Re: [ccp4bb] Question about small molecule crystallography

[Winter, Graeme (DLSLtd,RAL,LSCI)]

Hi Jon

Ambiguous phrasing, perhaps - the detector has a maximum count rate, as events 
per second, and it is easy to exceed this with a good quality small molecule 
crystal on an undulator beamline thus under record the intensity of strong 
reflections

Best wishes Graeme

On 8 Jun 2020, at 20:55, bogba...@yahoo.co.uk 
wrote:

Re: "it turns out to be very very easy to exceed the count rate where the 
detector electronics can keep up."

Sorry if this is obvious, but I take it you mean "_can't_" keep up?

Jon Cooper

On 4 Jun 2020 13:06, "Winter, Graeme (DLSLtd,RAL,LSCI)" 
mailto:graeme.win...@diamond.ac.uk>> wrote:
Dear All,

A small word of caution regarding chemical crystallography on an MX-like 
beamline - if you have a bright source, a well diffracting crystal and a pixel 
array detector it is perfectly possible to lose counts in the strongest 
reflections without noticing - certainly without going over the nominal 
detector count limits if your mosaic spread is very small

At Diamond we faced this issue with i19, which is a dedicated chemical 
crystallography beamline on an undulator source, with a Pilatus 2 detector - it 
turns out to be very very easy to exceed the count rate where the detector 
electronics can keep up. This is somewhat less of a problem with Pilatus 3 and 
Eiger 2X detectors.

So: I would strongly suggest really turning down the intensity on the beam, use 
fine slicing and be prepared to check that the data are OK before removing your 
sample. You can solve and refine the structure with e.g. SHELX and get an F^2 
calc vs. I ops plot which would show systematically under measured low angle 
reflections.

We also have a tool in development to bolt on to DIALS called screen19 which 
estimates the true peak photon rate from a “quick screening run” to offer 
insights into data collection options - https://github.com/xia2/screen19 - this 
is not perfect but you could find it useful. Our chemical crystallography users 
certainly find it helpful for planning their experiments.

Best wishes Graeme

On 4 Jun 2020, at 10:51, Alker, Andre M. 
<4599f25026c0-dmarc-requ...@jiscmail.ac.uk>
 wrote:

Dear Jiyuan,

maybe I can add something from the small molecule crystallographer view :-)

Crystallization:
For crystallization of small molecules you normally use solvents and water or 
mixtures as mentioned already before. At my lab the most successful way to 
crystallise is evaporation. Please use small glass vials (no plastic, some 
solvents will solute them too).

You can also use crystallization kits. Here you can use Bernhard Spinglers kit 
and or the Hampton kit. The Hampton kit didn't work so well for my molecules. I 
also bought Bernhard's kit but had no time to test it so far. I have to say I'm 
only using crystallization kits at the moment as last try. Maybe that changes 
in the future.

Measurement:
Of course you can use the synchrotron for small molecules at the protein 
beamline. I'm using the PXII protein beamline at the SLS (Swiss light source) 
for my small molecules if the crystals are too small for my inhouse system or 
there is a problem with my inhouse system. To get the resolution you need for 
structure solution and a good refinement you have to change the wavelength to 
0.7Å. Collect always at least 360 degrees  in steps of 0.5 degrees or smaller. 
Use high filters and short exposure times to secure your crystal against 
radiation damage. Normally 10 to 20% of the beam and 0.01 to 0.1 sec work fine 
depending on the crystal size. Do the measurement at low temperatures as usual 
for protein crystals. Here are my parameters for the SLS-PXII beamline equipped 
with an Eiger detector (wavelength 0.7Å, biggest aperture, 20% transmission, 
step 0.1 deg/0.01 sec, 1800 degrees, 100K).

Processing, structure solution and refinement:
I process the eiger data with XDS,
for structure solution I'm using shelxs or shelxd,
for structure refinement shelxl.

But as mentioned before there are a lot of programs doing processing, structure 
solution and refinement. I just started to use Olex as well for solution and 
refinement. In very earlier times I also used hkl2000 for data processing but 
in my opinion XDS is doing a very good job for small molecule data.

Last but not least I deeply agree with Navdeep to read Mueller et al.'s 
excellent book about Crystal Structure Refinement.

Hope this helps a little bit :-)

Best regards,
André






André Alker
Senior Scientist, pCMC Analytics
Roche Pharmaceutical Research and Early Development
Roche Innovation Center Basel
F. Hoffmann-La Roche Ltd
Grenzacherstrasse 124
4058 Basel, Switzerland
Phone: +41-61-6880935
email: andre_m.al...@roche.com

Upcoming absences:
...

Hinweis:
Der Inhalt dieser E-Mail kann vertrauliche Angaben enthalten, die nur für den 
(die) namentlich genannten Empfänger bestimmt sind. Falls Sie nicht der 
Adressat 

Re: [ccp4bb] Question about small molecule crystallography

[00000c2488af9525-dmarc-request]

Re: "it turns out to be very very easy to exceed the count rate where the detector electronics can keep up."Sorry if this is obvious, but I take it you mean "_can't_" keep up?Jon CooperOn 4 Jun 2020 13:06, "Winter, Graeme (DLSLtd,RAL,LSCI)"  wrote:
Dear All,


A small word of caution regarding chemical crystallography on an MX-like beamline - if you have a bright source, a well diffracting crystal and a pixel array detector it is perfectly possible to lose counts in the strongest reflections without
 noticing - certainly without going over the nominal detector count limits if your mosaic spread is very small


At Diamond we faced this issue with i19, which is a dedicated chemical crystallography beamline on an undulator source, with a Pilatus 2 detector - it turns out to be very very easy to exceed the count rate where the detector electronics can keep
 up. This is somewhat less of a problem with Pilatus 3 and Eiger 2X detectors.


So: I would strongly suggest really turning down the intensity on the beam, use fine slicing and be prepared to check that the data are OK before removing your sample. You can solve and refine the structure with e.g. SHELX and get an F^2 calc
 vs. I ops plot which would show systematically under measured low angle reflections. 


We also have a tool in development to bolt on to DIALS called screen19 which estimates the true peak photon rate from a “quick screening run” to offer insights into data collection options - https://github.com/xia2/screen19 -
 this is not perfect but you could find it useful. Our chemical crystallography users certainly find it helpful for planning their experiments. 


Best wishes Graeme


On 4 Jun 2020, at 10:51, Alker, Andre M. <4599f25026c0-dmarc-requ...@jiscmail.ac.uk> wrote:



Dear Jiyuan,


maybe I can add something from the small molecule crystallographer view :-)


Crystallization:
For crystallization of small molecules you normally use solvents and water or mixtures as mentioned already before. At my lab the most successful way to crystallise is evaporation. Please use small glass vials (no plastic, some solvents
 will solute them too). 


You can also use crystallization kits. Here you can use Bernhard Spinglers kit and or the Hampton kit. The Hampton kit didn't work so well for my molecules. I also bought Bernhard's kit but had no time to test it so far. I have to say
 I'm only using crystallization kits at the moment as last try. Maybe that changes in the future.


Measurement: 
Of course you can use the synchrotron for small molecules at the protein beamline. I'm using the PXII protein beamline at the SLS (Swiss light source) for my small molecules if the crystals are too small for my inhouse system or there is a problem
 with my inhouse system. To get the resolution you need for structure solution and a good refinement you have to change the wavelength to 0.7Å. Collect always at least 360 degrees  in steps of 0.5 degrees or smaller. Use high filters and short exposure times
 to secure your crystal against radiation damage. Normally 10 to 20% of the beam and 0.01 to 0.1 sec work fine depending on the crystal size. Do the measurement at low temperatures as usual for protein crystals. Here are my parameters for the SLS-PXII beamline
 equipped with an Eiger detector (wavelength 0.7Å, biggest aperture, 20% transmission, step 0.1 deg/0.01 sec, 1800 degrees, 100K).


Processing, structure solution and refinement:
I process the eiger data with XDS, 
for structure solution I'm using shelxs or shelxd, 
for structure refinement shelxl. 


But as mentioned before there are a lot of programs doing processing, structure solution and refinement. I just started to use Olex as well for solution and refinement. In very earlier times I also used hkl2000 for data processing but
 in my opinion XDS is doing a very good job for small molecule data.


Last but not least I deeply agree with Navdeep to read Mueller et al.'s excellent book about Crystal Structure Refinement. 


Hope this helps a little bit :-)


Best regards,
André



























































André Alker
Senior Scientist, pCMC Analytics
Roche Pharmaceutical Research and Early Development
Roche Innovation Center Basel

F. Hoffmann-La Roche Ltd
Grenzacherstrasse 124
4058 Basel, Switzerland
Phone: +41-61-6880935
email: andre_m.al...@roche.com



Upcoming absences: 
...


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Re: [ccp4bb] [EXTERNAL] [ccp4bb] CCP4I2: non standard ssh port for remote jobs

[Edward Berry]

>>> Michael Weyand  06/08/20 12:40 PM >>>
Dear CCP4I2 experts,

I'm trying to submit remote jobs via SSH within CCP4i2. Unfortunately,
we use a non standard SSH port.
So far, I'm not able to add any option within the CCP4I2 interface. For
job submission, I need something to do like

'ssh -p X -Y . ccp4i-specific-command ...'.

Is there any chance to enter this '-p' SSH option within CCP4i2? I tried
already to define a "ssh command" via "Preferences".
But so far without any success.
==
Not sure if this is applicable, but you can set an alias name
to be equivalent to a real host with a non-standard port.
Something like: 

in ~/.ssh/config or /etc/ssh/ssh_config:


Host oswego
   hostname sanpablo

   hostkeyalias "[sanpablo]:8123"

   port 8123



"hostkeyalias" refers to one key in ~/.ssh/known_hosts that looks like:
[sanpablo]:8101,[192.168.2.4]:8123 ecdsa-sha2-nist
I'm not sure if I entered that or it was made the first time I logged in and 
said "yes".

So I or a program I'm running can issue "ssh oswego" and get connected to port 
8123 on sanpablo without needing to enter a password.

I'm also wondering why there is a sshkey file option. If an user already
uses a ssh-key for a client/server connection, why is necessary to
re-input the key file again?
Any ssh between client and server should work from scratch ...

Any hints are highly appreciated,
Michael



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Re: [ccp4bb] Any advice on specs for a new Mac Laptop to run CCP4 and other Xtal Software?

[Goldman, Adrian]

I tend to agree - though I am still using a 15” machine myself - the lab has 
13” machines and at their desks they have a big monitor as well.  

Adrian

> On 8 Jun 2020, at 17:37, Harry Powell - CCP4BB 
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> Hi
> 
> I’d make the decision based largely on where I was going to use it, and how 
> much I was going to have to carry it (and if I ever wanted to use it in coach 
> class). If it was going to be my machine for “on the road”, I’d go for the 
> 13” one, but if it was going to sit on my desk most of the time (and do what 
> a traditional desktop does), I’d go for the larger one. 
> 
> I “traded down” to a 13” after many years using 15”+ laptops a few years ago 
> and have never regretted it, even when I have to put my reading glasses on to 
> read what’s on the screen.
> 
> However, if you _really_ need 64GB RAM, you don’t have much of a choice.
> 
> Just my two ha’porth
> 
> Harry
> 
>> On 8 Jun 2020, at 17:07, Diana Tomchick  
>> wrote:
>> 
>> Make sure the 13” display is large enough to display all the GUIs for 
>> program suites that you are interested in.
>> 
>> For example, in the past, the 13” Mac laptops couldn’t display the HKL2000 
>> GUI. Requirements are found here:
>> 
>> https://hkl-xray.com/hardware-operating-systems
>> 
>> Diana
>> 
>> **
>> Diana R. Tomchick
>> Professor
>> Departments of Biophysics and Biochemistry
>> UT Southwestern Medical Center
>> 5323 Harry Hines Blvd.
>> Rm. ND10.214A
>> Dallas, TX 75390-8816
>> diana.tomch...@utsouthwestern.edu
>> (214) 645-6383 (phone)
>> (214) 645-6353 (fax)
>> 
>> On Jun 8, 2020, at 10:56 AM, Scott Pegan  wrote:
>> 
>> 
>> EXTERNAL MAIL
>> 
>> 
>> Finally looking to replace my 2014 Mac Pro lap (duo core; 16 gb RAM. I would 
>> welcome any input or being put in the direction of some related to the 
>> following:
>> 
>> 13" versus 16"
>> 
>> I know the 16" has a better and standalone GPU.  Is there anyone using a 13" 
>> that finds that it works well? If so, what were the specs
>> 
>> Memory for the 16"
>> 
>> Torn between 16 gb and 32 gb RAM for the next computer.  Apple asks a 
>> premium for the 32 gb, but some say that now with the SSD's it's not as big 
>> of a deal. Any thoughts?
>> 
>> GPU
>> 
>> For the 15", apple has two 4 gb and an 8 gb. Does anyone have any experience 
>> on these for running CCP4 and other Xtal software on these?
>> 
>> Thanks for your help in advance, looking to get something that is a Mac, 
>> robust to last a while spec wise.  However, not looking to buy something 
>> that is the equivalent of a small car in price and overkill.
>> 
>> Scott
>> 
>> 
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>> 
>> 
>> CAUTION: This email originated from outside UTSW. Please be cautious of 
>> links or attachments, and validate the sender's email address before 
>> replying.
>> 
>> 
>> 
>> 
>> UT Southwestern 
>> 
>> Medical Center
>> 
>> The future of medicine, today.
>> 
>> 
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
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Re: [ccp4bb] CCP4I2: non standard ssh port for remote jobs

[Christian Becke]

Dear Michael,

I've been playing around a bit with remote job submission via SSH in 
CCP4 7.0. I remember I had to patch some files and upgraded a python lib 
to add support for ED25519 keys and to allow passing non-standard ports 
through the GUI. I never got around to wrap this up and forward it to 
the CCP4 devs. If you think this is useful (and I can port the patches 
to CCP4 7.1), I could have another look and wrap this up so I can share it.


All the best,

Christian

Am 08.06.20 um 18:39 schrieb Michael Weyand:

Dear CCP4I2 experts,

I'm trying to submit remote jobs via SSH within CCP4i2. Unfortunately,
we use a non standard SSH port.
So far, I'm not able to add any option within the CCP4I2 interface. For
job submission, I need something to do like

'ssh -p X -Y . ccp4i-specific-command ...'.

Is there any chance to enter this '-p' SSH option within CCP4i2? I tried
already to define a "ssh command" via "Preferences".
But so far without any success.

I'm also wondering why there is a sshkey file option. If an user already
uses a ssh-key for a client/server connection, why is necessary to
re-input the key file again?
Any ssh between client and server should work from scratch ...

Any hints are highly appreciated,
Michael



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[ccp4bb] CCP4I2: non standard ssh port for remote jobs

[Michael Weyand]

Dear CCP4I2 experts,

I'm trying to submit remote jobs via SSH within CCP4i2. Unfortunately,
we use a non standard SSH port.
So far, I'm not able to add any option within the CCP4I2 interface. For
job submission, I need something to do like

'ssh -p X -Y . ccp4i-specific-command ...'.

Is there any chance to enter this '-p' SSH option within CCP4i2? I tried
already to define a "ssh command" via "Preferences".
But so far without any success.

I'm also wondering why there is a sshkey file option. If an user already
uses a ssh-key for a client/server connection, why is necessary to
re-input the key file again?
Any ssh between client and server should work from scratch ...

Any hints are highly appreciated,
Michael



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Re: [ccp4bb] Any advice on specs for a new Mac Laptop to run CCP4 and other Xtal Software?

[Harry Powell - CCP4BB]

Hi

I’d make the decision based largely on where I was going to use it, and how 
much I was going to have to carry it (and if I ever wanted to use it in coach 
class). If it was going to be my machine for “on the road”, I’d go for the 13” 
one, but if it was going to sit on my desk most of the time (and do what a 
traditional desktop does), I’d go for the larger one. 

I “traded down” to a 13” after many years using 15”+ laptops a few years ago 
and have never regretted it, even when I have to put my reading glasses on to 
read what’s on the screen.

However, if you _really_ need 64GB RAM, you don’t have much of a choice.

Just my two ha’porth

Harry

> On 8 Jun 2020, at 17:07, Diana Tomchick  
> wrote:
> 
> Make sure the 13” display is large enough to display all the GUIs for program 
> suites that you are interested in.
> 
> For example, in the past, the 13” Mac laptops couldn’t display the HKL2000 
> GUI. Requirements are found here:
> 
> https://hkl-xray.com/hardware-operating-systems
> 
> Diana
> 
> **
> Diana R. Tomchick
> Professor
> Departments of Biophysics and Biochemistry
> UT Southwestern Medical Center
> 5323 Harry Hines Blvd.
> Rm. ND10.214A
> Dallas, TX 75390-8816
> diana.tomch...@utsouthwestern.edu
> (214) 645-6383 (phone)
> (214) 645-6353 (fax)
> 
> On Jun 8, 2020, at 10:56 AM, Scott Pegan  wrote:
> 
> 
> EXTERNAL MAIL
> 
> 
> Finally looking to replace my 2014 Mac Pro lap (duo core; 16 gb RAM. I would 
> welcome any input or being put in the direction of some related to the 
> following:
> 
> 13" versus 16"
> 
> I know the 16" has a better and standalone GPU.  Is there anyone using a 13" 
> that finds that it works well? If so, what were the specs
> 
> Memory for the 16"
> 
> Torn between 16 gb and 32 gb RAM for the next computer.  Apple asks a premium 
> for the 32 gb, but some say that now with the SSD's it's not as big of a 
> deal. Any thoughts?
> 
> GPU
> 
> For the 15", apple has two 4 gb and an 8 gb. Does anyone have any experience 
> on these for running CCP4 and other Xtal software on these?
> 
> Thanks for your help in advance, looking to get something that is a Mac, 
> robust to last a while spec wise.  However, not looking to buy something that 
> is the equivalent of a small car in price and overkill.
> 
> Scott
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 
> 
> CAUTION: This email originated from outside UTSW. Please be cautious of links 
> or attachments, and validate the sender's email address before replying.
> 
> 
> 
> 
> UT Southwestern 
> 
> Medical Center
> 
> The future of medicine, today.
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
> 



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Re: [ccp4bb] Any advice on specs for a new Mac Laptop to run CCP4 and other Xtal Software?

[Diana Tomchick]

Make sure the 13” display is large enough to display all the GUIs for program 
suites that you are interested in.

For example, in the past, the 13” Mac laptops couldn’t display the HKL2000 GUI. 
Requirements are found here:

https://hkl-xray.com/hardware-operating-systems

Diana

**
Diana R. Tomchick
Professor
Departments of Biophysics and Biochemistry
UT Southwestern Medical Center
5323 Harry Hines Blvd.
Rm. ND10.214A
Dallas, TX 75390-8816
diana.tomch...@utsouthwestern.edu
(214) 645-6383 (phone)
(214) 645-6353 (fax)

On Jun 8, 2020, at 10:56 AM, Scott Pegan 
mailto:scott.d.pe...@gmail.com>> wrote:


EXTERNAL MAIL

Finally looking to replace my 2014 Mac Pro lap (duo core; 16 gb RAM. I would 
welcome any input or being put in the direction of some related to the 
following:

13" versus 16"

I know the 16" has a better and standalone GPU.  Is there anyone using a 13" 
that finds that it works well? If so, what were the specs

Memory for the 16"

Torn between 16 gb and 32 gb RAM for the next computer.  Apple asks a premium 
for the 32 gb, but some say that now with the SSD's it's not as big of a deal. 
Any thoughts?

GPU

For the 15", apple has two 4 gb and an 8 gb. Does anyone have any experience on 
these for running CCP4 and other Xtal software on these?

Thanks for your help in advance, looking to get something that is a Mac, robust 
to last a while spec wise.  However, not looking to buy something that is the 
equivalent of a small car in price and overkill.

Scott






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or attachments, and validate the sender's email address before replying.





UT Southwestern


Medical Center



The future of medicine, today.




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[ccp4bb] Any advice on specs for a new Mac Laptop to run CCP4 and other Xtal Software?

[Scott Pegan]

Finally looking to replace my 2014 Mac Pro lap (duo core; 16 gb RAM. I
would welcome any input or being put in the direction of some related to
the following:

13" versus 16"

I know the 16" has a better and standalone GPU.  Is there anyone using a
13" that finds that it works well? If so, what were the specs

Memory for the 16"

Torn between 16 gb and 32 gb RAM for the next computer.  Apple asks a
premium for the 32 gb, but some say that now with the SSD's it's not as big
of a deal. Any thoughts?

GPU

For the 15", apple has two 4 gb and an 8 gb. Does anyone have any
experience on these for running CCP4 and other Xtal software on these?

Thanks for your help in advance, looking to get something that is a Mac,
robust to last a while spec wise.  However, not looking to buy something
that is the equivalent of a small car in price and overkill.

Scott



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[ccp4bb] Canceled: [ccp4bb] Cryo-EM for Drug Discovery | Virtual event | June 16, 2020

[Jorg Stetefeld]

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[ccp4bb] Cryo-EM for Drug Discovery | Virtual event | June 16, 2020

[Jorg Stetefeld]

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Re: [ccp4bb] Crosslinking software doubt

[Georg Mlynek]

Dear Jesus, you should look at

https://www.rappsilberlab.org/software/

or

https://www.maxquant.org/

Altough there have been huge strides in recent years in software 
development, XL-MS data processing need still some effort.


Br, Georg.

Am 2020-06-08 um 9:48 AM schrieb JESUS BALTANAS COPADO:


Hi all!

I am new in crosslinking,
We performed in our group some time ago crosslinking, and need help 
with the data processing.


We only have available the molecular weight of the crosslinked 
peptides, so the idea would be to find a free sofware in which you 
could enter the whole sequence of the protein undergone to 
crosslinking, as well as the molecular weights of the peptides as well 
as the molecular weight of the crosslinker, so the software could 
predict which combination of peptides give the unknown molecular 
weights. Do you know some software that could fit my needs?


Thank you very much for your help

Cheers

Jesús.



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[ccp4bb] Cryo-EM for Drug Discovery | Virtual event | June 16, 2020

[H. Raaijmakers]

Cryo-EM for Drug Discovery | June 16, 2020 

What if you could get structural insights at near-atomic resolution of
your most challenging drug targets at a pace that meets that of your
drug discovery projects? 

>From around the world you are invited to join Thermo Fisher Scientific
for Cryo-EM for Drug Discovery- a free, one-day virtual event featuring
the latest solution to address current challenges with SBDD. 

Session Title: How to solve structures at a perfected pace for drug
discovery
Times: 11:00 CEST/05:00 a.m. EDT and 17:00 CEST/11:00 a.m. EDT 

You will discover: 

* An innovative cryo-EM solution optimized for drug discovery
* How this solution can increase your chances in finding hits, lead
compounds and beyond
* Testimonials from your peers on this innovative solution and how
this improves their outcomes and results

This event also includes a virtual networking environment and exhibit
hall. 

Register here [1] 

Cheers, 

Hans 

If you can't join us live, be sure to still register. All registrants
will receive on-demand access to the material. 

Links:
--
[1]
https://www.thermofisher.com/us/en/home/about-us/events/industrial/structures-pace-drug-discovery.html?cid=3so-ccp4-ls



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Re: [ccp4bb] Crosslinking software doubt

[Eleanor Dodson]

Well - there is a CCP4 program seqwt which will give the molecular weight
of the given sequence (s).
You say you know the molecular weight of the crosslink and of the whole
complex..
But then I dont know of any software which can predict the composition - I
think you will have to do the arithmetic yourself .
Eleanor Dodson


On Mon, 8 Jun 2020 at 08:58, JESUS BALTANAS COPADO 
wrote:

> Hi all!
>
> I am new in crosslinking,
> We performed in our group some time ago crosslinking, and need help with
> the data processing.
>
> We only have available the molecular weight of the crosslinked peptides,
> so the idea would be to find a free sofware in which you could enter the
> whole sequence of the protein undergone to crosslinking, as well as the
> molecular weights of the peptides as well as the molecular weight of the
> crosslinker, so the software could predict which combination of peptides
> give the unknown molecular weights. Do you know some software that could
> fit my needs?
>
> Thank you very much for your help
>
> Cheers
>
> Jesús.
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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[ccp4bb] Crosslinking software doubt

[JESUS BALTANAS COPADO]

Hi all!

I am new in crosslinking, 
We performed in our group some time ago crosslinking, and need help  
with the data processing.


We only have available the molecular weight of the crosslinked  
peptides, so the idea would be to find a free sofware in which you  
could enter the whole sequence of the protein undergone to  
crosslinking, as well as the molecular weights of the peptides as well  
as the molecular weight of the crosslinker, so the software could  
predict which combination of peptides give the unknown molecular  
weights. Do you know some software that could fit my needs?


Thank you very much for your help

Cheers

Jesús.



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[ccp4bb] Multiple Postdoctoral Fellowships available at the “Multiscale Research Institute for Complex Systems” at Fudan University of Shanghai

[lyguo]

The Multiscale Research Institute for Complex Systems (MRICS) at Fudan 
University is located at the Zhangjiang Campus of Fudan University and is 
supported by the Shanghai High-level Talents Program.  MRICS is strongly 
committed to the development of novel and effective multi-scale imaging 
technology that spans microscopic molecular structures all the way to 
macroscopic medical imaging, with the aim to provide unprecedented spatial and 
temporal insights into the structures and functions of living beings at all 
levels (molecules, cells, tissues, organs and even whole organisms).  
Specifically for structural biology, MRICS is equipped with a state-of-the-art 
cryo-EM facility that includes FEI Titan Krios with Volta phase plate, Glacios, 
Talos and Aquilos.  MRICS is also located next to Shanghai Synchrotron 
Radiation Facility for X-ray crystallography.
 
Our team includes Nobel laureate and international leading interdisciplinary 
experts.
 
We have new openings for multiple postdoctoral fellows in structural biology 
who will mainly study important biological systems by means of cryo-electron 
microscopy including single-particle and tomography. 
   
Requirements: 
 
The applicants should have a recent Ph.D. degree (within two years of 
graduation) or will have a Ph.D. degree within the next six months in biology 
or chemistry-related fields, be devoted to excellence in scientific research, 
have strong sense of responsibility, and be highly motivated and hardworking.  
For these positions, extensive experience in protein expression and 
purification is a must, while prior experience in X-ray crystallography or 
cryo-EM is a plus, but is not required.  
 
Compensation: 
 
1)We offer internationally competitive salary, fringe benefits and yearly 
bonus.  The level of salary will be determined according to the applicant's 
experience and qualification; 
2)Low-rent housing on campus is provided; 
3)There are ample opportunities to collaborate with world-renown 
laboratories;
4)We provide support for applying for funding opportunities whenever 
applicable.  
 
Shanghai is one of the most cosmopolitan cities in China with strong economy 
and vibrant scientific community. 
 
For interested applicants, please submit postdoctoral application packages (a 
combined pdf) including resumes, representative publications, phone numbers and 
email addresses of three academic referees to mrics...@fudan.edu.cn.
 
We look forward to your joining of our first-class team!



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