Re: [ccp4bb] Regarding Patents

2017-11-03 Thread Francisco Tenjo 
You cannot patent the “binding site” because it is found in nature (you did
not invent it, you discovered it and patents are only granted for
inventions). I think you could patent compounds that bind that site if they
are not the exact natural ligands.

- Francisco

On Fri, Nov 3, 2017 at 9:14 PM Cheng Zhang  wrote:

>
> A related question. If you have a crystal structure and found a novel
> ligand binding site that can be used to regulate protein activity, could
> you patent such "binding site"? If not, how to make the best use of such
> findings?
>
> Thanks!
>
> Cheng
>
> On Sat, Nov 4, 2017 at 12:33 AM, James Phillips <
> phillipsjames...@gmail.com> wrote:
>
>> Realistically, if you live in the US and 5 SCOTUS judges agree you can
>> patent anything.
>>
>> On Fri, Nov 3, 2017 at 09:45 Francisco Tenjo  wrote:
>>
>>> Hi.
>>>
>>> A mutated DNA or protein molecule can be patented if the mutations are
>>> not present in nature and they have a technical effect (for example, in the
>>> case of antibodies, you could have increased affinity for an antigen if you
>>> make the right mutations of the CDRs). Also, the mutations should not have
>>> been published before you file your patent application.
>>>
>>> Regards,
>>>
>>> - Francisco
>>>
>>> 2017-11-03 6:26 GMT-04:00 Chris Morris :
>>>
 > Sorry for asking out of context question. Can a mutated DNA or
 protein molecule be patented.

 Yes and no. A molecule as such cannot be patented. But the use of a
 molecule for a specific purpose can be. There are many patents for small
 molecule drugs, and also for engineered antibodies, which are proteins.
 There are patents for industrial use of enzymes too.

 regards,
 Chris
 
 Chris Morris
 chris.mor...@stfc.ac.uk
 Tel: +44 (0)1925 603689  Fax: +44 (0)1925 603634
 Mobile: 07921-717915
 Skype: chrishgmorris
 http://www.citeulike.org/blog/chrishmorris
 STFC, Daresbury Laboratory, Sci-Tech Daresbury, Keckwick Lane,
 Daresbury, Warrington, WA4 4AD UK

>>>
>>>
>>>
>>> --
>>> Francisco Tenjo
>>>
>>
>
>
> --
> -
> Cheng Zhang
>
-- 
Francisco Tenjo

Re: [ccp4bb] Regarding Patents

2017-11-03 Thread Cheng Zhang 
A related question. If you have a crystal structure and found a novel
ligand binding site that can be used to regulate protein activity, could
you patent such "binding site"? If not, how to make the best use of such
findings?

Thanks!

Cheng

On Sat, Nov 4, 2017 at 12:33 AM, James Phillips 
wrote:

> Realistically, if you live in the US and 5 SCOTUS judges agree you can
> patent anything.
>
> On Fri, Nov 3, 2017 at 09:45 Francisco Tenjo  wrote:
>
>> Hi.
>>
>> A mutated DNA or protein molecule can be patented if the mutations are
>> not present in nature and they have a technical effect (for example, in the
>> case of antibodies, you could have increased affinity for an antigen if you
>> make the right mutations of the CDRs). Also, the mutations should not have
>> been published before you file your patent application.
>>
>> Regards,
>>
>> - Francisco
>>
>> 2017-11-03 6:26 GMT-04:00 Chris Morris :
>>
>>> > Sorry for asking out of context question. Can a mutated DNA or protein
>>> molecule be patented.
>>>
>>> Yes and no. A molecule as such cannot be patented. But the use of a
>>> molecule for a specific purpose can be. There are many patents for small
>>> molecule drugs, and also for engineered antibodies, which are proteins.
>>> There are patents for industrial use of enzymes too.
>>>
>>> regards,
>>> Chris
>>> 
>>> Chris Morris
>>> chris.mor...@stfc.ac.uk
>>> Tel: +44 (0)1925 603689  Fax: +44 (0)1925 603634
>>> Mobile: 07921-717915
>>> Skype: chrishgmorris
>>> http://www.citeulike.org/blog/chrishmorris
>>> STFC, Daresbury Laboratory, Sci-Tech Daresbury, Keckwick Lane,
>>> Daresbury, Warrington, WA4 4AD UK
>>>
>>
>>
>>
>> --
>> Francisco Tenjo
>>
>


-- 
-
Cheng Zhang

Re: [ccp4bb] Regarding Patents

2017-11-03 Thread James Phillips 
Realistically, if you live in the US and 5 SCOTUS judges agree you can
patent anything.

On Fri, Nov 3, 2017 at 09:45 Francisco Tenjo  wrote:

> Hi.
>
> A mutated DNA or protein molecule can be patented if the mutations are not
> present in nature and they have a technical effect (for example, in the
> case of antibodies, you could have increased affinity for an antigen if you
> make the right mutations of the CDRs). Also, the mutations should not have
> been published before you file your patent application.
>
> Regards,
>
> - Francisco
>
> 2017-11-03 6:26 GMT-04:00 Chris Morris :
>
>> > Sorry for asking out of context question. Can a mutated DNA or protein
>> molecule be patented.
>>
>> Yes and no. A molecule as such cannot be patented. But the use of a
>> molecule for a specific purpose can be. There are many patents for small
>> molecule drugs, and also for engineered antibodies, which are proteins.
>> There are patents for industrial use of enzymes too.
>>
>> regards,
>> Chris
>> 
>> Chris Morris
>> chris.mor...@stfc.ac.uk
>> Tel: +44 (0)1925 603689  Fax: +44 (0)1925 603634
>> Mobile: 07921-717915
>> Skype: chrishgmorris
>> http://www.citeulike.org/blog/chrishmorris
>> STFC, Daresbury Laboratory, Sci-Tech Daresbury, Keckwick Lane, Daresbury,
>> Warrington, WA4 4AD UK
>>
>
>
>
> --
> Francisco Tenjo
>

Re: [ccp4bb] another unknown density problem

2017-11-03 Thread Eleanor Dodson 
Well - I would stick in waters - they can be very well rdered in certain
environments.
Anecote: We have spent ages trying to put some interesting compound into a
"feature" in maps,
untill the crystals finally diffracted to 1.6A and in that map it is very
clear there are 4 beautifully shaped waters, with lots of hydrogen bonds to
the surrounding amino acides..

So all that intelligent interpretation was unnecessary!
Eleanor


On 3 November 2017 at 21:02, Abhishek Anan 
wrote:

> Dear all,
>
> My apology for the confusion!! I did mean the map radius is "truncated" at
> 5A. Poor choice of words :(
>
> Any thoughts on what this density could be are still welcome.
>
> Best regards,
> Abhishek
>
> On Fri, Nov 3, 2017 at 9:21 PM, Joern Krausze <
> j.krau...@tu-braunschweig.de> wrote:
>
>> Dear all,
>>
>> I think Abhishek means that the picture shows 5 A map radius.
>>
>> Best
>> Joern
>>
>> On 3. Nov 2017, at 18:42, Pavel Afonine  wrote:
>>
>> If by "it was truncated at 5A for clarity" you really mean you truncated
>> all low-resolution data from 5A and lower then I am not surprised you see
>> funny densities all over or don't see density where it is expected. Why?
>> Consult a textbook for the answer.
>>
>> All the best,
>> Pavel
>>
>> On Fri, Nov 3, 2017 at 3:10 AM, Abhishek Anan 
>> wrote:
>>
>>> Dear Prof Schreuder
>>>
>>> Here are another couple of perspectives from coot. The density is too
>>> far and isolated from the peptide chain to be an alternate conformation or
>>> conformational change. The density of the peptide chain does not look good
>>> because it was truncated at 5A for clarity.
>>>
>>> Best regards
>>> Abhishek
>>>
>>> On Fri, Nov 3, 2017 at 9:33 AM,  wrote:
>>>
 Dear Abhishek,



 To me, it looks like an alternative conformation of the peptide chain
 or maybe even a conformational change with respect to the starting model.
 The peptide chain does not look too well defined, despite high resolution
 electron density.



 Best,

 Herman



 *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag
 von *Abhishek Anan
 *Gesendet:* Freitag, 3. November 2017 09:26
 *An:* CCP4BB@JISCMAIL.AC.UK
 *Betreff:* [EXTERNAL] [ccp4bb] another unknown density problem



 Hi all,

 I have an "unknown" density in the map. I have tried to fit it to PEG
 but it doesn't fit very well. I was wondering if there are other
 PEG-related or other molecules I could try.

 The crystal grew in TRIS-HCl and PEG MME 2K.

 Thank you

 Abhishek

>>>
>>>
>>
>>
>

Re: [ccp4bb] another unknown density problem

2017-11-03 Thread Abhishek Anan 
Dear all,

My apology for the confusion!! I did mean the map radius is "truncated" at
5A. Poor choice of words :(

Any thoughts on what this density could be are still welcome.

Best regards,
Abhishek

On Fri, Nov 3, 2017 at 9:21 PM, Joern Krausze 
wrote:

> Dear all,
>
> I think Abhishek means that the picture shows 5 A map radius.
>
> Best
> Joern
>
> On 3. Nov 2017, at 18:42, Pavel Afonine  wrote:
>
> If by "it was truncated at 5A for clarity" you really mean you truncated
> all low-resolution data from 5A and lower then I am not surprised you see
> funny densities all over or don't see density where it is expected. Why?
> Consult a textbook for the answer.
>
> All the best,
> Pavel
>
> On Fri, Nov 3, 2017 at 3:10 AM, Abhishek Anan 
> wrote:
>
>> Dear Prof Schreuder
>>
>> Here are another couple of perspectives from coot. The density is too far
>> and isolated from the peptide chain to be an alternate conformation or
>> conformational change. The density of the peptide chain does not look good
>> because it was truncated at 5A for clarity.
>>
>> Best regards
>> Abhishek
>>
>> On Fri, Nov 3, 2017 at 9:33 AM,  wrote:
>>
>>> Dear Abhishek,
>>>
>>>
>>>
>>> To me, it looks like an alternative conformation of the peptide chain or
>>> maybe even a conformational change with respect to the starting model. The
>>> peptide chain does not look too well defined, despite high resolution
>>> electron density.
>>>
>>>
>>>
>>> Best,
>>>
>>> Herman
>>>
>>>
>>>
>>> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag
>>> von *Abhishek Anan
>>> *Gesendet:* Freitag, 3. November 2017 09:26
>>> *An:* CCP4BB@JISCMAIL.AC.UK
>>> *Betreff:* [EXTERNAL] [ccp4bb] another unknown density problem
>>>
>>>
>>>
>>> Hi all,
>>>
>>> I have an "unknown" density in the map. I have tried to fit it to PEG
>>> but it doesn't fit very well. I was wondering if there are other
>>> PEG-related or other molecules I could try.
>>>
>>> The crystal grew in TRIS-HCl and PEG MME 2K.
>>>
>>> Thank you
>>>
>>> Abhishek
>>>
>>
>>
>
>

Re: [ccp4bb] another unknown density problem

2017-11-03 Thread Joern Krausze 
Dear all,

I think Abhishek means that the picture shows 5 A map radius.

Best
Joern

> On 3. Nov 2017, at 18:42, Pavel Afonine  wrote:
> 
> If by "it was truncated at 5A for clarity" you really mean you truncated all 
> low-resolution data from 5A and lower then I am not surprised you see funny 
> densities all over or don't see density where it is expected. Why? Consult a 
> textbook for the answer.
> 
> All the best,
> Pavel
> 
> On Fri, Nov 3, 2017 at 3:10 AM, Abhishek Anan  > wrote:
> Dear Prof Schreuder
> 
> Here are another couple of perspectives from coot. The density is too far and 
> isolated from the peptide chain to be an alternate conformation or 
> conformational change. The density of the peptide chain does not look good 
> because it was truncated at 5A for clarity. 
> 
> Best regards
> Abhishek
> 
> On Fri, Nov 3, 2017 at 9:33 AM,  > wrote:
> Dear Abhishek,
> 
>  
> 
> To me, it looks like an alternative conformation of the peptide chain or 
> maybe even a conformational change with respect to the starting model. The 
> peptide chain does not look too well defined, despite high resolution 
> electron density.
> 
>  
> 
> Best,
> 
> Herman
> 
>  
> 
> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK 
> ] Im Auftrag von Abhishek Anan
> Gesendet: Freitag, 3. November 2017 09:26
> An: CCP4BB@JISCMAIL.AC.UK 
> Betreff: [EXTERNAL] [ccp4bb] another unknown density problem
> 
>  
> 
> Hi all,
> 
> I have an "unknown" density in the map. I have tried to fit it to PEG but it 
> doesn't fit very well. I was wondering if there are other PEG-related or 
> other molecules I could try.
> 
> The crystal grew in TRIS-HCl and PEG MME 2K.
> 
> Thank you
> 
> Abhishek
> 
> 
>

Re: [ccp4bb] another unknown density problem

2017-11-03 Thread Pavel Afonine 
If by "it was truncated at 5A for clarity" you really mean you truncated
all low-resolution data from 5A and lower then I am not surprised you see
funny densities all over or don't see density where it is expected. Why?
Consult a textbook for the answer.

All the best,
Pavel

On Fri, Nov 3, 2017 at 3:10 AM, Abhishek Anan 
wrote:

> Dear Prof Schreuder
>
> Here are another couple of perspectives from coot. The density is too far
> and isolated from the peptide chain to be an alternate conformation or
> conformational change. The density of the peptide chain does not look good
> because it was truncated at 5A for clarity.
>
> Best regards
> Abhishek
>
> On Fri, Nov 3, 2017 at 9:33 AM,  wrote:
>
>> Dear Abhishek,
>>
>>
>>
>> To me, it looks like an alternative conformation of the peptide chain or
>> maybe even a conformational change with respect to the starting model. The
>> peptide chain does not look too well defined, despite high resolution
>> electron density.
>>
>>
>>
>> Best,
>>
>> Herman
>>
>>
>>
>> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag
>> von *Abhishek Anan
>> *Gesendet:* Freitag, 3. November 2017 09:26
>> *An:* CCP4BB@JISCMAIL.AC.UK
>> *Betreff:* [EXTERNAL] [ccp4bb] another unknown density problem
>>
>>
>>
>> Hi all,
>>
>> I have an "unknown" density in the map. I have tried to fit it to PEG but
>> it doesn't fit very well. I was wondering if there are other PEG-related or
>> other molecules I could try.
>>
>> The crystal grew in TRIS-HCl and PEG MME 2K.
>>
>> Thank you
>>
>> Abhishek
>>
>
>

Re: [ccp4bb] AW: Re: [ccp4bb] another unknown density problem

2017-11-03 Thread Gloria Borgstahl 
If you mean you truncated the low resolution data to 5 angstrom, I
wouldn't recommend that.

On Fri, Nov 3, 2017 at 12:24 PM, Eleanor Dodson
 wrote:
> That map does not look like a 5A map?
> I guess you mean something else..
> Eleanor
>
> On 3 November 2017 at 11:00,  wrote:
>>
>> You are right. In this case, I would put some waters in it, refine and see
>> if the density gets any clearer. However, since from this perspective the
>> density is quite far away from the protein, it could be a very disordered
>> PEG, which, even at high resolution, might be impossible to fit.
>>
>>
>>
>> Best,
>>
>> Herman
>>
>>
>>
>> Von: Abhishek Anan [mailto:rendezvous.a...@gmail.com]
>> Gesendet: Freitag, 3. November 2017 11:10
>> An: Schreuder, Herman /DE
>> Cc: CCP4BB@jiscmail.ac.uk
>> Betreff: [EXTERNAL] Re: [ccp4bb] another unknown density problem
>>
>>
>>
>> Dear Prof Schreuder
>>
>> Here are another couple of perspectives from coot. The density is too far
>> and isolated from the peptide chain to be an alternate conformation or
>> conformational change. The density of the peptide chain does not look good
>> because it was truncated at 5A for clarity.
>>
>> Best regards
>>
>> Abhishek
>>
>>
>>
>> On Fri, Nov 3, 2017 at 9:33 AM,  wrote:
>>
>> Dear Abhishek,
>>
>>
>>
>> To me, it looks like an alternative conformation of the peptide chain or
>> maybe even a conformational change with respect to the starting model. The
>> peptide chain does not look too well defined, despite high resolution
>> electron density.
>>
>>
>>
>> Best,
>>
>> Herman
>>
>>
>>
>> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von
>> Abhishek Anan
>> Gesendet: Freitag, 3. November 2017 09:26
>> An: CCP4BB@JISCMAIL.AC.UK
>> Betreff: [EXTERNAL] [ccp4bb] another unknown density problem
>>
>>
>>
>> Hi all,
>>
>> I have an "unknown" density in the map. I have tried to fit it to PEG but
>> it doesn't fit very well. I was wondering if there are other PEG-related or
>> other molecules I could try.
>>
>> The crystal grew in TRIS-HCl and PEG MME 2K.
>>
>> Thank you
>>
>> Abhishek
>>
>>
>
>

Re: [ccp4bb] AW: Re: [ccp4bb] another unknown density problem

2017-11-03 Thread Eleanor Dodson 
That map does not look like a 5A map?
I guess you mean something else..
Eleanor

On 3 November 2017 at 11:00,  wrote:

> You are right. In this case, I would put some waters in it, refine and see
> if the density gets any clearer. However, since from this perspective the
> density is quite far away from the protein, it could be a very disordered
> PEG, which, even at high resolution, might be impossible to fit.
>
>
>
> Best,
>
> Herman
>
>
>
> *Von:* Abhishek Anan [mailto:rendezvous.a...@gmail.com]
> *Gesendet:* Freitag, 3. November 2017 11:10
> *An:* Schreuder, Herman /DE
> *Cc:* CCP4BB@jiscmail.ac.uk
> *Betreff:* [EXTERNAL] Re: [ccp4bb] another unknown density problem
>
>
>
> Dear Prof Schreuder
>
> Here are another couple of perspectives from coot. The density is too far
> and isolated from the peptide chain to be an alternate conformation or
> conformational change. The density of the peptide chain does not look good
> because it was truncated at 5A for clarity.
>
> Best regards
>
> Abhishek
>
>
>
> On Fri, Nov 3, 2017 at 9:33 AM,  wrote:
>
> Dear Abhishek,
>
>
>
> To me, it looks like an alternative conformation of the peptide chain or
> maybe even a conformational change with respect to the starting model. The
> peptide chain does not look too well defined, despite high resolution
> electron density.
>
>
>
> Best,
>
> Herman
>
>
>
> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag von
> *Abhishek Anan
> *Gesendet:* Freitag, 3. November 2017 09:26
> *An:* CCP4BB@JISCMAIL.AC.UK
> *Betreff:* [EXTERNAL] [ccp4bb] another unknown density problem
>
>
>
> Hi all,
>
> I have an "unknown" density in the map. I have tried to fit it to PEG but
> it doesn't fit very well. I was wondering if there are other PEG-related or
> other molecules I could try.
>
> The crystal grew in TRIS-HCl and PEG MME 2K.
>
> Thank you
>
> Abhishek
>
>
>

[ccp4bb] software to map surface residues

2017-11-03 Thread Kai Zhou 
Hello, is there an existing program that can extract the 3D coordinates of
the surface residues of a given protein/PDB file? Thanks so much~~

Kai

Buck Institute

[ccp4bb] EMBO Practical Course CEM3DIP 2018: of macromolecular assemblies and cellular tomography

2017-11-03 Thread Natesh Ramanathan 
*Second  Announcement:*


*Applicants from all over the world are eligible to apply.  Applicants from
EMBC member states  (http://www.embo.org/about-embo/member-states
) are in
particular encouraged  to apply.*


*EMBO Practical course Cryo Electron Microscopy and 3 Dimensional Image
Processing (CEM3DIP2018): **of Macromolecular assemblies and Cellular
tomography*

*18-29 March, 2018, at IIT Delhi, New Delhi, India.*


The *EMBO Practical Course *Cryo Electron Microscopy and 3
Dimensional Image Processing (*CEM3DIP 2018): of macromolecular assemblies
and cellular tomography* will be held at  IIT Delhi
 in New Delhi
, India.  This is an extensive 10
day course that will be held  from 18  March – 29 March 2018 at IIT Delhi
(with a 1 day break, to chill out at the backdrops of
Taj Mahal
, one of the seven wonders of
world).


For Course details  and to apply online go to the URL :


http://meetings.embo.org/event/18-
cem3dip




 Important dates :

*Registration Deadline : 15 November 2017*


   The course will focus on structural biology using Transmission
Electron Microscopy and aims to teach the participants the basic principles
and practical aspects of specimen preparation, Image processing and 3D
reconstruction in Single Particle Cryo Electron Microscopy(SPCryoEM) and
Cellular Tomography.  This is a hands-on course, in which theory and
practicals are tightly intertwined.  There will be practical session to
teach sample preparation for Single particle –ve stain and cryoEM.   The
topics covered will suit both the new entrants to the field as well as
those who wants to acquire an in-depth understanding  of  the fundamental
principles and practical aspects.   Applications are invited from PhD
students, Post Docs and Researchers (Faculties/PI’s and protein
crystallographers) who wish to acquire knowledge in SPCryoEM and Cellular
Tomography.  Applicants from all over the world are encouraged to
apply.  For more information please contact the course organizer at
*cem3dip2...@iisertvm.ac.in
*.


*The basic format of the course* will be theoretical lectures
in the mornings followed by hands on practical session on specimen
preparation and image processing on computer workstations in the afternoon.
  Evenings will be reserved for poster presentations by the participants
and research talks by the participants/instructors.


*The instructors/speakers for the course will include:*  Wah Chiu (Stanford
University), Jack Johnson (TSRI), Marin van Heel (Leiden University),
Edward Morris (ICR), Paula da Fonseca (MRC-LMB), Peter Rosenthal (TFCI),
Carsten Sachse (EMBL Heidelberg), Sara Sandin (NTU), Ardan Patwardhan
(EMBL-EBI), Maya Topf (Birkbeck), Srinivasan N (IISc), Tanmay Bharath (Dunn
School of Pathology), Agnel Praveen (Birkbeck), Tanveer
Hussain(IISc), Sonja Welsh (FEI - part of Thermo Fisher Scientific), Jayati
Sengupta (IICB), Manidipa Banerjee (IIT Delhi), Ramanathan Natesh (IISER
Thiruvananthapuram), Vinothkumar KR(NCBS), Partha Pratim Datta (IISER
Kolkota), Somnath Dutta (IISc).


For more details and to apply for this course kindly visit the course
website *http://meetings.embo.org/event/18-cem3dip*
*. *

The selection will be based on applicants CV, current research project,
relevant skills, future plans and most importantly the quality of the
submitted poster  abstract.  Applicants should include in the section “Current
research Project and Statement of Purpose” an explanation of why attendance
at the course would further the applicant's own research.   Having some
preliminary data or exposure to electron microscopy /cryoEM/ tomography
will be preferred.  PhD and Postdoctoral applicants should request their
supervisor to send a recommendation letter, before the application
deadline, by e-mail directly to the organizer at cem3dip2...@iisertvm.ac.in.
  Only selected people from the applicants will be contacted.  Based on
availability of funds, travel and/or registration, accommodation bursaries
for subset of selected applicants can be provided.  If you want to request
for registration and/or accommodation bursaries, mention that explicityly
in the space for ‘Justification for Travel Grant’ and Justify your
request.   All
registered participants have to present posters on their research work.  A
selection of participants will be invited to give oral presentation of
their ongoing research work.


We shall truly appreciate if this e-mail print out can be displayed at your
Institute notice board and

Re: [ccp4bb] Regarding Patents

2017-11-03 Thread Francisco Tenjo 
Hi.

A mutated DNA or protein molecule can be patented if the mutations are not
present in nature and they have a technical effect (for example, in the
case of antibodies, you could have increased affinity for an antigen if you
make the right mutations of the CDRs). Also, the mutations should not have
been published before you file your patent application.

Regards,

- Francisco

2017-11-03 6:26 GMT-04:00 Chris Morris :

> > Sorry for asking out of context question. Can a mutated DNA or protein
> molecule be patented.
>
> Yes and no. A molecule as such cannot be patented. But the use of a
> molecule for a specific purpose can be. There are many patents for small
> molecule drugs, and also for engineered antibodies, which are proteins.
> There are patents for industrial use of enzymes too.
>
> regards,
> Chris
> 
> Chris Morris
> chris.mor...@stfc.ac.uk
> Tel: +44 (0)1925 603689  Fax: +44 (0)1925 603634
> Mobile: 07921-717915
> Skype: chrishgmorris
> http://www.citeulike.org/blog/chrishmorris
> STFC, Daresbury Laboratory, Sci-Tech Daresbury, Keckwick Lane, Daresbury,
> Warrington, WA4 4AD UK
>



-- 
Francisco Tenjo

[ccp4bb] AW: Re: [ccp4bb] another unknown density problem

2017-11-03 Thread Herman . Schreuder 
You are right. In this case, I would put some waters in it, refine and see if 
the density gets any clearer. However, since from this perspective the density 
is quite far away from the protein, it could be a very disordered PEG, which, 
even at high resolution, might be impossible to fit.

Best,
Herman

Von: Abhishek Anan [mailto:rendezvous.a...@gmail.com]
Gesendet: Freitag, 3. November 2017 11:10
An: Schreuder, Herman /DE
Cc: CCP4BB@jiscmail.ac.uk
Betreff: [EXTERNAL] Re: [ccp4bb] another unknown density problem

Dear Prof Schreuder
Here are another couple of perspectives from coot. The density is too far and 
isolated from the peptide chain to be an alternate conformation or 
conformational change. The density of the peptide chain does not look good 
because it was truncated at 5A for clarity.
Best regards
Abhishek

On Fri, Nov 3, 2017 at 9:33 AM, 
> wrote:
Dear Abhishek,

To me, it looks like an alternative conformation of the peptide chain or maybe 
even a conformational change with respect to the starting model. The peptide 
chain does not look too well defined, despite high resolution electron density.

Best,
Herman

Von: CCP4 bulletin board 
[mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von 
Abhishek Anan
Gesendet: Freitag, 3. November 2017 09:26
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] another unknown density problem

Hi all,
I have an "unknown" density in the map. I have tried to fit it to PEG but it 
doesn't fit very well. I was wondering if there are other PEG-related or other 
molecules I could try.
The crystal grew in TRIS-HCl and PEG MME 2K.
Thank you
Abhishek

[ccp4bb] CryoEM postdoctoral position at the Wellcome Centre for Cell Biology, Edinburgh, UK | Corrected weblink

2017-11-03 Thread ARULANANDAM Jeyaprakash 
A Wellcome Trust funded postdoctoral position is available in Jeyapraksh (JP) 
Arulanandam’s lab at the Wellcome Centre for Cell Biology, University of 
Edinburgh. The JP lab (http://jeyaprakash.ed.ac.uk) aims to understand the 
structural level mechanistic details of processes regulating error-free 
chromosome segregation. The successful candidate will combine protein 
biochemistry and structural biology with mammalian cell based assays to dissect 
the molecular details of how specific intermolecular protein interactions 
achieve stable centromere maintenance and accurate chromosome segregation 
during cell division.

Applicants must have a PhD (or will shortly be awarded a PhD) with training in 
biochemistry and structural biology. The successful candidate will be a highly 
motivated and enthusiastic individual with an outstanding academic track 
record, good communication skills and the ability to work as a team. Applicants 
with experience in single particle cryoEM and biochemistry are encouraged to 
apply.

The post is for 24 months in the first instance with a possibility of extension.

Closing Date: 01Dec 2017 at 5pm GMT

For further particulars and to apply for this post, please follow 
https://www.vacancies.ed.ac.uk/pls/corehrrecruit/erq_jobspec_version_4.jobspec?p_id=041812


Dr. A. Jeyaprakash Arulanandam
Wellcome Senior Research Fellow
Wellcome Trust Centre for Cell Biology
University of Edinburgh
Michael Swann Building
Max Born Crescent
Edinburgh EH9 3BF
Tel: +44 131 6507113
Fax: +44 131 6080414
Web: http://jeyaprakash.bio.ed.ac.uk/




The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

[ccp4bb] CryoEM postdoctoral position at the Wellcome Centre for Cell Biology, Edinburgh, UK

2017-11-03 Thread ARULANANDAM Jeyaprakash 
A Wellcome Trust funded postdoctoral position is available in Jeyapraksh (JP) 
Arulanandam’s lab at the Wellcome Centre for Cell Biology, University of 
Edinburgh. The JP lab (http://jeyaprakash.ed.ac.uk) aims to understand the 
structural level mechanistic details of processes regulating error-free 
chromosome segregation. The successful candidate will combine protein 
biochemistry and structural biology with mammalian cell based assays to dissect 
the molecular details of how specific intermolecular protein interactions 
achieve stable centromere maintenance and accurate chromosome segregation 
during cell division.

Applicants must have a PhD (or will shortly be awarded a PhD) with training in 
biochemistry and structural biology. The successful candidate will be a highly 
motivated and enthusiastic individual with an outstanding academic track 
record, good communication skills and the ability to work as a team. Applicants 
with experience in single particle cryoEM and biochemistry are encouraged to 
apply.

The post is for 24 months in the first instance with a possibility of extension.

Closing Date: 01Dec 2017 at 5pm GMT
For further particulars and to apply for this post, please follow  
https://www.vacancies.ed.ac.uk/pls/corehrrecruit/erq_jobspec_version_4.jobspec?p_id=041812


Dr. A. Jeyaprakash Arulanandam
Wellcome Senior Research Fellow
Wellcome Trust Centre for Cell Biology
University of Edinburgh
Michael Swann Building
Max Born Crescent
Edinburgh EH9 3BF
Tel: +44 131 6507113
Fax: +44 131 6080414
Web: http://jeyaprakash.bio.ed.ac.uk/




The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.

Re: [ccp4bb] Regarding Patents

2017-11-03 Thread Chris Morris 
> Sorry for asking out of context question. Can a mutated DNA or protein 
> molecule be patented.

Yes and no. A molecule as such cannot be patented. But the use of a molecule 
for a specific purpose can be. There are many patents for small molecule drugs, 
and also for engineered antibodies, which are proteins. There are patents for 
industrial use of enzymes too. 

regards,
Chris

Chris Morris
chris.mor...@stfc.ac.uk
Tel: +44 (0)1925 603689  Fax: +44 (0)1925 603634
Mobile: 07921-717915
Skype: chrishgmorris
http://www.citeulike.org/blog/chrishmorris
STFC, Daresbury Laboratory, Sci-Tech Daresbury, Keckwick Lane, Daresbury, 
Warrington, WA4 4AD UK

[ccp4bb] AW: [ccp4bb] another unknown density problem

2017-11-03 Thread Herman . Schreuder 
Dear Abhishek,

To me, it looks like an alternative conformation of the peptide chain or maybe 
even a conformational change with respect to the starting model. The peptide 
chain does not look too well defined, despite high resolution electron density.

Best,
Herman

Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von Abhishek 
Anan
Gesendet: Freitag, 3. November 2017 09:26
An: CCP4BB@JISCMAIL.AC.UK
Betreff: [EXTERNAL] [ccp4bb] another unknown density problem

Hi all,
I have an "unknown" density in the map. I have tried to fit it to PEG but it 
doesn't fit very well. I was wondering if there are other PEG-related or other 
molecules I could try.
The crystal grew in TRIS-HCl and PEG MME 2K.
Thank you
Abhishek

Re: [ccp4bb] coot shelxl problem

2017-11-03 Thread Abhishek Anan 
Dear all,

A simple work around is to add HOH in coot, copy their coordinates into the
*.ins fil and refine shelxl from the command line. I have done it a few
time and it seems to refine fine.

Best regards,

Abhishek

On Thu, Nov 2, 2017 at 5:40 PM,  wrote:

> > I am using 0.8.8 that comes with ccp4 on a Mac 10.10.5. I will give it a
> > go with the pre-release.
>
>
> As far as I understand, stand-alone binaries for 10.6 - 10.10 are no
> longer supported for coot pre-release.
>
> I'd rather that that was not the case, but peanuts and monkeys, hey-ho.
>
> Paul.
>
>
>
>