Re: [ccp4bb] Broken Masks

Protein crystallography Programs for crystallography X-ray detectors
Basic tutorials:
Protein Peptide

CCP4bb navigation

CCP4bb <-- 2008 <-- March 2008 <-- 19 March 2008

Previous message:
Subject: cryoprotectant for crystals in isopropanol
From: shivesh kumar 2shivesh {- at -} GMAIL {- dot -} COM
Date: 2008-03-19

Next message:
Subject: The Lawnmower Man
From: Jordi Benach jbenach {- at -} CELLS {- dot -} ES
Date: 2008-03-19

Subject: Re: Broken Masks
From: Laurence Pearl Laurence {- dot -} Pearl {- at -} ICR {- dot -} AC {- dot -} UK
Date: 2008-03-19

I think it is a version bug of some sort - when I ran the same mask
creation run in CCP4i on my MacBook laptop (which has the most recent
CCP4) it displays fine and also worked perfectly in dm averaging,
turning a tangled mess into interpretable density.

The mask generated by NCSMASK on my desktop Mac displayed weirdly in
COOT on that machine, and crashed COOT on the laptop as soon as I treid
to display it.

Anyway the job is done - thanks for the advice.

Laurence

Daniel Anderson wrote:
> Could it be that NCSMASK folded the mask back into an asymmetric unit?
> My NCSMASK input file contains explicit xyzlim boundaries and "notrim"
> keyword.
>
> On Tue, 18 Mar 2008, Laurence Pearl wrote:
>
>> I'm trying to generate a mask around a molecule using NCSMASK under
>> the CCP4i interface, for ultimate use in NCS averaging and density
>> modification in dm. Being a little old-fashioned I wanted to check
>> that it covered the required molecule. However when displayed in
>> COOT, there seem to be arbitary flat slabs running through the mask,
>> with some sort of inversion or other transformation on the other side
>> of the slab. The mask has a similar appearance in the CCP4mg. The
>> flattenings are parallel to cell edges, and sometimes, but not always
>> adjacent to cell faces.
>>
>> Is this a known problem ? is it NCSMASK ? or is it COOT and CCP4mg ?
>>
>>
>

--
-------------------------------------------------------------
Laurence H. Pearl PhD FMedSci

Professor of Protein Crystallography and Section Chairman
Section of Structural Biology, Institute of Cancer Research
Chester Beatty Laboratories, 237 Fulham Road, London SW3 6JB
Phone +44-(0)20 7153 5422 : Secretary 5443 : FAX 5457
-------------------------------------------------------------
"Live Simply and do Serious Things .. "
- Dorothy Crowfoot Hodgkin
-------------------------------------------------------------

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.

CCP4bb navigation

CCP4bb <-- 2008 <-- March 2008 <-- 19 March 2008

Previous message:
Subject: cryoprotectant for crystals in isopropanol
From: shivesh kumar 2shivesh {- at -} GMAIL {- dot -} COM
Date: 2008-03-19

Next message:
Subject: The Lawnmower Man
From: Jordi Benach jbenach {- at -} CELLS {- dot -} ES
Date: 2008-03-19