Re: [ccp4bb] Linux Distro for setting up workstations - Is CentOS still a good choice?

[Folmer Fredslund]

Dear Tom

Be aware that python2 is currently not supported.  It is end-of-life since
1/1-2020 and is not part of Ubuntu 20.04

This might not be a big concern, bit depends on which software you use.


Best regards
Folmer



lør. 20. feb. 2021 21.50 skrev Peat, Tom (Manufacturing, Parkville)
:

> Speaking of Linux, but somewhat tangential to the thread:
> Ubuntu has recently released their newest version 20.04 (Focal Fossa).
> Has anyone implemented this and is there anything that doesn't work? Any
> gotchas that one might want to be aware of?
>
> Cheers, tom
>
> Tom Peat, PhD
> Proteins Group
> Biomedical Program, CSIRO
> 343 Royal Parade
> Parkville, VIC, 3052
> +613 9662 7304
> +614 57 539 419
> tom.p...@csiro.au
>
> --
> *From:* CCP4 bulletin board on behalf of Tim Gruene
> *Sent:* Sunday, February 21, 2021 2:35 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* Re: [ccp4bb] Linux Distro for setting up workstations - Is
> CentOS still a good choice?
>
> Hi Matthias,
>
> I have been using Debian for more than a decade. Every stable release
> is supported for at least 5 years.
> Many crystallographic libraries and some programs are part of the
> standard repository, like raster3d, pymol, shelxle, libccp4,
> libclipper, ...
>
> Debian is particularly stable, and requires little maintenance.
>
> Cheers,
> Tim
>
> On Fri, 19 Feb 2021 21:35:46 +0100
> Matthias Zeug  wrote:
>
> > Hi all,
> >
> >
> >
> > I just came across the (already quite old) news that Red-Hat switches
> > their support-policy for CentOS to a rolling preview model (replacing
> > CentOS Linux by CentOS Stream):
> >
> >
> https://www.zdnet.com/article/why-red-hat-dumped-centos-for-centos-stream/
> >
> >
> https://www.enterpriseai.news/2021/01/22/red-hats-disruption-of-centos-unlea
> > shes-storm-of-dissent/
> >
> >
> >
> > I wondered if that has any implications for the community, as
> > scientific programs - maybe except the big ones like coot, Phenix,
> > and ccp4 - are often not *that* well maintained for an extended
> > period. I had the impression CentOS was liked especially for its
> > "unbreakability,"  and it seems to be the main developing platform
> > for some widely used smaller programs (e.g., adxv).
> >
> >
> >
> > Do you think it would be advisable to switch to a Ubuntu-distro when
> > setting up new workstations in the future, or is it safe to stick to
> > CentOS?
> >
> >
> >
> > Please let me know what you think :-)
> >
> >
> >
> > Best,
> >
> >
> >
> > Matthias
> >
> >
> >
> >
> >
> > Matthias Zeug
> >
> > Buchmann Institute of Molecular Life Sciences
> >
> > Goethe University Frankfurt
> >
> >
> >
> >
> > 
> >
> > To unsubscribe from the CCP4BB list, click the following link:
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> >
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>
>
>
> --
> --
> Tim Gruene
> Head of the Centre for X-ray Structure Analysis
> Faculty of Chemistry
> University of Vienna
>
> Phone: +43-1-4277-70202
>
> GPG Key ID = A46BEE1A
>
> 
>
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Re: [ccp4bb] coot is drawing the unit cell away from the modelled molecule

[Folmer Fredslund]

Aside from Paul's instructions on how to manually choose a different
location from inside *Coot *perhaps using the

http://achesym.ibch.poznan.pl/

server would be a good idea for setting a position on the molecule that
should be more objective


Hope this helps,
Folmer



man. 1. feb. 2021 14.51 skrev Paul Emsley :

> On 01/02/2021 13:23, leo john wrote:
>
> >
> > I am sure this issue might have addressed before,
>
> Correct.
>
> > but somehow I am not able to find it.
>
> That's because email is a terrible system for archiving structural biology
> information. An that goes doubly
> so for the Jiscmail archive.
>
> We should use something better.
>
> > After refinement when I open the structure in coot and draw the unit
> cell, I find that the modeled molecule
> > is not centered in the cell (unitcell.png)
> > Please suggest me a way by which I can get the molecule centered.
>
> Centre (using middle mouse click) on an atom in the symmetry-related
> molecule that you would actually like
> to be the "main" molecule, then Calculate -> Modelling -> Symm Shift
> Reference Chain Here.
>
> > I have a Bromo-phenylalanine in the sequence that I have modeled, but I
> get the red and green density around
> > Br atom (brphe.png). What can be the possible reason and how can I get
> rid of it.
>
> Tha looks right out of Dale's "Introduction to Maps" presentation. It's
> anisotropy. Thing about what you'd
> get if you subtract a gaussian sphere from a gaussian ellipsoid. You can
> either model it with anisotropic
> B-factor refinement (perhaps just that atom) or maybe split the residue by
> adding an alt conf.
>
> Paul.
>
> 
>
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Re: [ccp4bb] how to swap chain IDs

[Folmer Fredslund]

Dear Christian

What exactly are you trying to accomplish?


I don't quite follow why you would expect the atom positions to change?
Unless I'm missing something?
Also, why would you expect the numbering to change when you edit the chain
ID?

After CIF conversion:
What do you mean by "original position"? What position where you expecting?

And you mention that chain A is not at the beginning of the sequence. What
sequence are you talking about?

Coot or pdbset can definitely do want you want, I'm just not sure what
exactly you're after.

Perhaps a more elaborate explanation would be good?

Best regards
Folmer Fredslund


man. 7. dec. 2020 18.49 skrev Christian GALICIA <
christian.galicia.diaz.sant...@vub.be>:

> Hello,
> I'm trying to swap the chain IDs of a structure. I tried changing the IDs
> in coot and with PDBset, both change labels of the chains but not the atom
> positions nor numbering.Also, after the pdb file is converted to cif for
> deposition it displays in pymol in the original position making chain A not
> to be at the beginning of the sequence. I would appreciate if you would
> suggest a good way to achieve this. The structure is otherwise finished and
> will no go any other rounds of refinement. Thanks
>
> Christian
> --
> *Christian Galicia*
> E-mail: cgali...@vub.be
>
>
>
> --
>
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Re: [ccp4bb] Phenix refine distorting a sidechain despite correct density

[Folmer Fredslund]

Dear Igor

There's a phenix bulletin board for question like this, which is where you
should post the question. ( I crosspost here)


I would choose to not do the real space refinement in phenix.refine during
the last rounds of refinement of a model, when sidechain positions are
essentially correct.


I hope this helps

Folmer



tor. 3. dec. 2020 05.48 skrev Igor Petrik :

> I am refining a 1.71A X-ray structure with phenix refine. I have
> everything modelled in - ~150 residues in the ASU and a heme - and my
> R-work/R-free is 0.17/0.22. But when I went to deposit it, PDB pointed out
> that two of my sidechains have distorted geometries. One is a His, and
> looking at it in Coot, I can clearly see the 2Fo-Fc density for the correct
> geometry, but the actual coordinates that phenix refine produce don't lie
> in that density; there are significant difference map peaks showing that
> the coordinates are in the wrong place. If I use real space refine in Coot
> to put the coordinates back into the correct density and refine it again in
> phenix, they get distorted again.
>
> What settings in phenix should I check to try to get it to properly refine
> the coordinates?
>
> Thanks,
> - Igor Petrik, PhD
>
> --
>
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Re: [ccp4bb] I cannot download xds

[Folmer Fredslund]

 Dear Murpholino,

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

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

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

Cheers

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

> Hello, it downloaded to my phone from the link on this page:
>
> http://xds.mpimf-heidelberg.mpg.de/html_doc/downloading.html
>
> It looks alright:
> http://u.cubeupload.com/jbcooper/20200628034613.jpg
>
> Jon Cooper
>
> On 28 Jun 2020 01:39, Murpholino Peligro  wrote:
>
> ```
> ~/Downloads$ aria2c
> ftp://ftp.mpimf-heidelberg.mpg.de/pub/kabsch/XDS-INTEL64_Linux_x86_64.tar.gz
>
> 06/27 19:36:10 [NOTICE] Downloading 1 item(s)
> [#3065b2 0B/10MiB(0%) CN:1 DL:0B]
> ```
>
> It stays there forever.
> Is there an alternative download url?
>
>
> Thanks
>
> --
>
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Re: [ccp4bb] Problem with structural alignment

[Folmer Fredslund]

Dear Ishan

Would it be possible for you to use a fitting of the atoms of the ligand?
I've done that with success before.

Hope this helps
Folmer


man. 16. dec. 2019 07.38 skrev Ishan Rathore :

> Hi,
>
> I am trying to compare multiple homologous structures of a protein, where
> I am analysing the active site residues and the bound substrate/peptide. I
> have used multiple methods for alignment in coot and pymol. Every
> method gives a slightly different orientation in the active site. Based on
> the analysis I am trying to propose a hypothesis for the catalytic
> mechanism of the protein. But, I am a bit wary of getting biased with the
> alignment if that supports my hypothesis.
>
> What are the parameters that have to be considered for a reliable
> alignment?
> What are the other Softwares available for alignment?
>
>
>
> Thanks and regards
> Ishan
>
> --
>
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Re: [ccp4bb] Coot on Macosx Catalina

[Folmer Fredslund]

Hi Jan

If I remember correctly, you need to start the program once by
right-clicking, and choosing "Open" from the menu. Then you can choose
"trust this program" (or something similar) and you should be able to use
it as normal after that small extra step.

Hope this helps,
Folmer Fredslund


lør. 19. okt. 2019 00.48 skrev Jan van Agthoven :

> Hi everyone,
> I'm running into issues installing coot on Macosx Catalina. When install
> the system using BINARY.setup the following message shows up:
>
> Does anyone else faced this problem? Is there a way to work around it?
> Thanks,
> J.
>
> --
>
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Re: [ccp4bb] Calculating RMSD of a loop

[Folmer Fredslund]

Dear Kyle,

As other non-CCP4 solutions have also been suggested, perhaps I can suggest
using PyMOL?
https://pymolwiki.org/index.php/Align
Here's a nice wiki article about what you can do with the align command.


If you're already familiar with scripting languages it's quite easy, and
you can load your already superimposed structures and calculate on the
selection you want.


Hope this helps,
Folmer Fredslund


tir. 17. sep. 2019 15.42 skrev Kyle Gregory <
3632e92fcc15-dmarc-requ...@jiscmail.ac.uk>:

> Hi all,
>
> What is the best/easiest way to calculate RMSD of a loop for 2 c-alpha
> aligned structures?
> Thought I could do this in Coot but I only see this if I align the
> specific loops, which I don't want to do.
>
> Thanks,
>
> Kyle
>
> --
>
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Re: [ccp4bb] PyMOL now packaged as a snap on Linux

[Folmer Fredslund]

Hi Darren,

That's brilliant!

I'll give it a spin and see how it works.

Best regards
Folmer


tor. 16. maj 2019 13.02 skrev Darren Hart :

> Since yesterday, PyMOL (open source version v2.3) has been packaged as a
> distro-independent "snap" that can be installed easily on linux
> platforms - no more cloning from gitlab and compiling after installing
> the dependencies.
>
> On Ubuntu, install from software centre or:
>
> sudo snap install pymol-oss
>
> Many distros have the snap architecture already installed. If not, you
> just need to install snapd in the regular way first (e.g. on Debian:
> sudo apt install snapd).
>
> Hope this is useful for some folks.
>
> Best regards,
>
> Darren
>
> 
>
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Re: [ccp4bb] PISA command line

[Folmer Fredslund]

Hi Wolfram,

I just tried running
pisa 5jju  -analyse 5jju.pdb
pisa 5jju -list interfaces

with
 PISA v.2.1.1 built 05-04-2017   with SSM v.1.4.0, SRS v.1.0.0, MMDB 
v.2,0.17


on Ubuntu 16.04
and that seems to work as expected.

Hope this helps,
Folmer


On 2018-07-06 19:54, wtempel wrote:

Hi,
has anyone of you performed a PISA command line analysis using the 
version distributed with CCP4 on ubuntu-16.04? My attempt to "-list 
interfaces" after seemingly successful "-analysis" resulted in a core 
dump:



 PISA v.2.1.1 built 05-04-2017   with SSM v.1.4.0, SRS v.1.0.0, MMDB 
v.2,0.17

 Session some_name
Segmentation fault (core dumped)


Any suggestions?
Thanks.
Wolfram Tempel



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Re: [ccp4bb] processing hd5 files from Dectris detector

[Folmer Fredslund]

Dear all,

With respect to the usage of the XDSAPP program, it depends on the
generate_XDS.INP script. For our local installation, I have edited the
script to include the "LIB=/path/to/dectrisneggia.so" in the resulting XDS
input file and this works as expected without any problems.
This does depend on knowing the location of the file on the filesystem, and
hence not really easily portable.

Nonetheless and easy and quick workaround for a local system.

Best regards


Folmer Fredslund
Staff scientist
DTU Biosustain


fre. 1. jun. 2018 11.04 skrev Harry Powell <
193323b1e616-dmarc-requ...@jiscmail.ac.uk>:

> Hi
>
> Laurent has contacted me off-board about this and sent me an example of a
> CBF file extracted from the HDF5.
>
> As far as I can see, there is no problem with the CBF file created by
> eiger2cbf - it can be processed correctly by iMosflm, and the miniCBF
> header is not missing any of the information that Mosflm requires.
>
> From this, I think that there's an issue with XDSAPP - so probably
> something for Manfred to have a look at!
>
> In answer to Kay's questions -
>
> (1) Massif-1
> (2) That would be my first port of call...
> (3) not tried yet...
> (4) the exact error messages start with what Laurent gave originally, i.e.
>  -
>
> Some important experimental parameters are missing from the images header
>
>
> which is not so useful, but there is an additional traceback -
>
> Some important experimental parameters are missing from the images header
> Traceback (most recent call last):
>  File "/mnt/maredsous/programs/bin/xdsit.py", line 4018, in 
>manual_process()
>  File "/mnt/maredsous/programs/bin/xdsit.py", line 3897, in manual_process
>manual_index()
>  File "/mnt/maredsous/programs/bin/xdsit.py", line 3885, in manual_index
>print(params['detector'])
> KeyError: ‘detector'
>
>
> Harry
> --
> Dr Harry Powell
> Chairman of European Crystallographic Association SIG9 (Crystallographic
> Computing)
>
>
>
>
> On 1 Jun 2018, at 07:21, Kay Diederichs wrote:
>
> Hi Laurent,
>
> this prompte a couple of questions -
> 1. where did you collect the data?
> 2. can this not be answered by the beamline staff? After all they should
> know their detector, and procedures for use of its data.
> 3. what are the exact error messages when using the neggia plugin? I guess
> Dectris would care if their plugin cannot read "their" data.
> 4. what are the exact error messages / missing items when using eiger2cbf
> / hdf2cbf-mini?
>
> best,
> Kay
>
> On Thu, 31 May 2018 14:58:52 +0200, maveyrau 
> wrote:
>
> Hi CCP4ers
>
>
> we recently collected many datasets on dectris detectors producing hd5
> files. I would like to use some auto processing tools to process them
> (xdsapp, xdsme…). As far as I can say, xdsapp or xdsme cannot process hd5
> natively. I tried to convert them to cbf format (eiger2cbf,
> hdf2mini-cbf,...), but then it seams that the header of the caf files are
> lacking some required informations…
>
>
> Any idea how to convert hd5 files to complete caf files ? Are there any
> plans for xdsapp to be able to work on hd5 files ?
>
>
> thanks for your help
>
>
> Laurent
>
> --
>
> Laurent Maveyraud laurent.maveyraud AT ipbs DOT fr
>
> P I C T   ---  Plateforme Intégrée de Criblage de Toulouse
>
> Université  Paul  Sabatier /  CNRS  /  I.P.B.S.  UMR  5089
>
> Département BiologieStructurale   et   Biophysique
>
> http://cribligand.ipbs.fr   http://www.ipbs.fr
>
> 205 route de Narbonne  31077 TOULOUSE Cedex FRANCE
>
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>
> --
>
>
>
>
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Re: [ccp4bb] mmCIF and CIF

[Folmer Fredslund]

Dear Oliviero,

The suggestion made by Tim Grüne is probably best, you didn't specify 
exactly what you have in the mmCIF file.


Anyway, openbabel should be able to read mmCIF files and write a CIF, 
(https://openbabel.org/wiki/MmCIF)


Best regards,
Folmer

On 2017-11-14 14:16, Oliviero Carugo wrote:

Dears,

does anybody know how to transform an mmCIF file of the Protein Data 
Bank into a CIF file (the slightly different format used in small 
molecule crystallography)?


Thanks,

Oliviero

Re: [ccp4bb] RMSD between superposed structures without moving

[Folmer Fredslund]

Hi Johannes,

Did you read the PymoWIKI entry on the align command?

https://pymolwiki.org/index.php/Align#RMSD

I think this should give you what you want within PyMOL.

Btw, there is a nice dedicated PyMOL mailing list
https://pymolwiki.org/index.php/PyMOL_mailing_list
It is rather low traffic, but the replies are generally from the 
developers or very knowledgeable users.


Hope this helps,
Folmer Fredslund

On 2017-08-27 13:09, Johannes Sommerkamp wrote:

Hello everybody,
I have superposed two structures based on the central beta-sheet CA 
atoms with the "super" command in Pymol.
Now, I want to calculate the RMSD between ALL atoms or ALL CA atoms 
without moving the structures again. The rms_cur command in Pymol 
would do that, but only works if all atom identifiers match. Adding 
"transform=0" to the super, oder align command still does the 
alignment and moves the structure but does not show the movement.


Is there an easy way to just calculate the all atom RMSD between two 
already superposed structures in pymol or any other programm?


Thanks in advance!
Johannes

Re: [ccp4bb] Remittance advice - Invitation to edit

[Folmer Fredslund]

Dear all,

Just to point out the obvious (I hope) this is spam and points to a scam 
site trying to acquire your Google account password (in case you have one).


Sorry to spam the list, just writing in case anyone stumbles upon it and 
thinks it's legit.


Best regards,
Folmer


On 2016-12-05 14:34, Yong-Fu Li wrote:

Please find attached for your review.
Regards.

Y.-F. Li

Re: [ccp4bb] Good 3D Monitor for Molecular Modelling

[Folmer Fredslund]

Hi Matt,

Have you tried looking at these pages:
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Stereo
https://pymolwiki.org/index.php/Stereo_3D_Display_Options

HTH,
Folmer Fredslund

On 2016-10-27 17:20, Matthew Graf wrote:

Hello All,
 I am looking for suggestions on a good, but not too costly, 3D 
monitor for visualizing pdb structures and looking at outputs of 
modelling programs. I am not personally a structural biologist, but am 
on the hunt for someone who is. All help appreciated.


Kind regards,
Matt

Re: [ccp4bb] completeness drops from conversion from XDS to Fs

[Folmer Fredslund]

Hi Tommi,

Could it be the bug that was reported in June?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1606=ccp4bb===119181

Obviously if you recently updated XDS is can't be that.

HTH,
Folmer

On 2016-10-21 18:00, Kajander, Tommi A wrote:
Problem solved, or well, circumvented - for the record: This seems to 
happen during XDSCONV indeed (F2MTZ seems to dump half the reflections?)
and running via aimless seems to work. Either there is a bug with the 
conversion in the SG or I made  some mistake (which i cant quite 
figure out now).


Thanks for comments!

Tommi




On Oct 21, 2016, at 6:11 PM, Kajander, Tommi A 
> wrote:


Hi,

This seems very stupid but I have some data sets processed with XDS 
with apparently close to 100% completeness (high symmetry F4132)
only 50 (or 100) degrees of data, fine, but still looks complete 
overall, given the high symmetry, though low res could be better.


After running it via XDSCONV to truncate for a check, or to phenix - 
I get a completeness of ca. 50% for the Fs…


… cant quite figure out where this is coming  from…? Never happened 
before. Too tired now. Any suggestions?


Tommi

Re: [ccp4bb] How many is too many free reflections?

[Folmer Fredslund]

Hi Graeme,

There's a very nice page on the (unofficial?) CCP4 wiki about it
http://strucbio.biologie.uni-konstanz.de/ccp4wiki/index.php/Test_set

For structures with a lot of reflections, a rule of thumb would be that
2000 free reflections would give an adequate reliability in the free R
factor.

Hope this helps,
Folmer Fredslund


2015-06-02 12:26 GMT+02:00 Graeme Winter graeme.win...@gmail.com:

 Hi Folks

 Had a vague comment handed my way that xia2 assigns too many free
 reflections - I have a feeling that by default it makes a free set of 5%
 which was OK back in the day (like I/sig(I) = 2 was OK) but maybe seems
 excessive now.

 This was particularly in the case of high resolution data where you have a
 lot of reflections, so 5% could be several thousand which would be more
 than you need to just check Rfree seems OK.

 Since I really don't know what is the right # reflections to assign to a
 free set thought I would ask here - what do you think? Essentially I need
 to assign a minimum %age or minimum # - the lower of the two presumably?

 Any comments welcome!

 Thanks  best wishes Graeme




-- 
Folmer Fredslund

Re: [ccp4bb] Cryo-EM

[Folmer Fredslund]

Hi Faisal,

I guess a start for you would be to go here:
http://www.ccpem.ac.uk/
and subscribe to that mailing list :-)

Best regards,
Folmer

2015-05-19 9:01 GMT+02:00 Faisal Tarique faisaltari...@gmail.com:

 Hi everyone

 A bit off topic..but..I request you to please suggest me some good
 readings related to Cryo-EM..

 Thanx in advance

 --
 Regards

 Faisal
 School of Life Sciences
 JNU




-- 
Folmer Fredslund

Re: [ccp4bb] Strange Ancient Diffraction Pattern...

[Folmer Fredslund]

Hi Julia,

This was clearly taken at MAXlab, since it's a very distinct Swedish
pattern. I would guess I911-2, unless of course it is a very old one from
I711.
There was a problem once, where the header of the file didn't get written
correctly.

Can you index it if you manually guess the beam position (somewhere behind
the beamstop) and input it to imosflm? It should work, although you might
have to try a number of guesses, seing the beamstop is so big.

HTH,
Folmer

2015-04-01 14:00 GMT+02:00 Julia Griese gri...@dbb.su.se:

  This one appears to be of a similar age. It has a most puzzling, but
 pretty pentagonal pattern (and a backstop). Unfortunately Mosflm doesn't
 appear to support the image format.

 /Julia



 On 01/04/15 13:08, Harry Powell wrote:

 Hi Jacob

  I noticed that there's no backstop shadow that might give a clue as to
 the direct beam position.

  Do you know what wavelength radiation was used to bake this?

  On 1 Apr 2015, at 12:03, Keller, Jacob wrote:

  Can anyone index this? It's got mostly split spots and a strange diffuse
 scattering background

 JPK

 ***
 Jacob Pearson Keller, PhD
 Looger Lab/HHMI Janelia Research Campus
 19700 Helix Dr, Ashburn, VA 20147
 email: kell...@janelia.hhmi.org
 ***


 roundmatzah.jpg


Harry
 --
Dr Harry Powell, MRC Laboratory of Molecular Biology, Francis
 Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH
 Chairman of International Union of Crystallography Commission on
 Crystallographic Computing
 Chairman of European Crystallographic Association SIG9 (Crystallographic
 Computing)











 --
 Dr. Julia Griese
 Postdoctoral Researcher
 Stockholm Center for Biomembrane Research
 Department of Biochemistry and Biophysics
 Stockholm University
 106 91 Stockholm
 Sweden

 phone: +46-(0)8-162 778
 email: gri...@dbb.su.se




-- 
Folmer Fredslund

Re: [ccp4bb] Absence of contact between layers in a crystal

[Folmer Fredslund]

Unfortunately, the structure and associated paper for PDB id 2hr0 has _not_
been retracted, or marked as invalid.

The University of Alabama had a note about it, but only some of the
affected PDB entries were removed.
http://www.uab.edu/reporterarchive/71570-uab-statement-on-protein-data-bank-issues

For 2hr0, the Nature letter (
http://www.nature.com/nature/journal/v444/n7116/full/nature05258.html)  and
the associated structure has not been removed from the archives.


Best regards,

Folmer Fredslund

Disclosure: I published the structure of native bovine C3 (2b39)



2015-02-06 12:08 GMT+01:00 David Briggs drdavidcbri...@gmail.com:

 Haven'tthat paper and the associated structure been retracted?

 http://www.nature.com/news/2009/091222/full/462970a.html

 There was a huge scandal when it was discovered that Krishna Murthy had
 falsified data, including the structure you refer to.

 See http://en.wikipedia.org/wiki/H.M._Krishna_Murthy

 A crystallographer with a wikipedia entry for all the wrong reasons...

 Dave


 On Fri Feb 06 2015 at 11:02:12 AM Kerff Fred fke...@ulg.ac.be wrote:

 Hello,

 Looking at structure 2HR0 (The structure of complement C3b provides
 insights into complement activation and regulation. »,Abdul Ajees, A.,
 Gunasekaran, K.,  Volanakis, J.E.,  Narayana, S.V.,  Kotwal, G.J.,  Krishna
 Murthy, H.M.;  (2006) Nature 444: 221-225), I noticed the absence of
 contacts between layers in the crystal. Is it something that has already
 been observed in other crystals?

 Best regards,

 Fred
 -
 Frédéric Kerff
 Chercheur qualifié F.R.S.-FNRS
 Cristallographie des protéines
 Centre d'Ingénierie des Protéines
 Université de Liège
 17, Allée du 6 Août - Bat B5a
 4000 Liège (Belgium)
 Tel.: +32 (0)4 3663620
 Fax: +32 (0)4 3663772



  Le 6 févr. 2015 à 10:12, Tim Gruene t...@shelx.uni-ac.gwdg.de a écrit :
 
  -BEGIN PGP SIGNED MESSAGE-
  Hash: SHA1
 
  Dear Smith,
 
  The sca file most likely does not contain flags. pointless can read
  the sca file, standardise it to ccp4 standards and freerflag marks
  random reflections. You should use the maximum of 500 unique
  reflections or 5% of the unique reflections, whichever is larger.
 
  Best,
  Tim
 
  On 02/06/2015 09:49 AM, Smith Lee wrote:
  Dear All, I have a sca file. Will you please tell me by which
  software or how I can know whether the sca file contains R-free
  tags? If not, by which software or how I can add the R-free tags?
  And how much of the reflections I add the R-free tags? I am looking
  forward to getting your reply. Smith
 
 
  - --
  - --
  Dr Tim Gruene
  Institut fuer anorganische Chemie
  Tammannstr. 4
  D-37077 Goettingen
 
  GPG Key ID = A46BEE1A
 
  -BEGIN PGP SIGNATURE-
  Version: GnuPG v1.4.12 (GNU/Linux)
 
  iD8DBQFU1IWVUxlJ7aRr7hoRAmZHAJ4+6wREnwkFN0EhfErAA0tPSopKKwCgiLdi
  j0JFZac4kAh8twpov71MG84=
  =XN57
  -END PGP SIGNATURE-




-- 
Folmer Fredslund

Re: [ccp4bb] Absence of contact between layers in a crystal

[Folmer Fredslund]

Hi Fred,



2015-02-06 11:58 GMT+01:00 Kerff Fred fke...@ulg.ac.be:

 Hello,

 Looking at structure 2HR0 (The structure of complement C3b provides
 insights into complement activation and regulation. »,Abdul Ajees, A.,
 Gunasekaran, K.,  Volanakis, J.E.,  Narayana, S.V.,  Kotwal, G.J.,  Krishna
 Murthy, H.M.;  (2006) Nature 444: 221-225), I noticed the absence of
 contacts between layers in the crystal. Is it something that has already
 been observed in other crystals?


Come to think of it, in the communication (
http://www.nature.com/nature/journal/v448/n7154/full/nature06103.html)
Ajees et al., mention that they actually don't have gaps, but just some low
occupancy contaminant that makes crystal contacts. So, even with this
structure being fraud, you would not be able to use it as an example of
absence of crystal contacts.

Best regards,
Folmer Fredslund




 Best regards,

 Fred
 -
 Frédéric Kerff
 Chercheur qualifié F.R.S.-FNRS
 Cristallographie des protéines
 Centre d'Ingénierie des Protéines
 Université de Liège
 17, Allée du 6 Août - Bat B5a
 4000 Liège (Belgium)
 Tel.: +32 (0)4 3663620
 Fax: +32 (0)4 3663772



  Le 6 févr. 2015 à 10:12, Tim Gruene t...@shelx.uni-ac.gwdg.de a écrit :
 
  -BEGIN PGP SIGNED MESSAGE-
  Hash: SHA1
 
  Dear Smith,
 
  The sca file most likely does not contain flags. pointless can read
  the sca file, standardise it to ccp4 standards and freerflag marks
  random reflections. You should use the maximum of 500 unique
  reflections or 5% of the unique reflections, whichever is larger.
 
  Best,
  Tim
 
  On 02/06/2015 09:49 AM, Smith Lee wrote:
  Dear All, I have a sca file. Will you please tell me by which
  software or how I can know whether the sca file contains R-free
  tags? If not, by which software or how I can add the R-free tags?
  And how much of the reflections I add the R-free tags? I am looking
  forward to getting your reply. Smith
 
 
  - --
  - --
  Dr Tim Gruene
  Institut fuer anorganische Chemie
  Tammannstr. 4
  D-37077 Goettingen
 
  GPG Key ID = A46BEE1A
 
  -BEGIN PGP SIGNATURE-
  Version: GnuPG v1.4.12 (GNU/Linux)
 
  iD8DBQFU1IWVUxlJ7aRr7hoRAmZHAJ4+6wREnwkFN0EhfErAA0tPSopKKwCgiLdi
  j0JFZac4kAh8twpov71MG84=
  =XN57
  -END PGP SIGNATURE-




-- 
Folmer Fredslund

Re: [ccp4bb] rebuild by coot

[Folmer Fredslund]

Dear Dialing,

You can use Rotate/Translate zone (
https://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/web/docs/coot.html#Rotate_002fTranslate-Zone)
to do that, just clicking twice on the same residue to chose a zone of one.

mvh
Folmer

2015-01-15 14:45 GMT+01:00 Dialing Pretty 
03f1d08ed29c-dmarc-requ...@jiscmail.ac.uk:

 Dear All,

 If I rebuild a 4-residue peptide, and the first 1 is leu. When I rebuild
 the first one, the sidechain of leu occupies the electron density of the
 first 3 residues. Can you tell me the method to turn the side chain of Leu
 from position of the first 3 residues to its sidechain position in the
 electron density may?

 In addition, for coot real space refinement, can you tell me how many
 residues or the length of the fragment one time can process?

 Dialing




-- 
Folmer Fredslund

Re: [ccp4bb] A Moleman alternative?

[Folmer Fredslund]

Dear Yong,

It's easy enough to get it,
http://xray.bmc.uu.se/markh/usf/

Even though there's no development or support.

Best regards,
Folmer Fredslund


2014-11-17 20:55 GMT+01:00 Yong Tang liutan...@gmail.com:

 Dear all, I have no access to Moleman now but I need to compile a
 statistics table for a structure, more specifically, for its atom numbers
 (protein/ligand/water), B factors, RMS deviations etc. Is there an
 alternative program for that in the CCP4 suite? Thank you in advance for
 your help, -yong




-- 
Folmer Fredslund

Re: [ccp4bb] How to run CCP4 without source command

[Folmer Fredslund]

Dear Peter,

Put your source command in your .bashrc file.

It's a hidden file (because of the dot in the start) in your home folder
and will be run every time you open a terminal, so any command inside
will be executed.

You can edit the file by typing
gedit .bashrc
Just after opening a terminal.

If you just started using Linux and you're interested in an introduction to
how Linux works, I'd recommend the Linux Foundations free online course
https://www.edx.org/course/linuxfoundationx/linuxfoundationx-lfs101x-2-introduction-5386

Especially if you are not working in a lab were people can help you with
questions like the one you just asked.

Venlig hilsen/Best regards
Folmer Fredslund
Den 16/11/2014 07.34 skrev 陈昂 angsc...@outlook.com:

 Dear all:

 I have installed CCP4 suit on my computer. The OS IS fedora 18. Every time
 I open the software, I have to

 use the command source. Does anyone else can run it in terminal without
 that command?

 Thank u so much!

 best regards,

 Peter

Re: [ccp4bb] Amino acid side chains without density

[Folmer Fredslund]

Dear Sasha,

There was a survey done by Ed Pozharski back in 2011

The results of the online survey on what to do with disordered side
chains (from total of 240 responses):

Delete the atoms 43%
Let refinement take care of it by inflating B-factors41%
Set occupancy to zero12%
Other 4%

Reference:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1103L=CCP4BBD=0P=321265

So, the other way (appart from what you mention) is to keep the atoms and
let the B-factors refine to relatively large values.

Best regards,
Folmer

2014-11-11 14:14 GMT+01:00 Sasha Pausch sashapau...@gmail.com:

 Dear CCP4bb,

 Sorry for asking a naive question.

 I am trying to deposit a structure in PDB. I would like to know whether we
 have to delete the side chains of amino acids for which we are not finding
 density or people prefer keeping the side chains occupancy zero? Is there
 any other way to do this?




-- 
Folmer Fredslund

Re: [ccp4bb] R free flag missing after ARP/wARP?

[Folmer Fredslund]

Dear Lu Zuokun,

The option you mention do not use the Free R flag, tells ARP/wARP to do
refinement without using the R-free flags, so it does not seem strange to
me that it would output a file without those labels.

I don't know why this would be a good idea, though, if you want to continue
building on this model with those same R-free flags.

The manual says:
The default is not to use Rfree, since the number of traced residues serves
as excellent indicator of the success of the job. You can certainly turn
the use of Rfree on.
(http://www.embl-hamburg.de/ARP/Manual/UserGuide7.4.html)

Maybe the thought is that the free reflections will be uncoupled during
further building and refinement?

Best regards,
Folmer Fredslund

2014-10-20 4:41 GMT+02:00 luzuok luzuo...@126.com:

 Dear all,
 I was using ARP/wARP in ccp4i, the input mtz file certainly has free R
 flag, but the output mzt file doesn't have the free R flag label?
 I chose  do not use the Free R flag in the ARP/wARP GUI. Can anyone tell
 me what's wrong with this?

 best reagrds!
 Lu Zuokun


 --
 卢作焜
 南开大学新生物站A202





-- 
Folmer Fredslund

Re: [ccp4bb] how to get a reflection cid file from PDB

[Folmer Fredslund]

Hi Yu (posting to the board for reference)

To get the cif files is quite easy
E.g. at http://pdb.org/pdb/explore/explore.do?structureId=2v5p you'd go to
the lower right part and get the structure factors from the experimental
details box.
At http://pdbe.org/2v5p you would click the experimental data link to be
able to download the file.


If you are using phenix (it looks like you are) then phenix.fetch_pdb is
much easier to use! There's also a phenix bulletin board you should use for
questions relating to phenix (
http://www.phenix-online.org/mailman/listinfo/phenixbb)

Also, if you have a recent version of COOT, then it can calculate a map for
you on-the-fly through the extensions - PDBe menu.
Be aware that the version of COOT distributed with CCP4 does not work, but
the versions from
http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot/devel/build-info.html
works. (The problem seem to be a change in the way PDBe was storing their
files)

Best regards,
Folmer



2014-08-21 9:53 GMT+02:00 Yamei Yu ymyux...@gmail.com:

 Hi all,

 I download the mmcif file from PDB entry 2V5P, and then I use 
 phenix.cif_as_mtz
  (or cif2mtz ) to try to convert the cid file to mtz file but I got the
 following error message:” Sorry: Please specify one reflection cif file.” I
 also tried several other PDB entries but got the same error message. Where
 is the reflection cif files located in PDB? How to get
 the original diffraction data from PDB?

 Thank you so much for your help!

 Best wishes!

 

 Yamei Yu
 Sichuan University,Chengdu,610041, P.R.China
 Tel: 15882013485
 Email: ymyux...@gmail.com
ymyux...@163.com
yamei...@scu.edu.cn




-- 
Folmer Fredslund

Re: [ccp4bb] IUCR bibtex

[Folmer Fredslund]

Hi Kavya,

If you mean the file located at ftp://ftp.iucr.org/templates/latex/iucr.bst
I have just sent it to you.

Best regards,
Folmer


2014-08-18 7:23 GMT+02:00 Kavyashree Manjunath ka...@ssl.serc.iisc.in:

 Dear users,

 Sorry for an off topic question.
 I would like to request if anyone can mail me the
 iucr.bst file for bibtex. The website hosting this
 file is not opening.

 Thank you
 Regards
 Kavya



 --
 This message has been scanned for viruses and
 dangerous content by MailScanner, and is
 believed to be clean.




-- 
Folmer Fredslund

Re: [ccp4bb] 100.000?

[Folmer Fredslund]

Hi Tim,

I think its easy to find:

pdbe.org/latest (found by googling around a little, and knowing that the
PDBe usually have some very nice short url's)

As far as I can see, the release for 2014-05-07 had 154 new structures in
the PDB.

Best regards,
Folmer



2014-05-10 22:00 GMT+02:00 Tim Gruene t...@shelx.uni-ac.gwdg.de:

 Hi Gerard,

 does that mean there are more than 70 structures released in a week? I
 know the number of entries grows exponentially, yet having it cut down
 to a graspable number makes it even more impressive.

 Cheers,
 Tim

 On 05/10/2014 09:33 PM, Gerard DVD Kleywegt wrote:
  See: http://www.wwpdb.org/news/news_2014.html#06-May-2014
 
  Even if you don't deposit anything, we'll reach the 100,000-entry
  milestone with next Wednesday's release :-)
 
  --Gerard
 
 
 
  On Fri, 9 May 2014, mesters wrote:
 
  Great, just a few more structures to deposit and then 100.000
  structures to celebrate and that in the IYCR2014 :-)
 
  - J .-
  --
  Dr.Jeroen R. Mesters
  Deputy, Senior Researcher  Lecturer
 
  Institute of Biochemistry, University of L?beck
  Ratzeburger Allee 160, 23538 L?beck, Germany
 
  phone: +49-451-5004065 (secretariate 5004061)
  fax: +49-451-5004068
 
  http://www.biochem.uni-luebeck.de Http://www.biochem.uni-luebeck.de
  http://www.iobcr.org Http://www.iobcr.org
 
 
  --
  If you can look into the seeds of time and tell which grain will grow
  and which will not, speak then to me who neither beg nor fear
  (Shakespeare's Macbeth, Act I, Scene 3)
  --
  Disclaimer
  * This message contains confidential information and is intended only
  for the individual named. If you are not the named addressee you
  should not disseminate, distribute or copy this e-mail. Please notify
  the sender immediately by e-mail if you have received this e-mail by
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  * E-mail transmission cannot be guaranteed to be secure or error-free
  as information could be intercepted, corrupted, lost, destroyed,
  arrive late or incomplete, or contain viruses. The sender therefore
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  --
 
 
 
 
  Best wishes,
 
  --Gerard
 
  **
 Gerard J. Kleywegt
 
http://xray.bmc.uu.se/gerard   mailto:ger...@xray.bmc.uu.se
  **
 The opinions in this message are fictional.  Any similarity
 to actual opinions, living or dead, is purely coincidental.
  **
 Little known gastromathematical curiosity: let z be the
 radius and a the thickness of a pizza. Then the volume
  of that pizza is equal to pi*z*z*a !
  **
 

 --
 Dr Tim Gruene
 Institut fuer anorganische Chemie
 Tammannstr. 4
 D-37077 Goettingen

 GPG Key ID = A46BEE1A




-- 
Folmer Fredslund

Re: [ccp4bb] CCP4 BB email change

[Folmer Fredslund]

Hi Arnau,

You can find all the information you need here:

http://www.ccp4.ac.uk/ccp4bb.php

Just subscribe with your new adress, and unsubscribe your old one.

Best regards,
Folmer

ps: actually the following information is available in the header of the
emails sent to the CCP4bb:

List-Help: https://www.jiscmail.ac.uk/cgi-bin/webadmin?LIST=CCP4BB,
   mailto:lists...@jiscmail.ac.uk?body=INFO%20CCP4BB
List-Unsubscribe: mailto:ccp4bb-unsubscribe-requ...@jiscmail.ac.uk
List-Subscribe: mailto:ccp4bb-subscribe-requ...@jiscmail.ac.uk
List-Owner: mailto:ccp4bb-requ...@jiscmail.ac.uk
List-Archive: https://www.jiscmail.ac.uk/cgi-bin/webadmin?LIST=CCP4BB




2014-02-20 10:29 GMT+01:00 Casañas Arnau acasa...@mol.biol.ethz.ch:

 Hi, is it possible to change the email to which my ccp4i bulletin board
 emails get sent?
 The new email address is arnau.casa...@psi.ch
 Thank you very much,

 Arnau Casañas, PhD
 Institute of Molecular Biology and Biophysics
 ETH Zurich
 Schafmattstr. 20 HPK H10
 8093 Zurich
 Switzerland
 +41.44.633845




-- 
Folmer Fredslund

Re: [ccp4bb] I/sigmaI or I/sigmaI

[Folmer Fredslund]

Dear Qixu Cai,

You can find information about where to find the archives here:

http://www.ccp4.ac.uk/ccp4bb.php#archives


Best regards,
Folmer


2014-02-19 14:44 GMT+01:00 Cai Qixu caiq...@gmail.com:

 Dear Richard Gillilan,

 Where to find the archives of Dec 2003? I can only find the archives until
 2007 at jiscmail.

 Thanks.

 Regards,

 Qixu Cai

 发件人: Richard Gillilan r...@cornell.edu
 答复: Richard Gillilan r...@cornell.edu
 日期: 2014年2月16日 星期日 上午12:19
 至: CCP4BB@JISCMAIL.AC.UK
 主题: Re: [ccp4bb] I/sigmaI or I/sigmaI

 There was an informative discussion on this very topic back in Dec 1-2,
 2003 if you browse the CCP4BB archives.

 Richard Gillilan
 MacCHESS

 On Feb 12, 2014, at 6:43 AM, Cai Qixu wrote:

 Dear all,

 Does the I/sigmaI in “Table 1” mean for I/sigmaI or I/sigmaI ?

 Thanks for your answer.

 Best wishes,

 Qixu Cai





-- 
Folmer Fredslund

Re: [ccp4bb] resubmission of pdb

[Folmer Fredslund]

Hi Faisal,

There is one thing I don't understand:

Some time back i had submitted a coordinate in PDB but because of
unacceptance of the manuscript we had to retract the submission

Why would you need to retract your deposited structure just because the
paper describing the structure didn't get accepted?

Venlig hilsen
Folmer Fredslund
On Jan 31, 2014 10:04 PM, Faisal Tarique faisaltari...@gmail.com wrote:

 Dear all

 Dear Dr. PDB,

 Some time back i had submitted a coordinate in PDB but because of
 unacceptance of the manuscript we had to retract the submission. During
 this procedure i got few zipped file from the annotator such as 1.
 rcsb0.cif-public.gz,  2. rcsb0.pdb.gz and  3.
 rcsb0-sf.cif.gz..Now i want to submit the same ..My question is what is
 the best way to do it again..??
 Should we start  from the beginning through ADIT Deposition tool and
 resubmit it with a new PDB id or there is some way to submit again those
 zip files which the annotator sent us after retraction..May you please
 suggest what could be the easiest way to submit our structure to PDB
 without much efforts.


 --
 Regards

 Faisal
 School of Life Sciences
 JNU

Re: [ccp4bb] How to show the ligands (both as sticks and sphere) as shown here in Pymol

[Folmer Fredslund]

Hi Wei,

I think it's easier to do with a surface representation.
I'd do something like this:

# start script 
fetch 3b6a, async=0
as cartoon
extract ligand, c. c and organic
util.chainbow(3b6a)
color green, elem c and ligand
color oxygen, elem o and ligand
show surface, ligand
set surface_mode, 1
set surface_color, yellow
set transparency=.5
show sticks, ligand
set stick_radius, 0.4
show sticks, c. c and i. 130
set cartoon_side_chain_helper, on
zoom ligand
# end script 



And then you'd have to mess around with the view/colors of course.


Hope this helps
Folmer

ps: there's actually a PyMOL bulletin board :-)
https://lists.sourceforge.net/lists/listinfo/pymol-users



2014/1/20 Wei Shi wei.shi...@gmail.com

 Hi all,
 Please see attached Fig where they show the ligand both as sticks and
 spheres at the same time. Does anyone happen to know how to display the
 ligand like this? Thank you so much!

 Best,
 Wei





-- 
Folmer Fredslund

Re: [ccp4bb] OT: Who's Afraid of Peer Review?

[Folmer Fredslund]

Hi Navdeep,

I feel disappointed. (not your fault)

I was hoping to see what kind of science was behind the computer program
that generated the unique papers. That doesn't seem to be contained in the
linked article.

The article does, however, seem to be lacking in peer review itself? Or can
anything be done in the name of journalism? Why were only open-access
journals selected? I guess I'm just repeating the questions that many
others have asked since the publication.

Best regards,
Folmer


2013/10/9 Navdeep Sidhu nsi...@shelx.uni-ac.gwdg.de

 John Bohannon wrote about his experience writing a computer program to
 generate hundreds of unique papers. Thought some of you might find it of
 interest:

 John Bohannon. Who's Afraid of Peer Review? Science 342 (Oct. 4, 2013)
 60-65.
 DOI: 10.1126/science.342.6154.60
 http://www.sciencemag.org/content/342/6154/60.full

 Best regards,
 Navdeep

 ---
 Navdeep Sidhu
 University of Goettingen
 ---




-- 
Folmer Fredslund

Re: [ccp4bb] Docking models into low-res SAD map

[Folmer Fredslund]

Hi Anindito Sen


2013/9/20 Anindito Sen andysen.to...@gmail.com

 skip



 . You can also use Pymol (but I think thats not free any more??).

 /skip


I do not know what your definition of free is, but PyMOL is an
open-source project. You can download the code from
http://sourceforge.net/projects/pymol/
To me, that means free.

It is also possible to pay for PyMOL http://www.pymol.org/pymol which will
give you an easy installer for windows and support amongst other things.

Sorry for the OT post,
Folmer

-- 
Folmer Fredslund

Re: [ccp4bb] I can not find edstat in ccp4i

[Folmer Fredslund]

Hi Ezequiel ,

It doesn't work on windows as far as I can see from the README file.

ftp://ftp.ccp4.ac.uk/ccp4/6.3.0/unpacked/src/edstats/README

Best regards,
Folmer


2013/9/9 Ezequiel Noguera back_nogu...@yahoo.com.ar

 I'm trying to run edstat, but I can not find it in the list of programs of
 CCP4-6.2 or -6.3. How I can run it under Windows? Thanks




-- 
Folmer Fredslund

Re: [ccp4bb] Off-topic, visualization

[Folmer Fredslund]

If you play around with the settings you can do something similar (this is
for surface, but should work for spheres also)
http://www-cryst.bioc.cam.ac.uk/members/zbyszek/figures_pymol#cut

mvh
Folmer


2013/9/5 Ethan A Merritt merr...@u.washington.edu

 On Thursday, 05 September, 2013 13:30:21 Arthur Glasfeld wrote:
  I am hoping to create some images of protein cross-sections where the
 atoms are depicted as spheres, and the spheres that are cut by the slab
 are shown as solids with the same color as the surface.  An example of what
 I'm after can be found here:
 
  people.reed.edu/~glasfeld/xsection.jpg
 
  Does anyone know of any software that can produce similar images?

 http://skuld.bmsc.washington.edu/raster3d/raster3d.html


 
  Thanks,
 
  Arthur Glasfeld
  Reed College
  Portland, OR




-- 
Folmer Fredslund

Re: [ccp4bb] a new version of XDS

[Folmer Fredslund]

Hi all,

Nice with a new version (I guess that means improvements :-)

Before I upgrade, I just have one question:

Does the change in the XPARM.XDS format mean that software such as xia2
will be broken?

Thanks,
Folmer


2013/5/29 Kay Diederichs kay.diederi...@uni-konstanz.de

 ... is available for academic users at http://homes.mpimf-heidelberg.**
 mpg.de/~kabsch/xds/ http://homes.mpimf-heidelberg.mpg.de/~kabsch/xds/
 Please note that there are some incompatibilities; most notably, the new
 format of XPARM.XDS is different so that the new INTEGRATE does not work
 with an old XPARM.XDS.

 best,

 Kay




-- 
Folmer Fredslund

Re: [ccp4bb] a new version of XDS

[Folmer Fredslund]

Hi Alun,

Thanks!

I should have checked the blog (xia2.blogspot.com) myself.

mvh
Folmer


2013/5/30 Alun Ashton alun.ash...@diamond.ac.uk

 Graeme is away this week but was working on the problem before he went
 away. Looking at his update on the XIA2 blog it does look like at least the
 SVN version of XIA2 should be ok, older versions/releases of XIA2 are
 unlikely to work.

 Alun
 ___
 Alun Ashton, alun.ash...@diamond.ac.ukmailto:alun.ash...@diamond.ac.uk
 Tel: +44 1235 778404
 Scientific Software Team Leader,  http://www.diamond.ac.uk/
 Diamond Light Source, Chilton, Didcot, Oxon, OX11 0DE, U.K.


 From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of
 Sebastiano Pasqualato
 Sent: 30 May 2013 07:55
 To: ccp4bb
 Subject: Re: [ccp4bb] a new version of XDS


 Hi Folmer,
 it's just a matter of time, you know, given the short-living license of
 XDS. ;-)

 Anyway, I second the request,
 ciao,
 s


 On May 30, 2013, at 8:50 AM, Folmer Fredslund folm...@gmail.commailto:
 folm...@gmail.com wrote:


 Hi all,
 Nice with a new version (I guess that means improvements :-)
 Before I upgrade, I just have one question:
 Does the change in the XPARM.XDS format mean that software such as xia2
 will be broken?
 Thanks,
 Folmer

 2013/5/29 Kay Diederichs kay.diederi...@uni-konstanz.demailto:
 kay.diederi...@uni-konstanz.de
 ... is available for academic users at
 http://homes.mpimf-heidelberg.mpg.de/~kabsch/xds/
 Please note that there are some incompatibilities; most notably, the new
 format of XPARM.XDS is different so that the new INTEGRATE does not work
 with an old XPARM.XDS.

 best,

 Kay



 --
 Folmer Fredslund

 --
 Sebastiano Pasqualato, PhD
 Crystallography Unit
 Department of Experimental Oncology
 European Institute of Oncology
 IFOM-IEO Campus
 via Adamello, 16
 20139 - Milano
 Italy

 tel +39 02 9437 5167
 fax +39 02 9437 5990








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-- 
Folmer Fredslund

Re: [ccp4bb] Rfree flag

[Folmer Fredslund]

Although it is not mandatory, I think it would be a very good idea,
especially if you have the exact same spacegroup and the native and
ligand-bound forms of your protein are essentially the same.

If you do not use the same reflections, you are actually not reporting an
independent (free) R-factor.




Best regards,
Folmer


2013/2/28 Prof. K. Sekar se...@physics.iisc.ernet.in

 Dear Kavya,

 It is not so.  It is not
 mandatory.

 best,

 Sekar


  Dear users,
 
  Is it mandatory to use the same reflections for
  Rfree calculations of a ligand bound data as that
  of its native?
 
  Thank you
  With Regards
  Kavya
 
 
  --
  This message has been scanned for viruses and
  dangerous content by MailScanner, and is
  believed to be clean.
 


 Could you kindly confirm the safe
 receipt of this mail please

 All best wishes and regards,

 Yours sincerely,

 Dr. K. Sekar, Ph.D.
 Associate Professor
 Bioinformatics
 Indian Institute of Science
 Bangalore 560 012
 INDIA

 E-mail:  se...@physics.iisc.ernet.in

 Tel: 91-(0)80-22933059, 23601409, 22932469
 Fax:91-(0)80-23600683, 23600551

 Homepage:   http://www.physics.iisc.ernet.in/~dichome/sekhome/index.html


 --
 This message has been scanned for viruses and
 dangerous content by MailScanner, and is
 believed to be clean.




-- 
Folmer Fredslund

[ccp4bb] Building sugars

[Folmer Fredslund]

Dear all,


What's the correct way to build and refine sugar polymers?

I am currently building several structures with different kinds of sugar
polymers bound to them.

Searching for similar ligands in the PDB, I end up with e.g.
trisaccharides that are named as one molecule, even though they are indeed
made up of three individual sugars with bonds between them.


Thank you for any pointers.

Best regards,
Folmer

-- 
Folmer Fredslund

Re: [ccp4bb] Building sugars

[Folmer Fredslund]

Hi all

Thank you all for your replies.

I might have expressed myself poorly, but I am not talking about covalently
linked sugar modifications, so for my purpose there's no need to be
concerned about insertion codes ;-)

The glycosciences.de link is really useful. There does not seem to be a
test to verify correct PDB nomenclature though. Or perhaps RAF (for
raffinose, a tri-saccharide) is OK to use?

Best regards,
Folmer




2013/2/21 Robbie Joosten robbie_joos...@hotmail.com

 Hi Folmer,

 Just to add some tips:

  Concerning the naming as one molecule: the sugar monomers get the same
  chain ID as the protein they are connected to and arbitrary residue
 numbers.
  I usually start numbering from 1000 to prevent overlap with the numbering
  of the amino acids.
 1) Just don't use insertion codes, some people find it upsetting ;) And
 keep
 the residue numbering consistent between NCS copies.

 2) The glycosciences.de portal has many tools for dealing with
 carbohydrates: http://www.glycosciences.de/
 I really like PDB-care and CARP for validation in the building and
 refinement process.

 3) When using TLS you should try to figure out whether it's useful to add
 the sugars to the group of the linked protein residue or to have specific
 groups for your sugar trees.

 Cheers,
 Robbie

  HS.
 
 
  
 
From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On
  Behalf Of Folmer Fredslund
Sent: Thursday, February 21, 2013 12:33 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Building sugars
 
 
Dear all,
 
 
 
What's the correct way to build and refine sugar polymers?
 
 
I am currently building several structures with different kinds of
 sugar
  polymers bound to them.
 
 
Searching for similar ligands in the PDB, I end up with e.g.
  trisaccharides that are named as one molecule, even though they are
 indeed
  made up of three individual sugars with bonds between them.
 
 
 
Thank you for any pointers.
 
 
Best regards,
Folmer
 
 
--
Folmer Fredslund
 




-- 
Folmer Fredslund

Re: [ccp4bb] Boveral in SFCheck

[Folmer Fredslund]

Hi,

Sorry Eric I don't have an answer for your question.

off topic:
From the University's announcement (
http://main.uab.edu/Sites/reporter/articles/71570/) you would have thought
that they had asked for this entry to be removed.

But if I understand correctly, this is is completely at the discretion of
the depositors in question.

mvh
Folmer Fredslund




2012/12/14 Zhijie Li zhijie...@utoronto.ca

 **
 Hi,

 Seems not officially retracted from Nature either. On the paper's web
 page, there was only a line in small font read like this:

  There is a Brief Communications 
 Arisinghttp://www.nature.com/uidfinder/10.1038/nature06102(9 August 2007) 
 associated with this document.
 It took me more than half an hour to find this line. I normally won't read
 any line above the title. Now it proves to be a bad habit.

 I am still trying to find this line in the PDF.

 Zhijie



  *From:* Michael Hadders mhadd...@gmail.com
 *Sent:* Friday, December 14, 2012 2:57 AM
 *To:* CCP4BB@JISCMAIL.AC.UK
 *Subject:* Re: [ccp4bb] Boveral in SFCheck

 Hi,

 2HR0 I would stay far away from that one! It is a made up model, not
 based on any real data. Unfortunately, for reasons unclear to me, this
 structure has still not been retracted from the PDB. This B factor could
 just be a figment of the senior authors imagination

 https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0912L=CCP4BBD=0P=88327

 Regards,

 Michael

 On Fri, Dec 14, 2012 at 3:34 AM, Eric Williams ericwilli...@pobox.comwrote:

 Please pardon me if this is a dumb question with an obvious answer...

 I'm parsing SFCheck's plain text output as part of my dissertation, and
 I'm having trouble identifying one of the values. There are three overall
 B-factor values reported, one based on the Patterson origin peak, one based
 on the Wilson plot, and one that remains a mystery to me. Here's the
 relevant line (from 2HR0) with some lines before and after for context:

   R_stand(I) = sig(I)/I :0.397
   Number of acceptable reflections:  194123
   for resolution :  45.33 -  2.26
   Optical Resolution:   1.80
   Boveral,Effres,Padd:   40.751   2.032 777.887
   Expected Optical Resolution for complete data set:   1.80
 / Optical resolution - expected minimal distance between
   two resolved peaks in the electron density map./
   Resmax_used(opt):  2.26

 The mystery value is Boveral. I've found no explanation for it in either
 the SFCheck manual or the original journal article. Perhaps I'm missing
 something obvious, but someone would really make my day if they could point
 me in the right direction. Thanks! :)

 Eric





-- 
Folmer Fredslund

Re: [ccp4bb] manipulation of water molecules in pdb files

[Folmer Fredslund]

Dear Zhiyi,

I think that sortwater (http://www.ccp4.ac.uk/html/sortwater.html), will do
something along what you want. Remember to read the documentation ;-)

Best regards,

Folmer

2012/7/30 Zhiyi Wei ustcwebri...@gmail.com

 Dear all,

 I have a refine structure with 8 ncs copies and several hundreds of
 water molecules (which was put in one chain). Now I try to separate
 these molecules by renaming to the chain id of each adjacent protein
 molecule. I know RCSB can do this during deposition process. Do anyone
 know a program can do a similar task? Many thanks!

 Best,
 Zhiyi




-- 
Folmer Fredslund

Re: [ccp4bb] pymol question

[Folmer Fredslund]

Hi Sebastiano

2012/5/18 Sebastiano Pasqualato sebastiano.pasqual...@gmail.com


 Hi all,

 is there a way in Pymol to have a loop/tube representation of the protein
 backbone that would pass through the N-CA-C-N(+1)-CA(+1)-C(+1) atoms rather
 than CA-CA(+1) atoms?


I know this is possibly not what you are after, but what about

show lines, name n+ca+c
or
show sticks, name n+ca+c
?
It won't be a smooth loop, but maybe usefull?




 I remember something like this (a loop vs turn representation) in
 Molscript or Ribbons, but can't find it in Pymol.
 I'm using Pymol 0.99rc6


You might want to consider upgrading. And also subscribe to the pymol users
mailing list https://lists.sourceforge.net/lists/listinfo/pymol-users

Hope this helps ,
Folmer


 Thanks all in advance,
 ciao,
 Sebastiano

 --
 Sebastiano Pasqualato, PhD
 Crystallography Unit
 Department of Experimental Oncology
 European Institute of Oncology
 IFOM-IEO Campus
 via Adamello, 16
 20139 - Milano
 Italy

 tel +39 02 9437 5167
 fax +39 02 9437 5990










-- 
Folmer Fredslund, Post doc
The MAX IV laboratory

Re: [ccp4bb] Ubuntu Maverick and coot menus

[Folmer Fredslund]

Dear David and everybody,

lørdag den 11. februar 2012 skrev David Schuller dj...@cornell.edu:
 On 02/11/12 14:15, Nat Echols wrote:

 On Sat, Feb 11, 2012 at 10:55 AM, hari jayaram hari...@gmail.com wrote:

 There has been a lot of opinions within the Ubuntu community about
 Unity..just wondering what coot-ers are using with the new Ubuntu(s).

 ... If this is a
 reliable indication of where Ubuntu is going in the future, I need to
 find a new favorite distribution.

 that seems to be a common sentiment:


http://www.zdnet.com/blog/hardware/ubuntu-sees-massive-slide-in-popularity-mint-sprints-ahead-but-why/16550

 

 Ubuntu sees massive slide in popularity, Mint sprints ahead...

Please note that this is based on pageranks from distrowatch, i.e. this
only shows something about what pages on distrowatch people have been
looking at. It shows absolutely nothing about what people actually use.


With respect to the ubuntu UI, I personally am happily using it.
As far as I understand, the old gnome UI was abandoned for version 3.0
and canonical (company behind ubuntu) decided to go somewhere else ( thats
the short description).

anyways:
You should be able to disable the global application menu as shown here:
http://askubuntu.com/questions/10481/how-do-i-disable-the-global-application-menu

Best regards

Folmer




 --
 ===
 All Things Serve the Beam
 ===
David J. Schuller
modern man in a post-modern world
MacCHESS, Cornell University
schul...@cornell.edu


-- 
Folmer Fredslund
Maj Allé 86
2730 Herlev
Mobil: (+45) 61 468 009
Mail: folm...@gmail.com

Re: [ccp4bb] Fwd: Installing ccp4-6.0.99e on 64 bit Ubuntu - Bioscreencast Wiki (works for 32-bit also)

[Folmer Fredslund]

Dear all,

I tend to use Google's cached versions or

The web archive
http://www.archive.org/web/web.php

leading to
http://web.archive.org/web/20100814204611/http://www.bioscreencastwiki.com/Crystallography_Howtos/Installing_ccp4-6.0.99e_on_64_bit_Ubuntu

Hope this helps someone...

Best regards,
Folmer


2011/10/4 Edward A. Berry ber...@upstate.edu

 I think I captured most of it in the attached. Hope this doesn't
 violate anyone's copyright:




-- 
Folmer Fredslund, Ph.D.

Re: [ccp4bb] unusual sighting of a crystal structure

[Folmer Fredslund]

Nice find! ;-)

Just in case anyone want to see it IRL
http://www.youtube.com/watch?v=4sYSyuuLk5ghd=1t=38s

Regards,
Folmer

2011/7/16 Artem Evdokimov artem.evdoki...@gmail.com:
 Fellow structural biologists,

 I just caught a brief glimpse of a crystal structure (looks like an Fv
 complex or maybe an IG-like receptor ectodomain complex?) in the trailer for
 the upcoming 'scary virus' movie Contagion and thought you'd want to share
 the amusement.

 Sorry about the 300K attachment :)

 Artem

Re: [ccp4bb] exploding hydrogens during real space refinement in coot

[Folmer Fredslund]

Dear Kendall

2011/2/10 Kendall Nettles knett...@scripps.edu:
 When I real space refine my ligand the hydrogens fly away. The ligand pdb 
 file and cif file were generated with progdr. I'm using Coot 0.6.2-pre-1.

 Kendall


This could be a problem with the naming conventions of pdb versions. I
don't remember which version Coot uses, but here is an old thread on
the subject http://www.mail-archive.com/coot@jiscmail.ac.uk/msg00405.html

Best regards,
-- 
Folmer Fredslund

Re: [ccp4bb] COOT water retention problem...

[Folmer Fredslund]

Dear Myron,

What is wrong with using the Delete Item option from the menu?
It's gives you a couple of choices, one of which is waters. Means that
you will only delete waters when selecting in the main window.

That is the way I do it anyway.

Best regards,
Folmer Fredslund


2010/11/10 Smith, Myron myron.sm...@evotec.com:
 Has anyone ever accidentally placed a water molecule onto the exact position
 of selected atom and tried to delete it? How was that achieved? I actually
 saved the pdb file and deleted the text line of the coordinates for the
 offending water, then reloaded the file. Is there any other procedure that
 does not require external manipulation of the file outside of COOT?





 Regards

 Myron

 Evotec (UK) Ltd is a limited company registered in England and Wales.
 Registration number:2674265.  Registered Office:  114 Milton Park, Abingdon,
 Oxfordshire, OX14 4SA, United Kingdom

Re: [ccp4bb] how to superpose density maps?

[Folmer Fredslund]

Hi Mark.

This is hidden in the Extensions menu.

Extenstions - Maps- Transform map by LSQ model fit

Or at least that is what I think you want.

Best regards,
Folmer Fredslund

On 28 January 2010 15:29, Matt Warkentin mattw...@gmail.com wrote:
 Hi all

 I have a seemingly simple task that I can't seem to figure out how to
 do:  I have a bunch of structures with same space/cell that I want to
 compare in coot.  It is easy to superpose the models, but I would also
 like to superpose the maps.  Is there a simple way to do this?  If
 not, is that because there is a good reason not to?

 Thanks

 Matt

Re: [ccp4bb] Electron Density Maps

[Folmer Fredslund]

Dear Pascal,

2009/8/10 Pascal Egea pas...@msg.ucsf.edu:
 Dear All,
 I am currently carrying the refinement of a structure and comparing the
 results obtained in Refmac, Phenix and CNS.
 While Phenix and Refmac write maps and their corresponding coefficients in
 mtz format allowing display of 2Fo-Fc and Fo-Fc maps in COOT, the
 corresponding Fo-Fc map as written by CNS does not show positive and
 negatives peaks. There is density but it does not look like why I would
 expect for a Fo-Fc map. Why is that?

Is your map read as an Fo-Fc map? I guess not...

I believe there is a way to tell COOT that you want to load you CNS
map as a difference map.
This section
http://www.ysbl.york.ac.uk/~emsley/coot/doc/chapters/user-manual_6.html#SEC160
of the user manual might explain better.


Hope this helps,
Folmer Fredslund

Re: [ccp4bb] Phaser SAD+MR followed by CNS

[Folmer Fredslund]

Dear Kelly-Anne

2009/3/27 Kelly-Anne Twist wils...@rockefeller.edu:
 Hello all,

 I have a structure that has been solved by MR and now have experimental SAD
 phases that I hope will improve the map.
 I used Phaser for this from within the CCP4i suite but I would like to take
 the solution and work with it further in CNS.

 Is there a way to generate a .hkl file from the Phaser output .mtz file?


There is also the possibility to check the CNS pages at
http://cns-online.org/v1.21/ (also nice to have if you get further
problems) and they also have a page on converting to hkl format:
http://cns-online.org/v1.21/tutorial/sf_convert/mtz_to_cns/text.html


Best regards,
Folmer

Re: [ccp4bb] two identical proteins in one asymmetric unit

[Folmer Fredslund]

Dear Sang

They are really different!

And I guess you would probably want to use NCS restraints depending on
your resolution.

Regards,
Folmer

2009/3/24 Sang Hoon Joo s...@duke.edu:
 I am refining my crystal structure in which I have two identical
 chains in one asymmetric unit.
 Space group is H32 and each chain yields me a biological trimer as expected.
 The problem is, do I have to assume they are identical, or they are
 really different.
 After each cycle of refinement, if I try to align two molecules I get
 ~ 0.17 RMSD.
 --
 Sang Hoon Joo, PhD
 Postdoctoral Associate
 Duke University
 239 Nanaline H. Duke
 Box 3711, DUMC
 Durham, NC 27710