Re: [ccp4bb] update manager
My mistake, that was on my Fedora 40 host, not my Alma 9 host. Installing libxcrypt-compat fixed the problem. === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu From: CCP4 bulletin board on behalf of David J. Schuller Sent: Sunday, May 5, 2024 10:01 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] update manager ccp4um does not work for me. # ccp4um /usr/local/xtal/ccp4_master/ccp4-8.0/libexec/python3.7: error while loading shared libraries: libcrypt.so.1: cannot open shared object file: No such file or directory --- I recently updated from Scientific Linux 7 to Alma 9. I don't know if this is part of the reason or not. I have version 8.0.017. === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu From: CCP4 bulletin board on behalf of Becker, Stefan Sent: Sunday, May 5, 2024 9:28 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] update manager Dear all, update manager on ccp4 8.0.017 doesn´t run (two new updates available). Did anyone else have this problem? Stefan To unsubscribe from the CCP4BB list, click the following link: https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1=05%7C02%7Cschuller%40CORNELL.EDU%7Cd332cf2471854e6276fc08dc6d073e6a%7C5d7e43661b9b45cf8e79b14b27df46e1%7C0%7C0%7C638505125087222895%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=YsWTr8%2BUg8MLH18E9igpA%2B1KdQ0%2FaPzELT4detk2lqc%3D=0<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1> This message was issued to members of https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BB=05%7C02%7Cschuller%40CORNELL.EDU%7Cd332cf2471854e6276fc08dc6d073e6a%7C5d7e43661b9b45cf8e79b14b27df46e1%7C0%7C0%7C638505125087231012%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=uZklXxinZnZMNPN4BhDAIxIh1T%2FDgL5humamL%2BQ%2BpdA%3D=0<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F=05%7C02%7Cschuller%40CORNELL.EDU%7Cd332cf2471854e6276fc08dc6d073e6a%7C5d7e43661b9b45cf8e79b14b27df46e1%7C0%7C0%7C638505125087235570%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=n5eK%2By9P5jcLxbZDZRHo%2Bl13cLhYu7%2FA3UinmayC4mk%3D=0<http://www.jiscmail.ac.uk/>, terms & conditions are available at https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F=05%7C02%7Cschuller%40CORNELL.EDU%7Cd332cf2471854e6276fc08dc6d073e6a%7C5d7e43661b9b45cf8e79b14b27df46e1%7C0%7C0%7C638505125087239973%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=Act7y17M9sSrM4QFwBoob3lh8wwgkNcfLP6EC08pDJs%3D=0<https://www.jiscmail.ac.uk/policyandsecurity/> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 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/
Re: [ccp4bb] update manager
ccp4um does not work for me. # ccp4um /usr/local/xtal/ccp4_master/ccp4-8.0/libexec/python3.7: error while loading shared libraries: libcrypt.so.1: cannot open shared object file: No such file or directory --- I recently updated from Scientific Linux 7 to Alma 9. I don't know if this is part of the reason or not. I have version 8.0.017. === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu From: CCP4 bulletin board on behalf of Becker, Stefan Sent: Sunday, May 5, 2024 9:28 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] update manager Dear all, update manager on ccp4 8.0.017 doesn´t run (two new updates available). Did anyone else have this problem? Stefan To unsubscribe from the CCP4BB list, click the following link: https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1=05%7C02%7Cschuller%40CORNELL.EDU%7Cd332cf2471854e6276fc08dc6d073e6a%7C5d7e43661b9b45cf8e79b14b27df46e1%7C0%7C0%7C638505125087222895%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=YsWTr8%2BUg8MLH18E9igpA%2B1KdQ0%2FaPzELT4detk2lqc%3D=0<https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1> This message was issued to members of https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2FCCP4BB=05%7C02%7Cschuller%40CORNELL.EDU%7Cd332cf2471854e6276fc08dc6d073e6a%7C5d7e43661b9b45cf8e79b14b27df46e1%7C0%7C0%7C638505125087231012%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=uZklXxinZnZMNPN4BhDAIxIh1T%2FDgL5humamL%2BQ%2BpdA%3D=0<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jiscmail.ac.uk%2F=05%7C02%7Cschuller%40CORNELL.EDU%7Cd332cf2471854e6276fc08dc6d073e6a%7C5d7e43661b9b45cf8e79b14b27df46e1%7C0%7C0%7C638505125087235570%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=n5eK%2By9P5jcLxbZDZRHo%2Bl13cLhYu7%2FA3UinmayC4mk%3D=0<http://www.jiscmail.ac.uk/>, terms & conditions are available at https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fpolicyandsecurity%2F=05%7C02%7Cschuller%40CORNELL.EDU%7Cd332cf2471854e6276fc08dc6d073e6a%7C5d7e43661b9b45cf8e79b14b27df46e1%7C0%7C0%7C638505125087239973%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=Act7y17M9sSrM4QFwBoob3lh8wwgkNcfLP6EC08pDJs%3D=0<https://www.jiscmail.ac.uk/policyandsecurity/> 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/
Re: [ccp4bb] Room temperature change from 25ºC to 20ºC
Looking forward to feedback from the Southern realms as to which should be higher; SSRT or WSRT. === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu From: CCP4 bulletin board on behalf of Nukri Sanishvili Sent: Monday, April 1, 2024 10:47 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Room temperature change from 25ºC to 20ºC Excellent idea, Mark! I think the solution to your dilemma is rather straightforward: we introduce a Winter Standard Room Temperature (WSRT) and a Summer Standard Room Temperature (SSRT). This way, the folks from locales closer to the equator can always use SSRT, while those from more temperate climates can take advantage of using both WSRT and SSRT. The added benefit of this approach will be inclusion of researchers closer to either of the poles (which, forgive me for saying it, you so egregiously omitted from your considerations). Similar to the tropics, they could use just one standard - WSRT. Hope it helps your and so many young scientists' careers. Best wishes, Nukri On Mon, Apr 1, 2024 at 9:29 AM Mark mailto:mjvanra...@cnb.csic.es>> wrote: Room temperature change from 25ºC to 20ºC As a member of the inter-society standards commission St-Incent I have been asked to take the bearings of the structural biology community regarding a proposal to lower the universally understood room temperature from 25ºC (77º Fahrenheit) to 20ºC (68º Fahrenheit). Obvious advantages would be less heating necessary for experiments at this standard temperature. Given that laboratories nowadays are not commonly heated to this high temperature anyway, it does appear to make sense. Members of tropical and subtropical countries have already expressed opposition to the proposal, because they have to reach room temperature by cooling rather than heating, so for them the proposal would mean more CO2 emissions, not less. Please express opinions to this list today, so that I have time to collate them before the local deadline of 28 December. Mark J van Raaij Dpto de Estructura de Macromoleculas, lab 20B Centro Nacional de Biotecnologia - CSIC calle Darwin 3 E-28049 Madrid, Spain To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 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/
Re: [ccp4bb] Combating disinformation in science and other areas
"Who is to be the arbiter of what is true and what is “misinformation”?
The way to uphold the integrity of science is with a free exchange of ideas,
not an app or document that decides which publication or which interpretation
of the data is real science and which is misinformation."
The problem with this approach is that not all participants are acting in good
faith.
===
All Things Serve the Beam
===
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
schul...@cornell.edu
From: CCP4 bulletin board on behalf of Daniel M.
Himmel, Ph. D.
Sent: Wednesday, February 14, 2024 10:40 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Combating disinformation in science and other areas
Dear all,
That’s a very nice idea to have an app to combat misinformation that can
undermine the integrity of science and foster mistrust of scientific inquiry.
But to launch such an app raises the obvious question:
Who is to be the arbiter of what is true and what is “misinformation”?
The way to uphold the integrity of science is with a free exchange of ideas,
not an app or document that decides which publication or which interpretation
of the data is real science and which is misinformation.
Thanks go to Bryan Lepore for pointing out that the work of Herbert Marcuse (a
strong advocate of a brand of Marxism once popular in Germany) led to much
violence in the USA. Violent revolutions are how a great deal of science has
been lost during the last several thousand years of human history, which is why
we’re first determining atomic and near-atomic resolution structures in the
20th and 21st centuries, not eons ago.
So, my humble request: Can we stick to crystallography and allied fields of
structure determination on this e-mail list, and not digress into divisive
politics, please?
Respectfully submitted,
Daniel
[https://ci3.googleusercontent.com/mail-sig/AIorK4yaaDCOito7kuxLPC8Vy7HwqDw5i6DzTzprxgG0ijHkV1cwNX6leSeq_9r7EK46_M0TzQrRM-c]
Daniel M. Himmel, Ph. D.
Principal, Himmel Sci Med Com, LLC
E-mail: danielmhim...@gmail.com<mailto:danielmhim...@gmail.com>
URL : https://himmelscimedcom.com<https://himmelscimedcom.com/>
On Wed, Feb 14, 2024 at 7:52 AM Bryan Lepore
mailto:bryanlep...@gmail.com>> wrote:
The idea of "Global Sustainability" can be found in the documents for the noted
projects, so the United Nations "Sustainable Development Goals" appear to be
worth reviewing as background - even though it appears the UN or UNESCO (below)
is irrelevant to them :
“Transformation is the red thread running through all the Sustainable
Development Goals, the United Nations’ agenda for responding to global
challenges facing humanity and the planet. Setting our world on a more
sustainable course requires radical shifts in current development paradigms
that are exacerbating inequalities and imperilling [sic] our common future.
This transition is dependent on new knowledge, research and competences that
only higher education institutions are in a position to provide, rooted in
their historic role of service to society.”
[...]
“In 1964, inspiring the 1968-student revolt a couple of years later, Herbert
Marcuse wrote a key text against “one dimensional man”, urging universities and
campuses around the world to become places that resisted reductionism. ”
Source:
Parr, et. al.
“Knowledge-driven actions: transforming higher education for global
sustainability”
2022
UNESCO
https://doi.org/10.54675/YBTV1653
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Re: [ccp4bb] Problem running CCP4I2 in CCP4 8
Similar messages appear on the Known Issues page:
https://www.ccp4.ac.uk/download/doc/known_issues_linux.html
"Download
find-missing-libs.sh<https://www.ccp4.ac.uk/download/doc/find-missing-libs.sh>
and run it as a normal user (not root). The script will advise on what to do
next."
===
All Things Serve the Beam
===
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
schul...@cornell.edu
From: CCP4 bulletin board on behalf of Pedro Matias
Sent: Tuesday, January 30, 2024 9:17 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Problem running CCP4I2 in CCP4 8
Hi Arnaud,
I have installed Fedora 38 from scratch and reinstalled CCP4 since the
previous FC version was too old to update. I will try again after the
next reboot.
Thanks,
Pedro
On 30/01/2024 13:44, Arnaud Basle wrote:
> Hi Pedro,
>
> Can you reboot your machine and try again?
>
> I have see this error before on linux mint/ubuntu. Did you also updated
> the OS?
>
> Cheers,
> Arnaud
>
>
> On 30/01/2024 11:43, Pedro Matias wrote:
>> ⚠ External sender. Take care when opening links or attachments. Do not
>> provide your login details.
>>
>> Dear All,
>>
>> After updating CCP4 to version 8, CCP4I2 stopped working with the
>> following error message:
>>
>>> Running CCP4i2 browser from:
>>> /home/pxsoft/ccp4/ccp4-8.0/lib/python3.7/site-packages/ccp4i2
>>> Python 3.7.12 (default, Jan 6 2022, 21:30:12)
>>> [GCC 8.2.1 20180905 (Red Hat 8.2.1-3)]
>>> Qt version 5.15.2
>>>
>>> qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in
>>> "/home/pxsoft/ccp4/ccp4-8.0/QtPlugins/" even though it was found.
>>> This application failed to start because no Qt platform plugin could
>>> be initialized. Reinstalling the application may fix this problem.
>>>
>>> Available platform plugins are: eglfs, linuxfb, minimal, minimalegl,
>>> offscreen, vnc, webgl, xcb.
>>>
>>> Abort (core dumped)
>> Apparently I am missing some library/package but I have no idea of which.
>>
>> Thanks & BR,
>>
>> Pedro
>>
>> --
>> Industry and Medicine Applied Crystallography
>> Macromolecular Crystallography Unit
>> ___
>> Phones : (351-21) 446-9100 Ext. 1669
>> (351-21) 446-9669 (direct)
>> Fax : (351-21) 441-1277 or 443-3644
>>
>> email : mat...@itqb.unl.pt
>>
>> https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.itqb.unl.pt%2Fresearch%2Fbiological-chemistry%2Findustry-and-medicine-applied-crystallography=05%7C02%7Cschuller%40CORNELL.EDU%7C7f66bb288389491fff2708dc219e486c%7C5d7e43661b9b45cf8e79b14b27df46e1%7C0%7C0%7C638422211033290359%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=ncoQvCe7uIZHrS4zwOGoyNMB5JCLrh78opYomjQzGqs%3D=0<http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography>
>>
>> https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.itqb.unl.pt%2Flabs%2Fmacromolecular-crystallography-unit=05%7C02%7Cschuller%40CORNELL.EDU%7C7f66bb288389491fff2708dc219e486c%7C5d7e43661b9b45cf8e79b14b27df46e1%7C0%7C0%7C638422211033298109%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=POb5gNKM12eJP6YY6Noq4zQpGRs4CkKkUzmzZYOcMMg%3D=0<http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit>
>>
>>
>> Mailing address :
>> Instituto de Tecnologia Quimica e Biologica António Xavier
>> Universidade Nova de Lisboa
>> Av. da República
>> 2780-157 Oeiras
>> PORTUGAL
>>
>> ITQB NOVA, a great choice for your PhD
>> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fyoutu.be%2Fde6j-aaTWNQ=05%7C02%7Cschuller%40CORNELL.EDU%7C7f66bb288389491fff2708dc219e486c%7C5d7e43661b9b45cf8e79b14b27df46e1%7C0%7C0%7C638422211033303516%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=IICjRQeYwqHmUqOtvC5V0q8COepe0G9Fs%2BWQ4oxCVKg%3D=0<https://youtu.be/de6j-aaTWNQ>
>>
>>
>> Master Programme in Biochemistry for Health
>> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fyoutu.be%2FUKstDCFjYI8=05%7C02%7Cschuller%40CORNELL.EDU%7C7f66bb288389491fff2708dc219e486c%7C5d7e43661b9b45cf8e79b14b27df46e1%7C0%
Re: [ccp4bb] Problems updating CCP4 via CCP4i
What is your operating system? I have encountered a problem on Scientific Linux 7 where ccp4um will not run correctly unless I clear out LD_LIBRARY_PATH first. This apparently happens because ccp4um requires certain libraries that ship with CCP4, and if the system libraries, which are a different version, appear in LD_LIBRARY_PATH ahead of the CCP4 libraries, trouble ensues. It is possible to put the CCP4 libraries at the start of LD_LIBRARY_PATH, but then that screws up every other program. csh/tcsh: unsetenv LD_LIBRARYPATH sh/bash: unset LD_LIBRARY_PATH === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu From: CCP4 bulletin board on behalf of Pedro Matias Sent: Tuesday, January 30, 2024 6:40 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Problems updating CCP4 via CCP4i Dear All, I am no longer able to update CCP4 via CCP4i [cid:part1.PIYkI0WM.u8Wjf4uA@itqb.unl.pt] When I click on "Proceed" Instead of opening the update window, I get back to exactly this view. Is it possible to update CCP4 via the command line? I haven't tried using CCP4I2 because it doesn't work on my PC (separate e-mail). Thanks & BR, Pedro -- Industry and Medicine Applied Crystallography Macromolecular Crystallography Unit ___ Phones : (351-21) 446-9100 Ext. 1669 (351-21) 446-9669 (direct) Fax : (351-21) 441-1277 or 443-3644 email : mat...@itqb.unl.pt<mailto:mat...@itqb.unl.pt> http://www.itqb.unl.pt/research/biological-chemistry/industry-and-medicine-applied-crystallography http://www.itqb.unl.pt/labs/macromolecular-crystallography-unit Mailing address : Instituto de Tecnologia Quimica e Biologica António Xavier Universidade Nova de Lisboa Av. da República 2780-157 Oeiras PORTUGAL ITQB NOVA, a great choice for your PhD https://youtu.be/de6j-aaTWNQ Master Programme in Biochemistry for Health https://youtu.be/UKstDCFjYI8 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 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/
Re: [ccp4bb] Fragile Crystals
There are multiple avenues you could explore.
If you think handling is an issue, you could look into growing and collecting
with "in situ" plates.
You could test for diffraction at room temp, or even get a full data set at
room temp by combining data from multiple crystals. If diffraction is not good
at room temp, it is probably not going to be better under cryo conditions.
As for cryo, instead of trying cryoprotectant A or cryoprotectant B, you could
try a mixture of multiple cryoprotectants:
https://pubs.acs.org/doi/abs/10.1021/acs.cgd.5b01692
Use of Multiple Cryoprotectants to Improve Diffraction Quality from Protein
Crystals
Senda, et al.
https://doi.org/10.1021/acs.cgd.5b01692
Evidence of Kinetic Cooperativity in Dimeric Ketopantoate Reductase from
Staphylococcus aureus
JE Sanchez, PG Gross, RW Goetze, RM Walsh Jr, WB Peeples, ZA Wood
Biochemistry 54 (21), 3360-3369
===
All Things Serve the Beam
===
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
schul...@cornell.edu
From: CCP4 bulletin board on behalf of Blake, Morgan
Elizabeth
Sent: Wednesday, November 22, 2023 11:44 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Fragile Crystals
Hello!
I am a PhD student working on a crystallography project to wrap up my
dissertation research. I have purified a complex of two proteins, and I can
consistently grow crystals in 10% PEG3350, 0.2M KSCN, 0.1M BIS-TRIS propane pH
7.5. These crystals have sharp edges and can grow to a large size (greater than
0.5 mm), but the crystals seem to be very fragile. When we open the drops to
harvest the crystals, we have little time to harvest the crystals before they
crack. When we move the crystals to a cryoprotectant, over time they start
fracturing. We've tried using different percentages of glycerol, ethylene
glycol, PEG400, and oil for cryoprotectants with no success. Needless to say,
the crystals do not diffract well, with spot patterns that look very
streaky/mosaic, which I presume is due to the defects that we see in
harvesting/handling. We have screened for alternate crystallization conditions,
but we seem to get the same morphology in other conditions. Does anyone have
suggestions for additives we could use post-crystallization to help stabilize
our crystals?
Thanks for your advice!
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Re: [ccp4bb] Dry shipper in limbo
FedEx missing deadlines on "overnight" shipments is not uncommon, I advise
everyone to ship dewars to arrive at least one extra day in advance.
Also, their online tracking page could be better. They show the original
expected delivery time even if the shipment has already missed an intermediate
transfer point. The delivery time does not get updated until the original
delivery time has been passed.
The multiple lost days and the international complication are unusual details
and I don't have any specific advice on that.
===
All Things Serve the Beam
===
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
schul...@cornell.edu
From: CCP4 bulletin board on behalf of Savvas Savvides
<9d24f7f13e09-dmarc-requ...@jiscmail.ac.uk>
Sent: Friday, July 28, 2023 3:56 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] Dry shipper in limbo
Dear Kevin,
A similar incident from just two weeks ago, in Europe in our case, was resolved
by travelling to the regional FedEx package collection/distribution center to
recover the dry-shipper in person. This involved gaining access to the FedEx
center and talking to the right people.
I would absolutely not wait this out because your shipment is probably
somewhere in the corner of a distribution center used as a seat by employees
taking a break. I can attest to the fact that they do have such corners where
“problematic" shipments are piled up!
Despite what you were told on the phone or could deduce from any online
tracking systems (in our case the dry-shipper was not even trackable), there is
still a (very good) chance that your shipment might still be at a regional
collection/distribution center.
The key is to get to any information about where this place might be, talk to
the local people, and find out what the actual route of the shipment might have
been after getting picked up from your lab. The routes often involve
intermediate collection/distribution sites.
To their credit, and in contrast to the general FedEx customer service, the
people at the regional FedEx distribution center (including the shift manager)
were very empathic and helpful, and used means that go above and beyond SOPs to
help. This included sharing photos of the shipment via WhatsApp with
drivers/employees of the three previous shifts etc… Despite the volumes of work
they handle, drivers and other courier employees actually do remember unusually
looking shipments, such as a shipping-case containing a dry-shipper!
Best of luck and wishes,
Savvas
On 28 Jul 2023, at 08:15, Savvas Savvides wrote:
Best wishes,
Savvas
Begin forwarded message:
From: "Dr. Kevin M Jude" mailto:kj...@stanford.edu>>
Date: 28 July 2023 at 05:16:39 CEST
To: CCP4BB@jiscmail.ac.uk<mailto:CCP4BB@jiscmail.ac.uk>
Subject: [ccp4bb] Dry shipper in limbo
Reply-To: "Dr. Kevin M Jude" mailto:kj...@stanford.edu>>
My first adventure in international crystallography is off to an inauspicious
start. On Monday, I sent a dry shipper “overnight” from California to
Saskatchewan, but it has been stuck in the Memphis FedEx facility for a few
days. I’ve gotten several conflicting explanations of the status from FedEx on
the phone, but the most likely seems that it has “pre-cleared” customs and yet
has not yet made it to Calgary. It’s not clear whether anyone actually knows
where the shipping case is, since I was asked to give a physical description of
it. Is there anything else I can do from a few thousand miles away, or do I
just have to wait this out?
--
Kevin Jude, PhD
Structural Biology Research Specialist, Garcia Lab
Howard Hughes Medical Institute
Stanford University School of Medicine
Beckman B177, 279 Campus Drive, Stanford CA 94305
Phone: (650) 723-6431
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Re: [ccp4bb] Error in xdsgui: you have to install generate_XDS.INP in your path
I am not familiar with Macs, but on Linux the first problem could be easily solved by having the desktop shortcut call a brief shell script rather than the executable. The script would first set up the environment properly, then call the executable. === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu From: CCP4 bulletin board on behalf of Kay Diederichs Sent: Sunday, June 4, 2023 8:43 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Error in xdsgui: you have to install generate_XDS.INP in your path Dear Zhen Gong, Installation of XDS and associated programs is documented in the "Installation" article in XDSwiki. If I google "XDSwiki installation article", it is the first hit. Your PATH is probably different when you double-click XDSGUI to start it, compared to what it is on the command line. So don 't double-click it! Start XDSGUI from the command line - this way you also see error messages from generate_XDS.INP, and output of POINTLESS and Coot. Use the latest versions of the programs. Concerning HDF5 processing, read the Installation article. As Graeme said, you need a library, and you need to tell XDS where it is, with a LIB= line in XDS.INP . There are different library versions for Intel Mac and Silicon Mac. if you have a Silicon Mac, I recommend to use the specific Silicon Mac versions of XDS, XDSGUI and the library. Hope this helps, Kay On Sat, 3 Jun 2023 18:24:24 +0100, Zhen Gong wrote: >Dear all, > >I have encountered this problem in xdsgui: you have to install >generate_XDS.INP in your path. Generate_XDS.INP works fine in command line but >not in the GUI. I saw the same question was raised up by another user >previously on CCP4bb but I was not able to see Key's reply any more. > >Thank you very much for your help! > >Best regards, >Zhen > > > >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<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list >hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions >are available at https://www.jiscmail.ac.uk/policyandsecurity/ 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<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ 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/
Re: [ccp4bb] Unknown electron density
Anomalous data might have been helpful. Zinc has an edge at 1.2837 A. === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu From: CCP4 bulletin board on behalf of Betty Chu Sent: Wednesday, April 19, 2023 12:58 PM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Unknown electron density Dear CCP4BB, I am working on a structure refinement and came across a blob of density that looks like an anvil (see link). Has anyone seen this before and have an idea of what it is? https://drive.google.com/file/d/1BGNwV3MujYjrV4W5m1bh3_WWd49RhJ1w/view?usp=sharing The protein is in potassium phosphate and the components in the crystallization/cryo condition are zinc acetate, PEG, and glycerol. Thank you in advance for your time and help! Betty To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 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/
[ccp4bb] Another folding AI
https://www.biorxiv.org/content/10.1101/2022.07.20.500902v2
Evolutionary-scale prediction of atomic level protein structure with a language
model<https://www.biorxiv.org/content/10.1101/2022.07.20.500902v2>
doi: https://doi.org/10.1101/2022.07.20.500902
Abstract
Artificial intelligence has the potential to open insight into the structure of
proteins at the scale of evolution. It has only recently been possible to
extend protein structure prediction to two hundred million cataloged proteins.
Characterizing the structures of the exponentially growing billions of protein
sequences revealed by large scale gene sequencing experiments would necessitate
a breakthrough in the speed of folding. Here we show that direct inference of
structure from primary sequence using a large language model enables an order
of magnitude speed-up in high resolution structure prediction. Leveraging the
insight that language models learn evolutionary patterns across millions of
sequences, we train models up to 15B parameters, the largest language model of
proteins to date. As the language models are scaled they learn information that
enables prediction of the three-dimensional structure of a protein at the
resolution of individual atoms. This results in prediction that is up to 60x
faster than state-of-the-art while maintaining resolution and accuracy.
Building on this, we present the ESM Metagenomic Atlas. This is the first
large-scale structural characterization of metagenomic proteins, with more than
617 million structures. The atlas reveals more than 225 million high confidence
predictions, including millions whose structures are novel in comparison with
experimentally determined structures, giving an unprecedented view into the
vast breadth and diversity of the structures of some of the least understood
proteins on earth.
Competing Interest Statement
The authors have declared no competing interest.
===
All Things Serve the Beam
===
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
schul...@cornell.edu
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[ccp4bb] Jenkins?
CCP4 8.0.004
Scientific Linux 7, kernel 3.10.0-1160.76.1.el7.x86_64
mate-desktop-1.16.2-1.el7.x86_64
This morning I updated my Nvidia graphics driver, then rebooted. When I logged
in again, my desktop (Mate) was all messed up, no applications menus, etc. I
perused the log files and found many lines similar to these in
/var/log/messages:
Sep 25 09:45:32 titan mate-session[1718]: WARNING: Could not connect to
Systemd: Failed to connect to socket
/home/jenkins/workspace/CCP4/series-8.0-linux/devtools/install/var/run/dbus/system_bus_socket:
No such file or directorySep 25 09:45:34 titan journal: Error connecting to
system bus: Failed to connect to socket
/home/jenkins/workspace/CCP4/series-8.0-linux/devtools/install/var/run/dbus/system_bus_socket:
No such file or directory
Sep 25 10:12:35 titan pulseaudio[22894]: [alsa-sink-ALC887-VD Analog]
core-util.c: Failed to connect to system bus: Failed to connect to socket
/home/jenkins/workspace/CCP4/series-8.0-linux/devtools/install/var/run/dbus/system_bus_socket:
No such file or directory
Sep 25 10:12:40 titan pulseaudio[23162]: [pulseaudio] core-util.c: Failed to
connect to system bus: Failed to connect to socket
/home/jenkins/workspace/CCP4/series-8.0-linux/devtools/install/var/run/dbus/system_bus_socket:
No such file or directory
Sep 25 10:12:40 titan pulseaudio[23162]: [pulseaudio] core-util.c: Failed to
connect to system bus: Failed to connect to socket
/home/jenkins/workspace/CCP4/series-8.0-linux/devtools/install/var/run/dbus/system_bus_socket:
No such file or directory
I do not have, and have never had, a user "jenkins" on my system. Note that the
CCP4 workspace is implicated.
I took the CCP4 startup stuff out of my .cshrc login script and restarted, and
everything appeared to be normal.
# source /usr/local/xtal/ccp4/bin/ccp4.setup-csh >& /dev/null
Why is jenkins mucking about with my desktop settings, and how do I keep him
from doing so?
===
All Things Serve the Beam
===
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
schul...@cornell.edu
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Re: [ccp4bb] PDBx-format utilities
I have a set of utilities for handling PDB files, known as "PDB Pipeline". Each
one does a single distinct thing: manipulate the spatial coordinates, reset the
B, pull out a particular subset of residue numbers, fix particular known
problems, etc. There are several dozen. They work very nicely with Linux
command line utilities such as grep and sed. They are so old that they were
written in Fortran-77 (with VMS FORTRAN extensions).
===
All Things Serve the Beam
===
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
schul...@cornell.edu
From: CCP4 bulletin board on behalf of Paul Emsley
Sent: Thursday, September 8, 2022 3:28 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] PDBx-format utilities
A spectre is haunting structural biology - it is the spectre of the PDBx
format.
We at CCP4 are interested in providing tools that are equivalents of
those that one might have trivially made with utilities such as grep or sed.
For example:
delete the hydrogen atoms
extract the hydrogen atoms
extract the SD of MET
find the atoms with B-factors greater than 100.0
So, what useful tool have you made can that works because it based on
the PDB format - that (of course) doesn't work with PDBx?
Thanks,
Paul.
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Re: [ccp4bb] Checking X-ray sequence (no more protein).
I don't know how much effort I would put into that, given how easy nucleic acid sequencing has become. === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu From: CCP4 bulletin board on behalf of Robbie Joosten Sent: Friday, July 29, 2022 9:56 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Checking X-ray sequence (no more protein). Hi Jon, There are placeholders for ASP/ASN and GLU/GLN ambiguities: ASX and GLX respectively. You can just use those. AFAICT there no such thing for VAL/THR ambiguities. You could look for the most likely canadidata based on multiple sequence alignments. Refinement of both alternatives can give hints in B-factors and if you are lucky in difference density. But if hydrogen bonding gives no hints, then the residues are also not in a place where the identity really matters. You can give your best guess with a CAVEAT record or use the name UNK to indicate that you do not know what the residue is. You would loose the knowledge that it is either VAL or THR in that case. Cheers, Robbie > -Original Message- > From: CCP4 bulletin board On Behalf Of Jon > Cooper > Sent: Friday, July 29, 2022 12:14 > To: CCP4BB@JISCMAIL.AC.UK > Subject: [ccp4bb] Checking X-ray sequence (no more protein). > > Hello, I am looking for suggestions of ways to check a 1.7 Angstrom X-ray > sequence for a protein where it is impractical to do experimental sequencing, > protein or DNA. The structure refines to publishable R/R-free and the main > ambiguities seem to be Thr/Val, Asp/Asn and Glu/Gln where alternative H- > bonding networks are possible. Running alpha-fold seems an interesting > option? Any suggestions much appreciated. > > Cheers, Jon.C. > > Sent from ProtonMail mobile > > > > > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 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<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk<http://www.jiscmail.ac.uk>, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ 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/
Re: [ccp4bb] ligand binds to one molecule
I think it would be a mistake to generalize. I have seen a situation in which 1 of 4 sites was occupied, the ligand was not included in the crystallization solution(which means it must have been bound beforehand) and the site participated in crystal contacts. I do not doubt that examples of the opposite causality exist. And the data I used to make my conclusions in my own example came from outside the structure itself. === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu From: CCP4 bulletin board on behalf of Palm, Gottfried Sent: Sunday, March 6, 2022 4:10 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] ligand binds to one molecule Dear all, I don't think, there is much to add to the statement of Bernhard or James that different protomers in the asymmetric unit (must) have some difference in there contacts and therefore often in their conformation. What it doesn't answer is a chicken or the egg question: do the different environments in the crystal allow or force different conformations (e.g. open or closed loops) and/or different (active) site occupancies or do different states in an oligomer allow or force crystallization only in a packing and space group with multiple states? Latter could be due to an anti-cooperative binding to a dimer. We have seen this in the dimeric Tet repressor: wt binds the ligand (a tetracycline) in each monomer of the dimer with one chain in the asymmetric unit, but some of the mutants bind only one ligand per dimer (confirmed by ITC, Biochimica et Biophysica Acta, 2020). Despite the same packing, this forces reduction of space group symmetry from I422 to P422 (omitting screws). >From the crystal structures alone, I think, one cannot prove what comes first. >From my gut feeling, in most cases multiple states in solution force multiple >states in the crystal - in other words - I tend to say, multiple states in the >crystal are "real" in the sense they also occur in solution. Does somebody >want to comment on this? Greetings Gottfried Am Sonntag, den 06-03-2022 um 00:40 schrieb Bernhard Rupp: As you stated, you have multiple protomers in the asymmetric unit, where they are free from crystallographic symmetry constraints. Generally that means different local environment for each protomer. Inspecting the sites in the different protomers (frequently related by various non-crystallographic symmetry operations) often can reveal plausible reasons for different occupancies. One hydrogen bond more or less for example can mean a difference of 4 orders of magnitude in Kd. Best, BR -Original Message- From: CCP4 bulletin board On Behalf Of Sent: Saturday, March 5, 2022 12:01 To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: [ccp4bb] ligand binds to one molecule Hello all, In homo-dimeric or homo-oligomeric protein crystal structures, what would be the reason for having a ligand (chemical compound or fragment) binds to one molecule and not all molecules in the asymmetric unit? I have soaked a fragment that has an affinity of 200 uM to a viral protein but I can only see it binds to one molecule (we have eight molecules in the AU). This is was also notable as well in some published PDB (dimeric protein). Any suggestions? Best wishes, Shymaa 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/ 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/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 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, ter
[ccp4bb] ccp4um log
Does ccp4um write a log file? Where does it go? Does it include everything that appears in the graphical window while the update is running? During an update, I noticed lines saying that something cannot be done, but they flew by too fast for me to inspect. === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu 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/
Re: [ccp4bb] nVidia 3D Vision2 glasses
Which Linux and which desktop? Attached find a typical functional /etc/X11/xorg.conf file for stereo use from a Scientific Linux 7 machine. The two notable things about this file: "STEREO" is enabled in the "Screen" section. "COMPOSITE" is disabled in the "Extensions" section. With some newer desktops such as Gnome 3 it is not possible to disable composite. Try using the XFCE or Mate desktop. On 2020-01-14 15:43, Oganesyan, Vaheh wrote: Colleagues, While on stereo issues here is problem I’m trying to resolve with community help: my hardware includes nVidia quadro FX1400, Xpand emiter and NewVision glasses. Driver taken from nVIDIA site specifically for Quadro FX 1400, long lived. On old Linux station these worked together fine for PyMOL and O. On newer machine PyMOL doesn’t complain but doesn’t show stereo either. “O” complains: freeglut (/home/Vaheh/o/bin/170211_lin64_ono): ERROR: Internal error in function fgOpenWindow and quits. Will appreciate help on resolving this issue. Regards, Vaheh Oganesyan, Ph.D. Scientist, Biologic Therapeutics AstraZeneca R | Antibody Discovery and Protein Engineering One Medimmune Way, Gaithersburg, MD 20878 T: 301-398-5851 vaheh.oganes...@astrazeneca.com<mailto:oganesy...@medimmune.com> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1<https://clicktime.symantec.com/33moye3DQdTgHFzwGL9vh2Q6H2?u=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DCCP4BB%26A%3D1> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- === All Things Serve the Beam =========== David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu<mailto:schul...@cornell.edu> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 # /etc/X11/nvidia-xorg.conf provided by http://elrepo.org Section "Device" Identifier "Videocard0" Driver "nvidia" EndSection Section "Monitor" Identifier "Monitor0" VendorName "Planar" ModelName"SA2311W" HorizSync30.0 - 140.0 VertRefresh 56.0 - 120.0 Option "DPMS" EndSection Section "Screen" Identifier "Screen0" Device "Device0" Monitor"Monitor0" DefaultDepth 24 Option "Stereo" "10" SubSection "Display" Modes "1920x1080" "1920x1080_120" Depth 24 EndSubSection EndSection Section "Extensions" Option "COMPOSITE" "Disable" EndSection To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Dead link
On this CCP4 documentation page:
http://www.ccp4.ac.uk/html/phaser.html
The link for "Full documentation" goes nowhere.
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Re: [ccp4bb] RAID array
I agree about the complexity of the RAID situation. But it can be narrowed down a bit. Since the claim is made there were only two hard drives, the only possibilities are: RAID 0 - "striping". In which case his data will probably not be recoverable, and he would be unable to boot. RAID 1 - "mirroring". In which case the data may be recoverable. This is probably the case, since from the description the machine is booting but the login process is unsuccessful. If the RAID is set up with hardware, there may be entry into the controller from the BIOS boot process. If the RAID is set up in Linux software, then you need to get logged in somehow with root privileges. Details may vary a bit depending on which Linux distribution is involved (which was not mentioned). You could try to boot into "rescue mode" from the Linux installation media (DVD or USB stick, usually). Or you could try to boot into "single user mode" by altering the boot command during the boot procedure (details will vary with distribution). Or you could try setting to boot up in nongraphical mode. Like I say, this varies with Linux distribution so I won't try to give a line by line set of instructions. My experience is all with Fedor and Scientific Linux. Once you are in, you need to assess the situation. If RAID is set up with software, there will be a configuration file, typically /etc/mdadm.conf, and a status file, typically /proc/mdstat. You can look for these files for clues to how the RAID is set up, and what its status is. You would need to figure out how your existing drive is configured by checking out the partition arrangement with /usr/sbin/fdisk or /usr/sbin/parted. Then you would need to set up partitions on the brand new drive in the same way. Once the partitions exist, you would try to add the partitions into the RAID volume with /usr/sbin/mdadm. You are going to need to read the man pages for mdadm and probably search for help online. Once the RAID set is successfully reconfigured, it would take probably a few hours to copy the data from the good device to the new one. BTW, if anyone is using HPE SSDs they need to be aware of this: https://www.zdnet.com/article/hpe-tells-users-to-patch-ssds-to-prevent-failure-after-32768-hours-of-operation/ HPE tells users to patch SSDs to prevent failure after 32,768 hours of operation On 2019-11-27 09:03, Kay Diederichs wrote: Hi Vaheh, RAID on Linux comes in different flavours and levels; the flavours are software RAID (mdadm) and hardware RAID (dedicated RAID controller or motherboard), and the levels are RAID0 RAID1 RAID5 RAID6 RAID10 and a few others. These details influence what the user will notice when a disk goes bad. Without knowing what you have, it is difficult to help. As an example, by default in my lab we have the operating system on mdadm RAID1 which consists of two disks that mirror each other. If one of the disks fails, typically we only notice this when inspecting the system log files. Replacing the disk, and re-silvering the RAID1 is not trivial and requires some reading of material on the web. It sounds like you don't have this type of RAID1, or maybe there is some mis-configuration. good luck, Kay On Tue, 26 Nov 2019 21:05:54 +, Oganesyan, Vaheh <mailto:vaheh.oganes...@astrazeneca.com> wrote: Hello ccp4-ers, A bit off topic (actually a lot off topic) question regarding RAID array system. On linux box one of two hard drives failed. I've found identical one and replaced it. Can someone point me in the direction where I can get instructions on what to do next to be able to login? Currently computer starts with no error messages, comes to the login window, takes username and password from me and then flashes and comes back to login window. Thank you for your help. Regards, Vaheh Oganesyan, Ph.D. Scientist, Biologic Therapeutics AstraZeneca R | Antibody Discovery and Protein Engineering One Medimmune Way, Gaithersburg, MD 20878 T: 301-398-5851 vaheh.oganes...@astrazeneca.com<mailto:vaheh.oganes...@astrazeneca.com><mailto:oganesy...@medimmune.com><mailto:oganesy...@medimmune.com> 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: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1 -- === All Things Serve the Beam ========
Re: [ccp4bb] difficult molecular replacement solution
Have you looked at a self-rotation function? Those can sometimes be very useful
in deciphering multiplicity.
On 2019-11-13 09:33, Robert S Phillips wrote:
I have been working on a protein structure which has been hard to solve by
molecular replacement.
Unit cell: (60.6, 172.34, 196.42, 90, 90, 90)
Space group: P 21 21 21
The problem is that the homologues have only ~20% identity, and there are
multiple chains in the asymmetric unit. The question is how many. It could be
4, 5, or 6 chains.
N solvent P
4 0.602 3.090.225
5 0.502 2.470.388
6 0.403 2.060.229
I have run PHASER with 4, 5 and 6 chains. I allowed it to search all possible
space groups, and P212121 was the best solution. These are the results.
N LLG TFZ
4 104.97.5
5 137.57.7
6 166.28.3
Am I correct to conclude that there are 6 chains in the asymmetric unit?
Rob
Robert S. Phillips
Professor of Chemistry and of Biochemistry and Molecular Biology
University of Georgia
Athens, GA 30602
Phone: (706) 542-1996
Fax: (706) 542-9454
E-mail: rsphill...@chem.uga.edu<mailto:rsphill...@chem.uga.edu>
Web:
http://tryptophan.net<https://pod51004.outlook.com/owa/redir.aspx?C=ccbf42ffea5f48b1bf8e9bb950454bab=http%3a%2f%2ftryptophan.net>
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modern man in a post-modern world
MacCHESS, Cornell University
schul...@cornell.edu<mailto:schul...@cornell.edu>
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[ccp4bb] Chiral
This would seem to be of interest as we all value chiral crystals. --- https://www.polygon.com/death-stranding-guide/2019/11/7/20948653/chiral-crystals-bts-farm-fight-collect-hermetic-grenades-standard-ammo Death Stranding guide: Fighting BTs to farm chiral crystals Take on BTs to collect thousands of chiral crystals -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu<mailto:schul...@cornell.edu> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Health study relevant to molecular modeling
http://www1.voanews.com/english/news/health/Research-Shows-3-D-Movies-Can-Cause-Eye-Strain-Headaches-84909757.html Research Shows 3-D Movies, TV Can Cause Eye Strain, Headaches Vidushi Sinha | Washington 21 February 2010 Three dimensional movies, like Avatar, are wowing us with their visual display. ... But a study at the University of California Berkeley found that 3-D movies can cause eye strain. ... Banks says younger viewers are more vulnerable. When you hit your 50s and 60s, we think that concern is going to be reduced, noted Banks. So that is probably more problematic for young adults, teenagers, et cetera. ... -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] anomalous difference fourier maps
On Fri, 2010-02-19 at 10:37 -0500, Edward A. Berry wrote: The problem is not that the phenix team was so quick to promote their software, but rather that now 14 hours after the original post, no one has answered the CCP4 question. The original poster returned to indicate that he had received multiple responses. I gather that he received them off-board. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] unknown density
On Wed, 2010-02-03 at 18:26 +0100, Mark J. van Raaij wrote: as it appears to bear near the guanidine group of an arginine, I would suggest it is a partially occupied and disordered sulphate and/or phosphate. If it's a sulphate, a look at the anomalous map should show something. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
[ccp4bb] 2010 Stereoscopic 3D Hardware Guide
This explains the various 3D technologies available http://www.mtbs3d.com/cgi-bin/newsletter.cgi?news_id=93 2010 Stereoscopic 3D Hardware Guide By Neil Schneider January 28, 2010 -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] question on the effect of a fire alarm on crystallization
If your crystals exploded, the alarm would provide warning to other residents of the building. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu On Fri, 2010-01-22 at 09:13 -0500, Jacqueline Vitali wrote: Dear all, Does anyone know the effect of a fire alarm placed in the same room where one grows crystals? (1) On trays placed inside styrofoam boxes (2) On trays placed inside an incubator which has not been tested as vibration free. Thank you. Jackie Vitali
Re: [ccp4bb] Stereo worked, but can't log back on after the screen lock Re: [ccp4bb] [COOT] 120hz LCDs and coot stereo
I don't recall which version of Linux you are using, but I have seen similar problems under some versions of Fedora, including F12, with some graphics drivers (but not specifically the nVidia proprietary driver). Some obvious solutions include: 1) setting the Power Management not to power down the display ever 2) setting the screensaver not to lock 3) setting the screensaver not to activate The first one is especially worth a try. -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu On Tue, 2010-01-19 at 07:05 -0500, Zheng Zhou wrote: Dear all Thanks for your input. With your help, I just installed the stereo on linux with two monitors using the clone mode. The coot and pymol stereo work beautifully. But I met some problem, every time I walked away from my computer to do some real work, the screensaver would be activated and I couldn't log back on. So I lost some part of my work. The virtual console Ctrl+Alt+F1~F6 worked. I tried to use kernel-devel to build the nvidia driver both the certified 190 version and the beta version 195.22 and 195.30. But none of these versions could correct the error. When I allowed the certified 190 driver to write the xorg.conf file, it worked. I googled it, but didn't find any answer. Has anyone encountered the similar problem? Thanks for your help in advance. Joe
Re: [ccp4bb] 3D monitors
On Fri, 2010-01-15 at 09:11 +0100, alexander.schif...@sanofi-aventis.com wrote: We had a demo of the ViewSonic FuHzion VX2265wm and Nvidia 3D Vision system yesterday. The VX2265wm is a 1680x1050 monitor. Reviews from last year generally pegged it as inferior to the Samsung 2233RZ, another 1680x1050 monitor. Soon a crop of 23.5 1920x1080 120 Hz LCD monitors compatible with active glasses (nVidia 3D vision) will appear on the market. The ViewSonic V3D241wm-LED has been announced as available in April. The Acer GD235HZ and GD245HW were anounced a month ago for january availability, but I haven't seen any for sale yet. These are the only 1920x1080 monitors listed on nVidia's Alienware (Dell) OptX AW2310 - available now? LG W2363D - no date on availability, but since LG is manufacturing the panels which will be used in all of these products, I presume they won't be last to market. I am guessing other manufacturers will follow suit, but I haven't seen anything from Samsung yet. Cheers, -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] Stereo TFT
On Fri, 2010-01-15 at 11:17 -0500, Yong Y Wang wrote: Alexander, I thought FX3700 would work. Good to hear confirmation from you. It would be nice a Linux driver is available to allow USB based stereo sync. No, not any Quadro card with stereo output will work. The old FX1400 does not work. Even the relatively new FX3500 does not work. The nVidia website has a list of cards that support 3D Vision. That should be consulted before purchasing even though the list was created for Windows. Here is nVidia's list http://www.nvidia.com/object/quadro_pro_graphics_boards.html This details which cards are supported for 3D vision and which have a 3 pin mini-DIN stereo connector. That page says cards without the connector can be used via USB, but I am not sure if that applies to Linux or just to Windows. FX1400 and FX3500 not working - are you just saying that because they do not appear on the list, or have you personally verified it? Those happen to be the cards I currently have. The FX3800 card can use a mini-DIN stereo plug on a separate PCI blank, which is sold separately. See for example: http://www.bhphotovideo.com/c/product/652465-REG/PNY_Technologies_900_50762__000_QUADRO_FX_3800_STEREO.html PNY Technologies Stereo Bracket for Quadro FX 3800 Someone posted a link for the release notes of the 195.30 beta driver last week. I can't find the link right now, but I believe it said that to be supported for 3D vision, the card has to be G82XL or newer. The Core designations for Quadro cards can be found at Wikipedia: http://en.wikipedia.org/wiki/Nvidia_Quadro -- === All Things Serve the Beam === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
[ccp4bb] Intel compiler in the news
This might be of interest to the scientific computing community: http://www.osnews.com/story/22683/Intel_Forced_to_Remove_Cripple_AMD_Function_from_Compiler_ Intel Forced to Remove Cripple AMD Function from Compiler? posted by Thom Holwerda on Sun 3rd Jan 2010 20:32 UTC Icon Here's something you probably don't know, but really should - especially if you're a programmer, and especially especially if you're using Intel's compiler. It's a fact that's not widely known, but Intel's compiler deliberately and knowingly cripples performance for non-Intel (AMD/VIA) processors. ... -- === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] [COOT] 120hz LCDs and coot stereo
On Thu, 2009-12-17 at 18:25 -0500, Ajit Datta wrote: I just talked to the NVIDIA pre-sales people and they told me that this driver (195.22 beta) should work with 120Hz lcd monitors together with Nvidia 3D vision kit on a quadro graphics card. Ajit B. http://www.phoronix.com/scan.php?page=news_itempx=NzczOQ NVIDIA Pushes Out 195.22 Beta Linux Driver ... Other changes include... support for NVIDIA 3D Vision Stereo on Linux with Quadro GPUs... -- === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] [COOT] 120hz LCDs and coot stereo
My current understanding is that 1) The new 120Hz LCD monitors are not compatible with the old goggles. Something about the type of polarization used for the shuttering effect. So if you were going to try out one of the new 120Hz monitors (~ $400) you might also want to spend on the nVidia glasses and emitter kit (~ $200) 2) The 120 Hz LCDs are not supported under Linux drivers by nVidia at present. Whether it might actually work or not, I can't say. I am encouraged by the mention that the nVidia emitter can accept a signal from the mini-DIN stereo port on some Quadro cards. http://www.nvidia.com/object/quadro_pro_graphics_boards.html 3) As someone mentioned already, the Zalman LCD monitors, which are not 120Hz and do not require goggles, but have diminished resolution, are currently supported. Cheers, -- === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu On Thu, 2009-12-17 at 11:09 -0500, Michael J Miley wrote: I have a linux workstation with a nvidia quadro graphics card and matching emitter/lcd glasses setup from realD. It is very hard to find CRTs that are able to support the high refresh rates needed for headache free 3D viewing. The old SGI one I have is terrible, as it flickers bad in 3d mode. My question is can i use one of these new 120hz LCD monitors with the above setup for coot. Basically just switch out the crt for the LCD. Has anyone tried this? I am aware that these monitors with a non-quadro nvidia card plus the nvidia emitter/glasses setup will not work with coot. But i think the reason is that the drivers for these non-quadro cards do not support true quad buffered stereo.
Re: [ccp4bb] [COOT] 120hz LCDs and coot stereo
On Thu, 2009-12-17 at 13:51 -0800, kai...@caltech.edu wrote: On this note, I recently bought a viewsonic 120hz LCD (VX2265wm) in the naïve believe it should work as it has the right refresh rate. I tried to run it with the normal setup, quadro with emitter via DIN, nuVision glasses, Linux. Here's the problem: I have stereo in the top and the bottom but not in the middle of the screen. The image is stable (no flickering or moving of the part that shows stereo). It seems that I got the right refresh rate (any way to check that?), but I don't understand at all what's going on. Any clues? Jens That monitor appears on the supported displays list: http://www.nvidia.com/object/3D_Vision_Requirements.html So the problem could be one (or more) of two things: 1) The glasses may be incompatible. You could try it out with the nVidia glasses. 2) The Linux driver may not be working properly yet. BTW, I see that some 1920x1080 monitors are listed on the above page, and should be available in January or so. -- === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] warning message: bound resonance
And a few guilty ones. - === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu On Fri, 2009-11-20 at 22:24 +0100, Gerard DVD Kleywegt wrote: 'Allo! 'Allo! I suspect that you are looking for the CCPN mailing list rather than the CCP4 one. You have just confused thousands of innocent crystallographers! --dvd
[ccp4bb] Stereo 3D notebook
http://www.xbitlabs.com/news/mobile/display/20091118173434_Nvidia_Adds_Stereo_3D_Vision_to_Notebooks.html Nvidia Adds Stereo 3D Vision to Notebooks. Asustek Computer to Add Stereo 3D to Mobile PCs This is the 120 Hz LCD technology. But still, no Linux drivers. - === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] crystallography teaching advice: f(S) ?
On Tue, 2009-10-20 at 11:45 +0100, Phil Evans wrote: On 20 Oct 2009, at 10:53, Kevin Cowtan wrote: I thought that the point of Enlightenment science was a rejection of (Aristotelian) authority, basing science of empirical observations. If properly conducted, Science is inherently not based on authority but on evidence... Indeed. The word expertise is more appropriate in science than authority. - === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] ALS cryopucks
Are you looking for the original ALS puck, or the Universal V1-Puck which is designed for compatibility with both ALS and SSRL systems? Uni-Puck: Crystal Positinoing Systems https://secure.crystalpositioningsystems.com/Uni-Puck.html - === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu On Mon, 2009-09-28 at 17:03 -0400, Alexandra Deaconescu wrote: Dear all: Does anyone know of a company other than Boyd Technologies that sells the ALS cryopucks? The item is no longer available from Boyd so I am trying to find alternative vendors... Thanks, Alex Alexandra M. Deaconescu Postdoctoral Fellow Grigorieff Laboratory Brandeis University Rosenstiel Center MS 029 415 South St. Waltham, MA 02454 USA For deliveries: Brandeis University Kalman Dock 415 South St. Waltham, MA 02454 USA
Re: [ccp4bb] Summary for weak magnet of goniometer of MAR345dtb
On Sun, 2009-08-30 at 22:13 +0800, aidong wrote: As a matter of fact, I believe that such a robot is really useless for home source X-ray. In my experience, the phrase as a matter of fact is more often followed by an opinion than a fact. - === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] space groups not supported by Refmac5
For the latter, P21221, you could reindex to get P21212, which is supported. - === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu On Mon, 2009-08-17 at 17:37 +0100, Arefeh Seyedarabi wrote: Hi, I have a question; recently I have encountered a few space groups which are not supported by Refmac5. Examples include I2 and P21221. Both these space groups have been identified as the best solutions for the two different datasets I am working on using Pointless. However, I am faced with difficulties in Refmac5, and the program fails to complete when I select refinement cycles with Arp-waters...with the message saying 'space group not supported'. Any suggestions on how this problem could be overcome? Regards, Arefeh Arefeh Seyedarabi, PhD Postdoctoral research assistant School of Biological and Chemical sciences Queen Mary, University of London Mile End road London E1 4NS Based at Joseph Priestley Building G.35 020 78828480
Re: [ccp4bb] Best 3D stereo combination for Linux
Warren: why should a 120 Hz LCD monitor with the nVidia USB emitter/glasses require a Quadro card? The system requirements for GeForce 3D Vision on Windows lists many GeForce cards as being supported: http://www.nvidia.com/object/GeForce_3D_Vision_Requirements.html GeForce GTX 200 series ... Geforce 9 series ... Geforce 8 series ... I should think it unlikely that the hardware requirements under Linux or MacOS would differ drastically, if and when those OSes are covered by a driver. - === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu Original message Date: Wed, 1 Jul 2009 01:31:12 -0700 From: Warren DeLano war...@delsci.com Subject: Re: [ccp4bb] Best 3D stereo combination for Mac OS X today To: CCP4BB@JISCMAIL.AC.UK Danny, Thank you (and Harry and Dirk) for pointing out the after-market PNY card -- I wasn't aware of that option. However, it is worth noting that PC users can access stereo 3D (via 3D Vision IR emitter glasses) with a $139 Quadro 300-series card whereas Mac users must spend 12X more for an ultra high-end 4000-series card (which will only work IF they happen to own a compatible Mac Pro model). Unfortunately, all the GPU power of an expensive ultra-high-end-card provides little (if any) benefit if all you're running is Coot, PyMOL, CCP4mg... Anyway, my point is that there is presently a significant (and possibly increasing) lack of parity for the Mac versus the other platforms with respect to stereo 3D. Furthermore, because of nVidia's introduction of their proprietary USB-based emitter (which syncs the 120 Hz LCDs), it isn't yet clear whether or these displays will work only on Windows, only on Windows and Linux, or indeed across all three platforms. Personally, I would want to know the answer to that question before spending $4-6k+ USD on a Quadro-equipped Mac Pro! Cheers, Warren -Original Message- From: Danny Smith [mailto:smi...@omrf.ouhsc.edu] Sent: Tue 6/30/2009 4:03 PM To: Warren DeLano Cc: Danny G Smith; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Best 3D stereo combination for Mac OS X today Warren, Thank you very much for the quick reply. I didn't see it directly with the mac, but this link still has it at the store, http://store.apple.com/AppleStore/WebObjects/BusinessCustom.woa/9554008/wa/PSLIDfind=Quadro+FX+4800+for+Macwosid=7Q4ITeYWEwd92YhZCy32JoVJnH4 . It is very expensive at $1,746.00. I also found this link, http://www3.pny.com/NVIDIA-Quadro-FX-4800-For-Mac-P2815C409.aspx . It looks like on that page that it is tested with Mac OS X v10.5.7, on MacPro3,1 or MacPro4,1 or later - Note: MacPro1,1 and MacPro2,1 are not compatible. I was just hoping to find a cheaper card. It does make me want to do more research with our sales rep. thanks, Danny G. Smith Sr. Programmer / Analyst Oklahoma Medical Research Foundation 825 N.E. 13th Street M.S. 11, Room E210.1 Oklahoma City, OK 73104 Phone: (405)271-8001 ext. 35535 Cell: (405)-202-6691 On Jun 30, 2009, at 5:25 PM, Warren DeLano wrote: Danny, Last I checked, Apple dropped the Quadro option from the Mac Pro, and a quick check on Apple.com seems to confirm that: http://store.apple.com/us_smb_78313/browse/home/shop_mac/family/ mac_pro Lacking indications to the contrary, we can only conclude that OpenGL stereo 3D support has an uncertain future on the Mac, whereas nVidia appears fully committed to supporting it under Windows XP, Vista, and Linux. 120 Hz LCDs are very close to being, but are not quite yet, a viable option. Hopelly that will change in a matter of weeks, however, they will likely require a quadro card, 3D vision emitter, and an appropriate driver from nVidia. Mac support for 120 Hz seems unlikely unless nVidia and Apple deliberately get together to create a joint solution. Due to proprietary aspects of each component (Mac OpenGL drivers, nVidia emitters), this isn't something either Apple or nVidia could accomplish alone. Zalman LCDs can do stereo 3D (with reduced vertical resolution) but they require software modifications or a Quadro card with the updated windows or linux driver
[ccp4bb] Sample shipping question
For your amusement/outrage: A user of our synchrotron shipped samples in a deWar from overseas. The deWar was held up by U.S. Customs, and we received the following from a FedEx employee: --- This shipment is delayed with US Customs. We need to know the amount of salt in the shipment in kilograms. I have attached the commercial invoice. Can you provide this info? Thank you. (name redacted) Senior ECO Import Coordinator FedEx Trade Networks --- - === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] protein folds
Concerning the number of proteins folds in existence vs. the number of folds already identified: Ed Berry had some good points regarding sample statistics, and I assume the mathematics of that sort of thing is formalized somewhere. The number of examples per protein fold will be skewed by the common use of molecular replacement for phasing and the tendency of researchers working in one field to solve several related structures. Keep in mind also the mechanism through which new folds have evolved; i.e. through the generation of new genes via duplication, insertion, deletions, point mutations, and the occasional frame shift. That should be enough text to give the impression that I am a serious person with serious ideas, without conveying any actual useful information; so that I now feel justified in changing the topic to a similar question in another field which was published a few years ago, work done by one of those ubiquitous and prolific Dodsons: Estimating the diversity of dinosaurs Steve C. Wang Peter Dodson PNAS September 12, 2006 vol. 103 no. 37 13601-13605 Published online before print September 5, 2006, doi: 10.1073/pnas.0606028103 http://www.pnas.org/content/103/37/13601.abstract Cheers, - === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu On Thu, 2009-02-26 at 14:19 +, ANDY DODDS wrote: The original poster may be interested in this paper from Phil Bourne's lab a few years ago which looked at the contribution of folds (among other things) by the Protein Structure Initiative, particularly Fig 5 and table 1. http://helix-web.stanford.edu/psb04/bourne.pdf The Status of Structural Genomics Defined Through the Analysis of Current Targets and Structures P.E. Bourne, C.K.J. Allerston, W. Krebs, W. Li, I.N. Shindyalov, A. Godzik, I. Friedberg, T. Liu, D. Wild, S. Hwang, Z. Ghahramani, L. Chen, and J. Westbrook ...
[ccp4bb] Replacement for arp_waters?
I note that in CCP4 6.1.0, arp_waters has been deprecated. Is there a program in the suite which fills the role formerly filled by arp_waters, of automatically adding waters? Cheers, - === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu
Re: [ccp4bb] Planar Systems monitor
RE LCD monitor for stereo viewing: No. That monitor, which looks like an ordinary 19 LCD monitor, is not capable of stereo viewing. LCD monitors are in general not fast enough for stereo. There are some new technology LCD monitors which claim to be able to do stereo, this is not one of them. http://www.reviewspring.com/3d-lcd-monitors-a80.php such monitors are more expensive than bog-standard monitors, and I don't know what the state of driver support is fro stereo viewing on them (not to mention you don't state your oeprating system.) Cheers, - === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University schul...@cornell.edu On Mon, 2008-12-15 at 09:26 -0500, Oganesyan, Vaheh wrote: I came across this LCD monitor with DVI connection. Would experts in the field recommend this monitor for stereo viewing? http://www.pcconnection.com/IPA/Shop/Product/Detail.htm?sku=6220485 Thank you. ___ Vaheh 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.
Re: [ccp4bb] protein crystallography universe
pxuniverse - so you want to start out by excluding the nucleic acids universe? ;) Also, I note that it ends in .com. Will this be a commercial site? Will you be selling ads or some such? Cheers, - === You can't possibly be a scientist if you mind people thinking that you're a fool. - Wonko the Sane === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University [EMAIL PROTECTED] On Tue, 2008-10-14 at 14:47 -0500, Paul Swepston wrote: Folks: While attending the ICSG meeting in Oxford last month it struck me that there might be a need for a general protein crystallography portal containing information about software, websites, jobs, journals, organizations, education, etc. While I realize that many people have created great lists of related websites for protein crystallography, I decided to create a new one and maintain it going forward. It can be found at www.pxuniverse.com. The inspiration for the name came from Ian Wilson's discussions about the structural biology universe and the impetus to create it came from Ian Wilson's discussion of XtalPred, Derewenda's talk on SERp, and Sussman's great presentation about Proteopedia; it is difficult to keep up with all the innovations and pxuniverse is an attempt to give easier access to all the available tools. If you have any links that you would like to see added please send them directly to me. If you have any suggestions about the organization, I will consider all suggestions. Thanks - Paul Swepston
Re: [ccp4bb] Crystallogrphy today
On Mon, 2008-09-22 at 10:52 -0500, Jacob Keller wrote: To understand the fundamentals of any discipline, I have always found it completely worthwhile to go back to the original source, where the idea was first discovered or presented. This is really, really valuable, although not always possible. I have found this to be not possible, and therefore not valuable, in the disciplines of fire-starting and wheel-building. - === With the single exception of Cornell, there is not a college in the United States where truth has ever been a welcome guest - R.G. Ingersoll === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University [EMAIL PROTECTED]
[ccp4bb] 6.0.99
Downloaded CCP4 6.0.99 core and phaser. Did gunzip and tar to extract. Next, the instructions say for the first 3 tarballs unpack into the same directory, then configure...make...make install. I did ./configure and got this: ! Please set environment variable BINSORT_SCR (see installation instructions). ! Please set environment variable CCP4_SCR (see installation instructions). ! Please set environment variable CINCL (see installation instructions). ! Please set environment variable CLIBD (see installation instructions). ! Please set environment variable CCP4_OPEN (see installation instructions). ! Please set environment variable PUBLIC_FONT84 (see installation instructions). So apparently a config file is necessary first. Oops. Full text of ./configure output is attached. - === With the single exception of Cornell, there is not a college in the United States where truth has ever been a welcome guest - R.G. Ingersoll === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University [EMAIL PROTECTED] # ./configure Please read the following NOTICE TO THE LICENSEE Please read the following Conditions of Use and the appropriate Licence Agreement carefully before completing the installation process and using the software. These Conditions and the Licence Agreement are legal documents, and together contain information on allowed usage of the software suite, warranty information and liability disclaimers. If you do not agree with these Conditions, then do not complete the installation and do not use the software. These conditions have been updated for release 6.0 of the CCP4 software suite, and all sites are required to agree to these conditions of use. You should only be prompted for this agreement once. The Conditions are as follows: a. For commercial users and those doing commercial work: Please contact CCP4 at [EMAIL PROTECTED] to arrange a commercial licence. If you have arranged or renewed a commercial licence in the last 12 months, then no action is required. By agreeing to these conditions, you confirm that you have a valid and current CCP4 commercial licence. b. For users at non-profit sites and not engaged in commercial work: Please print and complete an Academic licence, sign it and post or fax it to CCP4 at the address given on the licence (email is not acceptable). A new licence agreement is required for CCP4 version 6.0. This licence is valid for 6.0 and subsequent versions until further notice. Copies of the licence can be found in a variety of formats in the top directory of the CCP4 distribution (files academic_software_licence.*) and on the CCP4 web site at www.ccp4.ac.uk/ccp4license.html . By agreeing to these conditions, you confirm that you have returned a licence for CCP4 version 6.0 . It is sufficient to send the licence - there will be no confirmation that it has been received. I agree to the above conditions and have done the actions required. y/n [n] ?:y Thank you. The CCP4 configure will now run as normal. srcdir bindir libdir /usr/local/ccp4_master/ccp4-6.0.99e /usr/local/ccp4_master/ccp4-6.0.99e/bin /usr/local/ccp4_master/ccp4-6.0.99e/lib OK, setting up for a system type of `linux'... ! Using gnu fortran compiler. If you have an old fortran compiler, you may be better ! off using f2c, see --with-f2c option. Will attempt to install the xwindows programs from `x-windows'. This is not supported for all systems. please note the xwindows programs will be compiled with an option that means errors are ignored. This could result in some xwindows programs not being compiled. If you want to disable the xwindows programs use --disable-x The CCIF library will be built and installed. This has been tested on the most common systems, but if you have problems, use the --disable-ccif flag. The CCTBX library will be built and installed. If you have problems, use the --disable-cctbx flag. Phaser will be built and installed. If you have problems, use the --disable-phaser flag. The LAPACK linear algebra package will be included in the installation. Configure will search for existing LAPACK and BLAS libraries on on your system - if a version of LAPACK is not found then the NetLib version will be built for you automatically. If you want NetLib LAPACK and BLAS to be used regardless of system libraries then rerun configure using --with-netlib-lapack To disable inclusion of LAPACK, use the --disable-lapack flag (This is not recommended as some programs will fail to build) Configure will try
Re: [ccp4bb] Small lysozyme crystals protocol
Rigaku has a page of common crystallization recipes: http://www.rigaku.com/protein/crystallization.html Try the Lysozyme crystallization procedure for low temp use recipe. It contains ethylene glycol so the crystals are cryo-ready. To get a large number of smaller crystals, push the concentration of lysozyme solution up to 100 - 120 mg/ml. Cheers, - === With the single exception of Cornell, there is not a college in the United States where truth has ever been a welcome guest - R.G. Ingersoll === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University [EMAIL PROTECTED] On Thu, 2008-07-03 at 18:08 -0500, Jacob Keller wrote: Dear Crystallogrphers, does anybody here know a protocol to get consistently well-diffracting but smaller, ~50um, cryoprotect(ed/able) lysozyme crystals? Thanks, Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: [EMAIL PROTECTED] *** - Original Message - From: Ailong Ke [EMAIL PROTECTED] To: CCP4BB@JISCMAIL.AC.UK Sent: Thursday, July 03, 2008 4:13 PM Subject: [ccp4bb] air bubbles in the Bio-Rad Duoflow system Hello All, I own a Bio-Rad Duoflow system for almost a year. The machine lived up to some of the recommendations I saw on this board. However, there is this annoying problem with air bubbles entering columns and I cannot figure out the source. The system would be free of any air bubbles in the beginning, and performs fine when water is loaded using needle/syringe into the 5ml superloop and then injected into the column. When protein samples are injected the same way, a lot of air bubbles would appear and get trapped inside the ion exchange column, leaving yellowish marks on the Uno columns and eventually reducing their performance. I've been a FLC/AKTA user for about ten years and have never seen such problems. I doubt it is due to a faulty injection valve because we recently had it replaced for other reasons. We did move a backpressure generator (a little black piece) from post-column position to before-column, otherwise we cannot run sizing columns in a reasonable flow rate. I'd like to hear if you have similar experiences and how you fixed the problem. Thanks a lot! Ailong --
Re: [ccp4bb] stereo with Nvidia Quadro
The nVidia cards used for stereo are the Quadro FX series. The Quadro NVS series are for running multiple monitors, but not fancy 3D graphics. You can explore the manufacturer's web site for details. - === With the single exception of Cornell, there is not a college in the United States where truth has ever been a welcome guest - R.G. Ingersoll === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University [EMAIL PROTECTED] On Thu, 2008-05-08 at 15:01 +0200, Tim Gruene wrote: Good day, I have been trying to enable stereo mode on a PC (SuSE10.1) with an NVIDIA NV37GL [Quadro FX 330/Quadro NVS280] graphics card (according to Xorg.0.log). (--) PCI:*(5:0:0) nVidia Corporation NV37GL [Quadro FX 330/Quadro NVS280] rev 162, Mem @ 0xdd00/24, 0xc000/28, 0xde00/24, BIOS @ 0xdfc0/17 (II) NVIDIA(0): NVIDIA GPU Quadro NVS 280 PCI-E at PCI:5:0:0 (GPU-0) Accroding to some web page about O, the options are set to (**) NVIDIA(0): Option Stereo 3 (**) NVIDIA(0): Option NvAGP 1 (**) NVIDIA(0): Option IgnoreEDID false (**) NVIDIA(0): Option UseEdidFreqs true Yet, the log file says (WW) NVIDIA(0): Stereo is only available on Quadro cards (II) NVIDIA(0): Disabling stereo. I was wondering whether anyone could explain what is so un-Quadro about this card? (Currently, the display is an LCD, but the same messages came up when the display was a CRT) Thank you for your help, Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
[ccp4bb] Kay Diederichs and Novel_R source?
I would like to get a hold of the program Novel_R, the source code for which is supposed to be available on Kay Diederichs' web site. However, the links I have seem to be outdated. Does Diederichs have a new web site, and is the Novel_R source still available? The outdated link: http://strucbio.biologie.uni-konstanz.de/~kay Thanks, -- === With the single exception of Cornell, there is not a college in the United States where truth has ever been a welcome guest - R.G. Ingersoll === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University [EMAIL PROTECTED]
Re: [ccp4bb] Merging CCP4i projects from two computers
Unison is good, as is rsync, but in this particular case will be complicated (if ( understand correctly) by the use of the identical file names for different files on the two computers. I don't see an easy, automatic way around this. I would rename one or some of the directories, put them on the same computer, and then manually go through them and decide which ones are duplicates, and which are unique but identically named files, and rename those. If this is a Unix/Linux system, it might be useful to know that the diff command can work on an entire directory, if you plead with it sincerely enough and use the right parameters. In future, unison or rsync could be used on a regular basis to avoid another situation like this arising. Back in the good old days, we were able to share disks between computers with something called NFS, and even further back, file versioning in VMS might have been relevant and useful. But I am wandering. Cheers, - === With the single exception of Cornell, there is not a college in the United States where truth has ever been a welcome guest - R.G. Ingersoll === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University [EMAIL PROTECTED] On Fri, 2008-03-07 at 12:15 +, Johan Turkenburg wrote: Hi, The way I cope with this is by using synchronisation between directories (folders) on the two computers. In my case both are running linux, and the program Unison provides a simple tool to synchronise. If you make sure the projects have the same name on the two computers, the cpp4 database files copy over ok, and the interface copes ok. I am sure this method is easy to break, so be careful trying it out! Johan P.J.Briggs wrote: Hi Derek There's not really any way of doing what you're asking at present. If merging utility would be useful to others then I would be prepared to look into providing one, although there are a bunch of fiddly issues to deal with (e.g. keeping dates consistent, handling file name clashes and so on). Do any other readers of this list want to comment? Best wishes Peter Derek Logan wrote: Hi everyone, I've been working on a project using CCP4i on two separate computers in parallel and now unfortunately have jobs spread over the two locations. I would now like to consolidate these. Some of the new jobs on one computer will have the same run number as different ones on the other. Is there any convenient way to merge the projects? I guess the answer is no, or else the question would have been asked and answered already ;-) Thanks Derek -- Derek Logan tel: +46 46 222 1443 Molecular Biophysicsfax: +46 46 222 4692 Lund University mob: +46 76 8585 707 Box 124, Lund, Sweden
Re: [ccp4bb] Unknown density
Remember that since it is on a special position (2-fold?), you may not be looking at a single object, but an overlay from two or more positions. The anomalous map is very useful; the mystery molecule must have an anomalous scatterer. It would be even more helpful if you had mentioned the wavelength of the data. Anyway, the only thing in the list of mother liquor ingredients you provided that scatters anomalously is calcium, which fits in with the Asp ligands. The additional ligands for the calcium might be water or acetate. So: my guess would be two positions of Ca2+, one right on the axis and one off the axis (and doubled by the symmetry). You can try placing Ca atoms at these positions and see what the occupancies and thermal factors refine to. For example, start with an occupancy of 0.5 at each position and see if the thermal factors refine to a value comparable to nearby protein atoms. Cheers, - === With the single exception of Cornell, there is not a college in the United States where truth has ever been a welcome guest - R.G. Ingersoll === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University [EMAIL PROTECTED] On Mon, 2008-02-25 at 11:54 +0100, Franck Coste wrote: As Edward MITCHELL suggested, I made a phased anomalous difference map and could clearly see the S atom of my sulfide bridges and 1 Ca atom as I espected. Concerning the unknown density, the shape is the same as in the fo-fc map Updated images at : http://unknowndensity.blog4ever.com/blog/photo-183078.html In yellow is the phased anomalous difference map at 4 sigma. Franck.
Re: [ccp4bb] Engineering disulfide bonds
On Fri, 2008-02-08 at 10:44 -0500, Kendall Nettles wrote: Also, can I expect 100% disulfide formation from standard bacterial expression (assuming good geometry of the cysteines)? No, E. coli cells are a reducing environment. - === With the single exception of Cornell, there is not a college in the United States where truth has ever been a welcome guest - R.G. Ingersoll === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University [EMAIL PROTECTED]
Re: [ccp4bb] Web site GOOD, Attachment BAD
On Thu, 2008-01-31 at 08:12 -0500, Raji Edayathumangalam wrote: Can the CCP4BB provide something like a website to upload pictures and then have the BB-ers just post the link in their email. Please! These attachments are clogging my inbox... Thanks much. Raji If you're talking about an open site where anyone can post, then we could run a contest to predict how long it takes for it to be hacked and used for illegal file dispersal. If you're talking about a site where CCP4 personnel could remove attachments from incoming e-mail and post them on the site, I suspect that CCP4 personnel would prefer not to handle that extra work load. The same for a site where CCP4 personnel would administer private accounts for users to post. I think it's better if each person finds their own site where they can securely post. Cheers, - === With the single exception of Cornell, there is not a college in the United States where truth has ever been a welcome guest - R.G. Ingersoll === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University [EMAIL PROTECTED]
Re: [ccp4bb] Cocrystals - should they pop up under native conditions?
Don't call them co-crystals until you've actually shot them and seen the density. It will depend not only on the ligand but on the ligor(?) as well. You don't mention the identity of your ligand or ligor(?). You mention that some of your screens are under oil, so I will point out that some non-polar ligands might prefer to partition in the oil rather than the mother liquor. That would explain why the crystals look so much like the native. Posting to the BB is always a valuable way to fill time until you can collect the data which will answer the question. Cheers, - === With the single exception of Cornell, there is not a college in the United States where truth has ever been a welcome guest - R.G. Ingersoll === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University [EMAIL PROTECTED] On Tue, 2008-01-22 at 19:33 +, Brenda Patterson wrote: Hello all, I am expecting a somewhat homogeneous reply to this one, but that is fine and welcomed as are anecdotal experiences. I am running co crystallisation experiments and have thus far been trying under oil screens with some success (i.e. various hits in various conditions resulting in crystal growth). These conditions have varied from the native condition up until now. I have recently peered at some fairly old plates I set up under hanging drop under native conditions when running a co crystal trial and have found crystals. Their morphology is very similar to the 'native' form. I bit punier than them if I had to push. So, 1. Should I be surprised that co crystals pop up under native conditions or does it entirely depend on the ligand? 2. Is it probably not going to be a co crystal as usually they don't pop up under native conditions? 3. It totally depends and if I don't like it then I should get out of this beautiful game? I am going to shoot them either way, but just thought I would ask. cheers Brenda
Re: [ccp4bb] ideal bond length and bong angel
On Wed, 2008-01-09 at 12:47 +0100, Gerard DVD Kleywegt wrote: (rhetorical question of the day: just like teaching a person how to fish is better than to give them a fish, isn't providing the url to google or wikipedia better than providing an answer to a basic question?) You can read a few paragraphs about The spirit of helpfulness here: http://en.wikipedia.org/wiki/Wikipedia:Help_desk/How_to_answer - === With the single exception of Cornell, there is not a college in the United States where truth has ever been a welcome guest - R.G. Ingersoll === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University [EMAIL PROTECTED]
Re: [ccp4bb] Have a happy new year with your very own crystallography system!
On Mon, 2008-01-07 at 18:22 +, Erin Curry wrote: Tired of embarrassing incidents at the beamline?... Alright, who's been telling stories? - === With the single exception of Cornell, there is not a college in the United States where truth has ever been a welcome guest - R.G. Ingersoll === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University [EMAIL PROTECTED]
Re: [ccp4bb] detecting RNA from possible protein-RNA complex crystals
On Tue, 2007-12-11 at 13:00 -0500, Rongjin Guan wrote: Dear All I am trying to co-crystallize a protein and dsRNA complex, and looking for methods to detect RNA in the crystals. I am thinking about using Mass Spectrum, Nanodrop to measure OD280/260, etc, but I wonder if ther are some more sensitive and reliable ways. Sensitive and reliable - you could solve the crystal structure. - === With the single exception of Cornell, there is not a college in the United States where truth has ever been a welcome guest - R.G. Ingersoll === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University [EMAIL PROTECTED]
[ccp4bb] Installation problem on Fedora 8
I am attempting to install and compile CCP4-6.0.2 along with BLT,
Chooch, etc under Fedora 8. I am doing this under the root account, with
a default login shell of tcsh. When I run install.sh, BLT and Chooch
apear to install OK and then I get these error messages:
##
# CCP4 Installation #
##
Creating ccp4.setup file...
sed: can't read /root/ccp4-6.0.2/include/ccp4.setup-sh: No such file or
directory
./install.sh: line 477: /root/ccp4-6.0.2/include/ccp4.setup-sh: No such
file or directory
sed: can't read /root/ccp4-6.0.2/include/ccp4.setup-zsh: No such file or
directory
./install.sh: line 479: /root/ccp4-6.0.2/include/ccp4.setup-zsh: No such
file or directory
sed: can't read /root/ccp4-6.0.2/include/ccp4.setup-dist: No such file
or directory
./install.sh: line 481: /root/ccp4-6.0.2/include/ccp4.setup-dist: No
such file or directory
sed: can't read /root/ccp4-6.0.2/include/ccp4.setup-bash: No such file
or directory
./install.sh: line 483: /root/ccp4-6.0.2/include/ccp4.setup-bash: No
such file or directory
./install.sh: line 504: cd: ccp4-6.0.2: No such file or directory
cp: cannot stat `include/ccp4.setup-dist': No such file or directory
./install.sh: line 506: include/ccp4.setup-sh: No such file or directory
[EMAIL PROTECTED] ccp4_master]# pwd
/usr/local/ccp4_master
[EMAIL PROTECTED] ccp4_master]# echo $CCP4_MASTER
/usr/local/ccp4_master
--
The installation is by default supposed to happen in the current
directory, but references to the current directory in install.sh as
${current} seem to be failing, as though each command were instead being
executed from root's home directory. Help, anyone?
Cheers,
--
===
With the single exception of Cornell, there is not a college in the
United States where truth has ever been a welcome guest - R.G. Ingersoll
===
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
[EMAIL PROTECTED]
Re: [ccp4bb] speeding crystallisation
On Mon, 2007-08-06 at 15:50 -0400, Neeraj wrote: hi all, I am working on a protein for which we get nicely diffracting crystals but the problem is that the crystals grow from anywhere between 4-6 months. Does anyone has any general suggestions as to what things can be changed or tried to speed up the process. Any help or suggestions would be welcome as i am crawling towards getting enough crystals to make a synchroton visit:):) Perhaps some degradation such as proteolysis is necessary before crystallization. Try working in less clean conditions. Or, you could take some of your existing crystals and subject them to analysis, such as mass spec. If there is something like proteolysis occurring, you may be able to identify the site that way, and pre-cut your protein, or even engineer a shorter version. We did something similar to this for heme oxygenase. Cheers, -- === With the single exception of Cornell, there is not a college in the United States where truth has ever been a welcome guest - R.G. Ingersoll === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University [EMAIL PROTECTED]
Re: [ccp4bb] difference density ripples around Hg atoms
On Wed, 2007-08-01 at 09:35 +0200, Klemens Wild wrote: Dear friends of the Fourier transform, I am refining a structure with 2 adjacent Hg atoms bound to cysteines of different monomers in the crystal contacts, which means I need to refine them as well. While the structure nicely refines (2.2 A data), I do not get rid of negative density ripple layers next to them (-10 sigmas). My question: is this likely due to anistropy of the soft mercury atoms (anisotropic B refinement decreases the ripples) or is this likely a summation truncation effect prominent for heavy atoms? Can I just anistropically refine the mercuries while I keep the rest isotropic? Yes, that sounds worth a try. At 2.2 A you probably don't have the data/parameter ratio to justify anisotropic refinement for the whole molecule, but since you know the mercury atoms are not being treated adequately, adding an extra ~ 10 parameters to refine them as anisotropic is worth a try. Don't expect it to completely eliminate the ripples, but hopefully you can get some improvement on R/Rfree. Cheers, -- === With the single exception of Cornell, there is not a college in the United States where truth has ever been a welcome guest - R.G. Ingersoll === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University [EMAIL PROTECTED]
Re: [ccp4bb] Survey on computer usage in crystallography
On Tue, 2007-06-19 at 21:09 -0700, P Hubbard wrote: Hi all, I am doing a survey on computer usage in crystallography. The questionnaire can be found on the following web page: http://www.bioscienceforum.com/survey.html ... I don't care for the way several questions are posed. Examples: 4.What would you consider is a reasonable price to pay for a computer graphics workstation designed with crystallography in mind? A) USD $2000-3000 B) USD $3000-5000 C) USD $5000+ What, no option for I'd be willing to assemble one from parts for under USD $2000? ... If there were a choice, would you prefer stereo graphics displayed using LCD-shuttered glasses or a head mounted display (often referred to as a Virtual Reality headset)? That does not cover all the choices currently available, let alone what I wish were available. -- === With the single exception of Cornell, there is not a college in the United States where truth has ever been a welcome guest - R.G. Ingersoll === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University [EMAIL PROTECTED]
Re: [ccp4bb] image plate shadow
On Thu, 2007-05-03 at 19:51 -0300, Alejandro Buschiazzo wrote: Dear ccp4bb users, I have a question that concerns a problem with data collection (not directly related to CCP4). It might be a really stupid mistake I'm making... I'm attaching a diffraction frame where, as you can easily see, there is an annoying shadow... I agree with the others that the shadow could indeed be caused by your pin, and is not a problem as the software commonly in use corrects for local background. If you want to reduce the shadow, you could reduce the air scatter in between the collimator and the crystal. A shorter distance would mean less air scatter, but of course you don't want your collimator to impinge on your cryo stream. Possibly details of the collimator could be contributing, I don't know anything about hte design or quality of collimator you are using. Another way to reduce air scatter would be to reduce the air by putting the experiment in a helium box. -- === With the single exception of Cornell, there is not a college in the United States where truth has ever been a welcome guest - R.G. Ingersoll === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University [EMAIL PROTECTED]
Re: [ccp4bb] X-ray generator uninterruptible power supply
On Thu, 2007-03-22 at 18:54 -0400, [EMAIL PROTECTED] wrote: I never considered getting a UPS for my generator, even though our building has no backup power and Con Ed also forgets to feed their hamsters occasionally. What I did get was a UPS for my cryostream - I figured that the data collection can always be restarted if the generator died in the middle of the night, but once the crystal is gone, it's gone. I paid less than $10k for a UPS that can run my Cryojet for over 15 hours, so even if the power goes out in the middle of the night, I can come in and rescue the crystal the next day. That's a good idea, we do that now on our crystallography beamlines. -- === With the single exception of Cornell, there is not a college in the United States where truth has ever been a welcome guest - R.G. Ingersoll === David J. Schuller modern man in a post-modern world MacCHESS, Cornell University [EMAIL PROTECTED]
