Nope - LSQMAN would still be looking for stretches of sequentially ordered
residues and would only match atoms with identical names (" CB " with " CB ",
for instance).
--G
PS: Brownie points for the non-phenix solution, though!
On Fri, 26 Feb 2010, J?rgen Bosch wrote:
> How about LSQMAN ?
> with ATOM_types Side_chain ?
>
> That should do the trick.
>
> J?rgen
>
> P.S. sorry it's not really a CCP4 related program, but I use it very
> frequently in conjunction with the CCP4 suite :-)
>
> On Feb 26, 2010, at 11:22 AM, Ed Pozharski wrote:
>
>> On Fri, 2010-02-26 at 16:50 +0100, Gerard DVD Kleywegt wrote:
>>> But it still won't solve Miri's problem. I think what she is asking
>>> for is a
>>> program that detects which atoms should be matched to which,
>>> irrespective of
>>> their names (i.e., not assuming they are called " CA ") and order
>>> (i.e., not
>>> nicely sequential such as amino-acid residues), and then applies the
>>> operator
>>> that follows from that.
>>>
>>>
>>
>> How about FM option in molrep?
>> http://www.msg.ucsf.edu/local/programs/ccp4-6.0.2/html/molrep.html#FM
>>
>> Other MR programs can be used as well, just generate FC from one model
>> in a suitable cell and run search with another.
>>
>> HTH,
>>
>> Ed.
>>
>> --
>> Edwin Pozharski, PhD, Assistant Professor
>> University of Maryland, Baltimore
>> ----------------------------------------------
>> When the Way is forgotten duty and justice appear;
>> Then knowledge and wisdom are born along with hypocrisy.
>> When harmonious relationships dissolve then respect and devotion arise;
>> When a nation falls to chaos then loyalty and patriotism are born.
>> ------------------------------ / Lao Tse /
>
> -
> J?rgen Bosch
> Johns Hopkins Bloomberg School of Public Health
> Department of Biochemistry & Molecular Biology
> Johns Hopkins Malaria Research Institute
> 615 North Wolfe Street, W8708
> Baltimore, MD 21205
> Phone: +1-410-614-4742
> Lab: +1-410-614-4894
> Fax: +1-410-955-3655
> http://web.mac.com/bosch_lab/
>
Best wishes,
--Gerard
******************************************************************
Gerard J. Kleywegt
Dept. of Cell & Molecular Biology University of Uppsala
Biomedical Centre Box 596
SE-751 24 Uppsala SWEDEN
http://xray.bmc.uu.se/gerard/ mailto:[log in to unmask]
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