Re: [ccp4bb] Invisible atoms in ligands

2014-06-16 Thread James Holton
Thank you Pavel for the clarification! What I was really trying to point out is that a missing atom, occ=0.00 and occ=0.01 are not as similar as one might naiively think. Also, if you put a ligand into a pocket and the occupancy refines to 0, that does not necessarily mean the ligand is

Re: [ccp4bb] Invisible atoms in ligands

2014-06-16 Thread Hargreaves, David
@astrazeneca.commailto:name.surn...@astrazeneca.com Please consider the environment before printing this e-mail From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Frank von Delft Sent: 13 June 2014 10:45 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] Invisible atoms in ligands Hi

Re: [ccp4bb] Invisible atoms in ligands

2014-06-16 Thread Ian Tickle
Dear James You seem to be discounting the possibility of a true vacuum inside a structure, which is obviously not the same thing as 'something' (bulk solvent or whatever). I accept that this is unlikely in the case of ligand binding sites exposed to solvent, or indeed any site on the outer

Re: [ccp4bb] Invisible atoms in ligands

2014-06-16 Thread Daniel Picot
Dear Ian, This has been discussed in a review and related articles by Brian Matthews and Liljun Liu: Matthews BW, Liu L. A review about nothing: are apolar cavities in proteins really empty? Protein Sci. 2009 Mar;18(3):494-502. doi: 10.1002/pro.61. Review. PubMed PMID: 19241368; PubMed

Re: [ccp4bb] Invisible atoms in ligands

2014-06-16 Thread Ian Tickle
Dear Daniel Thanks for the info. I knew that Brian Matthews' group had done some work in this area. Cheers -- Ian On 16 June 2014 11:16, Daniel Picot daniel.pi...@ibpc.fr wrote: Dear Ian, This has been discussed in a review and related articles by Brian Matthews and Liljun Liu:

Re: [ccp4bb] Invisible atoms in ligands

2014-06-15 Thread James Holton
The principle difference between occ=0 and omitting the atom entirely is that occ=0 atoms exclude bulk solvent. Or at least they do for typical operation of contemporary refinement programs. So, by defining occ=0 you are forcing all map voxels within ~0.6A or so of your invisible atom to

Re: [ccp4bb] Invisible atoms in ligands

2014-06-15 Thread Pavel Afonine
Hi James, a remark: different programs may treat occ=0 differently. In phenix.refine (phenix.maps, etc) atoms with zero occupancy will be ignored for bulk-solvent mask calculation, unless you ask to do otherwise. For example, this means that if you want to calculate a ligand OMIT map both options

[ccp4bb] Invisible atoms in ligands

2014-06-13 Thread Frank von Delft
Hi all - talking about ligands, a quick question on that old conundrum, of what to do about invisible atoms -- build them with occ=0, or omit them? For bits of protein, I know all the arguments; personally I prefer omitting atoms because: * for amino acid sidechains, their presence is

Re: [ccp4bb] Invisible atoms in ligands

2014-06-13 Thread Tim Gruene
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Frank, if you can calculate their position, i.e. it is part of a rigid group, I would leave it. If it is flexible, I would remove it because the reader of my deposited structure may not be a crystallographer and misinterpret the result. If it is

Re: [ccp4bb] Invisible atoms in ligands

2014-06-13 Thread Marco Mazzorana
Hi Frank, I agree with what Tim has just posted. Personally I would not think occupancy=0, since this would mean the atom is not where you placed it (i.e. nowhere near). This could be useful if all your ligand has the same partial occupancy or, if you have multiple poses, the sum of occupancies

Re: [ccp4bb] Invisible atoms in ligands

2014-06-13 Thread Robbie Joosten
and leaves extra room for errors and misunderstandings. Cheers, Robbie -Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent: Friday, June 13, 2014 12:04 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Invisible atoms in ligands

Re: [ccp4bb] Invisible atoms in ligands

2014-06-13 Thread Tim Gruene
-Original Message- From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent: Friday, June 13, 2014 12:04 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Invisible atoms in ligands Hi Frank, if you can calculate their position, i.e. it is part of a rigid group, I

Re: [ccp4bb] Invisible atoms in ligands

2014-06-13 Thread Isaac Westwood
@JISCMAIL.AC.UK] On Behalf Of Tim Gruene Sent: Friday, June 13, 2014 12:04 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Invisible atoms in ligands -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Frank, if you can calculate their position, i.e. it is part of a rigid group, I

Re: [ccp4bb] Invisible atoms in ligands

2014-06-13 Thread Robbie Joosten
Joosten; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Invisible atoms in ligands -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Hi Robbie, maybe it is good not to use coordinates for calculations if you cannot measure the coordinates? Cheers, Tim On 06/13/2014 12:35 PM, Robbie Joosten

Re: [ccp4bb] Invisible atoms in ligands

2014-06-13 Thread Tim Gruene
modified. Cheers, Robbie -Original Message- From: Tim Gruene [mailto:t...@shelx.uni-ac.gwdg.de] Sent: Friday, June 13, 2014 13:37 To: Robbie Joosten; CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] Invisible atoms in ligands Hi Robbie, maybe it is good not to use coordinates