcing  effect.

Although structurally similar to
chlorofluorocarbons
(CFCs),
tetrafluoromethane does not deplete the ozone
layer.
This is because the depletion is caused by the chlorine atoms in CFCs,
which dissociate when struck by UV radiation. Carbon-fluorine bonds are
stronger and less likely to dissociate. According to Guinness World
Records
Tetrafluoromethane
is the most persistent greenhouse gas.
[edit
]Health risks

Depending on the concentration, inhalation of tetrafluoromethane can cause
headaches, nausea, dizziness and damage to the cardiovascular
system (mainly
the heart). Long-term exposure can cause severe heart damage.

Due to its density, tetrafluoromethane can displace air, creating an
asphyxiation  hazard in
inadequately ventilated areas.

On Mon, May 21, 2012 at 5:08 PM, Jim Pflugrath wrote:

>  Here is a trick which I will attribute to Cambridge:
>
>  Fill balloon with gas.  Put end of balloon over 15 ml Falcon tube.  Put
> Falcon tube in LN2.  No wasted gas.
>
>  I would recommend CF4 or carbon tetrafluoride instead of propane though.
>  CF4 is cheap and non-dangerous.
>
>  Jim
>
>
>  --
> *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Prince,
> D Bryan [dbryan.pri...@astrazeneca.com]
> *Sent:* Monday, May 21, 2012 4:15 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Propane still?
>
>Good afternoon fellow ccp4bb’rs,
>
>
>
> I was wondering if anyone knows if a still to condense gaseous propane to
> liquid propane using dry ice is commercially available. I want to make sure
> that it is not something I can purchase before I build one fit to purpose.
> I appreciate any advice and knowledge you can share.
>
>
>
> Regards,
>
> Bryan Prince
>
>  --
>
> *Confidentiality Notice: *This message is private and may contain
> confidential and proprietary information. If you have received this message
> in error, please notify us and remove it from your system and note that you
> must not copy, distribute or take any action in reliance on it. Any
> unauthorized use or disclosure of the contents of this message is not
> permitted and may be unlawful.
>
>
>
>


-- 
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] Propane still?

[Jim Pflugrath]

Here is a trick which I will attribute to Cambridge:

Fill balloon with gas.  Put end of balloon over 15 ml Falcon tube.  Put Falcon 
tube in LN2.  No wasted gas.

I would recommend CF4 or carbon tetrafluoride instead of propane though.  CF4 
is cheap and non-dangerous.

Jim



From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Prince, D Bryan 
[dbryan.pri...@astrazeneca.com]
Sent: Monday, May 21, 2012 4:15 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Propane still?

Good afternoon fellow ccp4bb’rs,

I was wondering if anyone knows if a still to condense gaseous propane to 
liquid propane using dry ice is commercially available. I want to make sure 
that it is not something I can purchase before I build one fit to purpose. I 
appreciate any advice and knowledge you can share.

Regards,
Bryan Prince



Confidentiality Notice: This message is private and may contain confidential 
and proprietary information. If you have received this message in error, please 
notify us and remove it from your system and note that you must not copy, 
distribute or take any action in reliance on it. Any unauthorized use or 
disclosure of the contents of this message is not permitted and may be unlawful.

Re: [ccp4bb] Propane still?

[Jacob Keller]

So much easier is to simply loop your favorite tubing a couple of times
through a small N2 dewar, then direct the output into a 15mL tube immersed
in same. Or, simply point the tubing directly into the immersed tube, and
flow slowly. In both cases, the cold N2 will condense the propane. Of
course, don't cap the 15mL tube and remove from the N2 (it will obviously
explode!).

JPK

On Mon, May 21, 2012 at 4:15 PM, Prince, D Bryan <
dbryan.pri...@astrazeneca.com> wrote:

>  Good afternoon fellow ccp4bb’rs, 
>
> ** **
>
> I was wondering if anyone knows if a still to condense gaseous propane to
> liquid propane using dry ice is commercially available. I want to make sure
> that it is not something I can purchase before I build one fit to purpose.
> I appreciate any advice and knowledge you can share. 
>
> ** **
>
> Regards, 
>
> Bryan Prince
>
>  --
>
> *Confidentiality Notice: *This message is private and may contain
> confidential and proprietary information. If you have received this message
> in error, please notify us and remove it from your system and note that you
> must not copy, distribute or take any action in reliance on it. Any
> unauthorized use or disclosure of the contents of this message is not
> permitted and may be unlawful.
>
>
>
>


-- 
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] Serine

[Uma Ratu]

Thank you All for you inputs.

Uma

On Mon, May 21, 2012 at 5:06 PM, Van Den Berg, Bert <
lambertus.vandenb...@umassmed.edu> wrote:

>  Yes, as Jacob says, alternative conformation of the serine. Quite common.
>
> Bert
>  --
> *From:* CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Uma Ratu
> [rosiso2...@gmail.com]
> *Sent:* Monday, May 21, 2012 4:57 PM
>
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Serine
>
>   Dear All:
>
> Some of serine residues in my model have extra positive Fo-Fc density at
> the edge of side chain. Some don't have. It is not like from phosphates.
>
> I am wondered what is the cause for these extra density. Could these
> serines be post-translational modified?
>
> I have the images attached. P289ser-0512-1 does not have the extra green,
> where P140ser-0512-1 has.
>
> Thank you for you advice and comment
>
> Uma
>

[ccp4bb] Propane still?

[Prince, D Bryan]

Good afternoon fellow ccp4bb'rs,



I was wondering if anyone knows if a still to condense gaseous propane
to liquid propane using dry ice is commercially available. I want to
make sure that it is not something I can purchase before I build one fit
to purpose. I appreciate any advice and knowledge you can share.



Regards,

Bryan Prince


--
Confidentiality Notice: This message is private and may contain confidential 
and proprietary information. If you have received this message in error, please 
notify us and remove it from your system and note that you must not copy, 
distribute or take any action in reliance on it. Any unauthorized use or 
disclosure of the contents of this message is not permitted and may be unlawful.
 

Re: [ccp4bb] Serine

[Van Den Berg, Bert]

Yes, as Jacob says, alternative conformation of the serine. Quite common.

Bert

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Uma Ratu 
[rosiso2...@gmail.com]
Sent: Monday, May 21, 2012 4:57 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Serine

Dear All:

Some of serine residues in my model have extra positive Fo-Fc density at the 
edge of side chain. Some don't have. It is not like from phosphates.

I am wondered what is the cause for these extra density. Could these serines be 
post-translational modified?

I have the images attached. P289ser-0512-1 does not have the extra green, where 
P140ser-0512-1 has.

Thank you for you advice and comment

Uma

Re: [ccp4bb] Serine

[Jacob Keller]

I believe that's an alternative conformationtry modeling as such and
see what happens.

Jacob

On Mon, May 21, 2012 at 3:57 PM, Uma Ratu  wrote:

> Dear All:
>
> Some of serine residues in my model have extra positive Fo-Fc density at
> the edge of side chain. Some don't have. It is not like from phosphates.
>
> I am wondered what is the cause for these extra density. Could these
> serines be post-translational modified?
>
> I have the images attached. P289ser-0512-1 does not have the extra green,
> where P140ser-0512-1 has.
>
> Thank you for you advice and comment
>
> Uma
>



-- 
***
Jacob Pearson Keller
Northwestern University
Medical Scientist Training Program
email: j-kell...@northwestern.edu
***

Re: [ccp4bb] color for metal ions

[mjvdwoerd]

There is a really nice web site that shows how colors are perceived by various 
color-blind readers. One of the journals I recently published in recommends it 
for consideration. If you are interested, have a look. The web site is made 
especially for people who publish scientific articles with color illustrations. 
It is not hard to be considerate.

http://jfly.iam.u-tokyo.ac.jp/html/color_blind/

Mark



-Original Message-
From: Artem Evdokimov 
To: CCP4BB 
Sent: Sun, May 20, 2012 2:54 pm
Subject: Re: [ccp4bb] color for metal ions


As long as you are considerate of the needs of colorblind people, I would vote 
that anything goes.
Artem 
On May 20, 2012 3:17 PM, "sujata halder"  wrote:

Hi all,

I was wondering if there is a rule for coloring metal ions a specific color. I 
am using pymol and was not sure if I have to use a specific color for calcium 
or magnesium ions for publication figures.

Thanks,

Sujata 


 

Re: [ccp4bb] Generating low resolution density maps from atomic models

[Tim Gruene]

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Hello ,
sfall from ccp4 can do that.

Regards,
Tim

On 05/21/12 14:48, Krithika Sundaram wrote:
> Hi all,
> 
> Just wanted to ask if anyone has generated low resoultion density
> maps before? If yes, can anyone help me with this or point me in
> the right direction?
> 
> Thanks in advance for your help!
> 

- -- 
- --
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/

iD8DBQFPukbHUxlJ7aRr7hoRAmGRAKD/nm5pZaI7aSb4fdfSDuGVyb9o1wCfWIBt
c0HQ+WUr1dX3pVmQlMsVU6k=
=nzpu
-END PGP SIGNATURE-

[ccp4bb] X-ray Crystallography Research Associate Position at Novartis in Cambridge, MA

[Sprague, Elizabeth]

Research Associate - X-ray crystallography

Job Description
The candidate will join a state-of-the art unit that provides structural 
biology information to expedite drug discovery projects undertaken at the NIBR 
Cambridge campus. The candidate will be part of the biomolecular structure 
group responsible for expression, purification, crystallization and structure 
determination of proteins and protein-ligand complexes. The candidate will be 
expected to be able to participate in experimental design and to independently 
conduct experiments in a priority-driven environment.

Minimum Requirements
B.S/M.S. in biochemistry or a related discipline with at least 2 years of 
research laboratory experience. Experience in protein chemistry (e.g. 
expression, purification and characterization) is required. Experience with 
crystallization, x-ray data collection, structure solution and/or biophysical 
characterization of proteins would be a decided asset.  The candidate must 
possess good oral and written communication skills and work well in a team.

For immediate consideration, please apply on-line at 
http://www.novartis.com/careers using Job Code 97236BR.  Novartis is committed 
to embracing and leveraging diverse backgrounds, cultures, and talents to 
achieve competitive advantage.  Novartis is an equal opportunity employer.  
M/F/D/V

[ccp4bb] Generating low resolution density maps from atomic models

[Krithika Sundaram]

Hi all,

Just wanted to ask if anyone has generated low resoultion density maps before? 
If yes, can anyone help me with this or point me in the right direction?

Thanks in advance for your help!

Re: [ccp4bb] problem in mtz2various

[Ian Clifton]

Sita Ram Meena  writes:

>Hello everyone
> I Was trying to convert my mtz output of the SCALA to CNS format in
>mtz2various but its gives some error
>please look at log file 

[...]

> Data line--- OUTPUT CNS
> Data line--- labin  FP=F_New SIGFP=SIGF_New FPH=F_New SIGFPH=SIGF_New
>DP=DANO_New SIGDP=SIGDANO_New FREE=FreeR_flag F(+)=F_New(+)
>SIGF(+)=SIGF_New(+) F(-)=F_New(+) SIGF(-)=SIGF_New(+)

[...]

>/home/ajay/programs/ccp4/ccp4-6.2.0/lib/data/syminfo.lib
> MTZ2VARIOUS:   *** You are inputting F(+) AND  FP  - incompatible ***

[...]

This just means you have to choose one of the sets {FP, SIGFP, DP,
SIGDP} or {F(+), F(-) SIGF(+), SIGF(-)} — you can’t have both.
-- 
Ian Clifton ⚗ Phone: +44 1865 275677
Chemistry Research Laboratory Fax:   +44 1865 285002
Oxford University ian.clif...@chem.ox.ac.uk
Mansfield Road   Oxford OX1 3TA   UK

[ccp4bb] X-ray Crystalographer Position - Evotec

[Richenburg, Alexandra]

 

 

 

Senior Scientist

X-Ray Crystallographer within our Structural Biology Department

 

 

Salary: £26,000 - £39,000 + benefits

Location: Oxfordshire, UK

Full time; Permanent or Temporary

Must be eligible to work in UK

 

 

Evotec (UK) Ltd is currently seeking an X-Ray Crystallographer for our 
Structural Biology Department based in Oxfordshire. X-Ray Crystallography works 
closely with our Discovery Chemistry Department and with clients to develop 
novel small molecule drugs.  The group is at the forefront of new science and 
technology, and is seeking to expand as business need grows.

 

The successful candidates will be part of the Structural Biology group 
responsible for expression, purification, crystallisation and structure 
determination of proteins and protein-ligand complexes. Knowledge of state of 
the art crystallographic methods is a must, along with skills in molecular 
biology and protein purification. Expertise in protein-ligand complex 
crystallisation problems would be an advantage though not essential.


You will have excellent written and verbal communication skills and will be a 
strong team player. Dynamic and innovative, you will be a self-starter with a 
flexible approach who enjoys a challenge. 


You will be PhD qualified or equivalent in Chemistry, Biochemistry, Molecular 
Biology or Biophysics, with experience in protein X-ray crystallography. 
Candidates will also be considered who have a Masters degree with extensive 
experience or equivalent.


We offer competitive salaries plus extensive benefits including annual bonus, 
pension plan, private medical and dental cover. 

 

If you feel that your skills and experience match what we are looking for, 
please apply via the website: http://www.evotec.com 

 

 


Evotec (UK) Ltd is a limited company registered in England and Wales. 
Registration number:2674265. Registered office: 114 Milton Park, Abingdon, 
Oxfordshire, OX14 4SA, United Kingdom.
<>

[ccp4bb] problem in mtz2various

[Sita Ram Meena]

Hello everyone

* *I Was trying to convert my mtz output of the SCALA to CNS format in
mtz2various but its gives some error

please look at log file 


 CCP4 6.2: MTZ2VARIOUS  version 6.2 : 17/08/09##

 User: unknown  Run date: 21/ 5/2012 Run time: 11:53:39


 Please reference: Collaborative Computational Project, Number 4. 1994.
 "The CCP4 Suite: Programs for Protein Crystallography". Acta Cryst. D50,
760-763.
 as well as any specific reference in the program write-up.

 Data line--- OUTPUT CNS
 Data line--- labin  FP=F_New SIGFP=SIGF_New FPH=F_New SIGFPH=SIGF_New
DP=DANO_New SIGDP=SIGDANO_New FREE=FreeR_flag F(+)=F_New(+)
SIGF(+)=SIGF_New(+) F(-)=F_New(+) SIGF(-)=SIGF_New(+)
 Data line--- end

FORMATTED  UNKNOWN file opened on unit  22
Logical name: HKLOUT, Filename:
/home/ajay/Desktop/cns/p212121-.2moz_scala2.hkl

 XPLOR/CNS output to ASCII file assigned to HKLOUT
 - format(A,3i5,A,f10.1,f10.1,A,f10.2,A,i6)

FORMATTED  SCRATCH file opened on unit  23
Logical name: MTZ2VSCR, Filename: /tmp/ajay/mtz2various_TMP.04363


 OPENED INPUT MTZ FILE
 Logical Name: HKLIN   Filename:
/home/ajay/Desktop/dpre3x6/allmtz_after_ICTP/p212121-.2moz_scala1.mtz

 * Title:

 [No title given]

 * Base dataset:

0 HKL_base
  HKL_base
  HKL_base

 * Number of Datasets = 1

 * Dataset ID, project/crystal/dataset names, cell dimensions, wavelength:

1 New
  New
  New
136.2400  261.8300  282.2798   90.   90.   90.
 0.97372

 * Number of Columns = 19

 * Number of Reflections = 261993

 * Missing value set to NaN in input mtz file

 * Column Labels :

 H K L FreeR_flag F_New SIGF_New DANO_New SIGDANO_New F_New(+) SIGF_New(+)
F_New(-) SIGF_New(-) ISYM_New IMEAN_New SIGIMEAN_New I_New(+) SIGI_New(+)
I_New(-) SIGI_New(-)

 * Column Types :

 H H H I F Q D Q G L G L Y J Q K M K M

 * Associated datasets :

 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1

 * Cell Dimensions : (obsolete - refer to dataset cell dimensions above)

  136.2400  261.8300  282.2798   90.   90.   90.

 *  Resolution Range :

0.30.13252 (191.965 -  2.747 A )

 * Sort Order :

  1 2 3 0 0

 * Space group = 'P 21 21 21' (number 19)

  (spacegroup is known)


 Spacegroup information obtained from library file:
 Logical Name: SYMINFO   Filename:
/home/ajay/programs/ccp4/ccp4-6.2.0/lib/data/syminfo.lib

 MTZ2VARIOUS:   *** You are inputting F(+) AND  FP  - incompatible ***
Times: User:   0.0s System:0.0s Elapsed: 0:00


***
* Information from CCP4Interface script
***
The program run with command:
/home/ajay/programs/ccp4/ccp4-6.2.0/bin/mtz2various HKLIN
"/home/ajay/Desktop/dpre3x6/allmtz_after_ICTP/p212121-.2moz_scala1.mtz"
HKLOUT "/home/ajay/Desktop/cns/p212121-.2moz_scala2.hkl"
has failed with error message
 MTZ2VARIOUS:   *** You are inputting F(+) AND  FP  - incompatible ***
***


#CCP4I TERMINATION STATUS 0 " MTZ2VARIOUS:   *** You are inputting F(+)
AND  FP  - incompatible ***"
#CCP4I TERMINATION TIME 21 May 2012  11:53:39
#CCP4I MESSAGE Task failed


Thanks
best regards

Sita Ram