Hi Sam,
some time ago I had a similar issue: refinement for a soaked crystal stuck
at 0.36/0.41 and there was no ligand density.
I tried to reprocess my dataset using different start/end frames and one of
the processing runs gave me a unit cell with a doubled axis a. Refinement
against this dataset
Dear Tom,
I updated the workstation with Ubuntu 16.04->20.04 This update broke 3d
vision and I am thinking about moving back to Ubuntu 16.04. Other programs
work well.
вс, 21 февр. 2021 г. в 10:59, Folmer Fredslund :
> Dear Tom
>
> Be aware that python2 is currently not supported. It is end-
Hi everyone,
I wanted to revive this discussion with a fresh paper from Cell journal:
https://www.cell.com/cell/fulltext/S0092-8674(20)31623-8
So one could use a smartphone camera for SARS-CoV-2 detection but you still
need some extra tools, like 488 nm laser.
пт, 10 апр. 2020 г. в 20:14, James Ho
Fred,
you could use the Academic version of Desmond freely available here:
https://www.deshawresearch.com/resources_desmond.html
The only difference from the commercial version is absence of OPLS3e force
field but you still could use GPU.
вт, 4 авг. 2020 г. в 10:08, Fred Vellieux :
> Hello,
>
>
Dear Javier,
It might be better to ask in the pymol mailing list.
See info here:
https://www.mail-archive.com/pymol-users@lists.sourceforge.net/info.html
вс, 14 июн. 2020 г. в 01:45, Javier Gonzalez :
> Hello,
> I'm attempting to build pymol on a laptop running MacOS Catalina 10.15.5,
> Process
Hi, Michael,
as a workaround you could create a tunnel (or port forwarding) from your
machine to the ssh server and bind port 22 on the local machine to the
non-standard ssh port of the remote host.
the command will look like this:
$ *ssh -L 127.0.0.1:22:remote-ssh-server:remote-ssh-port
remote-use
Dear CCP4 community,
the previous interface of search results in RCSB PDB website contained
"Ligands" tab but now it is gone.
Do someone knows how to browse ligands of the search results?
Thanks in advance!
--
Evgenii Osipov
Laboratory for Biocrystallography,
Department of Pharmaceutical Science
Dear Yong,
you could use freely available Chimera.Use Tools->Structure Editing-> Dock
prep. in order to add missing side chains to your protein.
Another option - Protein preparation tool from Schrodinger Suite. However,
it is non-free.
сб, 23 мая 2020 г. в 21:19, Yong Tang :
> Dear all, is there
Dear CCP4bb members,
how could I disable checks for nomenclature errors and get rid of "Fix
Nomenclature Errors" window at every Coot startup?
[image: image.png]
Thanks in advance,
--
Evgenii Osipov
Laboratory for Biocrystallography,
Department of Pharmaceutical Sciences,
KU Leuven O&N2
##
Dear Thierry,
Check here:
http://devtools.fg.oisin.rc-harwell.ac.uk/nightly/7.0/ccp4-src-7.0/
"Checkout" folder seems to contain the source code.
пн, 4 мая 2020 г. в 21:26, Fischmann, Thierry <
22f7fda0a875-dmarc-requ...@jiscmail.ac.uk>:
> Hello,
>
>
>
> This question is addressed to the CCP4
Hi, Sam,
it should be fine but as an additional safety measure I would recommend
installing miniconda and create separate virtual environment for cryoem
related software.
чт, 30 апр. 2020 г. в 13:45, Colin Palmer - UKRI STFC <
colin.pal...@stfc.ac.uk>:
> Hi Sam,
>
> There is no problem with this:
Dear CCP4 community,
In case if someone missed - Springer e-books are available for free
[Limited time]:
https://www.thebiomics.com/notes/springer-free-e-books-list.html
For example, do not miss the opportunity to grab "Structure Determination
by X-ray Crystallography":
https://link.springer.com/bo
y/tmp/', 'coot-download')
except:
pass
Thanks again for the advice!
ср, 22 апр. 2020 г. в 15:52, Paul Emsley :
>
> On 22/04/2020 14:43, Eugene Osipov wrote:
>
>
> is there a way to specify Coot download directory, like the way I
> can specify backup dir by
Dear CCP4BB members,
is there a way to specify Coot download directory, like the way I
can specify backup dir by COOT_BACKUP_DIR?
I did not find any guidelines in the Coot User Manual.
Thanks in advance
--
Evgenii Osipov
Laboratory for Biocrystallography,
Department of Pharmaceutical Sciences,
K
Dear Andre,
the easierst way is to place mirror next to the screen. You should be able
to see the mirror image of an existing map file
ср, 1 апр. 2020 г. в 14:56, Andre LB Ambrosio :
> Dear all,
> is it possible to generate a mirror image of an existing .ccp4 map file?
> Many thanks in advance.
>
Hi, Firdous,
Most modern force fields have a way to describe ions, small molecules or
modified residues for MD run. And they already contain description for
phosphorilated aminoacids. So you can choose whichever you want.
But it is more appropriate to ask in the specialized mailing list, like
CCPBi
Dear CCP4 developers,
ccp4wiki.org is throwing an exception:
*Fatal error*: Uncaught TypeError: Argument 1 passed to wfReportException()
must be an instance of Exception, instance of Error given, called in
/home/ccp4wiki/public_html/wiki/includes/Exception.php on line 205 and
defined in /home/ccp4
gt; Tel: +441235 77 8078
>
> Diamond Light Source Ltd.
> Diamond House
> Harwell Science & Innovation Campus
> Didcot
> Oxfordshire
> OX11 0DE
> --
> *From:* CCP4 bulletin board on behalf of Eugene
> Osipov
> *Sent:* 03 December 2019
Dear CCP4 community,
I can't figure out how to tell Dimple to use F(+)/F(-) columns and search
for anomalous peaks.
I was trying to run dimple in the next form:
dimple -R free.mtz --anode --fcolumn F output.mtz test.pdb dimple_dir
In the output mtz I get only 2Fo-Fc and Fo-Fc maps. When I try to
u
Dear Eleanor,
>From PDB files I see that the structures were solved by molecular
replacement using pdbid 1gci as a starting model. It is hard to say
definitely without the linked paper but may be the depositors made the same
error that I did some time ago: they solved both structures using molecul
Chris,
you can reduce occupancy of the water molecule, like: 0.5 if water lies on
2-fold axis, or 1/3 if it is on 3-fold axis and so on
ср, 6 нояб. 2019 г. в 11:18, Chris Fage :
> Dear BB Users,
>
> Within my unit cell, I see overlapping spherical blobs of Fo-Fc and 2Fo-Fc
> density in Coot. Thes
Ewa,
send the message '*unsubscribe ccp4bb'* to the *lists...@jiscmail.ac.uk
*
пт, 9 авг. 2019 г. в 03:10, Skrzypczak-Jankun, Ewa <
ewa.skrzypczak-jan...@utoledo.edu>:
> Please stop sending email to my address
>
> ewa.skrzypczak-jan...@utoledo.edu
>
> thank you
>
> --
Dear CCP4 developers,
I can't see any file or folder when I am trying to import file from ccp4i2
interface.
The only folder I see - my homefolder
Screenshot of the file selection dialog:
http://i.imgur.com/EDGn6Wj.png
note that "look in" path points to the root folder.
Software versions:
$ ccp4i2
R
Lumbini,
2.5A is close to the coordination bond length of sulfur-metal. Did you use
IMAC during purification?
ср, 10 июл. 2019 г. в 08:44, Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>:
> I am serious about checking the anomalous map!!
> (trivial from REFMAC - key word anom ma
Jonathan,
when you add a water molecule through "Place atom at Pointer..." change the
default option at the bottom of the popup window from "New molecule" to
your protein molecule. In this way water molecule will be placed directly
into your protein model and will be visible in symmetry mates.
вт,
Dear Aleix,
what is in the buffer and crystallization conditions? I have seen anomalous
signal at 0.99 angstroms because my crystallization conditions contain NaI.
And F'' (I) is around 3 at this wavelength.
I would follow Eleanor advice.
OR
Try to generate anomalous map if you can solve your struc
; ########
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>
--
Eugene Osipov
Junior Research Scientist
Laboratory of Enzyme Enginee
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>
--
Eugene Osipov
Junior Research Scientist
Laboratory of Enzyme Engineering
Research Center o
ap for my requirement.
>
>
>
> Thanks & Regards,
>
>
>
>
>
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
>
--
Eugene Osip
I found the solution by myself:
open pdb file in vim and replace segid by regexp
:%s/\S\S\S\s\s\(\S$\)/ \1/g
2018-07-05 14:33 GMT+03:00 Eugene Osipov :
> Hello everyone,
> is there any simple way in CCP4 to clear segid field?
> I used phenix.pdbtools but version 1.13 does not wor
Hello everyone,
is there any simple way in CCP4 to clear segid field?
I used phenix.pdbtools but version 1.13 does not work anymore.
--
Eugene Osipov
Junior Research Scientist
Laboratory of Enzyme Engineering
Research Center of Biotechnology
Russian Academy of Sciences
Leninsky pr. 33, 119071
ammannstr. 4,
> D37077 Goettingen, Germany
> Tel. +49-551-39-33021 or +49-5594-227312
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.a
made as
> specified by
> link information in the dictionary, then actually heme C (HEC) should be
> the same
> as heme b (protoheme).
>
>
> On 05/15/2018 04:35 AM, Eugene Osipov wrote:
>
>> Dear CCP4 developers,
>> please fix errors with heme c dictionary file
> >
> > The problem is not in the HEC.cif file but with the LINKs which modify
> the
> > chemistry. These were fixed a while ago and the LINKs were added to the
> > CCP4 dictionary. I thought these were released already. If not, they
> will be
> > soon.
> >
&g
of heme c.
--
Eugene Osipov
Junior Research Scientist
Laboratory of Enzyme Engineering
A.N. Bach Institute of Biochemistry
Russian Academy of Sciences
Leninsky pr. 33, 119071 Moscow, Russia
e-mail: e.m.osi...@gmail.com
nt - No diffraction (blank)
>>> with Ethylene glycol- No diffraction (blank)
>>> with PEG 3350 - 7A diffraction and No ice rings
>>> with Glycerol - 3.5A diffraction with ice rings
>>>
>>> I have tried soaking with glycerol different concentrations 10-30
their
expression level?
Thank you very much!
--
Eugene Osipov
Junior Research Scientist
Laboratory of Enzyme Engineering
A.N. Bach Institute of Biochemistry
Russian Academy of Sciences
Leninsky pr. 33, 119071 Moscow, Russia
e-mail: e.m.osi...@gmail.com
erably for some papers that describe PDB file
> formats, electron density refinements. A primer kind of for PDB,
> macromolecule world for teaching medicine students.
>
> Any suggestions gratefully recd,
> Veronica
>
--
Eugene Osipov
Junior Research Scientist
Laboratory of Enzy
ilano
> Italy
>
> tel +39 02 9437 5167
> fax +39 02 9437 5990
> web http://is.gd/IEOXtalUnit
>
>
--
Eugene Osipov
Junior Research Scientist
Laboratory of Enzyme Engineering
A.N. Bach Institute of Biochemistry
Russian Academy of Sciences
Leninsky pr. 33, 119071 Moscow, Russia
e-mail: e.m.osi...@gmail.com
_ASCII.HKL HKLOUT pointless.mtz
.
$aimless hklin pointless.mtz hklout aimless.mtz
After a program run with either "ANOMALOUS ON" or "ANOMALOUS OFF" I see
6629 reflections. Meanwile XDS and Phenix report 12 200 unique reflections.
Is it bug or I miss something?
--
Eugene Os
Hi,
Site http://ccp4wiki.org/ is not working.
E-mail of the responsible person (as fetched by whois service) c...@dl.ac.uk
is not accessible.
Can someone inform responsible person about this issue?
P.S.: It seems we read too much.
--
Eugene Osipov
Junior Research Scientist
Laboratory of Enzyme
2016-12-10 18:05 GMT+03:00 richard.gil...@diamond.ac.uk>>:
> "E.g. DIALS by default do not process reflections near ice rings,"
>
> I'm not sure where you got this information from, but this is not correct
> - by default DIALS will process all reflections.
>
&
>
> Cheers,
>
> Richard
>
> Dr Richard Gildea
> Data Analysis Scientist
> Tel: +441235 77 8078
>
> Diamond Light Source Ltd.
> Diamond House
> Harwell Science & Innovation Campus
> Didcot
> Oxfordshire
> OX11 0DE
> ________
> Fr
3.53 0.358 1430 0.3781.85 3248 0.185
> > 26 0.0835 3.46 -0.428 12 0.3301.38 22 0.138
> > 27 0.0868 3.39 0.390663 0.2851.73 1404 0.173
> > 28 0.0900 3.33 0.128 1443 0.2441.39 2946
them?
P.S.: I am trying to produce better crystals but this dataset is still the
best one I have.
--
Eugene Osipov
Junior Research Scientist
Laboratory of Enzyme Engineering
A.N. Bach Institute of Biochemistry
Russian Academy of Sciences
Leninsky pr. 33, 119071 Moscow, Russia
e-mail: e.
ishes,
>
> Didi
>
>
>
>
>
> Sent from Mail <https://go.microsoft.com/fwlink/?LinkId=550986> for
> Windows 10
>
>
>
--
Eugene Osipov
Junior Research Scientist
Laboratory of Enzyme Engineering
A.N. Bach Institute of Biochemistry
Russian Academy of Sciences
Leninsky pr. 33, 119071 Moscow, Russia
e-mail: e.m.osi...@gmail.com
t; current and planned beamlines at MAXIV?
>
> Best Regards, Hartelijke Groeten,
>
> Rik
>
>
>
--
Eugene Osipov
Junior Research Scientist
Laboratory of Enzyme Engineering
A.N. Bach Institute of Biochemistry
Russian Academy of Sciences
Leninsky pr. 33, 119071 Moscow, Russia
e-mail: e.m.osi...@gmail.com
>
> Please correct me if pertinent and provide additional examples if possible.
>
> Gratefully yours,
>
> Mark
>
> Mark J van Raaij
> Dpto de Estructura de Macromoleculas
> Centro Nacional de Biotecnologia - CSIC
> calle Darwin 3
> E-28049 Madrid, Spain
> tel. (+3
has encountered anything similar in the past, and if they managed to
> resolve the problem, how they went about it?
>
>
>
> Cheers in advance,
>
>
>
> Dave
>
>
> David C. Briggs PhD
> http://about.me/david_briggs
>
--
Eugene Osipov
Junior Research Scientist
Laboratory of Enzyme Engineering
A.N. Bach Institute of Biochemistry
Russian Academy of Sciences
Leninsky pr. 33, 119071 Moscow, Russia
e-mail: e.m.osi...@gmail.com
rectory C:/Ccp4/Temp/temp_6_topp_ for output files
In this directory after about 15 minutes (while I am typing this message)
is only two files: CHAR.CHA (inside only AUTO word) and empty file SEQ.CHA
So, can someone explain me what is the problem?
--
Eugene Osipov
Junior Research Scientist
Aug 19, 2013, at 11:49 PM, Mahesh Lingaraju
>>>> wrote:
>>>>
>>>> Hello people
>>>>
>>>> I recently obtained hexagonal rod like crystals (150x50x20 um) which
>>>> turned out to be non diffracting. What is the usual convention
advised to perform your own checks. Email
> communications with the University of Nottingham may be monitored as
> permitted by UK legislation.
>
>
--
Eugene Osipov
Junior Research Scientist
Laboratory of Enzyme Engineering
A.N. Bach Institute of Biochemistry
Russian Academy of Sciences
Leninsky pr. 33, 119071 Moscow, Russia
e-mail: e.m.osi...@gmail.com
атель "Eugene Osipov"
написал:
> Not only 118, look at 119 . It seems also that residues 82-88 incorrectly
> placed . I think that authors (if they are reading this board ) must fix
> errors. To be honest this is not first time I see such models.
> 12.04.2013 23:17 пользовател
Not only 118, look at 119 . It seems also that residues 82-88 incorrectly
placed . I think that authors (if they are reading this board ) must fix
errors. To be honest this is not first time I see such models.
12.04.2013 23:17 пользователь "Michel Fodje"
написал:
By the way, you will need to sho
ity
> analysis and rotamer analysis. The problem is that there are so many
> problems with my structure, that i dont know where to begin. Could you try
> some refinement for me, because this is first structure that i need to
> solve as a student and i dont have too many experience with it.
course if
someone already uses it)
3)Is there any advice for long-term diffraction image storage?
Thank you for your attention,
--
Eugene Osipov
Junior Research Scientist
Laboratory of Enzyme Engineering
A.N. Bach Institute of Biochemistry
Russian Academy of Sciences
Leninsky pr. 33, 119071 Moscow
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