Re: [COOT] (transparent) sphere

Hi Bernhard, both sound like good enough approximations to me. How would I do the dotted surface? Can I adjust the radius? -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Thu, 24 Sep 2009, Bernhard Lohkamp wrote: You currently can

Re: [COOT] NCS ghosts and map broken?

What's the 'proper' way to name nucleotides in Coot? (RNA) thanks FR On Sep 24, 2009, at 9:43 AM, Bernhard Lohkamp wrote: My (educated) guess is that Coot doesnt recognise your nucleotides as such and hence doesnt find any atoms to do the lsq superposition with. The different nucleotide name

Re: [COOT] NCS ghosts and map broken?

My (educated) guess is that Coot doesnt recognise your nucleotides as such and hence doesnt find any atoms to do the lsq superposition with. The different nucleotide name 'conventions' strike again B *** Dr. Bernhard Lohkamp Assistant Professor

Re: [COOT] (transparent) sphere

You currently cannot create a sphere as such (certainly not transparent). But you there is some workarounds: 1.) create a generic object and add a dot (although the dot will be a square esp when larger) 2.) put a dummy atom at the required position and display as ball'n'stick model (or for mock t

Re: [COOT] problem updating coot using fink

Dear Eleonore: As you mentioned, everyone who upgraded 32-bit fink on 10.6 runs into this. If you start fresh (either 32-bit or 64-bit), the problem doesn't arise. I hope you don't mind me cc-ing the cootbb, as this problem is a general one. The advice I was given, and with some reluct

[COOT] (transparent) sphere

Hi, is there a way to display a sphere with given radius at a specific position in coot? preferably semi-transparent? Otherwise I'd have to import a map into rasmol and I find that a little cumbersome. Cheers, Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goetti

[COOT] multimodel crash

Coot consistently crashes when I try to show the sequence of the pdb-file where some residues are labeled with insertion codes (column 27 of the ATOM record). I tested it on 64-bit Jaunty and 32-bit Hardy. Perhaps the problem is that there are multiple copies of the same residue number. Obvious w

[COOT] NCS ghosts and map broken?

Hi all It seems that adding ncs ghosts and then ncs maps is broken for my model / coot combo. Coot is at ver 0.6-pre-1 rev 2334. Thanks! This is what phenix.simple_ncs_from_pdb gives me Process input NCS or/and find new NCS NCS groups found

Re: [COOT] graphics window size

Thanks for the advice. I had managed to reduce the size by detaching the tool bar as you suggested. I can try unticking icons to see if this can do the job for me. Thanks Abhinav Stanford Synchrotron Radiation Lightsource Joint Center for Structural Genomics Mail Stop 99 Phone: (650) 926

Re: [COOT] - setting http_proxy

thanks, I don't know where to use the python command. Qiang > Date: Thu, 24 Sep 2009 08:59:38 +0200 > From: bernhard.lohk...@ki.se > Subject: Re: - setting http_proxy > To: COOT@JISCMAIL.AC.UK > > If you have a python enabled version, you should be able to set the > http_proxy in the shell wh

Re: [COOT] graphics window size

I assume you have a gtk2 Coot version. Here the y-size of the window size is dictated by the toolbar on the right. You cannot make the window smaller than the space needed for this (*). To make the toolbar smaller (or to not effect the window size) you can do the following: - undisplay icons via E

Re: [COOT] - setting http_proxy

If you have a python enabled version, you should be able to set the http_proxy in the shell where you start coot (bash, e.g.): http_proxy="http://myproxy:5050"; export http_proxy then use the following python command in Coot: get_ebi_pdb("id_code") not sure if this works for guile/scheme the sa