Re: [ccp4bb] Coot crashes on starting baton mode.

[Ray Changrui Lu]

Dave:

This may or may not help. I have not seen this particular error before, but
I I have discovered that sometimes coot can crash in newer versions of OSX.
I actually keep two "flavors" of coot in my system: one from the CCP4 suite
and the other from the Scott lab website. Somehow those two versions can
coexist just fine and I can run the other version when one of them crashes.

HTH

Ray

On Tue, Dec 20, 2016 at 10:10 PM, David Briggs 
wrote:

> Hi all,
>
> I'm running Coot 0.8.7 (as distributed with the CCP4 package) on OSX
> 10.11.6.
>
> As soon as I click to enter CA-baton mode, coot crashes (terminal output
> pasted below).
>
> All I have done prior to this is load a pdb and an mtz, build skeletons
> and pick a start point.
>
> Has anyone seen this before, and if so, how did they overcome the problem?
>
> Thanks in advance,
>
> Dave
>
> Symmetry available for this molecule
>
> INFO:: returning baton atom molecule 12
>
> -- baton_next_ca_options
>
>4e-12  xyz = (-16.27,-9.644, 24.54)
>
>4e-13  xyz = (-21.76,-12.59,  26.3)
>
>4e-13  xyz = (-21.32,-13.01, 25.91)
>
>4e-13  xyz = (-21.21,-9.022, 20.87)
>
>4e-13  xyz = (-21.41,-8.895, 20.97)
>
>4e-13  xyz = (-20.59,-13.48, 23.92)
>
>4e-13  xyz = (-20.59,-13.51, 24.55)
>
>4e-13  xyz = (-20.68,-13.39, 25.33)
>
>4e-13  xyz = ( -20.6,-9.633, 20.66)
>
>4e-13  xyz = (-20.56,-6.015, 23.94)
>
>4e-13  xyz = (-19.93,-13.38, 23.31)
>
>4e-13  xyz = ( -16.4,-8.755,  24.6)
>
>4e-13  xyz = (-16.27,-9.623, 24.57)
>
>4e-13  xyz = (-20.62,-11.67, 21.18)
>
>4e-13  xyz = (-21.17,-12.03, 21.58)
>
>4e-14  xyz = (-20.65, -6.04, 23.86)
>
>4e-14  xyz = (-20.78,-6.085, 23.73)
>
>4e-14  xyz = ( -20.6,-10.28, 20.69)
>
>4e-14  xyz = (-20.67,-11.09, 20.91)
>
>1e-15  xyz = (-20.64,-12.43, 21.78)
>
>9e-16  xyz = (-19.34,-13.12, 22.81)
>
>4e-16  xyz = (-19.93,-12.74, 22.08)
>
>0  xyz = (-18.76,-10.22, 27.96)
>
>0  xyz = (-18.75,-9.646, 27.98)
>
> --
>
> Creating a molecule for Baton Atom Guide Points
>
> !! Warning:: No symmetry available for this molecule
>
> No Symmetry for this model
>
> INFO:: Creating directory coot-backup
>
> INFO:: backup file coot-backup/Baton_Atom_Guide_
> Points_Tue_Dec_20_13:53:53_2016_modification_0.pdb.gz
>
> /Applications/ccp4-7.0/bin/coot: line 284: 20534 Segmentation fault: 11  
> $coot_bin
> "$@"
>
> coot-exe: "/Applications/ccp4-7.0/libexec/coot-bin"
>
> coot-version:
>
> /Applications/ccp4-7.0/libexec/coot-bin
>
> platform:
>
> /usr/bin/uname
>
> core: #f
> --
>
>
> [image: --]
>
> David Briggs PhD
> [image: https://]about.me/david_briggs
>
> 
>

[ccp4bb] 3D Viewing on Budget

[Ray Changrui Lu]

Dear CCP4 Community:

Happy Holidays!

Sorry for bringing up this old topic again. However after some recent
struggle with rather poor crystals and my deteriorating eye sights, I have
decided I need a couple 3D capable (cheap) workstations in lab.

After reviewing previous posts and the two web-pages suggested by Folmer,
I understand that active stereo is still the preferred method, just like
many years ago with CRT, emitters and expensive quadro cards. However,
since I cannot just buy and tryout hardware, I have the following questions:

1. Will any high refresh rate LCD work? The ones suggested in the guide and
by Jeroen are either unavailable or expensive.

2. High end 3-pin Quadro card are a bit out of reach at the moment, can I
just use consumer grade Geforce with NV3D vision 2? The most expensive ones
I have are a few GTX 460, 950, 750Ti (I even have an ancient FX1400 but the
guide says it doesn't work). Of course I can buy better GTX cards if needed
as long as I don't have to buy quadros--they are really expensive and hard
to find here.

3. Is there a cheap option to enable 3D under linux or OSX? I do prefer OSX
but I can live with any OS as long as I get 3D to work with coot.

Thank you so much for your time.

Changrui Lu
Nucleic Acid and Structural Biology Group
College of Chemistry, Chemical Engineering and Bioengineering
Donghua University
2999 North Ren Min Road, Shanghai 201620, China
Tel: 86-21-67792740  Fax: 86-21-67792740
E-mail: c...@dhu.edu.cn

[ccp4bb] Rational design of ligands

[Ray Changrui Lu]

Hello all,

Does anybody happen to know any programs capable of designing small
inhibitors from a known protein-ligand crystal structure? Many thanks.

best,
Ray Changrui Lu
Cornell University

Re: [ccp4bb] Vista

[Changrui Lu]

Hi all,

Vista has tons of compatibility issues, especially with opengl. As far as I 
know pymol, swisspdbviewer and a number of other opengl based programs do not 
work on vista. (Coot has some compatibility problem with Aeroglass, and pymol 
might have a stable release for vista soon.) More programs are being upgraded 
to support vista but you might find yourself in trouble with legacy programs 
that are no longer supoorted. I would not suggest running crystal graphic 
softwares on vista (or xp) unless you have a good reason. But to choose the 
lesser of 2 evils I would go for xp. If price is an issue then you should go 
for linux, as many of us already suggusted.

cheers,
Ray


  - Original Message - 
  From: deena 
  To: CCP4BB@JISCMAIL.AC.UK 
  Sent: Wednesday, February 20, 2008 3:11 PM
  Subject: [ccp4bb] Vista


  Hi All,
  I am about to buy a laptop and find that the XP is twice the price of Vista. 
Does anyone have positive experience using Vista for crystallographic packages: 
CCP4, Coot, O, X-plor?  or must I still avoid it?


  Thanks,


  Deena


  Deena Abells Oren, PhD
  Manager, Structural Biology Resource Center
  Rockefeller University
  1230 York Avenue
  New York, NY 10065-6399
  phone: 212- 327-7429
  fax: 212-327-7389

[ccp4bb] Dual Head Stereo On FireGL

[Ray Changrui Lu]

Hello all,

I have 2 21inch CRTs connected to a stereo capable firegl card and I am
hoping to enable the active stereo on the extended desktop. Stereo works on
a single screen setup but does not on the extended desktop on 2 monitors. I
have a similar setup on an nvidia quadro card using xinerama that everything
works fine. Does anyone have a working xorg.conf on the ati setup? I am
beginning to suspect that the ati driver does not support dual monitor with
stereo flipping. Any comment is appreciated.

Thanks in advance.

Ray
Cornell University

[ccp4bb] SAM phasing

[changrui lu]

Hello all,

Does anyone know where I can obtain heavy atom-derivatized
S-adenosylmethionine? I am wondering if anyone has experienced or heard of
successful instances where heavy atom-derivatized SAM has been used for
phasing molecules that binds SAM? Thanks a lot!

Ray