Re: [ccp4bb] malware in ccp4?

[Andy Purkiss]

Hi Andrea,

I would suggest that this is probably a false positive down to the way your 
anti-virus software detects threats. Searching for this particular threat gives 
several similar examples from even very simple Python code.

On my home PC, a scan of the CCP4 installation with Windows Defender doesn't 
report any issues.

Hope that helps,

Andy


From: CCP4 bulletin board  on behalf of Andrea Smith 

Sent: 28 August 2024 12:05
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] malware in ccp4?


External Sender: Use caution.


Hi,



I updated to ccp4-9 a couple of days ago (windows, package manager) and today 
my antivirus moved one of the ccp4 files to a quarantine. It was:

CCP4-9/WinCoot1/lib/python.3.11/site-packages/rdkit/Chem/rdDistGeom.pyd


It claims the threat is Win64:Evo-gen [Trj].



Is this an issue or did my antivirus just delete an actual part of a software?



Thank you,

Andrea



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Re: [ccp4bb] Lattice expansion

[Andy Purkiss]

Hi Charlie,

With xia2 you can try to reprocess and force the spacegroup to be P222 and the 
cell dimensions to be the larger option with the following options:

-spacegroup P212121    
-cell 80,80,120,90,90,90  

This can also be done with other processing pipelines.

I've seen similar cases before and you may find that the P222 cell was found 
but then discarded during the automatic processing as F222 fit just a little 
bit better. If collecting data at Diamond, it is worth uploading the expected 
spacegroup / cell dimensions and then the pipelines will try to process the 
data in the given cell as well as 'ab initio'.

Hope this helps,

Andy



From: CCP4 bulletin board  on behalf of Nichols, Charlie 

Sent: 08 July 2024 12:07
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] Lattice expansion


External Sender: Use caution.


Hi,



I am trying to recapitulate a published crystallisation system. The published 
crystal form is P212121 approx cell dimensions 80, 80, 120 // 90, 90, 90 with 
one trimer in the ASU



We did not get any crystals in the published conditions but have found a new 
condition giving data to a much higher resolution than the published one but 
there is a problem…



New crystal form is F222 with approx cell dimensions 40, 40, 120 // 90, 90, 90 
– this cell is too small to fit one monomer let alone one trimer.



The prep is remarkably clean and there is a high volume of crystals in the drop 
so unlikely to be a contaminant. I have tried molrep with individual domains in 
case there has been degradation during crystallisation but this does not look 
at all promising.



I am wondering, given the almost exact halving of the a/b cell dimensions and 
almost exact equivalence of the c cell dimension, whether this is a 
particularly egregious form of twinning where the twin is three 2-fold screw 
axes to cause an apparent reduction in the unit cell.



Is there a way to expand the data from the current 40, 40, 120 // 90, 90, 90 
unit cell to the larger ‘super-cell’ 80, 80, 120 // 90, 90, 90 with four copies 
of the data to then attempt either molep or just twin refinement with the 
original published model?



Any comments / help appreciated – NB: I can’t share the actual data or even the 
target as they are confidential client data…



Thanks, take care,

Charlie Nichols



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Re: [ccp4bb] Off-topic: UCSF Chimera Download

[Andy Purkiss]

According to X, there is electrical work yesterday and today.

Downtime: The ChimeraX web site, web services (Blast Protein, Modeller tools, 
sequence realignment), mailing lists, and bug reporting will be down 9 AM 
Pacific time Monday June 17 to 5 PM Tuesday June 18 for building electrical 
upgrades.

Hope this helps.

Andy


From: CCP4 bulletin board  on behalf of Nicholas Clark 

Sent: 18 June 2024 17:09
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Off-topic: UCSF Chimera Download


External Sender: Use caution.

Thanks for the responses. I’ve made multiple attempts over the last few days 
which is why I reached out. Maybe it’s just high traffic and I’ll have to keep 
trying.

Oleksiy, thanks for the offer but I’m on MacOS.

Best,

Nick


On Tue, Jun 18, 2024 at 12:07 PM Kovtun, Oleksiy 
mailto:oleksiy.kov...@mpinat.mpg.de>> wrote:
Hi Nick,

their web site goes offline from time to time. If you are on linux, I can share 
recent binaries.

Best,

Oleksiy


On 18. Jun 2024, at 17:53, Nicholas Clark 
>
 wrote:

I’m trying to navigate to the download page for UCSF Chimera but it does not 
seem to be working. Does anyone know of an alternative location?

Thanks,

Nick Clark




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Re: [ccp4bb] Topology diagram

[Andy Purkiss]

Dear Lionel and Xavier,

Unfortunately TOPDRAW doesn't interpret a pdb file, it just allows you to draw 
your own topology diagram.

PDBSUM (available from https://www.ebi.ac.uk/thornton-srv/software/PDBsum1/) 
has a topology diagram as part of the output.

You can also access a database of released structures here: 
https://www.ebi.ac.uk/thornton-srv/databases/pdbsum/ and there is a link to the 
Generate webpage there allows you to  securely upload a pdb file if you don't 
wish to install the software yourself.

Hope this helps,

Andy Purkiss


From: CCP4 bulletin board  on behalf of Xavier 
Brazzolotto 
Sent: 30 May 2024 16:39
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Topology diagram


External Sender: Use caution.

My Google search led directly to

<https://www.ccp4.ac.uk/html/topdraw.html>
TOPDRAW (CCP4: Supported Program) — CCP4 
documentation<https://www.ccp4.ac.uk/html/topdraw.html>
ccp4.ac.uk<https://www.ccp4.ac.uk/html/topdraw.html>
[favicon.ico]<https://www.ccp4.ac.uk/html/topdraw.html>

HTH

Le 30 mai 2024 à 17:32, Lionel  a écrit :

Dear community,

A biochemist asks me if I knew a webserver/tool to draw topology diagram of 
protein from a deposited pdb or part of it, ideally allowing edition (label, 
colour, etc...).

For a better understanding, the topology diagram’s representation is as the 
picture attached, which I believe is a “key notation” topology diagram.

It’s possible to get such diagram from PDBsum but they are fixed (pdf, ps) and 
I would say (without offence) a bit ugly.

After an extensive Google/Ccp4DB/ChatGPT search, for my surprise, I found 
nothing helpful.
It seems that “old” tools like pro-origami are gone/unavailable.

I would greatly appreciate any advice on possible website or more specialized 
program (even if I would do the “webserver” task myself).

Best,
Lionel




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Re: [ccp4bb] a dinosaur asks ... PDB format query

[Andy Purkiss]

For those wanting a text editor solution, there is the purpose built pdb-mode 
plugin for (x)emacs which works under most operating systems.

The download location has moved around a bit, but a current version is 
available from
https://github.com/mmagnus/emacs-pdb-mode/

with more details at
https://bondxray.org/software/pdb-mode/

Hope this helps,

Andy Purkiss


From: CCP4 bulletin board  on behalf of Hughes, Jonathan 

Sent: 15 May 2024 13:11
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] AW: [ccp4bb] a dinosaur asks ... PDB format query


External Sender: Use caution.


hello CCP4 people,
rather off-topic: is there a purpose-written windows editor for PDF files? with 
interleaved anisotropy lines, missing column delimiters etc., simply extracting 
the B-factors for Ca atoms is hard work using a standard character editor. 
would anyone think of working with DNA without proper tools?
best
jon

--
Prof. Dr. Jon Hughes
Department of Physics
Free University of Berlin
&
Institute for Plant Physiology
Justus Liebig University
Giessen
Germany




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Re: [ccp4bb] replacement for Scientific Linux

[Andy Purkiss]

Hi Harry,

We've been migrating to Rocky Linux as it is built on RHEL in a similar way to 
Scientific Linux. Most things compiled on Centos 7 (our default for a while) 
work in Rocky Linux version 9. For compilers etc., I use the Software 
Collections / devtoolsets to run later versions than the default OS.

Hope this helps,

Andy


From: CCP4 bulletin board  on behalf of Harry Powell 
<193323b1e616-dmarc-requ...@jiscmail.ac.uk>
Sent: 26 April 2024 16:46
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] replacement for Scientific Linux


External Sender: Use caution.


Hi folks

For many years I’ve been using Scientific Linux as my OS of choice (when not 
using my Mac) - but it’s been discontinued. SL was based on RHEL, and had 
useful things like a less-buggy Fortran/C/C++ compiler than that released by RH.

What do people here recommend as a replacement?

Harry


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Re: [ccp4bb] add ligand with AceDRG

[Andy Purkiss]

Hi Stefanie,

In CCP4Cloud, the equivalent task will generate the files using a 'free', 
unused code, if nothing is entered in the relevant box. However, not sure if 
CCP4I2's task will do the same, but worth trying.

Hope this helps,

Andy


From: CCP4 bulletin board  on behalf of FREITAG-POHL, 
STEFANIE 
Sent: 25 April 2024 13:01
To: CCP4BB@JISCMAIL.AC.UK 
Subject: [ccp4bb] add ligand with AceDRG


External Sender: Use caution.

Hi all,

I have trouble adding a ligand with AceDRG in CCP4i2 into my refinement:

I put in a smilesstring and the ligand is written ok, but since I can only 
chose already 'taken' 3-letter-codes the refinement always crashes as there is 
a clash with existing library entries.
Is there any way around this? How do I add a novel ligand?

Thanks so much for your help.

Best wishes,
Stefanie




Dr. Stefanie Freitag-Pohl (she/her)

Durham University

Department of Chemistry

South Road, Durham

DH1 3LE

United Kingdom

0191 334 2596

stefanie.freitag-p...@durham.ac.uk



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Re: [ccp4bb] Is there a bulletin board (similar to ccp4bb) for small molecule crystallography

[Andy Purkiss]

Dear Fred,

You need to register for the Windows (and other OS) installers if you want the 
stand-alone version of Shelx.

The form is at https://shelx.uni-goettingen.de/register.php

We have it running on Windows, although this version came with our Bruker X-ray 
generator.

Hope this helps,

Andy



From: CCP4 bulletin board  on behalf of Fred Vellieux 

Sent: 12 March 2024 09:38
To: CCP4BB@JISCMAIL.AC.UK 
Subject: Re: [ccp4bb] Is there a bulletin board (similar to ccp4bb) for small 
molecule crystallography


External Sender: Use caution.


Hello and thanks for the reply.

My input file came from my checking SHELX manuals and SHELX instructions on the 
web, and trying to modify them to suit my case.

I tried olex2 on a Windows computer (somehow olex2 did not run on my Linux box, 
and only v1.3 was able to install on that Windows machine and not the latest 
v1.5). However, olex2 (the installation program) does not come with Shelx 
program executables, and I could not locate the installers for the shelx 
software on Windows.

Hence I am running SHELXL in line command mode on my Linux box.

Thank you again,

Fred.

On 12/03/2024 10:12, David Waterman wrote:
Hi Fred,

I find Olex2 and shelxle are both convenient interfaces to SHELXL refinement, 
that take care of some of the details of .ins file format for you. However, 
maybe you are stuck in the starting gate, depending on what is malformed in 
your input file. Where did your input files come from?

Cheers
-- David


On Tue, 12 Mar 2024 at 09:01, Fred Vellieux 
mailto:frederic.velli...@lf1.cuni.cz>> wrote:
Hi folks,

I have a simple question: is there an electronic bulletin board for
small-molecule crystallography? I have checked the list of CCP projects
and there is no CCP-project for small molecule crystallography in the list.

I am trying to run SHELXL, and it fails with the cryptic message "** BAD
ATOM OR UNKNOWN INSTRUCTION **".

The alternative for me would be of course to use software meant for
macromolecular cystallography (that I know) on small molecule
diffraction data. And using the small molecule coordinate files
transformed to a suitable format. I don't know if this is feasible or
even advised. Probably not.

Thanks,

Fred.

--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic



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--
MedChem, 1st F. Medicine, Charles University
BIOCEV, Vestec, Czech Republic



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Re: [ccp4bb] Rejected posting to CCP4BB@JISCMAIL.AC.UK

[Andy Purkiss-Trew]

Hi Ian and list,

I don't know about rejected postings, as I've not made any recently, but
I am getting two copies of each posting made and the second has gone
through the same server as below:

Received: from ms1.kissei.co.jp ([210.238.65.82]) by
a12536.general.kissei.co.jp (Lotus Domino Release 6.5.4FP2) with
ESMTP id 2007081510253541-2677 ; Wed, 15 Aug 2007 10:25:35 +0900
Received: from ictmailer1.itd.rl.ac.uk (ictmailer1.itd.rl.ac.uk
[130.246.192.56]) by ms1.kissei.co.jp (8.11.6/3.7W) with ESMTP
id l7F1PYJ20264 for <[EMAIL PROTECTED]>; Wed, 15 Aug 2007
10:25:34 +0900

Looks like problem with someone's e-mail system to me.

Andy

On Wed, 2007-08-15 at 11:03 +0100, Ian Tickle wrote:
> All - is anyone else getting this response every time they post a
> message or is it just me?  The received header shows
> <[EMAIL PROTECTED]> (ms1.kissei.co.jp [210.238.65.82]).
> 
> -- Ian
> 
> > -Original Message-
> > From: JISCMAIL LISTSERV Server (14.5) 
> > [mailto:[EMAIL PROTECTED] 
> > Sent: 15 August 2007 10:51
> > To: Ian Tickle
> > Subject: Rejected posting to CCP4BB@JISCMAIL.AC.UK
> > 
> > Your message is  being returned to you unprocessed because  
> > it appears to have
> > already been distributed to the CCP4BB list. That is, a 
> > message with identical
> > text (but  possibly with different mail  headers) has been 
> > posted  to the list
> > recently, either by you or by someone  else. If you have 
> > reason to resend this
> > message to the list (for instance because you have been 
> > notified of a hardware
> > failure with loss of  data), please alter the text of the  
> > message in some way
> > and resend it  to the list. Note  that altering the 
> > "Subject:"  line or adding
> > blank lines at the top or bottom  of the message is not 
> > sufficient; you should
> > instead add a sentence or two at  the top explaining why you 
> > are resending the
> > message, so  that the other  subscribers understand  why they 
> > are  getting two
> > copies of the same message.
> > 
> 
> 
> Disclaimer
> This communication is confidential and may contain privileged information 
> intended solely for the named addressee(s). It may not be used or disclosed 
> except for the purpose for which it has been sent. If you are not the 
> intended recipient you must not review, use, disclose, copy, distribute or 
> take any action in reliance upon it. If you have received this communication 
> in error, please notify Astex Therapeutics Ltd by emailing [EMAIL PROTECTED] 
> and destroy all copies of the message and any attached documents. 
> Astex Therapeutics Ltd monitors, controls and protects all its messaging 
> traffic in compliance with its corporate email policy. The Company accepts no 
> liability or responsibility for any onward transmission or use of emails and 
> attachments having left the Astex Therapeutics domain.  Unless expressly 
> stated, opinions in this message are those of the individual sender and not 
> of Astex Therapeutics Ltd. The recipient should check this email and any 
> attachments for the presence of computer viruses. Astex Therapeutics Ltd 
> accepts no liability for damage caused by any virus transmitted by this 
> email. E-mail is susceptible to data corruption, interception, unauthorized 
> amendment, and tampering, Astex Therapeutics Ltd only send and receive 
> e-mails on the basis that the Company is not liable for any such alteration 
> or any consequences thereof.
> Astex Therapeutics Ltd., Registered in England at 436 Cambridge Science Park, 
> Cambridge CB4 0QA under number 3751674
-- 
Cat, n.: Lapwarmer with built-in buzzer.
+--+
| Andy Purkiss-Trew, School of Crystallography,Birkbeck College,London |
|   E-mail   [EMAIL PROTECTED]|
+--+

Re: [ccp4bb] The CCP4 license is ambiguous

[Andy Purkiss]

Quoting Kjeldgaard Morten <[EMAIL PROTECTED]>:

> > The CCP4 license does explicitly allow you to redistribute library  
> > code
> > Phil
> 
> That's not the way I read the license. There are two sections of the  
> license that are contradictory, 2.1 and 2.2. Both place restrictions  
> on your use of the software. According to 2.1 you can distribute CCP4  
> software to third parties, but according to 2.2 you can't. 2.3 limits  
> the license to academic use. None of this is compliant with the GPL,  
> and the inclusion of GPL as appendixes to the CCP4 license is  
> incomprehensible at best, but could be viewed as fraudulent.
> 

If you read the licence properly, you will see that section 2.1 covers the
libraries, whilst 2.2 covers the applications. 

It also reads to me, that the only software covered by the LGPL is any which
would come under section 2.5 and so is not covered by the CCP4 licence (much as
section 2.6 covers third party software included with its own licence, e.g.
Astexviewer). I don't have time to examine the licences for each bit of code,
but with software from so many sources, I'm sure that some of the code is under
the LGPL, and not the CCP4 licence.

-- 
"We are the Kitten. Lower your weapons and open your arms. 
Your refrigerators and sofas will be utilized for our comfort. 
Your society will be assimilated to nurture and care for our own. 
Resistance is Furry."
+-+
|  Andy Purkiss, School of Crystallography, Birkbeck College, London  |
|   E-mail   [EMAIL PROTECTED]   |
+-+



This message was sent using IMP, the Internet Messaging Program.

Re: [ccp4bb] Phaser TFZ=100.0 ?

[Andy Purkiss]

Quoting Andrew Wong <[EMAIL PROTECTED]>:

> I was using Phaser for some MR with a data set in P1 (may not actually be 
> P1, but..), and in every run I always got a list of "solutions" that all 
> have TFZ=100.0, with a very small LLG (around 0 or even in the negative). 
> The RFZ is like 4 or less. The solution(s) are definitely wrong, but I'm 
> just curious why Phaser is doing that? Could the TFZ=100.0 'solutions" 
> possibly mask out the real solutions?
> 

Is this not because the translation search has no fixed origin (for the first
molecule). In other words, all points are the same and placing the molecule
fixes the origin allowing search for a second molecule. I will check what my P1
search showed, when I get into work!


-- 
"We are the Kitten. Lower your weapons and open your arms. 
Your refrigerators and sofas will be utilized for our comfort. 
Your society will be assimilated to nurture and care for our own. 
Resistance is Furry."
+-----+
|  Andy Purkiss, School of Crystallography, Birkbeck College, London  |
|   E-mail   [EMAIL PROTECTED]   |
+-+



This message was sent using IMP, the Internet Messaging Program.

Re: [ccp4bb] Summary crystallisation of an extremely soluble protein

[Andy Purkiss-Trew]

On Thu, 2007-02-22 at 16:32 -0600, Carlos Huerta wrote:
> This may sound like hocus-pocus but it worked for me and may work in other 
> conditions.  Try chilling your solution in ice, or prepare your plate with 
> reservoir solution and chill the plate in a tub of ice (surround the plate 
> with ice, do not place the plate on top of the ice).  Finishing setting the 
> plate in the ice and place you plate at cooler temperatures such as 4-16 
> degrees Celcius after set-up.
> 
> My progress was substantially improved with this method.  I previously had 
> crystals that were small and diffracted anisotropically.  I tried other 
> screens to improve crystal size such as additive screen, slowing vapor 
> diffusion using oils and incubating at different temperatures after setting 
> up at room temperature.  The crystal grew at a lower concentration of PEG 
> that originally gave precipitation setting up at RT and placing at different 
> incubation temperatures.  The end result the crystal increased in size by 5x 
> and gave isotropic diffraction to high-resolution.

Well, this isn't really hocus-pocus. Remember that the entropy term when
calculating a free energy change is -T{delta}S

So, if altering the sidechains of a protein to reduce entropy works in
some cases, so will reducing the temperature!! Of course, you might have
to go to very low temperatures (where the solution will be frozen) to
get the same effect as a good mutation :)

Hope this helps

Andy

- 
Cat, n.: Lapwarmer with built-in buzzer.
+------+
| Andy Purkiss-Trew, School of Crystallography,Birkbeck College,London |
|   E-mail   [EMAIL PROTECTED]|
+--+

Re: ccp4bb on new site

[Andy Purkiss-Trew]

Well, having got around to getting a password and exploring the
www.jiscmail.ac.uk website, I see that I can get a list title back,
using the subscription settings for the list. The option is

Mail Header Style, option 2:
LISTSERV-style, with list name in subject

gives me a [CCP4BB] added to the start of the subject line, so I'm happy
now.

Andy

On Fri, 2007-01-19 at 18:57 +0000, Andy Purkiss-Trew wrote:
> Dear Charles (and the rest of the bulletin board)
> 
> I have a question regarding the new version of the software.
> 
> Can the [ccp4bb] be put in front of the message subjects again? I use
> this in my e-mail filtering, to get the ccp4 stuff out from under the
> groaning weight of spam into its own folder.
> 
> Andy
> 
-- 
Cat, n.: Lapwarmer with built-in buzzer.
+----------+
| Andy Purkiss-Trew, School of Crystallography,Birkbeck College,London |
|   E-mail   [EMAIL PROTECTED]|
+--+

Re: ccp4bb on new site

[Andy Purkiss]

Quoting Juergen Bosch <[EMAIL PROTECTED]>:

> Andy Purkiss-Trew wrote:
> 
> >Dear Charles (and the rest of the bulletin board)
> >
> >I have a question regarding the new version of the software.
> >
> >Can the [ccp4bb] be put in front of the message subjects again? I use
> >this in my e-mail filtering, to get the ccp4 stuff out from under the
> >groaning weight of spam into its own folder.
> >
> >Andy
> >
> >  
> >
> Just add an additional criteria to your filter e.g. to [EMAIL PROTECTED]
> 
> That's easy to fix.
> 

I know that it is an easy fix :) 

However, nearly all of the lists that I am on use the [listname] notation and
this makes it a bit easier to sort out the lists from the personal mail. I'm
more likely to look at something with [ccp4bb] and not just skip over it.

This is, however, only a personal preference and I just suggesting that the
marker be put back in, once the wrinkles of the software have been explored.

Andy

-- 
"We are the Kitten. Lower your weapons and open your arms. 
Your refrigerators and sofas will be utilized for our comfort. 
Your society will be assimilated to nurture and care for our own. 
Resistance is Furry."
+-+
|  Andy Purkiss, School of Crystallography, Birkbeck College, London  |
|   E-mail   [EMAIL PROTECTED]   |
+-+



This message was sent using IMP, the Internet Messaging Program.

Re: ccp4bb on new site

[Andy Purkiss-Trew]

Dear Charles (and the rest of the bulletin board)

I have a question regarding the new version of the software.

Can the [ccp4bb] be put in front of the message subjects again? I use
this in my e-mail filtering, to get the ccp4 stuff out from under the
groaning weight of spam into its own folder.

Andy

-- 
Cat, n.: Lapwarmer with built-in buzzer.
+--+
| Andy Purkiss-Trew, School of Crystallography,Birkbeck College,London |
|   E-mail   [EMAIL PROTECTED]|
+--+