Re: [ccp4bb] coot & other graphics programs draw too many bonds

[Johannes Cramer]

Hi Fred,

are you using the output from vina directly (I think it is called pdbrq)?
If so, you could try converting it to mol2, before loading it into pymol.

Cheers,
Johannes

Am Do., 1. Apr. 2021 um 15:59 Uhr schrieb Robbie Joosten <
robbie_joos...@hotmail.com>:

> Hi Fred,
>
> I think this is a problem of not having the right description of the
> compound. Have you tried using a restraint file for the compound in Coot so
> the bonds are properly defined? Note sure if Coot uses them, but perhaps
> also remove all the CONECT records.
>
> Cheers,
> Robbie
>
> > -Original Message-
> > From: CCP4 bulletin board  On Behalf Of Fred
> > Vellieux
> > Sent: Thursday, April 1, 2021 15:02
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: [ccp4bb] coot & other graphics programs draw too many bonds
> >
> > Hello there,
> >
> > After running autodock vina on certain small molecules, the graphics
> > software I am using (e.g. Pymol, Coot) draws far too many bonds on the
> > docked small molecule. See enclosed screen capture.
> >
> > Is there any way to prevent this from happening? This isn't very
> satisfactory
> > of you wish to produce figures for a presentation or for publication.
> >
> > Ta,
> >
> > Fred.
> >
> > --
> > MedChem, 1st F. Medicine, Charles University BIOCEV, Vestec, Czech
> > Republic
> >
> >
> > ###
> > #
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> >
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> 
>
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Re: [ccp4bb] Rigaku CrystalTrak Web not working

[Johannes Cramer]

Hi Pavel,

what I meant is, that the crystal hotel usually has a computer attached to
it and it has the software on it. This software is not a browser/flash
based program. So if you can physically go to the location where your
crystals are stored, you can use the local computer that is hosting the
webserver and look at it there. At least that is the way it is setup in our
facility.

Cheers,
Johannes

Am Fr., 19. Feb. 2021 um 16:55 Uhr schrieb Pavel Mader <
mader.pa...@seznam.cz>:

> Hi Johannes,
>
> just making sure that there is no misunderstanding. I am currently working
> in Dr. Frank Sicheri lab at Mount Sinai Hospital in Toronto, ON, Canada. Is
> this the local installation you are talking about? I am just using my Czech
> email account, since I have the CCP4BB already set up on this account...
>
> Thanks,
>
> Pavel
>
> -- Původní e-mail --
> Od: Johannes Cramer 
> Komu: Pavel Mader 
> Datum: 19. 2. 2021 7:04:48
> Předmět: Re: [ccp4bb] Rigaku CrystalTrak Web not working
>
>   Hey Pavel,
>
> afaik our local installation of the software still works. So if going
> there physically is an option for you, you can try that.
>
> Cheers,
> Johannes
>
> Am Do., 18. Feb. 2021 um 18:21 Uhr schrieb Pavel Mader <
> mader.pa...@seznam.cz>:
>
> Hello everyone,
>
> is there anyone else, who is using Rigaku CrystalTrak Web system (in our
> case version 2.3.4) for checking images of crystallization experiments?
> Recently (on January 14, 2021) the Adobe has stopped supporting the Flash
> support needed for the CrystalTrak web version from being fully functional.
>
> Is there anyone else, who has been facing this problem? Is there any good
> solution?
>
> Thanks,
>
> Pavel Mader
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
>



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Re: [ccp4bb] Rigaku CrystalTrak Web not working

[Johannes Cramer]

  Hey Pavel,

afaik our local installation of the software still works. So if going there
physically is an option for you, you can try that.

Cheers,
Johannes

Am Do., 18. Feb. 2021 um 18:21 Uhr schrieb Pavel Mader <
mader.pa...@seznam.cz>:

> Hello everyone,
>
> is there anyone else, who is using Rigaku CrystalTrak Web system (in our
> case version 2.3.4) for checking images of crystallization experiments?
> Recently (on January 14, 2021) the Adobe has stopped supporting the Flash
> support needed for the CrystalTrak web version from being fully functional.
>
> Is there anyone else, who has been facing this problem? Is there any good
> solution?
>
> Thanks,
>
> Pavel Mader
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



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Re: [ccp4bb] wsl2 Ubuntu 20.04

[Johannes Cramer]

Dear Tim, Victor and Peter,

Thank you for your quick reply! I found some of the posts you mentioned,
but wasn't sure if it was related and how to change the parameters.

For those googling after me:
close your wsl distro
in windows: make a file with a texteditor that is able to do a utf8
encoding (e.g. notepad++) %userprofile%/.wslconfig (e.g.
C:\Users\yourname\.wslconfig) and add the following lines:


[wsl2]
kernelCommandLine = vsyscall=emulate


in powershell execute

wsl --shutdown


then restart your wsl-distro and it should state something like this when
typing

cat /proc/cmdline
initrd=\initrd.img panic=-1 pty.legacy_count=0 nr_cpus=16 vsyscall=emulate

If your distro does not start it is probably due to wrong formatting of the
.wslconfig file.

This solved both my arp warp and my shelx problem.

Cheers,
Johannes

Am Mo., 7. Dez. 2020 um 15:02 Uhr schrieb Peter Keller <
pkel...@globalphasing.com>:

> Dear Johannes,
>
> On 07/12/2020 13:21, Tim Gruene wrote:
> > Dear Johannes,
> >
> > w.r.t. shelx-binaries:
> >
> > you can check with
> > #> cat /proc/cmdline
> > whether the linux-kernel option include 'vsyscall=emulate'.
> >
> > Quite some time ago, the linux kernel made vsyscall obsolete. The
> > SHELX-binaries are probably compiled with an old compiler on an
> > old linux system, and require this kernel option to run.
>
> There has been some correspondence about this on the CCP4 list in
> October last year, in the context of static executables not working on
> Debian 10. The thread starts here:
> <https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=CCP4BB;e91ed61d.1910>,
> and my own substantive reply is here:
> <
> https://www.jiscmail.ac.uk/cgi-bin/wa-jisc.exe?A2=ind1910&L=CCP4BB&D=0&P=44830>.
>
> Tim is right. Traditionally, compiling static executables on an old
> system is a technique used to try to ensure compatibility with newer
> distributions, on the basis that building on a new system is more likely
> to break with older systems than the other way around.
>
> However, when kernel options like this are changed so as to break
> backwards compatibility, then building static executables on an old
> system ensures INcompatibility with newer systems.
>
> > Otherwise they trigger a segmentation fault.
> >
> > vsyscall's are considered a small security hole, but unless you run a
> > safety-critical machine, you can probably risk to open this hole in
> > your kernel at the benefit of running the SHELX programs.
>
> That is a decision for you of course. This may not be an option for
> everyone though. The universal solution is for SHELX executables that
> don't require vsyscall to be made available, but we rely on the SHELX
> maintainers for that.
>
> Regards,
>
> Peter.
>
> >
> > This link might be related:
> > https://github.com/microsoft/WSL/issues/4694
> >
> > Cheers,
> > Tim
> >
> >
> > On Mon, 7 Dec 2020 13:50:23 +0100
> > Johannes Cramer  wrote:
> >
> >> Dear board,
> >>
> >> has anyone gotten ccp4 (specifically shelx and arpwarp) installed and
> >> working under wsl2 (windows subsystem for linux)?
> >> arp warp refuses to install with the following error:
> >>
> >> Segmentation fault
> >> *** ERROR ***
> >> This machine cannot run ARP/wARP executables that
> >> are statically linked to glibc.
> >>
> >> shelx does not complain during installation, but when I type shelxc
> >> (or shelxd, shelxe, shelxl, shelxt)  I get immediately to the promt.
> >> No error message or anything.
> >> I am using Ubuntu 20.04 LTS.
> >>
> >> Any help would be appreciated.
> >>
> >> Cheers,
> >> Johannes
> >>
> >> 
> >>
> >> To unsubscribe from the CCP4BB list, click the following link:
> >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
> >>
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> >> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
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> >
> >
>
> 
>
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[ccp4bb] wsl2 Ubuntu 20.04

[Johannes Cramer]

Dear board,

has anyone gotten ccp4 (specifically shelx and arpwarp) installed and
working under wsl2 (windows subsystem for linux)?
arp warp refuses to install with the following error:

Segmentation fault
*** ERROR ***
This machine cannot run ARP/wARP executables that
are statically linked to glibc.

shelx does not complain during installation, but when I type shelxc (or
shelxd, shelxe, shelxl, shelxt)  I get immediately to the promt. No error
message or anything.
I am using Ubuntu 20.04 LTS.

Any help would be appreciated.

Cheers,
Johannes



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Re: [ccp4bb] cannot access ccp4 download webpage

[Johannes Cramer]

Dear all,

seems like one just needs to complain about it... It works again ;)

Thanks to all who replied!

Cheers,
Johannes

Am Do., 3. Dez. 2020 um 15:54 Uhr schrieb Jon Cooper <
jon.b.coo...@protonmail.com>:

> Works for me. Cheers, Jon.C.
>
>
> Sent from ProtonMail mobile
>
>
>
>  Original Message ----
> On 3 Dec 2020, 14:47, Johannes Cramer < johannes.cra...@gmail.com> wrote:
>
>
> Dear all,
>
> I cannot access the ccp4 downloads webpage from my institute's pc or
> mobile.
> Is it just me? Is it a known problem? I get a 502 Proxy Error.
>
> http://www.ccp4.ac.uk/download/
>
> Cheers,
> Johannes
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>
>



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[ccp4bb] cannot access ccp4 download webpage

[Johannes Cramer]

Dear all,

I cannot access the ccp4 downloads webpage from my institute's pc or
mobile.
Is it just me? Is it a known problem? I get a 502 Proxy Error.

http://www.ccp4.ac.uk/download/

Cheers,
Johannes



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[ccp4bb] ftp://strucbio.biologie.uni-konstanz.de/pub down?

[Johannes Cramer]

Dear collegues,

I am trying to install xdsgui, however, I cannot access any files on the
ftp server ftp://strucbio.biologie.uni-konstanz.de/pub.
https://www.isitdownrightnow.com/ suggests, that it is not just me, but the
server is really down.
Does anyone have information about whether or when the server is back up
and running?
Alternatively/additionally, could anyone provide the required linux
binaries?

I wish you a nice christmas and a happy new year,
Johannes



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[ccp4bb] unable to run Jligand

[Johannes Cramer]

Dear ccp4bb,

I am trying to start JLigand from a ccp4 installation on a Windows7
VirtualBox host running a kubuntu 18.04 client, but I get the following
error:

Exception in thread "main" java.lang.ExceptionInInitializerError
> at JLigand.main(JLigand.java:35)
> Caused by: java.lang.NullPointerException
> at java.base/java.io.Reader.(Reader.java:82)
> at
> java.base/java.io.InputStreamReader.(InputStreamReader.java:72)
> at CharArray.append(CifFile.java:614)
> at CharArray.(CifFile.java:610)
> at Env.(T.java:312)
> ... 1 more


java --version outputs:

openjdk 10.0.2 2018-07-17
> OpenJDK Runtime Environment (build 10.0.2+13-Ubuntu-1ubuntu0.18.04.4)
> OpenJDK 64-Bit Server VM (build 10.0.2+13-Ubuntu-1ubuntu0.18.04.4, mixed
> mode)


The same happens, when I manually start the .jar with Java.
java -jar ${CBIN}/JLigand.jar
Has anyone experienced anything like this and is able to share a workaround?


Cheers,
Johannes



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[ccp4bb] definition of "apo" and alternatives?

[Johannes Cramer]

Dear collegues,

a while ago, there was a discussion in the board on the term apo-structure
as a way to descibe a native, free, or unbound protein (no ligands). I
think the conclusion was that an apo-form is a halo enzyme lacking a
cofactor and should not be used as a substitute for "unbound".
We were recently asked by a reviewer to change "unbound" to "apo" in a
text. We are weighing our options at the moment. Just comply and change it
or "teach" the reviewer something...
Can anyone share experiences with similar situations? Can anyone point out
a publication on the term?

Cheers,
Johannes

Re: [ccp4bb] cavities in protein structures

[Johannes Cramer]

Hi Claudia,

another program that I used with success is Hollow (
https://www.ncbi.nlm.nih.gov/pubmed/19014592).
It is really easy to use. You can get is here http://hollow.sourceforge.net/
It finds pockets in a defined area, fills them with water molecules and
generates a pdb with those waters. You can then import it into pymol and
represent it however you think is fitting.

Cheers,
Johannes

2018-01-30 14:20 GMT+01:00 Vipul Panchal :

> Hi Claudia,
> For the identification of cavities and residues linning them, metapocket
> is one of the preferred choice as it uses prediction from various program.
> Output of the server is pdb file.
>
> I found caver program represent cavities in a best manner. There is caver
> plugin available for pymol. Output is tunnel like representation with
> different colours. Interestingly, it also provides tunnel length, radius
> and list of residues linning the bottle-neck of each of the cavity. As a
> input for the presentation of cavities, you need to provide list of
> residues lining cavities. Identified by other programs.
>
> All the best!
>
>
> On 30-Jan-2018 6:28 PM, "Boaz Shaanan"  wrote:
>
> Hi Claudia,
>
> Another possibility is CastP: http://sts.bioe.uic.edu/castp/index.html
>
> They also have a Pymol plugin. I have not used this plugin since I'm
> displaying the CastP o/p files in UCSF-chimera which handles them nicely.
>
>
> Cheers,
>
>
> Boaz
>
>
>
>
>
>
>
>
>
>
>
>
> *Boaz Shaanan, Ph.D. Dept. of Life
> Sciences  Ben-Gurion University of the
> Negev  Beer-Sheva
> 84105
> Israel
> E-mail:
> bshaa...@bgu.ac.il  Phone: 972-8-647-2220  Skype:
> boaz.shaanan  Fax:   972-8-647-2992 or 972-8-646-1710*
>
>
>
>
>
>
>
> --
> *From:* CCP4 bulletin board  on behalf of Claudia
> Binda 
> *Sent:* Tuesday, January 30, 2018 1:51 PM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] cavities in protein structures
>
> Hi everyone,
>
> I need suggestions to calculate and represent cavities of protein
> structures. For years I have been using Voidoo that produces maps in ezd
> format which could be converted in map format (ccp4) using the online
> server http://xray.bmc.uu.se/cgi-bin/gerard/mapman_server.pl. However,
> this does not work anymore. Is there another way to do it? What is the best
> tool to calculate cavities and draw them by Pymol or ccp4mg?
>
> Thank you
> Claudia
>
>
>
>
>
>
>
> --
> Claudia Binda
> University of Pavia
> Dept. Biology and Biotechnology
> via Ferrata 1, 27100 Pavia - Italy
> Phone: +39-0382-985535 <+39%200382%20985535>
> Fax: +39-0382-528496 <+39%200382%20528496>
> E-mail: claudia.bi...@unipv.it
> Web: http://www.unipv.it/biocr 
>
>

Re: [ccp4bb] proxy settings for ccp4 package manager

[Johannes Cramer]

Thanks for this reply
I exported http_proxy... It is not like the ccp4um does not have a
connection.
It can determine that there are updates and downloads and installs small
updates (up to a handfull of MB) without a problem.
Larger updates start downloading at ridiculously low speeds, then suddenly
finish and generate a MD5 checksum error.
Is our proxy just weird?!?

Cheers,
Johannes

2018-01-11 0:19 GMT+01:00 Takanori Nakane :

> Hi Johannes,
>
> On RHEL 6.7, setting "http_proxy" was sufficient.
>
> Best regards,
>
> Takanori Nakane
>
> On 2018/01/09 13:18, Johannes Cramer wrote:
>
>> Dear CCP4bb,
>>
>> does anyone know how I can make the ccp4 package manager use a proxy for
>> downloading in Linux 64bit versions?
>> This would make installing and updating a whole lot easier for me...
>>
>> I exported http_proxy, https_proxy, ftp_proxy (and all their capital
>> letter
>> equivalents) and setup the system proxy in kde (although I think this only
>> matters for kde programs). I am using the 10.17 version of kubuntu, but
>> would also be interested in a solution that works for Mac.
>>
>> Cheers,
>> Johannes
>>
>>
>

[ccp4bb] proxy settings for ccp4 package manager

[Johannes Cramer]

Dear CCP4bb,

does anyone know how I can make the ccp4 package manager use a proxy for
downloading in Linux 64bit versions?
This would make installing and updating a whole lot easier for me...

I exported http_proxy, https_proxy, ftp_proxy (and all their capital letter
equivalents) and setup the system proxy in kde (although I think this only
matters for kde programs). I am using the 10.17 version of kubuntu, but
would also be interested in a solution that works for Mac.

Cheers,
Johannes

Re: [ccp4bb] PyMol question

[Johannes Cramer]

you can try the 'hide cell' command. This should hide the unit cell box,
however, I don't know why it is not displayed in your 'unrendered' gui...

Cheers,
Johannes

2017-12-11 23:47 GMT+01:00 Cygler, Miroslaw :

> Hi,
> When I loaded the ed map into PyMol v1.8.4.1 and used iso mesh around part
> of the protein all is well until I use the RAY command. In the ray traced
> image I see the unit cell box that does not show on the image in the normal
> view. How can I remove the box from the ray traced image?
> Thanks for your help,
>
> Mirek
>
>
>
>

Re: [ccp4bb] 3D stereo and pymol

[Johannes Cramer]

Hi Christine,

as far as I know, it does not work at all with Geforce cards. The Nvidia
drivers do not support windowed quad buffered GL, which you need for
coot/pymol. It does not matter whether you use Windows or Linux.
But this is based on my personal experience from around Oct. 2016. Maybe
something changed quietly since then. Again, as far as I know, you need a
Quadro card.

Cheers,
Johannes

2017-11-06 21:24 GMT+01:00 Christine Gee :

> Hi,
>
> I have looked in the archive for posts about this, but there hasn't been
> one for about a year. Can anyone comment on whether they have managed to
> get a linux flavor and GeForce cards to work with pymol and/or coot 3D
> stereo? Geforce cards supposedly support openGL, but posts from October
> last year on the BB suggests that it only works in windows unless you have
> a monitor with a built in emitter. I would appreciate any feedback.
>
> Regards
> Christine
>
>

[ccp4bb] ccp4i2 crashes on start

[Johannes Cramer]

Dear CCP4 bb,

I would like to use ccp4i2, but every time I try to start it via command
line, I get the following error message:

Running CCP4i2 browser from: /home/cramejo/programs/ccp4-7.0/share/ccp4i2
> Python 2.7.10 (default, Aug 28 2015, 12:10:46)
> [GCC 4.8.2 20140120 (Red Hat 4.8.2-15)]
> Qt version 4.8.7
>
> 440 367
> Segmentation fault (core dumped)


Has anyone experienced this behavior? How (where) can I get a more detailed
log file? ccp4i (old GUI) works perfectly fine, but the session log that is
accessible via the interface is only valid for the current session.
I am running 64 bit Kubuntu 10.16 on a windows host virtualbox.

Cheers,
Johannes

Re: [ccp4bb] Ligand building in real space

[Johannes Cramer]

Hey Mohamed,

I am not sure, if this is what you want, but you can import different PEG
molecules from coot's "File-> Get monomer". A list of different length PEGs
three letter codes can be found on page 1278 of this paper:

Naschberger et al., (2016) http://doi.org/10.1107/S205979831601723X.

I think you must have ccp4 installed, for this to work, but I am not 100%
sure.

Cheers,
Johannes


2017-04-10 9:44 GMT+02:00 Mohamed Noor :

> Dear all
>
> Is it possible to directly build a ligand in real space (in Coot?) and
> then generate a SMILES string for restraint generation. I have some unknown
> blobs in my density where they look like PEG molecules but these do not
> really fit the density (local CC of 0.7).
>
> I am already using Polder and omit maps that confirm these are not noise.
>
> Thanks.
> Mohamed
>

Re: [ccp4bb] suggestion on protein crystallization optimization from phase separation

[Johannes Cramer]

Dear Joseph,

You have probably already done so, but have you tried in- or decreasing your
protein+DNA concentration?
I had a similar problem with proteins that were concentrated too low. I had
to increase protein and decrease Ammonium sulfate (precipitant in my case)
concentration.

Cheers,
Johannes


2017-04-06 17:16 GMT+02:00 Joseph Ho :

> Dear all:
>
> I would like to seek your suggestion on protein crystallization from
> phase separation.
> We recently observed many small round droplets shown in our
> protein/DNA crystallization. Condition are 0.8M-1.6M LiSO4; 20mM
> MgCl2; pH 5-8;  protein conc. ~15mg/ml). The UV microscope confirms
> those are protein-rich phase separation.
> We have tried to change conc. of LiSO4 and pH. Still we got different
> size and amount of small round droplets. At 20 degree, those droplets
> appear within one day and at 4 degree, it takes two-three days.  We
> also tried additive and silver bullet screen. So far, we have not
> found a condition to have protein crystals. The protein is already
> truncated. Several DNA constructs are on-going.
> At this point, I would like to seek your advice on the method to
> optimize the condition. Based on
>
>
> PS. Any people have luck with protein crystallization by streaking the
> Gelationous protein to new drop as shown in
> http://xray.bmc.uu.se/terese/tutorial3.html . Can you please share
> your experience with us?
>
> Thanks for your help.
>
> Joseph Ho
>

Re: [ccp4bb] ligand with out space group information

[Johannes Cramer]

Hi,

I had the same problem once. Some chemistry programs are not really good at
exporting to pdb. Check the file format definition of pdb files, here:
ftp://ftp.wwpdb.org/pub/pdb/doc/format_descriptions/Format_v33_A4.pdf
Most interesting for you is probably pp. 174.
Also make sure, there is an "END" at the end.
It might help, if you send a link to the ligand file.

Cheers,
Johannes

2017-03-30 19:41 GMT+02:00 Paul Emsley :

> On 30/03/17 14:59, chemocev marker wrote:
>
>> Hi
>>
>
> Hi.
>
> I have model of ligand molecule and it does not open in coot. Its not a
>> crystal structure. I can view it in the pymol or chimera but not in the
>> coot. It gives error that it does not have any space group information. Is
>> there is a way to open it in coot.
>>
>>
> If there is not a CRYST1 card in your pdb file, then Coot will warn you
> that your molecule does not have symmetry.  It is merely a warning, not an
> error.
>
> If coot can't read the pdb file it's likely (it seems to me) that it's not
> actually a (specifications-compliant) pdb file.  Coot should give you an
> error about any line that it particularly doesn't like.
>
>
> Paul.
>

Re: [ccp4bb] modifying the ligand

[Johannes Cramer]

Hi Adriana,

when I am at home, I do the following. Use zinc structure search (
http://zinc.docking.org/search/structure) to generate a smiles code (or any
other website that can do this), then take that code to phenix elbow and
generate the ligand including cif.
Other softwares that can do this off the top of my head are chemoffice and
schrödinger.

I hope this helps,
Cheers,
Johannes

2017-03-29 14:36 GMT+02:00 Adriana Sene :

> Hi
> I am new here, I am looking for some way to modify one of my ligand. I
> have some cl atoms in the ligand which I wanted to remove and add other
> functional groups. If some one can tell me, how it can be done or which
> tools either free or paid can be used to do that.
>
> bet
>
> Adiana
>

Re: [ccp4bb] intermolecular dissulphides

[Johannes Cramer]

Dear Eleanor,

sorry for the late reply. I found a similar case (id: 2OEF, Cys 92). I
mutated the Cys to Ser, but it did not change anything (xtal conditions and
quality remained the same). In solution the protein is a monomer.
However, adding 1 mM DTT resulted in a significant increase in crystal
quality (larger 3D crystals with better resolution). I don't know why,
though...

Cheers,
Johannes

2017-02-01 20:45 GMT+01:00 Tom Peat :

> Hello Eleanor,
>
>
> We found some intermolecular vicinal disulfides recently that we think are
> 'real'. This class of proteins forms tetramers and in one version we find
> these intermolecular disulfides across molecules. We did some tests and
> found that oxidation or reduction has an effect on the stability of the
> protein. ​We also saw this was consistent across multiple space groups. If
> you would like to have a look, they were just released: 5HY0, 5HY2, 5HY4.
>
> As a comparison to another protein in this fold class that doesn't have
> the disulfide is 5HWE.
>
>
> cheers, tom
>
>
> Tom Peat
> Proteins Group
> Biomedical Program, CSIRO
> 343 Royal Parade
> Parkville, VIC, 3052
> +613 9662 7304 <+61%203%209662%207304>
> +614 57 539 419
> tom.p...@csiro.au
> --
> *From:* CCP4 bulletin board  on behalf of Eleanor
> Dodson 
> *Sent:* Thursday, February 2, 2017 2:17 AM
> *To:* CCP4BB@JISCMAIL.AC.UK
> *Subject:* [ccp4bb] intermolecular dissulphides
>
> Does anyone know of examples of these?
> I have found one - 2WQW with these SSBOND records
> 2WQW
> SSBOND   1 CYS A  206CYS A  227  1555   6556
> 2.07
> SSBOND   2 CYS B  206CYS B  227  1555   5556
> 2.15
>
> We seem to have one but it would have to form after crystalisation?
>
> Eleanor
>
>
>

Re: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card under Windows 10

[Johannes Cramer]

Hi Xiao,

did you try manually changing the Hz in the nvidia system control panel?
It is somewhere under Resolution-> adapt (or something like that, sorry, I
don't have an english version). There you can change the frequency.
If it doesn't work and you only see a black screen, the system switches
back to the previous setting. So what I am saying is: Maybe the system does
not recognize its 144hz ability. For me, that war the case about a year ago.

Cheers,
Johannes

2017-01-31 5:50 GMT+01:00 Xiao Lei :

> Taka,
>
> I really appreciate this information! I do have Displayport cable and can
> connect the card and Asus VG248QE both via the DP cable, somehow on the
> Nvidia control panel in Windows 10, I do not have an option of choosing
> "120HZ" or "144Hz", I only have option choosing "60Hz" or below, which
> sounds weird to me. Windows 10 should make things easier not harder. If
> CentOS 6 works then Windows 10 should work, I guess I have to go back to
> Windows 7 if needed, but as I already ordered the DP to DVI active cable,
> I'll test this cable first and update CCP4bb later.
>
> On Mon, Jan 30, 2017 at 7:50 PM,  wrote:
>
>> Xiao,
>>
>>
>>
>> If you connect the board and monitor by DisplayPort cable directly, it
>> should work.
>>
>> I confirmed with Quadro M4000 and BenQ XL2420Z on CentOS 6, though not
>> tested on Windows.
>>
>>
>>
>> Taka
>>
>>
>>
>> *From:* Xiao Lei [mailto:xiaolei...@gmail.com]
>> *Sent:* Tuesday, January 31, 2017 10:08 AM
>> *Cc:* CCP4BB@JISCMAIL.AC.UK
>> *Subject:* Re: [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card
>> under Windows 10
>>
>>
>>
>> I changed my mind, I should order the usb- powered DP to DVI dual link...
>>
>>
>>
>> On Mon, Jan 30, 2017 at 5:02 PM, Christine Gee  wrote:
>>
>> Hi Xiao,
>>
>>
>>
>> I can confirm you need to buy an active adapter if you want to convert
>> the display port on the graphics card to DVI. The one that they supply with
>> the graphics card is passive and won't work. I was in the same boat about a
>> year ago. I bought a USB powered active adapter which allowed 120htz. My
>> monitor only had DVI input so I didn't try a direct display port
>> connection. I can't comment on why that didn't work.
>>
>>
>>
>> Cheers
>>
>> Christine
>>
>>
>>
>> Sent from my iPhone
>>
>>
>> On Jan 30, 2017, at 4:25 PM, Takaaki Fukami 
>> wrote:
>>
>> Dear Xiao,
>>
>>
>>
>> You need an active converter from DP to DVI.  You can't get 120Hz if you
>> use a passive converter, even with a DVI dual link cable.  If you used an
>> adapter come with the board, it's probably passive.
>>
>>
>>
>> Taka
>>
>>
>>
>>
>>
>> *From:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK
>> ] *On Behalf Of *Xiao Lei
>> *Sent:* Tuesday, January 31, 2017 9:10 AM
>> *To:* CCP4BB@JISCMAIL.AC.UK
>> *Subject:* [ccp4bb] Coot and Pymol 3D in Quadro M4000 Graphics Card
>> under Windows 10
>>
>>
>>
>> Dear All,
>>
>>
>>
>> I tried to make Coot and Pymol 3D working for a HP Workstation with
>> Quadro M4000 graphics card, the card has four displayport. I also has a
>> Asus 24 inch 3D monitor. I tried to connect  the graphics card with the
>> monitor through displayport to displayport connection and displayport to
>> DVI-D dual link connection but failed to set the monitor run on 120Hz. It
>> seems I have to follow the old way of using  DVI-D dual link connection for
>> both graphic card and monitor, but the problem is that the graphics card
>> does not have a DVI-D dual link socket, it only have displayport.
>>
>>
>>
>> I appreciate any suggestions.
>>
>>
>>
>>
>>
>>
>>
>
>

Re: [ccp4bb] ccp4 package manager

[Johannes Cramer]

Dear Edwin,

I had a similar problem and it had to do with our institutions proxy
settings. The proxy settings in ccp4i did not affect the updater settings.
I could not resolve it and always had to manually download the full update
package.

Cheers,
Johannes


2016-11-29 21:02 GMT+01:00 Edwin Pozharski :

> CCP4 package manager doesn't work for me when I try a fresh ccp4
> installation.  It goes through all the question dialogs, but then fails to
> download the actual installation package, complaining of broken network
> connection.  Multiple tries don't help.  Obviously, I can get around this
> by downloading the full 750Mb suite directly, which works fine. This might
> be something on my end, of course.  However, I've seen this twice now on
> quite different network connections.  In fact, I haven't installed CCP4
> using the package manager since what could have been couple of years.
>
> Cheers,
>
> Ed.
> ---
> Hurry up, before we all come to our senses!
> Julien, King of Lemurs
>

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

[Johannes Cramer]

Hi Matt,

I guess you are talking about hardware. For a year or so, this should have
become quite cheap. A recent Nvidia Geforce card, a 120 Hz 3D Monitor and a
3D vision kit should do the trick. However, personally I only have
experiences with the "professional" NVidia quadro grafics card series.
Can anyone in the CCP4BB confirm that Geforce cards work with coot, as
suggested on the pymolwiki site:


>- GeForce Cards from series 400 onward have gained OpenGl support in
>recent Nvidia driver iterations (314+). This allows Pymol to be viewed in
>3D using the quad buffered stereo setting with a GeForce card, 120Hz screen
>and 3D Vision kit.
>
>
Cheers,
Johannes

2016-10-27 20:11 GMT+02:00 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
>
>
>