Re: [ccp4bb] MOOC "Voyage au coeur du vivant avec les rayons X : la cristallographie"

[LEDU Marie-Helene]

The Université of Paris-Saclay is pleased to present the MOOC " Voyage au cœur 
du vivant avec les rayons X : la cristallographie", which results from a tight 
collaboration between the CEA, the Synchrotron Soleil, the Ecole Polytechnique, 
and the CNRS.



The use of three-dimensional structures of biological macromolecules is part of 
the daily life of many biologists. The major approach to solve the 
three-dimensional structure of biological macromolecules is X-ray 
crystallography.


This MOOC constitutes a complete initiation to biological crystallography: from 
the history of the method to its concrete tools.


The course, which begins on November 6th, is designed for biology students from 
the Master's level, thesis students, postdoctoral fellows, engineers or biology 
researchers.

The MOOC is in French with English subtitles.

Access is free on the France University website: https://goo.gl/dkDZEx


Register and circulate information around you.


Marie-Hélène Le Du, for the MOOC team


CEA/DRF/ISVFJ
Laboratoire de Biologie Structurale et Radiobiologie
Bât 144, CEA Saclay
91191, Gif-sur-Yvette, France
email: marie-helene.l...@cea.fr
tel: (33) (0)1 69 08 71 35
URL: http://www.i2bc.paris-saclay.fr/spip.php?article168

Re: [ccp4bb] OFF topic (Protein degrades during Dailysis)

[Éverton D'Andréa]

   Hi Anamika,

As it was said before, a cocktail of protease inhibitors should be
fine. But let`s say you can not overcome the problem. It is not specified
if you are doing this dialysis to cleave or not your His-tagged protein but
even this you could try getting samples in 1 hour intervals then you could
monitor the stability (and/or cleavage) of your protein. Another thing is
if you are doing this at room temperature or at 4C.

Best regards,

Everton.

On Thu, Oct 26, 2017 at 5:11 PM, Smith Liu  wrote:

> suppose protease is the issue, then avoid overnight dialysis
>
>
> 发自网易邮箱大师
>
> 在2017年10月26日 22:18，Anamika Singh  写道：
> Dear All,
>
> I am purifying the His-tagged proteins ( 21Kda) using buffer 20mM Tris,
> 150mM Nacl, and 5mM MgCl2 with 500mM imidazole. Earlier I was facing the
> precipitation problem during dialysis but with the addition of 50mM L-Arg
> somehow managed to overcome the precipitation issue. But this time I have
> seen after overnight dialysis there are degradation products on SDS page. I
> have used protease inhibitor (PMSF) in my sonication buffer.
>
> Please suggest me to overcome this problem.
>
> Thanks
> --
> Anamika
>
>
>
> 【网易自营】好吃到爆！鲜香弹滑加热即食，经典13香/麻辣小龙虾仅75元3斤>>
> 
>
>



-- 
Éverton Dias D'Andréa

Re: [ccp4bb] OFF topic (Protein degrades during Dailysis)

[Smith Liu]

suppose protease is the issue, then avoid overnight dialysis


发自网易邮箱大师


在2017年10月26日 22:18，Anamika Singh 写道：
Dear All,


I am purifying the His-tagged proteins ( 21Kda) using buffer 20mM Tris, 150mM 
Nacl, and 5mM MgCl2 with 500mM imidazole. Earlier I was facing the 
precipitation problem during dialysis but with the addition of 50mM L-Arg 
somehow managed to overcome the precipitation issue. But this time I have seen 
after overnight dialysis there are degradation products on SDS page. I have 
used protease inhibitor (PMSF) in my sonication buffer. 


Please suggest me to overcome this problem. 



Thanks
--

Anamika

Re: [ccp4bb] efresol download?

[Alexandre Ourjoumtsev]

Dear Johan 

one more copy :-) 
Yes, you can get it from 

http://www-ibmc.u-strasbg.fr/spip-arn/spip.php?rubrique2=en 

Sorry for inconvenience and answering so late... 
Luca, Daniel and Pavel, many thanks for your help ! 

Sacha Urzhumtsev 

- Le 26 Oct 17, à 18:50, Hattne, Johan  a écrit : 

> Thanks a lot, Luca, Pavel, and Daniel! I now have sufficiently many copies to
> last me well into 2020!

> // Cheers; Johan

> > On Oct 26, 2017, at 11:58, Bonsor, Daniel  wrote:

> > Is this not it?

> > http://www-ibmc.u-strasbg.fr/spip-arn/rubrique257?lang=en

> > At the bottom of the page.


> > Daniel A Bonsor PhD.
> > Sundberg Lab
> > Institute of Human Virology
> > University of Maryland, Baltimore
> > 725 W Lombard Street N370
> > Baltimore
> > Maryland
> > MD 21201
> > Tel: (410) 706-7457


>> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Pavel
> > Afonine
> > Sent: Thursday, October 26, 2017 11:54 AM
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: Re: [ccp4bb] efresol download?

> > Johan,

>> core functionality described in that paper is implemented in cctbx. Re the
> > stand-alone program -- I'm cc'ing to the author.

> > Pavel

> > On Thu, Oct 26, 2017 at 8:39 AM, Hattne, Johan  
> > wrote:
> > Dear all;

>> Would anybody know where I can find efresol (as detailed in
>> http://dx.doi.org/10.1107/S0907444913016673) these days? Googling lead me to 
>> a
>> 2014 post
>> (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1406=ccp4bb===155751),
> > but those links result in 403 Forbidden as of right now.

> > // Best wishes; Johan


> > Research Specialist @ Gonen Lab
> > 
> > Janelia Research Campus * 19700 Helix Drive
> > Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376

> Research Specialist @ Gonen Lab
> 
> Janelia Research Campus * 19700 Helix Drive
> Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376

Re: [ccp4bb] efresol download?

[Alexandre Ourjoumtsev]

Dear Johan 

one more copy :-) 
Yes, you can get it from 

http://www-ibmc.u-strasbg.fr/spip-arn/spip.php?rubrique2=en 

Sorry for inconvenience... 
Luca, Daniel and Pavel, m 

- Le 26 Oct 17, à 17:39, Hattne, Johan  a écrit : 

> Dear all;

> Would anybody know where I can find efresol (as detailed in
> http://dx.doi.org/10.1107/S0907444913016673) these days? Googling lead me to a
> 2014 post
> (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1406=ccp4bb===155751),
> but those links result in 403 Forbidden as of right now.

> // Best wishes; Johan

> Research Specialist @ Gonen Lab
> 
> Janelia Research Campus * 19700 Helix Drive
> Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376

Re: [ccp4bb] blast pdb for a very short sequence (3 amino acids)

[Xiao Lei]

Dear All,

Thanks. I tried PDBemotif, indeed, it works very well!

On Thu, Oct 26, 2017 at 10:04 AM, Andrew Lovering <
andrewleelover...@googlemail.com> wrote:

> The backbone psi phi angle option in pdbemotif should limit hits to a
> particular secondary structure.
>
> Good luck!
> Andy
>
> On 26 Oct 2017 5:54 pm, "xiaolei...@gmail.com" 
> wrote:
>
>> Dear All,
>>
>> Thanks for the suggestions!  I tried MPI pattern search, MOTIF2 as Andrew
>> suggested, they worked fine to pull out of the PDB containing short
>> sequences. What I need to do is a little bit more, I'd also like to know my
>> hit region's secondary structure (helix, sheet, or loop), MPI and MOTIF2
>> usually pulls out tons of sequences, then at this stage I have to manually
>> go to each PDB, check the hit region's secondary structure. I wonder if
>> there is a tool to do both, i.e., let's say I could search for short
>> sequences in only helix region or loop region of PDB files?
>>
>>
>>
>> On Thu, Oct 26, 2017 at 1:28 AM, Andrew Lovering 
>> wrote:
>>
>>> I would guess that you want to search PDB for a small motif you've
>>> observed in a structure of yours, looking to find examples of it used in
>>> same context?
>>>
>>> If that's true, I would recommend PDBemotif, put the sequence in, and
>>> then use the backbone psi phi angles of your motif as a secondary
>>> constraint in the search, increasing/decreasing the angle tolerance as
>>> appropriate.
>>>
>>> If I’m incorrect, and you just want to find examples of a short motif,
>>> this webserver is awesome – you can also limit it by taxonomy:
>>>
>>> http://www.genome.jp/tools/motif/MOTIF2.html
>>>
>>>
>>>
>>> Best
>>>
>>> Andy
>>>
>>>
>>>
>>> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf
>>> Of *xiaolei...@gmail.com
>>> *Sent:* 26 October 2017 04:40
>>> *To:* CCP4BB@JISCMAIL.AC.UK
>>> *Subject:* [ccp4bb] blast pdb for a very short sequence (3 amino acids)
>>>
>>>
>>>
>>> Dear CCP4BB members,
>>>
>>>
>>>
>>> Sorry this post is off-topic. I am asking is there a way to blast pdb
>>> for a very short sequence like 2 or 3 amino acids?  I tried this for a
>>> positive control in pdb database but returned that "Your search parameters
>>> were adjusted to search for a short input sequence."  and "No significant
>>> similarity found. ".
>>>
>>>
>>>
>>>
>>>
>>
>>

Re: [ccp4bb] blast pdb for a very short sequence (3 amino acids)

[Andrew Lovering]

The backbone angle search in pdbemotif should limit it to particular secondary 
structure.

Good luck!
Andy

From: xiaolei...@gmail.com [xiaolei...@gmail.com]
Sent: October 26, 2017 5:53 PM
To: Andrew Lovering; Joana Pereira
Cc: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] blast pdb for a very short sequence (3 amino acids)

Dear All,

Thanks for the suggestions!  I tried MPI pattern search, MOTIF2 as Andrew 
suggested, they worked fine to pull out of the PDB containing short sequences. 
What I need to do is a little bit more, I'd also like to know my hit region's 
secondary structure (helix, sheet, or loop), MPI and MOTIF2 usually pulls out 
tons of sequences, then at this stage I have to manually go to each PDB, check 
the hit region's secondary structure. I wonder if there is a tool to do both, 
i.e., let's say I could search for short sequences in only helix region or loop 
region of PDB files?



On Thu, Oct 26, 2017 at 1:28 AM, Andrew Lovering 
> wrote:
I would guess that you want to search PDB for a small motif you've observed in 
a structure of yours, looking to find examples of it used in same context?
If that's true, I would recommend PDBemotif, put the sequence in, and then use 
the backbone psi phi angles of your motif as a secondary constraint in the 
search, increasing/decreasing the angle tolerance as appropriate.
If I’m incorrect, and you just want to find examples of a short motif, this 
webserver is awesome – you can also limit it by taxonomy:
http://www.genome.jp/tools/motif/MOTIF2.html

Best
Andy

From: CCP4 bulletin board 
[mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
xiaolei...@gmail.com
Sent: 26 October 2017 04:40
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] blast pdb for a very short sequence (3 amino acids)

Dear CCP4BB members,

Sorry this post is off-topic. I am asking is there a way to blast pdb for a 
very short sequence like 2 or 3 amino acids?  I tried this for a positive 
control in pdb database but returned that "Your search parameters were adjusted 
to search for a short input sequence."  and "No significant similarity found. ".

Re: [ccp4bb] blast pdb for a very short sequence (3 amino acids)

[Xiao Lei]

Dear All,

Thanks for the suggestions!  I tried MPI pattern search, MOTIF2 as Andrew
suggested, they worked fine to pull out of the PDB containing short
sequences. What I need to do is a little bit more, I'd also like to know my
hit region's secondary structure (helix, sheet, or loop), MPI and MOTIF2
usually pulls out tons of sequences, then at this stage I have to manually
go to each PDB, check the hit region's secondary structure. I wonder if
there is a tool to do both, i.e., let's say I could search for short
sequences in only helix region or loop region of PDB files?



On Thu, Oct 26, 2017 at 1:28 AM, Andrew Lovering 
wrote:

> I would guess that you want to search PDB for a small motif you've
> observed in a structure of yours, looking to find examples of it used in
> same context?
>
> If that's true, I would recommend PDBemotif, put the sequence in, and then
> use the backbone psi phi angles of your motif as a secondary constraint in
> the search, increasing/decreasing the angle tolerance as appropriate.
>
> If I’m incorrect, and you just want to find examples of a short motif,
> this webserver is awesome – you can also limit it by taxonomy:
>
> http://www.genome.jp/tools/motif/MOTIF2.html
>
>
>
> Best
>
> Andy
>
>
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of *
> xiaolei...@gmail.com
> *Sent:* 26 October 2017 04:40
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] blast pdb for a very short sequence (3 amino acids)
>
>
>
> Dear CCP4BB members,
>
>
>
> Sorry this post is off-topic. I am asking is there a way to blast pdb for
> a very short sequence like 2 or 3 amino acids?  I tried this for a positive
> control in pdb database but returned that "Your search parameters were
> adjusted to search for a short input sequence."  and "No significant
> similarity found. ".
>
>
>
>
>

Re: [ccp4bb] efresol download?

[Hattne, Johan]

Thanks a lot, Luca, Pavel, and Daniel!  I now have sufficiently many copies to 
last me well into 2020!

// Cheers; Johan

> On Oct 26, 2017, at 11:58, Bonsor, Daniel  wrote:
> 
> Is this not it?
>  
> http://www-ibmc.u-strasbg.fr/spip-arn/rubrique257?lang=en
>  
> At the bottom of the page.
>  
>  
> Daniel A Bonsor PhD.
> Sundberg Lab
> Institute of Human Virology
> University of Maryland, Baltimore
> 725 W Lombard Street N370
> Baltimore
> Maryland
> MD 21201
> Tel: (410) 706-7457
>  
>  
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Pavel 
> Afonine
> Sent: Thursday, October 26, 2017 11:54 AM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] efresol download?
>  
> Johan,
>  
> core functionality described in that paper is implemented in cctbx. Re the 
> stand-alone program -- I'm cc'ing to the author.
>  
> Pavel
>  
> On Thu, Oct 26, 2017 at 8:39 AM, Hattne, Johan  
> wrote:
> Dear all;
> 
> Would anybody know where I can find efresol (as detailed in 
> http://dx.doi.org/10.1107/S0907444913016673) these days?  Googling lead me to 
> a 2014 post 
> (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1406=ccp4bb===155751),
>  but those links result in 403 Forbidden as of right now.
> 
> // Best wishes; Johan
> 
> 
>   Research Specialist @ Gonen Lab
> 
> Janelia Research Campus * 19700 Helix Drive
> Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376

  Research Specialist @ Gonen Lab

Janelia Research Campus * 19700 Helix Drive
Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376

Re: [ccp4bb] Unknown electron density

[Nick Pearce]

I agree that the difference density isn’t “noise". However, just because it’s 
not noise doesn’t mean that it is modellable (with an atomic model) — the 
crystallographic density is an average over billions of molecules, and if its 
not obvious at 1.6Å what is bound, then it’s probably a superposition of states 
(or a highly disordered molecule with large B-factors, which in this case 
amounts to pretty much the same thing). When it’s a superposition of states in 
solvent regions, there are too many free parameters to build a reliable model: 
you don’t know how many alternate conformations to model, or how many species 
of molecules there are. It could be 1 conformer of PEG with 1 superposed 
conformer of water or 2 of PEG + 1 of water or 1 of PEG + 1 of something else + 
1 of water… or literally anything…

So unless you have some prior information as to what is bound, I would play it 
safe and model nothing — the conservative approach.

Thanks,
Nick

—

Nick (Nicholas) Pearce
Post-doctoral Researcher
Lab of Piet Gros
Crystal & Structural Chemistry Group
Universiteit Utrecht

> On 26 Oct 2017, at 18:00, Vijaykumar Pillalamarri  
> wrote:
> 
> Thanks Nick.
> 
> May be it is not that weak. The blue map contour level was set to 1.5. I have 
> attached another image in which the blue map is contoured to 1.0. I feel the 
> green density (contoured at 3.0) is not just some noise.
> 
> On 26 October 2017 at 20:38, Nick Pearce  > wrote:
> Hi,
> 
> Given the weakness and shapelessness of the density I doubt it is "one 
> conformation of one thing", but rather a superposition of "one or more 
> conformations of one or more things”. If that is the case then there probably 
> isn’t enough information in the electron density or enough prior information 
> to restrain a modelling approach — i.e. you could build a model that fit the 
> density, but you could never determine if it was “correct”. I would probably 
> just leave that bit un-modelled.
> 
> Thanks,
> Nick
> 
> —
> 
> Nick (Nicholas) Pearce
> Post-doctoral Researcher
> Lab of Piet Gros
> Crystal & Structural Chemistry Group
> Universiteit Utrecht
> 
>> On 26 Oct 2017, at 16:53, Vijaykumar Pillalamarri > > wrote:
>> 
>> Dear Dr. Vaheh,
>> 
>> I tried fitting waters around Co but the positive density is still present 
>> even after refinement.
>> 
>> Thanks,
>> Vijaykumar
>> 
>> On 26 October 2017 at 20:19, Oganesyan, Vaheh > > wrote:
>> Water molecules completing Co coordination?
>> 
>>  
>> 
>> Regards,
>> 
>>  
>> 
>> Vaheh Oganesyan
>> 
>> www.medimmune.com 
>>  
>> 
>> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK 
>> ] On Behalf Of Vijaykumar Pillalamarri
>> Sent: Thursday, October 26, 2017 10:24 AM
>> To: CCP4BB@JISCMAIL.AC.UK 
>> Subject: [ccp4bb] Unknown electron density
>> 
>>  
>> 
>> Dear ccp4bb,
>> 
>>  
>> 
>> I am solving the structure of a 1.6 Angstrom data of a metallo protein. 
>> While everything else is straight forward, this density (see the picture) 
>> seems unfamiliar to me. I don't see any thing fits in the density. This 
>> density present just above Histidine-Cobalt. What ever I try to fit, the 
>> molecule clahes with histidine ( I mean the distance between His and 
>> molecule is <2 Angstrom). 
>> 
>>  
>> 
>> The crystallization condition is 0.1M Bistris, 19% PEG 3350 and 50% glycerol.
>> 
>>  
>> 
>> Any suggestions?
>> 
>>  
>> 
>> Thanks,
>> 
>> Vijaykumar Pillalamarri
>> 
>> UGC-SRF
>> 
>> C/O: Dr. Anthony Addlagatta
>> 
>> Principal Scientist
>> 
>> CSIR-IICT, Tarnaka
>> 
>> Hyderabad, India-57
>> 
>> Mobile: +918886922975
>> 
>> To the extent this electronic communication or any of its attachments 
>> contain information that is not in the public domain, such information is 
>> considered by MedImmune to be confidential and proprietary. This 
>> communication is expected to be read and/or used only by the individual(s) 
>> for whom it is intended. If you have received this electronic communication 
>> in error, please reply to the sender advising of the error in transmission 
>> and delete the original message and any accompanying documents from your 
>> system immediately, without copying, reviewing or otherwise using them for 
>> any purpose. Thank you for your cooperation.
>> 
>> 
>> 
>> -- 
>> Vijaykumar Pillalamarri
>> UGC-SRF
>> C/O: Dr. Anthony Addlagatta
>> Principal Scientist
>> CSIR-IICT, Tarnaka
>> Hyderabad, India-57
>> Mobile: +918886922975
> 
> 
> 
> 
> -- 
> Vijaykumar Pillalamarri
> UGC-SRF
> C/O: Dr. Anthony Addlagatta
> Principal Scientist
> CSIR-IICT, Tarnaka
> Hyderabad, India-57
> Mobile: +918886922975

Re: [ccp4bb] efresol download?

[Bonsor, Daniel]

Is this not it?

http://www-ibmc.u-strasbg.fr/spip-arn/rubrique257?lang=en

At the bottom of the page.


Daniel A Bonsor PhD.
Sundberg Lab
Institute of Human Virology
University of Maryland, Baltimore
725 W Lombard Street N370
Baltimore
Maryland
MD 21201
Tel: (410) 706-7457


From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Pavel 
Afonine
Sent: Thursday, October 26, 2017 11:54 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] efresol download?

Johan,

core functionality described in that paper is implemented in cctbx. Re the 
stand-alone program -- I'm cc'ing to the author.

Pavel

On Thu, Oct 26, 2017 at 8:39 AM, Hattne, Johan 
> wrote:
Dear all;

Would anybody know where I can find efresol (as detailed in 
http://dx.doi.org/10.1107/S0907444913016673) these days?  Googling lead me to a 
2014 post 
(https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1406=ccp4bb===155751),
 but those links result in 403 Forbidden as of right now.

// Best wishes; Johan


  Research Specialist @ Gonen Lab

Janelia Research Campus * 19700 Helix Drive
Ashburn, VA 20147 * +1 (571) 209-4000 extension 
3376

Re: [ccp4bb] efresol download?

[Pavel Afonine]

Johan,

core functionality described in that paper is implemented in cctbx. Re the
stand-alone program -- I'm cc'ing to the author.

Pavel

On Thu, Oct 26, 2017 at 8:39 AM, Hattne, Johan 
wrote:

> Dear all;
>
> Would anybody know where I can find efresol (as detailed in
> http://dx.doi.org/10.1107/S0907444913016673) these days?  Googling lead
> me to a 2014 post (https://www.jiscmail.ac.uk/
> cgi-bin/webadmin?A2=ind1406=ccp4bb===155751), but those links
> result in 403 Forbidden as of right now.
>
> // Best wishes; Johan
>
>
>   Research Specialist @ Gonen Lab
> 
> Janelia Research Campus * 19700 Helix Drive
> Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376
>

[ccp4bb] efresol download?

[Hattne, Johan]

Dear all;

Would anybody know where I can find efresol (as detailed in 
http://dx.doi.org/10.1107/S0907444913016673) these days?  Googling lead me to a 
2014 post 
(https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1406=ccp4bb===155751),
 but those links result in 403 Forbidden as of right now.

// Best wishes; Johan


  Research Specialist @ Gonen Lab

Janelia Research Campus * 19700 Helix Drive
Ashburn, VA 20147 * +1 (571) 209-4000 extension 3376

Re: [ccp4bb] Unknown electron density

[Nick Pearce]

Hi,

Given the weakness and shapelessness of the density I doubt it is "one 
conformation of one thing", but rather a superposition of "one or more 
conformations of one or more things”. If that is the case then there probably 
isn’t enough information in the electron density or enough prior information to 
restrain a modelling approach — i.e. you could build a model that fit the 
density, but you could never determine if it was “correct”. I would probably 
just leave that bit un-modelled.

Thanks,
Nick

—

Nick (Nicholas) Pearce
Post-doctoral Researcher
Lab of Piet Gros
Crystal & Structural Chemistry Group
Universiteit Utrecht

> On 26 Oct 2017, at 16:53, Vijaykumar Pillalamarri  
> wrote:
> 
> Dear Dr. Vaheh,
> 
> I tried fitting waters around Co but the positive density is still present 
> even after refinement.
> 
> Thanks,
> Vijaykumar
> 
> On 26 October 2017 at 20:19, Oganesyan, Vaheh  > wrote:
> Water molecules completing Co coordination?
> 
>  
> 
> Regards,
> 
>  
> 
> Vaheh Oganesyan
> 
> www.medimmune.com 
>  
> 
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK 
> ] On Behalf Of Vijaykumar Pillalamarri
> Sent: Thursday, October 26, 2017 10:24 AM
> To: CCP4BB@JISCMAIL.AC.UK 
> Subject: [ccp4bb] Unknown electron density
> 
>  
> 
> Dear ccp4bb,
> 
>  
> 
> I am solving the structure of a 1.6 Angstrom data of a metallo protein. While 
> everything else is straight forward, this density (see the picture) seems 
> unfamiliar to me. I don't see any thing fits in the density. This density 
> present just above Histidine-Cobalt. What ever I try to fit, the molecule 
> clahes with histidine ( I mean the distance between His and molecule is <2 
> Angstrom). 
> 
>  
> 
> The crystallization condition is 0.1M Bistris, 19% PEG 3350 and 50% glycerol.
> 
>  
> 
> Any suggestions?
> 
>  
> 
> Thanks,
> 
> Vijaykumar Pillalamarri
> 
> UGC-SRF
> 
> C/O: Dr. Anthony Addlagatta
> 
> Principal Scientist
> 
> CSIR-IICT, Tarnaka
> 
> Hyderabad, India-57
> 
> Mobile: +918886922975
> 
> To the extent this electronic communication or any of its attachments contain 
> information that is not in the public domain, such information is considered 
> by MedImmune to be confidential and proprietary. This communication is 
> expected to be read and/or used only by the individual(s) for whom it is 
> intended. If you have received this electronic communication in error, please 
> reply to the sender advising of the error in transmission and delete the 
> original message and any accompanying documents from your system immediately, 
> without copying, reviewing or otherwise using them for any purpose. Thank you 
> for your cooperation.
> 
> 
> 
> -- 
> Vijaykumar Pillalamarri
> UGC-SRF
> C/O: Dr. Anthony Addlagatta
> Principal Scientist
> CSIR-IICT, Tarnaka
> Hyderabad, India-57
> Mobile: +918886922975

Re: [ccp4bb] Unknown electron density

[Parthasarathy Sampathkumar]

Hi Vijay,

Why there is no 2mFo-DFc (blue) feature on this mFo-DFc (green) map?!! Is
the contour level for blue map set high?!! If there is no 2mFo-DFc density,
should this be consider as noise?!!

Hope this helps,
Best Wishes,
Partha


On Thu, Oct 26, 2017 at 10:23 AM, Vijaykumar Pillalamarri <
vijaypkuma...@gmail.com> wrote:

> Dear ccp4bb,
>
> I am solving the structure of a 1.6 Angstrom data of a metallo protein.
> While everything else is straight forward, this density (see the picture)
> seems unfamiliar to me. I don't see any thing fits in the density. This
> density present just above Histidine-Cobalt. What ever I try to fit, the
> molecule clahes with histidine ( I mean the distance between His and
> molecule is <2 Angstrom).
>
> The crystallization condition is 0.1M Bistris, 19% PEG 3350 and 50%
> glycerol.
>
> Any suggestions?
>
> Thanks,
> Vijaykumar Pillalamarri
> UGC-SRF
> C/O: Dr. Anthony Addlagatta
> Principal Scientist
> CSIR-IICT, Tarnaka
> Hyderabad, India-57
> Mobile: +918886922975 <+91%2088869%2022975>
>

Re: [ccp4bb] Unknown electron density

[Vijaykumar Pillalamarri]

Dear Dr. Vaheh,

I tried fitting waters around Co but the positive density is still present
even after refinement.

Thanks,
Vijaykumar

On 26 October 2017 at 20:19, Oganesyan, Vaheh 
wrote:

> Water molecules completing Co coordination?
>
>
>
> *Regards,*
>
>
>
> *Vaheh Oganesyan*
>
> *www.medimmune.com *
>
>
>
> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *On Behalf Of 
> *Vijaykumar
> Pillalamarri
> *Sent:* Thursday, October 26, 2017 10:24 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] Unknown electron density
>
>
>
> Dear ccp4bb,
>
>
>
> I am solving the structure of a 1.6 Angstrom data of a metallo protein.
> While everything else is straight forward, this density (see the picture)
> seems unfamiliar to me. I don't see any thing fits in the density. This
> density present just above Histidine-Cobalt. What ever I try to fit, the
> molecule clahes with histidine ( I mean the distance between His and
> molecule is <2 Angstrom).
>
>
>
> The crystallization condition is 0.1M Bistris, 19% PEG 3350 and 50%
> glycerol.
>
>
>
> Any suggestions?
>
>
>
> Thanks,
>
> Vijaykumar Pillalamarri
>
> UGC-SRF
>
> C/O: Dr. Anthony Addlagatta
>
> Principal Scientist
>
> CSIR-IICT, Tarnaka
>
> Hyderabad, India-57
>
> Mobile: +918886922975
> To the extent this electronic communication or any of its attachments
> contain information that is not in the public domain, such information is
> considered by MedImmune to be confidential and proprietary. This
> communication is expected to be read and/or used only by the individual(s)
> for whom it is intended. If you have received this electronic communication
> in error, please reply to the sender advising of the error in transmission
> and delete the original message and any accompanying documents from your
> system immediately, without copying, reviewing or otherwise using them for
> any purpose. Thank you for your cooperation.
>



-- 
Vijaykumar Pillalamarri
UGC-SRF
C/O: Dr. Anthony Addlagatta
Principal Scientist
CSIR-IICT, Tarnaka
Hyderabad, India-57
Mobile: +918886922975

Re: [ccp4bb] OFF topic (Protein degrades during Dailysis)

[Ruud Hovius]

Hello,

PMSF inhibits only 1 class of proteinases

You can try to add other inhibitors :
e.g. for purification from yeast I used the following in addition to PMSF:

1000 x stock individual inhibitors

pepstatin5 mg/ml methanol

chymostatin1 mg/mlDMSO

antipain3 mg/mlmethanol (sonicate to dissolve)

aprotinin2 mg/mlwater

leupeptin1 mg/ml water

E-642 mg/ml50 % ethanol

bestatin5 mg/mlmethanol

as well as EDTA for metallo-proteases

Some suppliers like Roche sell pre-made mixtures like protease inhibitor 
pills.



Also be as fast as possible with all steps and keep on ice


Best of luck,


Ruud



On 26/10/17 16:18, Anamika Singh wrote:

Dear All,

I am purifying the His-tagged proteins ( 21Kda) using buffer 20mM 
Tris, 150mM Nacl, and 5mM MgCl2 with 500mM imidazole. Earlier I was 
facing the precipitation problem during dialysis but with the addition 
of 50mM L-Arg somehow managed to overcome the precipitation issue. But 
this time I have seen after overnight dialysis there are degradation 
products on SDS page. I have used protease inhibitor (PMSF) in my 
sonication buffer.


Please suggest me to overcome this problem.

Thanks
--
Anamika


--

Ruud Hovius
EPFL SB ISIC LIP
BCH 4209
CH-1015 Lausanne
+41-21-693-9442
http://lip.epfl.ch

[ccp4bb] OFF topic (Protein degrades during Dailysis)

[Anamika Singh]

Dear All,

I am purifying the His-tagged proteins ( 21Kda) using buffer 20mM Tris,
150mM Nacl, and 5mM MgCl2 with 500mM imidazole. Earlier I was facing the
precipitation problem during dialysis but with the addition of 50mM L-Arg
somehow managed to overcome the precipitation issue. But this time I have
seen after overnight dialysis there are degradation products on SDS page. I
have used protease inhibitor (PMSF) in my sonication buffer.

Please suggest me to overcome this problem.

Thanks
-- 
Anamika

Re: [ccp4bb] mtzdmp gives segmentation fault

[Graeme Winter]

Sorry all this was obviously meant for the helpdesk...

Best wishes Graeme

From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Graeme Winter 
[graeme.win...@diamond.ac.uk]
Sent: 26 October 2017 14:56
To: ccp4bb
Subject: [ccp4bb] mtzdmp gives segmentation fault

Folks

I have a data set with 50 wavelengths in - mtzdmp dies as follows:

mtzdmp 
/dls/mx-scratch/gw56/LCY/50/process-all-merge-sep/LCY15/scale/LCY_LCY15_sorted.mtz

 





###
###
###
### CCP4 7.0.044: MTZDUMP  version 1.1 : ##
###
User: gw56  Run date: 26/10/2017 Run time: 14:55:18


Please reference: Collaborative Computational Project, Number 4. 2011.
"Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
as well as any specific reference in the program write-up.





Optional input follows.

Keywords: RESO STATS LRESO HEAD NREF START SKIP SYMM
   BATCH FORMAT RUN/GO/END
RESO max min - resolution limits for listing (default all)
STATS [NBIN num] [RESO max min] - no. of reso. bins and limits for stats.
LRESO -  S is given for each listed reflection
HEAD - print MTZ file header only
NREF num - number of reflections listed (default 10)
START H0 K0 L0 - first reflection listed (default first)
SKIP nskip - no. of refls. skipped before listing (default 0)
SYMMETRY - list symmetry info
VALM num - missing data set to this value
BATCH - list batch orientation blocks

FORMAT fmt - format of listed refls. .e.g. '(3i4,10f8.2)'
RUN/GO/END - to start dump


OPENED INPUT MTZ FILE
Logical Name: HKLIN   Filename: 
/dls/mx-scratch/gw56/LCY/50/process-all-merge-sep/LCY15/scale/LCY_LCY15_sorted.mtz


Program received signal 11 (SIGSEGV): Segmentation fault.

Backtrace for this error:
#0  0x0037a40ac794 in wait () from /lib64/libc.so.6
#1  0x7f863fdb3fdd in ?? () from 
/dls_sw/apps/ccp4/x86_64/7.0/update44/ccp4-7.0/bin/../lib/libgfortran.so.3
#2  0x7f863fdb584e in ?? () from 
/dls_sw/apps/ccp4/x86_64/7.0/update44/ccp4-7.0/bin/../lib/libgfortran.so.3
#3  0x7f863fdb46aa in ?? () from 
/dls_sw/apps/ccp4/x86_64/7.0/update44/ccp4-7.0/bin/../lib/libgfortran.so.3
#4  
#5  0x7f864009df61 in ccp4_lrbats () from 
/dls_sw/apps/ccp4/x86_64/7.0/update44/ccp4-7.0/bin/../lib/libccp4c.so.0
#6  0x0040469b in _start ()
[gw56@cs04r-sc-com99-01 process-all-merge-sep]$ du -hs 
/dls/mx-scratch/gw56/LCY/50/process-all-merge-sep/LCY15/scale/LCY_LCY15_sorted.mtz
188M
/dls/mx-scratch/gw56/LCY/50/process-all-merge-sep/LCY15/scale/LCY_LCY15_sorted.mtz

Is this expected?

Thanks Graeme

--
This e-mail and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
necessarily of Diamond Light Source Ltd.
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

[ccp4bb] mtzdmp gives segmentation fault

[Graeme Winter]

Folks

I have a data set with 50 wavelengths in - mtzdmp dies as follows:

mtzdmp 
/dls/mx-scratch/gw56/LCY/50/process-all-merge-sep/LCY15/scale/LCY_LCY15_sorted.mtz

 





###
###
###
### CCP4 7.0.044: MTZDUMP  version 1.1 : ##
###
User: gw56  Run date: 26/10/2017 Run time: 14:55:18


Please reference: Collaborative Computational Project, Number 4. 2011.
"Overview of the CCP4 suite and current developments". Acta Cryst. D67, 235-242.
as well as any specific reference in the program write-up.





Optional input follows.

Keywords: RESO STATS LRESO HEAD NREF START SKIP SYMM
   BATCH FORMAT RUN/GO/END
RESO max min - resolution limits for listing (default all)
STATS [NBIN num] [RESO max min] - no. of reso. bins and limits for stats.
LRESO -  S is given for each listed reflection
HEAD - print MTZ file header only
NREF num - number of reflections listed (default 10)
START H0 K0 L0 - first reflection listed (default first)
SKIP nskip - no. of refls. skipped before listing (default 0)
SYMMETRY - list symmetry info
VALM num - missing data set to this value
BATCH - list batch orientation blocks

FORMAT fmt - format of listed refls. .e.g. '(3i4,10f8.2)'
RUN/GO/END - to start dump


OPENED INPUT MTZ FILE
Logical Name: HKLIN   Filename: 
/dls/mx-scratch/gw56/LCY/50/process-all-merge-sep/LCY15/scale/LCY_LCY15_sorted.mtz


Program received signal 11 (SIGSEGV): Segmentation fault.

Backtrace for this error:
#0  0x0037a40ac794 in wait () from /lib64/libc.so.6
#1  0x7f863fdb3fdd in ?? () from 
/dls_sw/apps/ccp4/x86_64/7.0/update44/ccp4-7.0/bin/../lib/libgfortran.so.3
#2  0x7f863fdb584e in ?? () from 
/dls_sw/apps/ccp4/x86_64/7.0/update44/ccp4-7.0/bin/../lib/libgfortran.so.3
#3  0x7f863fdb46aa in ?? () from 
/dls_sw/apps/ccp4/x86_64/7.0/update44/ccp4-7.0/bin/../lib/libgfortran.so.3
#4  
#5  0x7f864009df61 in ccp4_lrbats () from 
/dls_sw/apps/ccp4/x86_64/7.0/update44/ccp4-7.0/bin/../lib/libccp4c.so.0
#6  0x0040469b in _start ()
[gw56@cs04r-sc-com99-01 process-all-merge-sep]$ du -hs 
/dls/mx-scratch/gw56/LCY/50/process-all-merge-sep/LCY15/scale/LCY_LCY15_sorted.mtz
188M
/dls/mx-scratch/gw56/LCY/50/process-all-merge-sep/LCY15/scale/LCY_LCY15_sorted.mtz

Is this expected?

Thanks Graeme

-- 
This e-mail and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If you 
are not the intended addressee or an authorised recipient of the addressee 
please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to the e-mail.
Any opinions expressed within this e-mail are those of the individual and not 
necessarily of Diamond Light Source Ltd. 
Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments 
are free from viruses and we cannot accept liability for any damage which you 
may sustain as a result of software viruses which may be transmitted in or with 
the message.
Diamond Light Source Limited (company no. 4375679). Registered in England and 
Wales with its registered office at Diamond House, Harwell Science and 
Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

[ccp4bb] X-ray Lab Manger Birbeck University of London- Permanent Post

[Nicholas Keep]

There is a vacancy for an X-Ray Laboratory Manager at the Institute for 
Structural and Molecular Biology at Birkbeck/UCL based at Birkbeck, 
University of London.


see https://tinyurl.com/y7jgfmr5

This is a permanent University Funded post.  A brief description of the 
role is below and informal enquiries can be made to me 
(n.k...@mail.cryst.bbk.ac.uk).  Closing date is the end of the 10th 
December 2017.


Best wishes

Nick


The Laboratory Manager role will ensure efficient day-to-day running of 
the X-ray Laboratory (including X-ray generators, detectors and 
crystallisation robots) for research staff and students in Biological 
Sciences, the ISMB and for external collaborators and hirers of the 
equipment; ensure that all safety procedures in the laboratory are 
implemented; provide training in use of equipment and to give general 
assistance in crystallography to students and research staff; keep 
abreast of new technologies and methodologies and assess and advise on 
the purchase of new equipment, software, and reagents.
The role holder will coordinate trips to synchrotrons and organise 
Beamline applications. The role holder will also contribute to teaching 
in the department through design, deliver and supervision of practicals, 
tutorials and projects in the general area of molecular biology and 
crystallography


--
Prof Nicholas H. Keep
Executive Dean of School of Science
Professor of Biomolecular Science
Crystallography, Institute for Structural and Molecular Biology,
Department of Biological Sciences
Birkbeck,  University of London,
Malet Street,
Bloomsbury
LONDON
WC1E 7HX

emailn.k...@mail.cryst.bbk.ac.uk
Telephone 020-7631-6852  (Room G54a Office)
  020-7631-6800  (Department Office)
Fax   020-7631-6803
If you want to access me in person you have to come to the crystallography 
entrance
and ring me or the department office from the internal phone by the door

[ccp4bb] Post-doctoral fellowship in Structural Molecular Biology

[Mario Tyago Murakami]

Post-doctoral position in Structural Biology at UFSCAR (Federal University of 
São Carlos) / CNPEM (National Center for Research in Energy and Materials) 
within a Thematic Project on bioluminescence supported by FAPESP, to work with 
Profs. Mario Murakami and Vadim Viviani. Expertise required in protein 
expression and purification, molecular biology, X-ray crystallography and other 
biophysical methods (SAXS and spectroscopy).

Please send CV and two recommendation letters to Mario Murakami 
(mario.murak...@ctbe.cnpem.br) and to 
vivi...@ufscar.br.

This opportunity is open to candidates of any nationalities. The selected 
candidate will receive a FAPESP's Post-Doctoral fellowship in the amount of R$ 
7.174,80 monthly and a research contingency fund, equivalent to 15% of the 
annual value of the fellowship which should be spent in items directly related 
to the research activity.

More information about the fellowship is at: 
www.fapesp.br/en/5427.

Kind regards

[ccp4bb] Seeking information of structural biology PhD programs.

[sadik sattar]

Esteemed members of the structural biology community, 

I am Shadikejiang (preferably Sadiq) from the University of Glasgow. I have recently finished my master’s study and am currently looking for a PhD position in the field of structural biology. I completed my undergraduate study at Shanghai Jiao Tong University, one of the highest-ranked universities within mainland China. After that I was admitted to the Msc Biotechnology program at the University of Glasgow and recently received my Msc degree with distinction. During my master’s project, I worked on crystallysation of a membrane protein from purple bacteria.  I have grown crystals and tested them at Diamond Light Sources (DLS), Oxford, UK. Ever since that project, I have been fervently drawn toward structural biology, and crystallography in particular. I have excellent knowledge of recombinant protein over _expression_, purification, high throughput screening, data collection, and crystal symmetry. I am currently looking for a PhD program in which I can learn more about crystallography, solving the crystal structure as well as other structural biology methods such as cryo-EM. I am writing this message in hopes that you may provide me with valuable information on PhD programs that would be suited to my interests and skill set. I have attached my CV. Any suggestions are highly appreciated. 

Cheers,Sadiq.

Sadiq-CV.pdf
Description: Adobe PDF document

[ccp4bb] Reminder: Travel bursaries to CCP4 Study Weekend 2018 - deadline for applications 31st October 2017 - i.e. next Tuesday

[Karen McIntyre]

TRAVEL BURSARIES

Limited funds have been made available to help pay travel costs for students 
and young post-docs from non-UK laboratories.

Please send a separate letter, signed by your supervisor and stating the 
expected cost of travel in pounds sterling, to justify applications for travel 
support. Supervisors are asked to nominate only one candidate from their 
Laboratory.

Delegates are expected to travel by the most economic means possible.

Candidates from less favoured regions will be given preference.

Applications should be sent to:

Helen Walker
CCP4 Study Weekend Travel Bursary
Science and Technology Facilities Council
Rutherford Appleton Laboratory
RCaH 1.22
Harwell Oxford
Didcot
OX11 0FA, UK

You can also fax copies of your letters to Helen on +44 (0)1235 567720 or 
e-mail ccp4_study_week...@stfc.ac.uk .

Applications for Travel Assistance MUST be received by 31 October 2017.

Regards

Karen McIntyre
CCP4 Study Weekend Local Organising Committee
Scientific Computing Department - CCP4
R92 1.22 RCaH

Science & Technology Facilities Council
Rutherford Appleton Laboratory
Harwell Campus
Didcot
Oxfordshire
OX11 0FA

Tel +44 (0) 1235 44 5790
Fax  +44 (0) 1235 56 7720

[*] @ccp4_mx

[cid:image002.png@01D34736.25FD26F0]

**Please note that I only work part-time until 1.30pm**

Re: [ccp4bb] blast pdb for a very short sequence (3 amino acids)

[Andrew Lovering]

I would guess that you want to search PDB for a small motif you've observed in 
a structure of yours, looking to find examples of it used in same context?
If that's true, I would recommend PDBemotif, put the sequence in, and then use 
the backbone psi phi angles of your motif as a secondary constraint in the 
search, increasing/decreasing the angle tolerance as appropriate.
If I’m incorrect, and you just want to find examples of a short motif, this 
webserver is awesome – you can also limit it by taxonomy:
http://www.genome.jp/tools/motif/MOTIF2.html

Best
Andy

From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of 
xiaolei...@gmail.com
Sent: 26 October 2017 04:40
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] blast pdb for a very short sequence (3 amino acids)

Dear CCP4BB members,

Sorry this post is off-topic. I am asking is there a way to blast pdb for a 
very short sequence like 2 or 3 amino acids?  I tried this for a positive 
control in pdb database but returned that "Your search parameters were adjusted 
to search for a short input sequence."  and "No significant similarity found. ".