Re: [ccp4bb] Finding Homologs with Specific Residues Conserved

[Joana Pereira]

I am also not sure of what your goal is, but you can build a sequence profile 
for your sequence and use that profile as input instead of your sequence. You 
can do this by aligning a set of sequences homologous to your target sequence, 
and use that alignment as input for, for example, HMMER or HHPred. You can also 
let HMMER or HHPred build these profiles for you by giving your sequence as 
input and play with the parameters.

Best,

Dr. Joana Pereira
--
Postdoctoral Researcher
Department of Protein Evolution

Max Planck Institute for Developmental Biology
Spemannstraße 35
72076 Tübingen
GERMANY

> On 20 Dec 2017, at 18:35, Keller, Jacob  wrote:
> 
> Dear Crystallographer-Bioinformaticians,
>  
> Is anyone aware of a way to tweak BLAST or similar software to be able to 
> specify certain residues to be absolutely required, e.g., active site 
> residues? I guess one can winnow broad-scale resuts with scripts, but it 
> would seem to be a pretty common type of thing to do, and might change 
> results slightly a la psi-BLAST.
>  
> All the best,
>  
> Jacob Keller
>  
> +
> Jacob Pearson Keller
> Research Scientist / Looger Lab
> HHMI Janelia Research Campus
> 19700 Helix Dr, Ashburn, VA 20147
> (571)209-4000 x3159
> +
>  
> The content of this email is confidential and intended for the recipient 
> specified in message only. It is strictly forbidden to share any part of this 
> message with any third party, without a written consent of the sender. If you 
> received this message by mistake, please reply to this message and follow 
> with its deletion, so that we can ensure such a mistake does not occur in the 
> future.

Re: [ccp4bb] cannot read h5 data file

[Kay Diederichs]

Dear Shijun,

it is always difficult to answer such questions without very specific 
information, like e.g. exact error messages, and exact description what was 
done. 

In addition to what others wrote, I see two general ways to solve the problem:
a) talk to the beamline people. They should know very well how to process the 
data collected at their beamline, and the procedures should be documented on 
the beamline web pages (though I did not find anything at 
http://ssrf.sinap.ac.cn/english/3/BL17U1.htm).
b) make a dataset available by Dropbox or Google Drive or the like, and ask the 
software developers for help

In the specific case of XDS, there are several ways to obtain XDS.INP: 
1) the beamline software should write it
2) try
generate_XDS.INP .h5
but important details may be wrong if the developers of generate_XDS.INP don't 
know the specifics of the particular beamline (the XDSwiki article called 
"Beamline notes" indicates that ROTATION_AXIS=-1 0 0 should probably be used). 
This is why a dataset from that beamline would be useful.
3) there is a nice script XDS_from_H5.py that can be obtained from 
https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Eiger#Script_for_generating_XDS.INP_from_master.h5
 which should generate a good XDS.INP

In case of XDSGUI, either H5ToXds must be installed, or the Neggia plugin must 
be available and specified in menu/settings - but this is _only_ needed to show 
a frame in the "Frame" tab, _not_ for running XDS by XDSGUI.

HTH,

Kay

On Wed, 20 Dec 2017 16:50:11 +0800, 张士军 <21620150150...@stu.xmu.edu.cn> wrote:

> Dear all
>
>  I just collected some data with Eiger16M whose file format is *.h5. But I 
> cannot read it with HKL2000, because I don't have the Eiger16M 
> detector license now, while, I have *.cbf detector license. So I transfered 
> the *.h5 to *.cbf files, but the problem is  XDSGUI still cannot read
> them,and HKL2000 can read it, can search peak, but cannot index it with 
> warning me ''no enough peaks to index the data'',when I check the
> peaks are much enough to index, whearas dials can read  it, but the cell 
> parameters are not the same with before. Anyone can tell me what's
> wrong with it? Thanks a lot !!!
>
> Best Regards
>
> Shijun

Re: [ccp4bb] Finding Homologs with Specific Residues Conserved

[Christian Roth]

Not sure if I understand the question right, but wouldn't phi-blast do
trick. You supply on too your conserved pattern and blast again.

Christian

Am 20.12.2017 19:37 schrieb "Keller, Jacob" :

> Dear Crystallographer-Bioinformaticians,
>
>
>
> Is anyone aware of a way to tweak BLAST or similar software to be able to
> specify certain residues to be absolutely required, e.g., active site
> residues? I guess one can winnow broad-scale resuts with scripts, but it
> would seem to be a pretty common type of thing to do, and might change
> results slightly a la psi-BLAST.
>
>
>
> All the best,
>
>
>
> Jacob Keller
>
>
>
> +
>
> Jacob Pearson Keller
>
> Research Scientist / Looger Lab
>
> HHMI Janelia Research Campus
>
> 19700 Helix Dr, Ashburn, VA 20147
> 
>
> (571)209-4000 x3159 <(571)%20209-4000>
>
> +
>
>
>
> The content of this email is confidential and intended for the recipient
> specified in message only. It is strictly forbidden to share any part of
> this message with any third party, without a written consent of the sender.
> If you received this message by mistake, please reply to this message and
> follow with its deletion, so that we can ensure such a mistake does not
> occur in the future.
>
>
>

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[Joseph Batchelor]

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[ccp4bb] Finding Homologs with Specific Residues Conserved

[Keller, Jacob]

Dear Crystallographer-Bioinformaticians,

Is anyone aware of a way to tweak BLAST or similar software to be able to 
specify certain residues to be absolutely required, e.g., active site residues? 
I guess one can winnow broad-scale resuts with scripts, but it would seem to be 
a pretty common type of thing to do, and might change results slightly a la 
psi-BLAST.

All the best,

Jacob Keller

+
Jacob Pearson Keller
Research Scientist / Looger Lab
HHMI Janelia Research Campus
19700 Helix Dr, Ashburn, VA 20147
(571)209-4000 x3159
+

The content of this email is confidential and intended for the recipient 
specified in message only. It is strictly forbidden to share any part of this 
message with any third party, without a written consent of the sender. If you 
received this message by mistake, please reply to this message and follow with 
its deletion, so that we can ensure such a mistake does not occur in the future.

Re: [ccp4bb] average B-factors

[Tristan Croll]

This is quite straightforward in any package with a reasonable scripting 
interface. In ChimeraX, for example:


-load your model
-make your selection 
(https://www.rbvi.ucsf.edu/chimerax/docs/user/selection.html)

-open the shell (Tools/General/Shell), and in it, type:

from chimerax.core.atomic import selected_atoms
sel = selected_atoms(session)
sel.bfactors.mean()

Hope this helps,

Tristan

On 2017-12-20 15:02, Amir Khan wrote:

Dear all,

Sorry for naive CCP4 question, is there a simple way to calculate
average B-factors (side chain, backbone, all)
for only part of a model, such as a domain, loop, etc…

Thanks,
Amir

Re: [ccp4bb] cannot read h5 data file

[Emilia C. Arturo (Emily)]

Shijun,

I have processed .h5 format data successfully that was collected at NSLS II
AMX (this beamline has a Eiger 9M, not 16M, incidentally, but I don't think
that this matters). I used XDSGUI without converting to .cbf format. To do
so, and without knowing what the error messages are that you are receiving
as output, it is important that you include the following two lines, at
minimum, in your XDS.INP file: DETECTOR= EIGER and include the correct
'LIB=' line; for instructions on the latter, see the XDSWiki page here:
https://strucbio.biologie.uni-konstanz.de/xdswiki/index.php/Eiger#Script_for_generating_XDS.INP_from_master.h5
, and get the XDS Neggia plugin here:
https://www.dectris.com/company/news/newsroom/news-details/process-eiger-data-with-xds-fast
. nb You will need to register to download the plugin, and *do* read the
README file.  :-)

Wishing you well,

Emily.

On Wed, Dec 20, 2017 at 3:50 AM, 张士军 <21620150150...@stu.xmu.edu.cn> wrote:

> Dear all
>
>I just collected some data with Eiger16M whose file format is *.h5. But
> I cannot read it with HKL2000, because I don't have the Eiger16M detector
> license now, while, I have *.cbf detector license. So I transfered the *.h5
> to *.cbf files, but the problem is  XDSGUI still cannot read them,and
> HKL2000 can read it, can search peak, but cannot index it with warning me
> ''no enough peaks to index the data'',when I check the peaks are much
> enough to index, whearas dials can read  it, but the cell parameters are
> not the same with before. Anyone can tell me what's wrong with it? Thanks a
> lot !!!
>
> Best Regards
>
> Shijun
>



-- 
"Study as if you were going to live forever; live as if you were going to
die tomorrow." - Maria Mitchell

"I'm not afraid of storms for I'm learning to sail my ship."  - Louisa May
Alcott

Re: [ccp4bb] average B-factors

[Eleanor Dodson]

Easy with GUI2
Import coordinates and select the part you want

Under validation and analysis

Choose analysis Bs etc and you will get your answer

BAVERAGE will give you Bs for main chain & side chain for each monomer but
there is no selection option - you would have to do that in some other way

Eleanor

On 20 December 2017 at 15:02, Amir Khan  wrote:

> Dear all,
>
> Sorry for naive CCP4 question, is there a simple way to calculate average
> B-factors (side chain, backbone, all)
> for only part of a model, such as a domain, loop, etc…
>
> Thanks,
> Amir

[ccp4bb] average B-factors

[Amir Khan]

Dear all,

Sorry for naive CCP4 question, is there a simple way to calculate average 
B-factors (side chain, backbone, all)
for only part of a model, such as a domain, loop, etc…

Thanks,
Amir

Re: [ccp4bb] cannot read h5 data file

[Harry Powell]

Hi Graeme and Shijun

eiger2cbf was indeed used for the conversion - so the metadata should be in the 
CBF headers (unless the H5 files produced do not conform to what eiger2cbf 
expects). The most recent version of eiger2cbf should be used rather than the 
one on the Mosflm website!

My guess is that the images are from the Shanghai synchrotron, where they have 
a 16M. In which case, the beam centre and the direction of rotation should be 
checked carefully. 

Since the images are now in CBF format, even if Shijun wanted to continue 
processing in another package, I would recommend reading them into iMosflm and 

(a) making sure that the displayed beam centre cross corresponds to where the 
beam position is likely to be

(b) checking that there are plenty of spots displayed (I think the iMosflm 
display should be able to add the CBFs for display purposes, but I can't 
remember if this feature made it into the release copy before I left LMB early 
in 2016)

(c) provided that (a) and (b) are okay, then Shijun should index with 

(i) one image at the start of data collection
(ii) one image around 90º away

(iii) check the answer is the same (within experimental error) for (i) 
and (ii)

then 

(iv) index with both the images used in (i) and (ii) together.
(v) check the answer is the same as in (i) and (ii).

Success at (i) and (ii) followed by failure at (iv) and/or (v) is often a good 
indication that the spindle rotation is opposite to what is expected. 

Harry
--
Dr Harry Powell
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 




On 20 Dec 2017, at 09:12, Graeme Winter wrote:

> Dear Shijun
> 
> How did you convert?
> 
> If H5ToXDS it throws away all header information - this tool will preserve 
> the metadata:
> 
> https://github.com/biochem-fan/eiger2cbf
> 
> which should allow XDSGUI to work. If DIALS can read the data but comes out 
> with the wrong answer, please could you provide some more information (off 
> list) so that we can assist?
> 
> There was a thread a couple of days ago re: HKL with Eigers - short version 
> is that you need an update, apparently.
> 
> While writing I see your subsequent question:
> 
> "When I run dials.index it result me "Sorry: No suitable lattice could be 
> found", but the other software can give me C2 space group. How could I DO 
> with this situation"
> 
> Check the meta data - look at the images, is the beam centre in about the 
> correct position? Is the spindle rotation correct?
> 
> Best wishes Graeme
> 
> 
> 
> From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of 张士军 
> [21620150150...@stu.xmu.edu.cn]
> Sent: 20 December 2017 08:50
> To: ccp4bb
> Subject: [ccp4bb] cannot read h5 data file
> 
> 
> Dear all
> 
>   I just collected some data with Eiger16M whose file format is *.h5. But I 
> cannot read it with HKL2000, because I don't have the Eiger16M detector 
> license now, while, I have *.cbf detector license. So I transfered the *.h5 
> to *.cbf files, but the problem is  XDSGUI still cannot read them,and HKL2000 
> can read it, can search peak, but cannot index it with warning me ''no enough 
> peaks to index the data'',when I check the peaks are much enough to index, 
> whearas dials can read  it, but the cell parameters are not the same with 
> before. Anyone can tell me what's wrong with it? Thanks a lot !!!
> 
> Best Regards
> 
> Shijun
> 
> -- 
> 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

Re: [ccp4bb] cannot read h5 data file

[Graeme Winter]

Dear Shijun

How did you convert?

If H5ToXDS it throws away all header information - this tool will preserve the 
metadata:

https://github.com/biochem-fan/eiger2cbf

which should allow XDSGUI to work. If DIALS can read the data but comes out 
with the wrong answer, please could you provide some more information (off 
list) so that we can assist?

There was a thread a couple of days ago re: HKL with Eigers - short version is 
that you need an update, apparently.

While writing I see your subsequent question:

"When I run dials.index it result me "Sorry: No suitable lattice could be 
found", but the other software can give me C2 space group. How could I DO with 
this situation"

Check the meta data - look at the images, is the beam centre in about the 
correct position? Is the spindle rotation correct?

Best wishes Graeme



From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of 张士军 
[21620150150...@stu.xmu.edu.cn]
Sent: 20 December 2017 08:50
To: ccp4bb
Subject: [ccp4bb] cannot read h5 data file


Dear all

   I just collected some data with Eiger16M whose file format is *.h5. But I 
cannot read it with HKL2000, because I don't have the Eiger16M detector license 
now, while, I have *.cbf detector license. So I transfered the *.h5 to *.cbf 
files, but the problem is  XDSGUI still cannot read them,and HKL2000 can read 
it, can search peak, but cannot index it with warning me ''no enough peaks to 
index the data'',when I check the peaks are much enough to index, whearas dials 
can read  it, but the cell parameters are not the same with before. Anyone can 
tell me what's wrong with it? Thanks a lot !!!

Best Regards

Shijun

-- 
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] Dials

[张士军]

Dear all

When I run dials.index it result me "Sorry: No suitable lattice could be 
found", but the other software can give me C2 space group. How could I DO with 
this situation

Best Regards

Shijun

[ccp4bb] cannot read h5 data file

[张士军]

Dear all

   I just collected some data with Eiger16M whose file format is *.h5. But I 
cannot read it with HKL2000, because I don't have the Eiger16M detector license 
now, while, I have *.cbf detector license. So I transfered the *.h5 to *.cbf 
files, but the problem is  XDSGUI still cannot read them,and HKL2000 can read 
it, can search peak, but cannot index it with warning me ''no enough peaks to 
index the data'',when I check the peaks are much enough to index, whearas dials 
can read  it, but the cell parameters are not the same with before. Anyone can 
tell me what's wrong with it? Thanks a lot !!!

Best Regards

Shijun