Re: [ccp4bb] Coot Crashed

2012-02-28 Thread Bernhard C. Lohkamp

Dear Ros,

I believe I have fixed this in the newer versions. So please update to 
the latest pre-release 
(http://www.ysbl.york.ac.uk/~lohkamp/coot/wincoot_newest_download.php) 
and it should work fine. If the problem persists please let me know.


B


Dear All:
I am having trouble with Coot.
The program keeps crashing when I click on rotamer analysis. Other 
functions, sych as geometry analysis all worked fine.
It runs normal before, and only happened when I added the ligands into 
the model.

I am using WinCoot_0.7_pre-1-revision-3772, and window vista.
Thank you for advices.
Ros

No virus found in this message.
Checked by AVG - www.avg.com http://www.avg.com
Version: 2012.0.1913 / Virus Database: 2114/4835 - Release Date: 02/27/12



[ccp4bb] Introducing mrprep

2012-02-28 Thread Tim Gruene
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1

Dear all,

I wrote a little program called 'mrprep' which helped me prepare PDB
files to be used with Rob Nicholls' excellent ProSMART for the
generation of external restraints for refmac5. It might also be useful
for the preparation of MR models, but I have not tested this, yet.

If you are interested, take a look at
http://shelx.uni-ac.gwdg.de/~tg/research/programs/mrprep/

The program might do something similar to chainsaw and sculptor, but I
could not get chainsaw to work with a multi-subunit PDB-file I was
working on, and my concept of using a computer program seems so
fundamentally different from the phenix philosophy that I could not be
bothered to read the sculptor manual, even though sculptor is probably
more sophisticated (it takes more information into account)m so I wrote
my own program (which was of course a lot more exciting than reading a
manual, and my GUI simply pops up on my computer so I don't need to wait
until phenix has initialised itself ;-) ).

It is not thoroughly tested, and please read the Limitations section
on the above url, but it works for me.
Feel free to contact me with suggestions and criticism, I am happy to
improve the program if I can.

Cheers,
Tim

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

GPG Key ID = A46BEE1A

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[ccp4bb] Beamline Scientist position in SAXS@EMBL Hamburg

2012-02-28 Thread Margret Fischer

Reminder!
Deadline for application: 4th March 2012

--

Vacancy Notice/Job Description

The European Molecular Biology Laboratory (EMBL) is one of the highest
ranked scientific research organisations in the world. The Headquarters
Laboratory is located in Heidelberg (Germany) and the outstations are in 
Grenoble (France),

Hamburg (Germany), Hinxton (UK) and Monterotondo (Italy).

Applications are invited for a Staff Scientist position at the Structural
Biology Unit of the EMBL in Hamburg, Germany. The position is within the
biological SAXS group, which runs a high brilliance user-oriented
synchrotron radiation P12 beamline on the storage ring PETRA 3. This
beamline is part of the integrated facilityofEMBL@PETRA3. The  successful
candidate will play a major role in scientific maintenance (development of
the beamline facilities, methods and technology), external user support and
collaborative projects at the beamline. The post is expected to be involved
in novel biological SAXS developments in collaboration with the other 
groups

of the EMBL@PETRA 3. There will be opportunities to link related
research activities with the operation of the beamline.

Qualifications and Experience

Applicants should have a PhD in a relevant field, proven record of
independent research, significant scientific accomplishments and expertise
in structure analysis of biological macromolecules using small-angle X-ray
scattering. Previous experience in hardware and/or software development for
synchrotron radiation beamlines is required.

Experience in work at a large-scale user-oriented facility, excellent
communication skills and ability to supervise and collaborate in
international team environment will be essential.

Please apply online throughwww.embl.org/jobs


Re: [ccp4bb] Desalting columns

2012-02-28 Thread Christian Roth
If you want test a lot of different conditions a Thermofluorecence assay might 
work for your protein and you may find a condition which stabilise your 
protein. However there is no warranty that it crystallise better afterwards.

Christian

Am Montag 27 Februar 2012 17:01:33 schrieb Sangeetha Vedula:
 Dear bb users,
 
 I am trying to crystallize a ~320 kDa protein that crashes out if
 concentrated past about 3 mg/mL.
 
 I would like to try to exchange it into various buffer-salt-additive
 combinations to see which buffer works. For a starting point, I'd like to
 use desalting colums.
 
 Does anyone have suggestions for good buffer exchange and sample recovery?
 I woud like to load about 250 uL onto each column.
 
 Thanks a lot!
 
 Best regards,
 
 Sangeetha.
 


Re: [ccp4bb] Sad News

2012-02-28 Thread Smita Mohanty
Yes, this is of course a scam.  My husband was almost duped by someone
who wrote in the name of a close friend saying that he got mugged in
Europe and to send money to return to USA. My husband of course was
ready to send for his colleague but just gave a call to his friend to
make this not a scam.  Of course, it was a scam.  

Only last night we saved ourselves from another scam.  I think it is
good share with the group.  My son (in high school) found a 2005 BMW X5
on an internet site.  The car's blue book price is $26,000 but the
asking price by the seller is $2775.  Sounds too good to be true.   But
when my son (who dreams to own a BMW) contacted the owner (Amanda
Stone), she replied him immediately saying her son died two months back
in an automobile accident hit by a drunk driver while riding his
fiancee's car.  She simply wants to sell the car so that someone else
can use it and she is not interested in making money.  She said that she
has a deal with e-bay and that the car will be shipped by e-bay to the
buyer once the buyer pays the price that will be hold by e-bay.  The
buyer has 5 days to check the car out and if decides not to buy, the car
will be shipped back to e-bay at seller's cost and buyer gets back his
money.  She sent an invoice that was from e-bay with e-bay logo and
exactly looking genuine.

She sent car pictures and Vin and my husband checked the car out with
car fax.  She wanted the money to be sent to a e-bay financial expert
through moneygram although she sent name and address of an e-bay expert.
 That is when my husband called up e-bay just to make sure before he
send the moneygram out.  That is when e-bay told him this is a scam and
that e-bay never asks for moneygram.  That all transactions are done on
e-bay site only and that e-bay does not get any contract like the one we
had.  E-bay told us that their logo has/can be copied to make an invoice
appears to have come from them.  Of course, we went all communications
and invoice to e-bay.  We lost only $35 for car fax.

Lesson: we need to be aware of any advertisements on internet or
unsolicited e-mails.  Here is a site to read about different scams-

http://www.fbi.gov/scams-safety/be_crime_smart 

Thanks,

Smita 

 Vellieux Frederic frederic.velli...@ibs.fr 2/28/2012 7:01 AM 
From: regnicat@, reply to: regniica@...

Somehow I don't believe someone in such a situation would write to 
ccp4bb instead of calling the family back home. Using Skype since there

is apparently internet access !

And I rather view with my mind's eye someone sitting in an internet
cafe 
in (say) Lagos, or the Paris suburbs or Kingston or...

Fred

Catherine Regni wrote:
 I'm writing this with tears in my eyes,my family and I came over here

 to Madrid,Spain for a short vacation. unfortunately,we were  mugged
at 
 the park of the hotel where we stayed,all cash and credit card were 
 stolen off us but luckily for us we still have our passports with
us.

  We've been to the Embassy and the Police here but they're not
helping 
 issues at all and our flight leaves in few hours from now but we're 
 having problems settling the hotel bills and the hotel manager won't

 let us leave until we settle the bills. Well I really need your 
 financial assistance..Please, Let me know if you can help us out? Am

 freaked out at the Moment.

 Catherine Regni..

 Catherine Regni, Ph.D.



Re: [ccp4bb] Sad News

2012-02-28 Thread Gerard Bricogne
Dear Smita,

 For me, your story mostly illustrates the grave dangers of wanting to
own a BMW while still in high school ... ;-) . 


 With best wishes,
 
  Gerard.

--
On Tue, Feb 28, 2012 at 09:02:42AM -0600, Smita Mohanty wrote:
 Yes, this is of course a scam.  My husband was almost duped by someone
 who wrote in the name of a close friend saying that he got mugged in
 Europe and to send money to return to USA. My husband of course was
 ready to send for his colleague but just gave a call to his friend to
 make this not a scam.  Of course, it was a scam.  
 
 Only last night we saved ourselves from another scam.  I think it is
 good share with the group.  My son (in high school) found a 2005 BMW X5
 on an internet site.  The car's blue book price is $26,000 but the
 asking price by the seller is $2775.  Sounds too good to be true.   But
 when my son (who dreams to own a BMW) contacted the owner (Amanda
 Stone), she replied him immediately saying her son died two months back
 in an automobile accident hit by a drunk driver while riding his
 fiancee's car.  She simply wants to sell the car so that someone else
 can use it and she is not interested in making money.  She said that she
 has a deal with e-bay and that the car will be shipped by e-bay to the
 buyer once the buyer pays the price that will be hold by e-bay.  The
 buyer has 5 days to check the car out and if decides not to buy, the car
 will be shipped back to e-bay at seller's cost and buyer gets back his
 money.  She sent an invoice that was from e-bay with e-bay logo and
 exactly looking genuine.
 
 She sent car pictures and Vin and my husband checked the car out with
 car fax.  She wanted the money to be sent to a e-bay financial expert
 through moneygram although she sent name and address of an e-bay expert.
  That is when my husband called up e-bay just to make sure before he
 send the moneygram out.  That is when e-bay told him this is a scam and
 that e-bay never asks for moneygram.  That all transactions are done on
 e-bay site only and that e-bay does not get any contract like the one we
 had.  E-bay told us that their logo has/can be copied to make an invoice
 appears to have come from them.  Of course, we went all communications
 and invoice to e-bay.  We lost only $35 for car fax.
 
 Lesson: we need to be aware of any advertisements on internet or
 unsolicited e-mails.  Here is a site to read about different scams-
 
 http://www.fbi.gov/scams-safety/be_crime_smart 
 
 Thanks,
 
 Smita 
 
  Vellieux Frederic frederic.velli...@ibs.fr 2/28/2012 7:01 AM 
 From: regnicat@, reply to: regniica@...
 
 Somehow I don't believe someone in such a situation would write to 
 ccp4bb instead of calling the family back home. Using Skype since there
 
 is apparently internet access !
 
 And I rather view with my mind's eye someone sitting in an internet
 cafe 
 in (say) Lagos, or the Paris suburbs or Kingston or...
 
 Fred
 
 Catherine Regni wrote:
  I'm writing this with tears in my eyes,my family and I came over here
 
  to Madrid,Spain for a short vacation. unfortunately,we were  mugged
 at 
  the park of the hotel where we stayed,all cash and credit card were 
  stolen off us but luckily for us we still have our passports with
 us.
 
   We've been to the Embassy and the Police here but they're not
 helping 
  issues at all and our flight leaves in few hours from now but we're 
  having problems settling the hotel bills and the hotel manager won't
 
  let us leave until we settle the bills. Well I really need your 
  financial assistance..Please, Let me know if you can help us out? Am
 
  freaked out at the Moment.
 
  Catherine Regni..
 
  Catherine Regni, Ph.D.
 


Re: [ccp4bb] Desalting columns

2012-02-28 Thread Prince, D Bryan
Actually, I would refer the ccp4-bbs to Journal of Structural Biology
175 (2011) pp216-223 for the use of fluorescence in relation to protein
crystallization.

Regards,
Bryan


--
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.
 
-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
Christian Roth
Sent: Tuesday, February 28, 2012 8:09 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Desalting columns

If you want test a lot of different conditions a Thermofluorecence assay
might
work for your protein and you may find a condition which stabilise your
protein. However there is no warranty that it crystallise better
afterwards.

Christian

Am Montag 27 Februar 2012 17:01:33 schrieb Sangeetha Vedula:
 Dear bb users,

 I am trying to crystallize a ~320 kDa protein that crashes out if
 concentrated past about 3 mg/mL.

 I would like to try to exchange it into various buffer-salt-additive
 combinations to see which buffer works. For a starting point, I'd like
to
 use desalting colums.

 Does anyone have suggestions for good buffer exchange and sample
recovery?
 I woud like to load about 250 uL onto each column.

 Thanks a lot!

 Best regards,

 Sangeetha.



Re: [ccp4bb] Sad News, Defend our CCP4BB community

2012-02-28 Thread Wenhua Zhang

Dear all,

  I see that the CCP4BB community is becoming less pure due to our 
failure to post structure determination-oriented inquiries and questions 
that can't be answered by googling them.

  Let's filter our questions before attempting to post.

  Wenhua

On 2/28/2012 4:16 PM, Gerard Bricogne wrote:

Dear Smita,

  For me, your story mostly illustrates the grave dangers of wanting to
own a BMW while still in high school ... ;-) .


  With best wishes,

   Gerard.

--
On Tue, Feb 28, 2012 at 09:02:42AM -0600, Smita Mohanty wrote:

Yes, this is of course a scam.  My husband was almost duped by someone
who wrote in the name of a close friend saying that he got mugged in
Europe and to send money to return to USA. My husband of course was
ready to send for his colleague but just gave a call to his friend to
make this not a scam.  Of course, it was a scam.

Only last night we saved ourselves from another scam.  I think it is
good share with the group.  My son (in high school) found a 2005 BMW X5
on an internet site.  The car's blue book price is $26,000 but the
asking price by the seller is $2775.  Sounds too good to be true.   But
when my son (who dreams to own a BMW) contacted the owner (Amanda
Stone), she replied him immediately saying her son died two months back
in an automobile accident hit by a drunk driver while riding his
fiancee's car.  She simply wants to sell the car so that someone else
can use it and she is not interested in making money.  She said that she
has a deal with e-bay and that the car will be shipped by e-bay to the
buyer once the buyer pays the price that will be hold by e-bay.  The
buyer has 5 days to check the car out and if decides not to buy, the car
will be shipped back to e-bay at seller's cost and buyer gets back his
money.  She sent an invoice that was from e-bay with e-bay logo and
exactly looking genuine.

She sent car pictures and Vin and my husband checked the car out with
car fax.  She wanted the money to be sent to a e-bay financial expert
through moneygram although she sent name and address of an e-bay expert.
  That is when my husband called up e-bay just to make sure before he
send the moneygram out.  That is when e-bay told him this is a scam and
that e-bay never asks for moneygram.  That all transactions are done on
e-bay site only and that e-bay does not get any contract like the one we
had.  E-bay told us that their logo has/can be copied to make an invoice
appears to have come from them.  Of course, we went all communications
and invoice to e-bay.  We lost only $35 for car fax.

Lesson: we need to be aware of any advertisements on internet or
unsolicited e-mails.  Here is a site to read about different scams-

http://www.fbi.gov/scams-safety/be_crime_smart

Thanks,

Smita


Vellieux Fredericfrederic.velli...@ibs.fr  2/28/2012 7:01 AM

From: regnicat@, reply to: regniica@...

Somehow I don't believe someone in such a situation would write to
ccp4bb instead of calling the family back home. Using Skype since there

is apparently internet access !

And I rather view with my mind's eye someone sitting in an internet
cafe
in (say) Lagos, or the Paris suburbs or Kingston or...

Fred

Catherine Regni wrote:

I'm writing this with tears in my eyes,my family and I came over here
to Madrid,Spain for a short vacation. unfortunately,we were  mugged

at

the park of the hotel where we stayed,all cash and credit card were
stolen off us but luckily for us we still have our passports with

us.

  We've been to the Embassy and the Police here but they're not

helping

issues at all and our flight leaves in few hours from now but we're
having problems settling the hotel bills and the hotel manager won't
let us leave until we settle the bills. Well I really need your
financial assistance..Please, Let me know if you can help us out? Am
freaked out at the Moment.

Catherine Regni..

Catherine Regni, Ph.D.



Re: [ccp4bb] Sad News, Defend our CCP4BB community

2012-02-28 Thread Debasish Chattopadhyay
I wonder if it is time to restrict users who places these discussions on the 
board.  If each of us spend even a minute on such a subject, it is such a huge 
waste of time.

-Original Message-
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Wenhua 
Zhang
Sent: Tuesday, February 28, 2012 11:13 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Sad News, Defend our CCP4BB community

Dear all,

   I see that the CCP4BB community is becoming less pure due to our 
failure to post structure determination-oriented inquiries and questions 
that can't be answered by googling them.
   Let's filter our questions before attempting to post.

   Wenhua

On 2/28/2012 4:16 PM, Gerard Bricogne wrote:
 Dear Smita,

   For me, your story mostly illustrates the grave dangers of wanting to
 own a BMW while still in high school ... ;-) .


   With best wishes,

Gerard.

 --
 On Tue, Feb 28, 2012 at 09:02:42AM -0600, Smita Mohanty wrote:
 Yes, this is of course a scam.  My husband was almost duped by someone
 who wrote in the name of a close friend saying that he got mugged in
 Europe and to send money to return to USA. My husband of course was
 ready to send for his colleague but just gave a call to his friend to
 make this not a scam.  Of course, it was a scam.

 Only last night we saved ourselves from another scam.  I think it is
 good share with the group.  My son (in high school) found a 2005 BMW X5
 on an internet site.  The car's blue book price is $26,000 but the
 asking price by the seller is $2775.  Sounds too good to be true.   But
 when my son (who dreams to own a BMW) contacted the owner (Amanda
 Stone), she replied him immediately saying her son died two months back
 in an automobile accident hit by a drunk driver while riding his
 fiancee's car.  She simply wants to sell the car so that someone else
 can use it and she is not interested in making money.  She said that she
 has a deal with e-bay and that the car will be shipped by e-bay to the
 buyer once the buyer pays the price that will be hold by e-bay.  The
 buyer has 5 days to check the car out and if decides not to buy, the car
 will be shipped back to e-bay at seller's cost and buyer gets back his
 money.  She sent an invoice that was from e-bay with e-bay logo and
 exactly looking genuine.

 She sent car pictures and Vin and my husband checked the car out with
 car fax.  She wanted the money to be sent to a e-bay financial expert
 through moneygram although she sent name and address of an e-bay expert.
   That is when my husband called up e-bay just to make sure before he
 send the moneygram out.  That is when e-bay told him this is a scam and
 that e-bay never asks for moneygram.  That all transactions are done on
 e-bay site only and that e-bay does not get any contract like the one we
 had.  E-bay told us that their logo has/can be copied to make an invoice
 appears to have come from them.  Of course, we went all communications
 and invoice to e-bay.  We lost only $35 for car fax.

 Lesson: we need to be aware of any advertisements on internet or
 unsolicited e-mails.  Here is a site to read about different scams-

 http://www.fbi.gov/scams-safety/be_crime_smart

 Thanks,

 Smita

 Vellieux Fredericfrederic.velli...@ibs.fr  2/28/2012 7:01 AM
 From: regnicat@, reply to: regniica@...

 Somehow I don't believe someone in such a situation would write to
 ccp4bb instead of calling the family back home. Using Skype since there

 is apparently internet access !

 And I rather view with my mind's eye someone sitting in an internet
 cafe
 in (say) Lagos, or the Paris suburbs or Kingston or...

 Fred

 Catherine Regni wrote:
 I'm writing this with tears in my eyes,my family and I came over here
 to Madrid,Spain for a short vacation. unfortunately,we were  mugged
 at
 the park of the hotel where we stayed,all cash and credit card were
 stolen off us but luckily for us we still have our passports with
 us.
   We've been to the Embassy and the Police here but they're not
 helping
 issues at all and our flight leaves in few hours from now but we're
 having problems settling the hotel bills and the hotel manager won't
 let us leave until we settle the bills. Well I really need your
 financial assistance..Please, Let me know if you can help us out? Am
 freaked out at the Moment.

 Catherine Regni..

 Catherine Regni, Ph.D.



Re: [ccp4bb] Sad News

2012-02-28 Thread William G. Scott
I thought it was some sort of allegory for tenure-track faculty positions.


-- Bill



On Feb 28, 2012, at 7:16 AM, Gerard Bricogne wrote:

 Dear Smita,
 
 For me, your story mostly illustrates the grave dangers of wanting to
 own a BMW while still in high school ... ;-) . 
 
 
 With best wishes,
 
  Gerard.
 
 --
 On Tue, Feb 28, 2012 at 09:02:42AM -0600, Smita Mohanty wrote:
 Yes, this is of course a scam.  My husband was almost duped by someone
 who wrote in the name of a close friend saying that he got mugged in
 Europe and to send money to return to USA. My husband of course was
 ready to send for his colleague but just gave a call to his friend to
 make this not a scam.  Of course, it was a scam.  
 
 Only last night we saved ourselves from another scam.  I think it is
 good share with the group.  My son (in high school) found a 2005 BMW X5
 on an internet site.  The car's blue book price is $26,000 but the
 asking price by the seller is $2775.  Sounds too good to be true.   But
 when my son (who dreams to own a BMW) contacted the owner (Amanda
 Stone), she replied him immediately saying her son died two months back
 in an automobile accident hit by a drunk driver while riding his
 fiancee's car.  She simply wants to sell the car so that someone else
 can use it and she is not interested in making money.  She said that she
 has a deal with e-bay and that the car will be shipped by e-bay to the
 buyer once the buyer pays the price that will be hold by e-bay.  The
 buyer has 5 days to check the car out and if decides not to buy, the car
 will be shipped back to e-bay at seller's cost and buyer gets back his
 money.  She sent an invoice that was from e-bay with e-bay logo and
 exactly looking genuine.
 
 She sent car pictures and Vin and my husband checked the car out with
 car fax.  She wanted the money to be sent to a e-bay financial expert
 through moneygram although she sent name and address of an e-bay expert.
 That is when my husband called up e-bay just to make sure before he
 send the moneygram out.  That is when e-bay told him this is a scam and
 that e-bay never asks for moneygram.  That all transactions are done on
 e-bay site only and that e-bay does not get any contract like the one we
 had.  E-bay told us that their logo has/can be copied to make an invoice
 appears to have come from them.  Of course, we went all communications
 and invoice to e-bay.  We lost only $35 for car fax.
 
 Lesson: we need to be aware of any advertisements on internet or
 unsolicited e-mails.  Here is a site to read about different scams-
 
 http://www.fbi.gov/scams-safety/be_crime_smart 
 
 Thanks,
 
 Smita 
 
 Vellieux Frederic frederic.velli...@ibs.fr 2/28/2012 7:01 AM 
 From: regnicat@, reply to: regniica@...
 
 Somehow I don't believe someone in such a situation would write to 
 ccp4bb instead of calling the family back home. Using Skype since there
 
 is apparently internet access !
 
 And I rather view with my mind's eye someone sitting in an internet
 cafe 
 in (say) Lagos, or the Paris suburbs or Kingston or...
 
 Fred
 
 Catherine Regni wrote:
 I'm writing this with tears in my eyes,my family and I came over here
 
 to Madrid,Spain for a short vacation. unfortunately,we were  mugged
 at 
 the park of the hotel where we stayed,all cash and credit card were 
 stolen off us but luckily for us we still have our passports with
 us.
 
 We've been to the Embassy and the Police here but they're not
 helping 
 issues at all and our flight leaves in few hours from now but we're 
 having problems settling the hotel bills and the hotel manager won't
 
 let us leave until we settle the bills. Well I really need your 
 financial assistance..Please, Let me know if you can help us out? Am
 
 freaked out at the Moment.
 
 Catherine Regni..
 
 Catherine Regni, Ph.D.
 


Re: [ccp4bb] Any calculation function in CCP4 to analyze coordinate file?

2012-02-28 Thread Eleanor Dodson
There are tools to do this - eg REFMAC will tell you no of residues and 
atoms. PDBSET baverage/ rwcontents etc all offer bits of info, but i guess 
it would be useful to have a more organised report..


Eleanor

On Feb 27 2012, Jan Dohnalek wrote:


We have been doing a bit of this using a simple program under Linux -
pdbskim.
A linux binary available on request. Very simple output though, focused on
infromation on occ, Bs alternatives, etc to help make decisions during
structure refinement.

Jan


On Sat, Feb 25, 2012 at 11:59 PM, WENHE ZHONG
wenhezhong.xmu@gmail.comwrote:


Dear members,

Just have a silly question past my mind: is there any program in CCP4 
can be used to analyze coordinate file (.pdb format) to have a very 
general/overall discription about the structure? --such as the total 
number of protein residues/water/ligand, the total atoms of 
protein/water/ligand, the average b-factor of protein/water/ligand, the 
number of residues which have alternative side chians, and so on.


Thank you.

King regards,
Wenhe








--
Professor Eleanor Dodson
YSNL, Dept of Chemistry
University of York
Heslington YO10 5YW
tel: 00 44 1904 328259
Fax: 00 44 1904 328266


Re: [ccp4bb] change in unit cell parameters and difficult MR

2012-02-28 Thread Eleanor Dodson
 Well, there is an obvious relation between cell dimensions - what is the 
translation vector you find at 41%


You say the native structure has 3 monomers - I would send those 
coordinates to the PISA application at the EBI, and see what the interfaces 
are and make sure you are using closely packed search models - eg you may 
find there is a closely packed trimer which is built using symmetry 
equivalent molecules to your native solution..


Hard to answer without more information though.
ie space group, relative size od protein and complex etc..
Eleanor



On Feb 27 2012, intekhab alam wrote:


Hi all
I have collected 2 datasets; one for the native proteins (2.3Å resolution)
while other is for a protein-protein complex (3.5Å resolution). The unit
cell parameters for the native are a=120, b=196, c=109, a=g=90, b=114,
while for the complex data it is a=122, b=197, c=300, a=g=90, b=93. I have
successfully got a MR solution and refined the native dataset with 3
monomers in the asymmetric unit. Analysis of the protein complex dataset
shows 41% pseudo translation and so far there is no success in molecular
replacement for this dataset. Can anyone please suggest me ways to solve
this problem. i already have tried different templates like monomer, dimer,
trimer, tetramer etc with truncations of loop region. i am using phaser as
well as molrep programs.

Regards



--
Professor Eleanor Dodson
YSNL, Dept of Chemistry
University of York
Heslington YO10 5YW
tel: 00 44 1904 328259
Fax: 00 44 1904 328266


Re: [ccp4bb] Heterotetrameric protein

2012-02-28 Thread Eleanor Dodson

All haemoglobins do..
Eleanor

On Feb 26 2012, Koustav Maity wrote:


Hi all,

 does anyone know a protein which make hetero tetramer of A2B2 which
arrange as[image: Inline image 1]  and NOT as [image: Inline image 2]?


Its great if these proteins are small? All the hetero tetramer I found was
of [image: Inline image 3] type.


Thanks

Dhiraj



--
Professor Eleanor Dodson
YSNL, Dept of Chemistry
University of York
Heslington YO10 5YW
tel: 00 44 1904 328259
Fax: 00 44 1904 328266


[ccp4bb] CCP4i Reflection DataUtilities: Convert to/modify/extend MTZ does not work

2012-02-28 Thread Dialing Pretty


Dear All,

I want to use CCP4i Reflection DataUtilities: Convert to/modify/extend MTZ to 
change a RCSB mmCIF file into MTZ file.

It shows there are a lot of data name (related to _pdbx_.or something else) not 
present in dictionary, and shows CCP4I termination status 0 child process 
excited anormally.

I am looking forward to getting a reply from you on how to solve the problem.

Cheers,

Dialing