Re: [ccp4bb] Biological assembly

2011-10-21 Thread Kayashree M
Respected Sir, Thank you for the efforts and nice depiction of the problem. The Dimeric assembly that is solved and the one predicted by PISA is depicted in the attachment. This is the arrangement I wanted to describe. The protein overall appears like a "C". Thanking you With Regards KavyaSince

Re: [ccp4bb] Biological assembly

2011-10-20 Thread James Stroud
Since a crystallographic 3-fold generates the trimer (of dimers) then A1-B2 can be the ASU in this case.Just generate the symmetry mates with the A1-B1 dimer and then make a new PDB of A1-B2 then generate the symmetry mates of A1-B2 to see that the lattice is complete.I compulsively made and attach

Re: [ccp4bb] Biological assembly

2011-10-20 Thread eugene . krissinel
Dear Bostjan, >> In case when ASU has the same multiplicity (number of chains) as the >> probable biological assembly, the latter is an ASU as well. In such a >> case, the PDB suggests to choose ASU in the form of that assembly, purely >> for simplicity. It seems to me that this is not an unreason

Re: [ccp4bb] Biological assembly

2011-10-20 Thread Kayashree M
ya>> -CCP4 bulletin board  wrote: ->>      To: CCP4BB@JISCMAIL.AC.UK>      From: James Stroud>      Sent by: CCP4 bulletin board>      Date: 10/19/2011 10:41PM>      Subject: Re: [ccp4bb] Biological assembly>>      On Oct 19, 2011, at 4:36 AM, Kayashree M wrote:>&

Re: [ccp4bb] Biological assembly

2011-10-20 Thread Eleanor Dodson
Stroud Sent by: CCP4 bulletin board Date: 10/19/2011 10:41PM Subject: Re: [ccp4bb] Biological assembly On Oct 19, 2011, at 4:36 AM, Kayashree M wrote: We have a structure which is a homodimer in the asymmetric unit. PISA predicts most probable assembly as a dimer but

Re: [ccp4bb] Biological assembly

2011-10-20 Thread Kayashree M
Thank you Sir for the suggestions. Hi,If, in your case, no possible asymmetric unit can contain A1-B2, then you deposit A1-B1 (or I suppose A2-B2...) and indicate to the PDB (like placing cards in the header cards) the operator to be used (and the subunit it applies to) in order to generate the mos

Re: [ccp4bb] Biological assembly

2011-10-20 Thread Vellieux Frederic
: [ccp4bb] Biological assembly On Oct 19, 2011, at 4:36 AM, Kayashree M wrote: We have a structure which is a homodimer in the asymmetric unit. PISA predicts most probable assembly as a dimer but this dimeric assembly is different from what is solved (offcourse we can generate the

Re: [ccp4bb] Biological assembly

2011-10-19 Thread Kayashree M
Respected Sir, The space group is H3. if I generate the symmetry, it appears to be a dimer of trimers stacked one above the other with a rotation of 60 deg wrt each other, like this -  A1, A2, A3 (in one trimer) stacked uponB1, B2, B3 (second trimer). So structure that is in the ASUis with A1-B1 wh

Re: [ccp4bb] Biological assembly

2011-10-19 Thread Bostjan Kobe
On 19/10/11 9:19 PM, "eugene.krissi...@stfc.ac.uk" wrote: >In case when ASU has the same multiplicity (number of chains) as the >probable biological assembly, the latter is an ASU as well. In such a >case, the PDB suggests to choose ASU in the form of that assembly, purely >for simplicity. It see

Re: [ccp4bb] Biological assembly

2011-10-19 Thread James Stroud
On Oct 19, 2011, at 4:36 AM, Kayashree M wrote: > We have a structure which is a homodimer in the asymmetric unit. > PISA predicts most probable assembly as a dimer but this > dimeric assembly is different from what is solved (offcourse > we can generate the symmetry equivalent molecule and get tha

Re: [ccp4bb] Biological assembly

2011-10-19 Thread Kayashree M
Dear users,Thank you all for the suggestions.With RegardsKavya-- This message has been scanned for viruses and dangerous content by MailScanner, and is believed to be clean.

Re: [ccp4bb] Biological assembly

2011-10-19 Thread Ed Pozharski
> My question is - is it necessary that we deposit a structure, which > PISA predicted as most probable assembly in PDB as an > asymmetric unit & biological assembly or can we deposit a dimer > (asymmetric unit) and give explanation for the biological assembly > according to what PISA predicted. >

Re: [ccp4bb] Biological assembly

2011-10-19 Thread eugene . krissinel
Dear Kavya, If I understand your question correctly, it is about the choice of asymmetric unit for your deposition. In case of dimeric asymmetric unit (ASU), there are, indeed, a few valid possibilities and you arrive to just one of them in the course of structure solution. What you decide to d

Re: [ccp4bb] Biological assembly

2011-10-19 Thread Frederic VELLIEUX
P4BB@JISCMAIL.AC.UK > Copie à : > Objet : [ccp4bb] Biological assembly > > Dear users, We have a structure which is a homodimer in the asymmetric unit. PISA predicts most probable assembly as a dimer but this dimeric assembly is different from what is solved (offcourse we can generate

[ccp4bb] Biological assembly

2011-10-19 Thread Kayashree M
Dear users, We have a structure which is a homodimer in the asymmetric unit.PISA predicts most probable assembly as a dimer but thisdimeric assembly is different from what is solved (offcoursewe can generate the symmetry equivalent molecule and get that).My question is - is it necessary that we dep