Re: [ccp4bb] MOLREP

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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

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Subject: Re: ACORN2 in ccp4
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-10-01

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Subject: Postdoctoral Fellow for the Structural Biology group at ESRF
From: Daniele de Sanctis de {- dot -} sanctisd {- at -} GMAIL {- dot -} COM
Date: 2009-10-01

Subject: Re: MOLREP
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-10-01

Then I suspect the sequence is overriding the model.

My preferred approach.
Get a sequence alignment from somewhere and use CHAINSAW to edit the
model you want to use. That is documented! And it will edit both
monomers in turn I believe..

Then you will have a dimer with the appropriate sequence editing done
for you.

Now give that toMOLREP without any sequence. Now I am pretty sure it
will use your whole model.
It will determine the non-cryst tramslation and apply it automatically
to all copies I guess but if you have strong NCT then it usually more or
less relates allmolecules..
.

Pseudo centring - what do you mean by that?

Twinning - Aaagh
Eleanor

tommi kajander wrote:
> yes i am, i haven't got a clue, it always seems to be doing somethig
> other than i want it to..
> to be honest the manual is prety obsolete and non-existent, would be
> nice if the authors provided
> more info on current vresion.
>
> tommi
>
>
> On 1.10.2009, at 11.10, Eleanor Dodson wrote:
>
>> How can that be! Are you also providing a sequence?
>>
>> Eleanor
>>
>> Tommi Kajander wrote:
>>> Hi,
>>> I have been using a dimer as a search model in MOLREP (there will be
>>> several in AU),
>>> for some reason the program tends to break the dimer into monomers
>>> wihtout asking me..
>>> how is this determined in the program... a more detailed manual
>>> would be nice, also on the output
>>> as the different contrasts and their meaning appear bit cryptic to
>>> me. (i am beginning to get the hang of it
>>> but its still bit fuzzy..)
>>>
>>> Also if i am searching for number of say these dimers and there is a
>>> speudo-translation vector
>>> should it be used all the time? (i would assume not all the searched
>>> unit are related necessarily by the
>>> translational NCS) (to make it even merrier, there is both proper
>>> speudo centering and "just" translational
>>> NCS .. and you can only specify one vector... if we are lucky its
>>> also twinned...
>>>
>>> thanks for comments,
>>> Tommi
>>>
>>>
>>
>>
>
> Tommi Kajander, Ph.D.
> Macromolecular X-ray Crystallography
> Research Program in Structural Biology and Biophysics
> Institute of Biotechnology
> P.O. Box 65 (Street: Viikinkaari 1, 4th floor)
> University of Helsinki
> FIN-00014 Helsinki, Finland
> Tel. +358-9-191 58903
> Fax +358-9-191 59940
>
>
>

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999

Previous message:
Subject: Re: ACORN2 in ccp4
From: Eleanor Dodson ccp4 {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-10-01

Next message:
Subject: Postdoctoral Fellow for the Structural Biology group at ESRF
From: Daniele de Sanctis de {- dot -} sanctisd {- at -} GMAIL {- dot -} COM
Date: 2009-10-01