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)
:
> Sp
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 s
rate 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 lab
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
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 us
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 th
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,
Fo
sy, 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 calculat
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
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,
h
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 <
193323b1e6
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 w
, 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 Pym
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:
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
Hi Tommi,
Could it be the bug that was reported in June?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1606&L=ccp4bb&F=&S=&P=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
actor.
Hope this helps,
Folmer Fredslund
2015-06-02 12:26 GMT+02:00 Graeme Winter :
> 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
ated to Cryo-EM..
>
> Thanx in advance
>
> --
> Regards
>
> Faisal
> School of Life Sciences
> JNU
>
>
--
Folmer Fredslund
ographic 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
/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,
Folme
-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
gt; 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
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 :
> Dear all, I have no access to Moleman now but I need to compile a
> statistics table
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" :
> Dear all:
>
> I have installed CCP4 suit on my computer. The OS IS fedora 18. Every time
> I open the software, I
f 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
erGuide7.4.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 :
> Dear all,
> I was using ARP/wARP in ccp4i, the input mtz file certainly has free R
> flag, but the
riginal 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
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
;
> > 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
sa...@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
3 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 / or ?
>
> Thanks for your answer.
>
> Best wishes,
>
> Qixu Cai
>
>
>
--
Folmer Fredslund
ture didn't get accepted?
Venlig hilsen
Folmer Fredslund
On Jan 31, 2014 10:04 PM, "Faisal Tarique" 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 t
w how to display the
> ligand like this? Thank you so much!
>
> Best,
> Wei
>
>
>
--
Folmer Fredslund
> due to the general overload with Emails I would like to unsubscribe to the
> CCP4BB Mailinglist. Does anybody know how to do that?
>
> Thanks.
>
--
Folmer Fredslund
tent/342/6154/60.full
>
> Best regards,
> Navdeep
>
> ---
> Navdeep Sidhu
> University of Goettingen
> ---
>
--
Folmer Fredslund
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
6.2 or -6.3. How I can run it under Windows? Thanks
>
--
Folmer Fredslund
> >
> > 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
t;
>
> 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.com>> wrote:
>
>
> Hi all,
>
DS.
>
> best,
>
> Kay
>
>
--
Folmer Fredslund
IA
>
> 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
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.
> >
> >
> > ____
>
olecule, 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
letely at the discretion of
the depositors in question.
mvh
Folmer Fredslund
2012/12/14 Zhijie Li
> **
> 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
f
> 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!
>
> Be
t; 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
===
> All Things Serve the Beam
> ===
>David J. Schuller
>modern man in a post-modern world
> MacCHESS, Cornell University
>
gards,
Folmer
2011/10/4 Edward A. Berry
> I think I captured most of it in the attached. Hope this doesn't
> violate anyone's copyright:
>
--
Folmer Fredslund, Ph.D.
Nice find! ;-)
Just in case anyone want to see it IRL
http://www.youtube.com/watch?v=4sYSyuuLk5g&hd=1&t=38s
Regards,
Folmer
2011/7/16 Artem Evdokimov :
> Fellow structural biologists,
>
> I just caught a brief glimpse of a crystal structure (looks like an Fv
> complex or maybe an IG-like recepto
ns. 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
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
2
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 wrote:
> Hi all
>
> I have a seemingly simple
ay 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
Dear Kelly-Anne
2009/3/27 Kelly-Anne Twist :
> 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
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 :
> I am refining my crystal structure in which I have two identical
> chains in one asymmetric unit.
> Space group is H32 and eac
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