Re: [ccp4bb] Pymol questions

Hi Eric, On Wed, 4 May 2011, jlliu liu wrote: Hi All, I have two questions for Pymol. the pymol wiki is your friend (http://www.pymolwiki.org/index.php/Main_Page) as is the pymol users mailing list (http://sourceforge.net/mail/?group_id=4546). Follow the link to subscribe. 1. Can you w

Re: [ccp4bb] Pymol questions

1. Yes, just "Save Molecule" (individually) after align 2. > show stick, &HETATM around 4 ( is your pdb name, 4 = 4 angstrom) On Wed, May 4, 2011 at 3:26 PM, jlliu liu wrote: > Hi All, > > I have two questions for Pymol. > > 1. Can you write out the PDB file after structural align

[ccp4bb] Pymol questions

Hi All, I have two questions for Pymol. 1. Can you write out the PDB file after structural alignment? 2. How to only show structure that is several angstrom from the ligand? Thanks a lot in advance! Eric

Re: [ccp4bb] Anomalous substructure solution at data with 37% completeness

I think that two issues are being confused here. When the anomalous signal is very weak, e.g. for sulfur-SAD phasing, the anomalous differences are comparable with the intensity esds. By averaging over many measurements we can reduce these esds and so improve the signal to noise ratio and the ch

Re: [ccp4bb] Zotero style

I made one some time ago (attached). It's not perfect (missing definitions for e.g. books) but works well for article-references. -Bjørn -- Bjørn Panyella Pedersen Macromolecular Structure Group Dept. of Biochemistry and Biophysics University of California, San Francisco On 2011-05-04 05:32,

[ccp4bb] Where is multillog for dmmulti?

Can someone return their full path of the location of multilog (used for browsing dmmulti output)? I can't find it in my ccp4-6.1.13 installed from Mr Scott's distrib. Thanks! F - Francis E. Reyes M.Sc. 215 UCB University of Colorado at Boulder

Re: [ccp4bb] Insertion codes

Robbie Joosten wrote: Hi Ed, > Personally I don't care one way or the other, but it may be pointed out > that if D25 is actually number 37 in a homologous protein, it should be > D37. Just as acknowledgement of the (somewhat purist) point of view > that the residue number should denote its l

[ccp4bb] Ion Channel Structure at UCSF- Postdoctoral Positions

UNIVERSITY OF CALIFORNIA SAN FRANCISCO (UCSF) POSTDOCTORAL POSITIONS, MINOR LAB Crystallographic studies of ion channels involved in pain and depression Postdoctoral positions in Ion Channel Structural Biology are available immediately for highly motivated individuals with a strong interest in c

[ccp4bb] PhD position at the Genome Damage and Stability Centre, University of Sussex

UNIVERSITY OF SUSSEX An MRC-funded PhD position is available immediately in the Genome Damage and Stability Centre, School of Life Sciences, University of Sussex. The student will be supervised jointly by the laboratories of Professor Keith Caldecott and Dr Antony Oliver, and will experimental

Re: [ccp4bb] Anomalous substructure solution at data with 37% completeness

[switch not too serious mode on]: well, it is lysozyme, which, according to diffraction properties, should perhaps be classified as a salt (LyCl7), not a protein... :-) Mark J van Raaij Laboratorio M-4 Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3, Campu

[ccp4bb] Anomalous substructure solution at data with 37% completeness

Dear all, We have solved the sturcture of hen egg white lysozyme with a barium ion at 2.7 fold data redundancy. Data collected at in-house copper K-alpha source to 2.22 A resolution with 1 degree oscillation step per frame. The substructure was correctly identified with just 8

[ccp4bb] Joint PhD position at the University of Sussex

UNIVERSITY OF SUSSEX An MRC-funded PhD position is available immediately in the Genome Damage and Stability Centre, School of Life Sciences, University of Sussex. The student will be supervised jointly by the laboratories of Professor Keith Caldecott and Dr Antony Oliver, and will experimental

Re: [ccp4bb] Zotero style

Hi Darren, Thank you for the link. It may be a usefull tool. Unfortunately, the site was buggy in IE9. It worked much better in FF4, but it stopped when I tried to generate the final style file. It turns out that you can also import an EndNote style into Zotero. I tried this for the .ens fil

Re: [ccp4bb] Zotero style

Hi Ian, Indeed the word 2007 template is very good (I never got the 2003 version working well), but it becomes a problem when your co-authors are Mac users with old Word versions. Cheers, Robbie > Date: Wed, 4 May 2011 12:18:59 +0100 > Subject: Re: [ccp4bb] Zotero style > From: ianj...@gma

Re: [ccp4bb] Coot: Residue number conflicts during model building

On 04/05/11 12:54, Jacob Wong wrote: Thanks Tim for the timely tips. I haven't tried Arp/wARP but will follow your recommendation right away. I haven't installed Resolve yet but will look into it and Buccaneer as well I would recommend buccaneer too. - I was having fun modeling some of the a

Re: [ccp4bb] Python problem

On 04/05/11 14:11, Phil Evans wrote: > Is that dangerous? > > If I move it I then get > > ImportError: Bad magic number in > /System/Library/Frameworks/Python.framework/Versions/2.5/lib/python2.5/site.pyc > > after moving that I then get > > ImportError: Bad magic number in > /System/Library/

Re: [ccp4bb] Coot: Residue number conflicts during model building

Thanks Tim for the timely tips. I haven't tried Arp/wARP but will follow your recommendation right away. I haven't installed Resolve yet but will look into it and Buccaneer as well - I was having fun modeling some of the apparent fragments into the density but with a protein so big, I ran exhausted

Re: [ccp4bb] Zotero style

You can use this http://www.somwhere.org/csl/ to build your style. Darren On 4 May 2011 09:05, Robbie Joosten wrote: > Hi Everyone, > > Does anyone have a Zotery style template for Acta Cryst and the like, (s)he > wishes to share? I cannot find it in the repository, but perhaps someone has

Re: [ccp4bb] Zotero style

Hi Robbie My understanding is that the templates for Acta Cryst. are here: http://journals.iucr.org/services/wordstyle.html or here: http://journals.iucr.org/d/services/latexstyle.html At least that's what I've always used. Cheers -- Ian On Wed, May 4, 2011 at 8:05 AM, Robbie Joosten wrote

Re: [ccp4bb] Coot: Residue number conflicts during model building

Dear Jacob Wong, have you tried arp warp for model building? It should do a reasonably good job at 2.3A resolution. Alternatively buccaneer or resolve might also help. For the overlapping: Does it help to give the subsequent fragment a different chain ID? Tim On Wed, May 04, 2011 at 02:48:11AM

[ccp4bb] Zotero style

Hi Everyone, Does anyone have a Zotery style template for Acta Cryst and the like, (s)he wishes to share? I cannot find it in the repository, but perhaps someone has made one for private use. Cheers, Robbie Joosten Biochemistry Netherlands Cancer Institute

Re: [ccp4bb] Insertion codes

Hi Ed, > Personally I don't care one way or the other, but it may be pointed out > that if D25 is actually number 37 in a homologous protein, it should be > D37. Just as acknowledgement of the (somewhat purist) point of view > that the residue number should denote its linear distance from the > N