Re: [ccp4bb] I cannot download xds

2020-06-28 Thread 00000c2488af9525-dmarc-request 
With wget you can pretend to be somewhere else with the: --referer "http://www../"option. You could even put in the heidelberg url and then the server thinks your request comes from there ;-0Might help ;-?Jon CooperOn 29 Jun 2020 02:17, Murpholino Peligro  wrote:Dear Kay, I can download anything from ftp://ftp.wwpdb.org/pub/pdb/data/structures/divided/mmCIF/ and it is ftp. Something else I guess.ThanksEl dom., 28 de jun. de 2020 a la(s) 14:43, Kay Diederichs (kay.diederi...@uni-konstanz.de) escribió:The problem could be that your current network / firewall does not allow FTP transfer, whereas it does allow HTTP.
HTH
Kay


On Sun, 28 Jun 2020 13:56:34 -0500, Murpholino Peligro  wrote:

>Dear Gianluca and bogbasic, the provided link will send  to a page where if
>you click on "XDS-INTEL64_Linux_x86_64.tar.gz
>"
>it will redirect you to
>ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-INTEL64_Linux_x86_64.tar.gz,
>which was what I already did (from the command line with wget, as suggested
>by Folmer, or aria2c, which are two command line programs to download stuff
>from the web)...
>
>Dear Folmer, I might be a bit unlucky.
>I can download other things (PDFs, some raw frames, etc). Is not my Fedora
>as I get the same result from my girlfriend's macbook and my cell phone
>(png attached).
>
>Dear all, I still can not download XDS from
>ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-INTEL64_Linux_x86_64.tar.gz,
>but if I try from the wiki page
>https://strucbio.biologie.uni-konstanz.de/pub/xds/XDS-INTEL64_Linux_x86_64.tar.gz
>it downloads the compressed folder without any problems.
>
>El dom., 28 de jun. de 2020 a la(s) 10:49, 
>escribió:
>
>> A quick Google search for "download xds" will lead you to this page
>>
>> http://xds.mpimf-heidelberg.mpg.de/html_doc/downloading.html
>>
>>
>>
>> On June 28, 2020 2:39:56 AM GMT+02:00, Murpholino Peligro <
>> murpholi...@gmail.com> wrote:
>>>
>>> ```
>>> ~/Downloads$ aria2c
>>> ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-INTEL64_Linux_x86_64.tar.gz
>>>
>>> 06/27 19:36:10 [NOTICE] Downloading 1 item(s)
>>> [#3065b2 0B/10MiB(0%) CN:1 DL:0B]
>>> ```
>>>
>>> It stays there forever.
>>> Is there an alternative download url?
>>>
>>>
>>> Thanks
>>>
>>> --
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>>
>>
>> --
>> Sent from my Android device with K-9 Mail. Please excuse my brevity.
>>
>
>
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Re: [ccp4bb] I cannot download xds

2020-06-28 Thread Kay Diederichs 
The problem could be that your current network / firewall does not allow FTP 
transfer, whereas it does allow HTTP.
HTH
Kay


On Sun, 28 Jun 2020 13:56:34 -0500, Murpholino Peligro  
wrote:

>Dear Gianluca and bogbasic, the provided link will send  to a page where if
>you click on "XDS-INTEL64_Linux_x86_64.tar.gz
>"
>it will redirect you to
>ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-INTEL64_Linux_x86_64.tar.gz,
>which was what I already did (from the command line with wget, as suggested
>by Folmer, or aria2c, which are two command line programs to download stuff
>from the web)...
>
>Dear Folmer, I might be a bit unlucky.
>I can download other things (PDFs, some raw frames, etc). Is not my Fedora
>as I get the same result from my girlfriend's macbook and my cell phone
>(png attached).
>
>Dear all, I still can not download XDS from
>ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-INTEL64_Linux_x86_64.tar.gz,
>but if I try from the wiki page
>https://strucbio.biologie.uni-konstanz.de/pub/xds/XDS-INTEL64_Linux_x86_64.tar.gz
>it downloads the compressed folder without any problems.
>
>El dom., 28 de jun. de 2020 a la(s) 10:49, 
>escribió:
>
>> A quick Google search for "download xds" will lead you to this page
>>
>> http://xds.mpimf-heidelberg.mpg.de/html_doc/downloading.html
>>
>>
>>
>> On June 28, 2020 2:39:56 AM GMT+02:00, Murpholino Peligro <
>> murpholi...@gmail.com> wrote:
>>>
>>> ```
>>> ~/Downloads$ aria2c
>>> ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-INTEL64_Linux_x86_64.tar.gz
>>>
>>> 06/27 19:36:10 [NOTICE] Downloading 1 item(s)
>>> [#3065b2 0B/10MiB(0%) CN:1 DL:0B]
>>> ```
>>>
>>> It stays there forever.
>>> Is there an alternative download url?
>>>
>>>
>>> Thanks
>>>
>>> --
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>>
>>
>> --
>> Sent from my Android device with K-9 Mail. Please excuse my brevity.
>>
>
>
>
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Re: [ccp4bb] I cannot download xds

2020-06-28 Thread Murpholino Peligro 
Dear Gianluca and bogbasic, the provided link will send  to a page where if
you click on "XDS-INTEL64_Linux_x86_64.tar.gz
"
it will redirect you to
ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-INTEL64_Linux_x86_64.tar.gz,
which was what I already did (from the command line with wget, as suggested
by Folmer, or aria2c, which are two command line programs to download stuff
from the web)...

Dear Folmer, I might be a bit unlucky.
I can download other things (PDFs, some raw frames, etc). Is not my Fedora
as I get the same result from my girlfriend's macbook and my cell phone
(png attached).

Dear all, I still can not download XDS from
ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-INTEL64_Linux_x86_64.tar.gz,
but if I try from the wiki page
https://strucbio.biologie.uni-konstanz.de/pub/xds/XDS-INTEL64_Linux_x86_64.tar.gz
it downloads the compressed folder without any problems.

El dom., 28 de jun. de 2020 a la(s) 10:49, 
escribió:

> A quick Google search for "download xds" will lead you to this page
>
> http://xds.mpimf-heidelberg.mpg.de/html_doc/downloading.html
>
>
>
> On June 28, 2020 2:39:56 AM GMT+02:00, Murpholino Peligro <
> murpholi...@gmail.com> wrote:
>>
>> ```
>> ~/Downloads$ aria2c
>> ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-INTEL64_Linux_x86_64.tar.gz
>>
>> 06/27 19:36:10 [NOTICE] Downloading 1 item(s)
>> [#3065b2 0B/10MiB(0%) CN:1 DL:0B]
>> ```
>>
>> It stays there forever.
>> Is there an alternative download url?
>>
>>
>> Thanks
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
>
> --
> Sent from my Android device with K-9 Mail. Please excuse my brevity.
>



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Re: [ccp4bb] Energy minimization and explicit solvent model

2020-06-28 Thread Daniel M. Himmel, Ph. D. 
The Schrodinger software suite may also have a module that you can use
(https://www.schrodinger.com/platform#product-list-collapse).  You can
contact technical help
for advice.

Daniel


On Wed, Jun 24, 2020 at 7:54 PM Andre LB Ambrosio  wrote:

> Dear Sorin, many thanks for this. Very useful.
>
> By probing the conformational space around the model, I meant to try and
> predict how specific solvent conditions may (or may not) induce
> rearrangement, both intra and intermolecule, within an oligomeric
> multidomain protein compared to it in a crystalline state.
>
> I will have an immediate look at the software and documentation you
> recommended and may eventually reach out for extra help.
>
> With best wishes
>
> Andre.
>
> Em qua., 24 de jun. de 2020 às 16:18, Sorin Draga 
> escreveu:
>
>> Dear Andre,
>>
>> I am not sure what you mean by conformational space around the model, but
>> to answer your question: short energy minimization can be done using, for
>> example, deep view/swiss pdb viewer. However, I think that you are most
>> likely looking for a short bout of molecular dynamics, in which you can use
>> explicit solvent and a proper ionic envelope. There you have a few options
>> - GROMACS, NAMD, AMBER etc. The first 2 are free for academia, but if you
>> have no prior knowledge of MD it can be a little bit tricky to set the
>> system up correctly. Let me know if I can help further.
>>
>> Best,
>>
>> Sorin
>>
>> On Wed, Jun 24, 2020 at 10:08 PM Andre LB Ambrosio 
>> wrote:
>>
>>> Dear colleagues,
>>>
>>> could you please suggest a computational tool to perform energy
>>> minimization of a crystal structure under explicit solvent conditions (i.e,
>>> types and concentrations of ions, pH)?
>>>
>>> I want to observe the solvent effects on the conformational space around
>>> a starting model, all-atom, while preserving its geometry (I guess it can
>>> be better expressed as relaxation).
>>>
>>> Thank you in advance.
>>>
>>> --
>>> Andre LB Ambrosio
>>>
>>> --
>>>
>>> To unsubscribe from the CCP4BB list, click the following link:
>>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>>
>>
>
> --
> Andre LB Ambrosio
>
> --
>
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Re: [ccp4bb] I cannot download xds

2020-06-28 Thread Gianluca Santoni 
A quick Google search for "download xds" will lead you to this page

http://xds.mpimf-heidelberg.mpg.de/html_doc/downloading.html



On June 28, 2020 2:39:56 AM GMT+02:00, Murpholino Peligro 
 wrote:
>```
>~/Downloads$ aria2c
>ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-INTEL64_Linux_x86_64.tar.gz
>
>06/27 19:36:10 [NOTICE] Downloading 1 item(s)
>[#3065b2 0B/10MiB(0%) CN:1 DL:0B]
>```
>
>It stays there forever.
>Is there an alternative download url?
>
>
>Thanks
>
>
>
>To unsubscribe from the CCP4BB list, click the following link:
>https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
>mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
>available at https://www.jiscmail.ac.uk/policyandsecurity/

-- 
Sent from my Android device with K-9 Mail. Please excuse my brevity.



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Re: [ccp4bb] How many microfocus beamlines are in the world?

2020-06-28 Thread CHAVAS Leonard 
I tend to like considering below 10microns as a micro-focus, below the micron 
as a sub-micron beamline. I don't know if any nano-focus, sort to say. XFELs 
are dealing with 100 nm, without the wings, which is really sub-micron to me.

Regards, Leo

-
Leonard Chavas
-
Synchrotron SOLEIL
PROXIMA-1
L'Orme des Merisiers
Saint-Aubin - BP 48
91192 Gif-sur-Yvette Cedex
France
-
Phone : +33 169 359 746
Mobile : +33 644 321 614
E-mail : leonard.cha...@synchrotron-soleil.fr
-

> On 27 Jun 2020, at 14:35, John R Helliwell  wrote:
> 
> Hi,
> At the ISDSB 2019 in Osaka last November I asked Stephen Burley about the 
> BioSync pages, commending how useful they are. Stephen said they had asked 
> for a budget line in their last renewal to help keep the pages up to date but 
> it had been cut. At the next renewal, or earlier, we should write our Letters 
> of Support for the BioSync pages.
> Best wishes,
> John
> Emeritus Professor John R Helliwell DSc
> 
> 
> 
> 
>> On 27 Jun 2020, at 10:41, Rasmus Fogh  wrote:
>> 
>> Dear All,
>> 
>> The link http://biosync.rcsb.org/index.jsp looked very interesting, but a 
>> cursory look found the following line in a beamline description:
>> 
>> "Next proposal submission period Mid 2013"
>> 
>> Not 100% up to date, then.
>> 
>> Yours,
>> Rasmus
>> 
>>> On 25/06/2020 09:36, Andrew Leslie wrote:
>>> Dear Morpholino,
>>> I think 10 microns or under is a reasonable way to define a micro focus 
>>> beam line. There is a list of all MX beamlines at the following web site:
>>> http://biosync.rcsb.org/index.jsp
>>> This gives details of each beam line, including beam size, but you would 
>>> have to go through them all to find the actual number. Also I’m not totally 
>>> sure how often this is updated.
>>> Best wishes,
>>> Andrew
> On 24 Jun 2020, at 23:23, Murpholino Peligro  > wrote:
 
 That's a good point...
 I was thinking that a decent crystal has a size in the hundreds of 
 micrometers (say 100 in a, b and c). So, with such a specimen we can use 
 any MX beamline.
 But if the crystal is smaller (say 10 micrometers in a, b and c) You must 
 use a microfocus beamline.
 *Please correct me if I am wrong.*
 So what are the number of MX beamlines that can get useful data from 
 smaller crystals (as defined above)?
 
 Thanks again
 
 El mié., 24 de jun. de 2020 a la(s) 13:02, James Holton (jmhol...@lbl.gov 
 ) escribió:
 
   Define "micro focus" ?
 
   -James Holton
   MAD Scientist
 
   On 6/24/2020 9:18 AM, Murpholino Peligro wrote:
>   I would like to know how many MX beamlines are micro focus?
> 
> 
>   Thanks.
> 
>   
> 
>   To unsubscribe from the CCP4BB list, click the following link:
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> 
 
 
 
 
 To unsubscribe from the CCP4BB list, click the following link:
 https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
 
>>> 
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>> 
>> 
>> 
>> -- 
>> Rasmus H. Fogh   Tel.: +44 (0)1223 353033
>> Global Phasing Ltd., Fax.: +44 (0)1223 366889
>> Sheraton House,
>> Castle Park,
>> Cambridge CB3 0AX
>> United Kingdom
>> 
>> 
>> 
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Re: [ccp4bb] dewar horror stories

2020-06-28 Thread CHAVAS Leonard 
Users had issues, back at SOLEIL in France, with FedEx, DHL, UPS, French 
post... at many levels. I guess it just depends on luck, or bad luck in the 
present case. The worst case encountered so far though was Dewars lost in 
transit for a couple of weeks. Not to mention countries where import taxes are 
so expensive that it becomes cheaper to buy new Dewars...

Regards, Leo

-
Leonard Chavas
-
Synchrotron SOLEIL
PROXIMA-1
L'Orme des Merisiers
Saint-Aubin - BP 48
91192 Gif-sur-Yvette Cedex
France
-
Phone : +33 169 359 746
Mobile : +33 644 321 614
E-mail : leonard.cha...@synchrotron-soleil.fr
-

> On 27 Jun 2020, at 01:57, Minmin 
> <3d6c0e364a92-dmarc-requ...@jiscmail.ac.uk> wrote:
> 
> A collaborated group met the similar situation with FedEx before and they 
> switched to World courier afterwards. 
> 
> When your shipping dewar is no longer leaking of course, maybe you would like 
> to check out the following link below. According to our users, crystals 
> stored in the CombiPuck seem to get less or no ice up after shipment, 
> possibly because the vials inside the puck helped keep the LN2 temp well.  
> The 16pins puck base format of the CombiPuck is the same format as the 
> UniPuck. It is easy to switch from crystals stored in canes or any other 
> formats of the pucks to the CombiPuck. It is also easy to retrieve the 
> crystals from the CombiPuck back to the canes or any other pucks when needed.
> 
> https://www.mitegen.com/product/combipuck-system/
> 
> 
> 
> On Thu, 25 Jun 2020 at 7:34, Jan Dohnalek
>  wrote:
> We have the suspicion (after several heavy FEDEX failures) they just toss 
> them around ... then the neck easily breaks off.
> That only explains everything we have seen with completely damaged samples, 
> lost, flying around the dewar etc ...
> When trying to communicate seriously with FEDEX about these issues - they 
> even did not reply ...
> 
> Jan
> 
> 
> 
> On Wed, Jun 24, 2020 at 9:27 PM Patrick Loll  wrote:
> Hello community,
> 
> We recently had a dry shipping dewar fail catastrophically (while en route to 
> the beam line, so, major trauma). I sent it to a company that specializes in 
> repair and refurbishing of cryogenic tanks, and they told me it has an 
> internal leak, and hence is not reparable. I was expecting that the valve had 
> failed, so the internal leak diagnosis came as a surprise.
> 
> Has anyone else had a similar experience? Any ideas about how an internal 
> leak might come about? The dewar is (was) a Taylor/Wharton CX100, and it was 
> traveling in its bespoke shipping case.
> 
> Thanks for any insights that might satisfy my curiosity and/or prevent future 
> mishaps of this sort.
> 
> Cheers,
> 
> Pat
> 
> __
> 
> Patrick J.  Loll, PhD
> Professor of Biochemistry & Molecular Biology
> Drexel University College of Medicine
> Room 10-102 New College Building
> 245 N. 15th St.
> Philadelphia, PA 19102-1192 USA
> 
> (215) 762-7706
> pj...@drexel.edu
> 
> 
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> 
> 
> 
> -- 
> Jan Dohnalek, Ph.D
> Institute of Biotechnology
> Academy of Sciences of the Czech Republic
> Biocev
> Prumyslova 595
> 252 50 Vestec near Prague
> Czech Republic
> 
> Tel. +420 325 873 758
> 
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Re: [ccp4bb] I cannot download xds

2020-06-28 Thread Folmer Fredslund 
 Dear Murpholino,

Perhaps you accidentally came upon a rare server outage? Or perhaps you had
a problem locally?
Did you try other programs to download or investigate the problem in any
other ways?

Historically and anecdotally, I've never had issues downloading XDS from
the website.
I normally use wget from a bash script.

As John wrote there doesn't seem to be any issues now.

Cheers

søn. 28. jun. 2020 04.50 skrev <
0c2488af9525-dmarc-requ...@jiscmail.ac.uk>:

> Hello, it downloaded to my phone from the link on this page:
>
> http://xds.mpimf-heidelberg.mpg.de/html_doc/downloading.html
>
> It looks alright:
> http://u.cubeupload.com/jbcooper/20200628034613.jpg
>
> Jon Cooper
>
> On 28 Jun 2020 01:39, Murpholino Peligro  wrote:
>
> ```
> ~/Downloads$ aria2c
> ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-INTEL64_Linux_x86_64.tar.gz
>
> 06/27 19:36:10 [NOTICE] Downloading 1 item(s)
> [#3065b2 0B/10MiB(0%) CN:1 DL:0B]
> ```
>
> It stays there forever.
> Is there an alternative download url?
>
>
> Thanks
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>
>
> --
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[ccp4bb] unable to launch ccp4 old interface on mac

2020-06-28 Thread Luca Mazzei 
Dear CCP4 people,
Can you help me with this?
At the end of installation of CCP4 7.1 on Mac with OS Mojave, CCP4 folder 
contains ccp4i2 icon, whereas ccp4 icon is not present. This way I can not 
launch the old interface, neither by clicking on the invisible icon nor using 
the terminal. I just fixed the problem by a copy-and-paste of the ccp4 icon 
coming from another Mac on which CCP4-7.0 is installed and It seems to work 
well (I ran Refmac, Coot and Molrep with success usingthe old interface)! Do 
you have any suggestion on why this occurs and how to overcome this problem in 
a more efficient way?

Thanks in advance,

Luca 

Luca Mazzei - PhD
Department of Pharmacy and Biotechnology
University of Bologna
Viale Giuseppe Fanin, 40 - 40127
Bologna - Italy



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