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Re: [ccp4bb] Bad geometry for alt. conformation refined in Refmac5
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CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
Previous message:
Subject: Bad geometry for alt. conformation refined in Refmac5
From: John Pascal John {- dot -} Pascal {- at -} JEFFERSON {- dot -} EDU
Date: 2009-11-25		Next message:
Subject: Re: Help request: Failed MR using the same molecule as model
From: Roger Rowlett rrowlett {- at -} COLGATE {- dot -} EDU
Date: 2009-11-25


Subject: Re: Bad geometry for alt. conformation refined in Refmac5
From: Garib Murshudov garib {- at -} YSBL {- dot -} YORK {- dot -} AC {- dot -} UK
Date: 2009-11-25

Could you please try the version from York:

www.ysbl.york.ac.uk/refmac/latest_refmac.html

I think probkem you mention is related with compilation or something.
At least I cannot repat it on my computer

regards
Garib

On 25 Nov 2009, at 16:18, John Pascal wrote:

> Hello All,
>
> We are trying to refine ARG residues with two conformations in
> Refmac5, and the
> refined atom positions in the output PDB file are all over the
> place, as if the
> geometry restraints are not well defined.
>
> We've tried several different formats for the input file, based on
> previous
> postings to the bulletin board and the PDB standard (two examples
> below), but
> the result is always the same.
>
> We are using Refmac5 in CCP4 Suite 6.1.2, GUI 2.0.5 on Mac OSX.
>
> We'd appreciate any suggestions. Thanks. -John
>
> Examples of ARG format:
>
> 1)
> ATOM 1472 N ARG A 1 -5.737 26.887 38.372 1.00
> 29.53 C N
> ATOM 1473 CA ARG A 1 -5.445 25.560 37.882 1.00
> 30.24 C C
> ATOM 1474 CB ARG A 1 -5.314 24.548 39.036 1.00
> 30.63 C C
> ATOM 1475 CG ARG A 1 -5.426 23.052 38.627 1.00
> 34.81 C C
> ATOM 1476 CD AARG A 1 -4.827 22.075 39.644 0.50
> 37.09 C C
> ATOM 1477 CD BARG A 1 -4.301 22.419 39.279 0.50
> 37.09 C C
> ATOM 1478 NE AARG A 1 -3.430 21.777 39.304 0.50
> 42.71 C N
> ATOM 1479 NE BARG A 1 -4.482 21.902 40.627 0.50
> 42.71 C N
> ATOM 1480 CZ AARG A 1 -2.998 20.868 38.402 0.50
> 44.91 C C
> ATOM 1481 CZ BARG A 1 -3.648 22.142 41.638 0.50
> 44.91 C C
> ATOM 1482 NH1AARG A 1 -3.841 20.117 37.678 0.50
> 45.20 C N
> ATOM 1483 NH1BARG A 1 -2.584 22.912 41.464 0.50
> 45.20 C N
> ATOM 1484 NH2AARG A 1 -1.688 20.715 38.210 0.50
> 44.99 C N
> ATOM 1485 NH2BARG A 1 -3.878 21.619 42.831 0.50
> 44.99 C N
> ATOM 1486 C ARG A 1 -6.518 25.176 36.830 1.00
> 29.97 C C
> ATOM 1487 O ARG A 1 -7.675 25.501 36.971 1.00
> 31.02 C O
>
> 2)
> ATOM 44 N AARG A 1 26.671 62.112 46.990 0.50
> 30.13 A N
> ATOM 45 CA AARG A 1 26.970 63.346 47.667 0.50
> 30.65 A C
> ATOM 46 CB AARG A 1 27.172 64.495 46.676 0.50
> 31.07 A C
> ATOM 47 CG AARG A 1 27.152 65.897 47.322 0.50
> 34.20 A C
> ATOM 48 CD AARG A 1 27.993 66.976 46.599 0.50
> 37.16 A C
> ATOM 49 NE AARG A 1 27.726 67.425 45.342 0.50
> 42.06 A N
> ATOM 50 CZ AARG A 1 28.315 67.639 44.168 0.50
> 44.78 A C
> ATOM 51 NH1AARG A 1 29.525 67.160 43.918 0.50
> 45.37 A N
> ATOM 52 NH2AARG A 1 27.690 68.340 43.240 0.50
> 45.67 A N
> ATOM 53 C AARG A 1 25.839 63.640 48.622 0.50
> 30.37 A C
> ATOM 54 O AARG A 1 24.690 63.377 48.340 0.50
> 31.24 A O
> ATOM 55 N BARG A 1 26.667 62.080 47.010 0.50
> 30.13 A N
> ATOM 56 CA BARG A 1 26.921 63.329 47.640 0.50
> 30.65 A C
> ATOM 57 CB BARG A 1 27.108 64.390 46.581 0.50
> 31.07 A C
> ATOM 58 CG BARG A 1 27.138 65.756 47.103 0.50
> 34.20 A C
> ATOM 59 CD BARG A 1 28.447 66.452 46.933 0.50
> 37.16 A C
> ATOM 60 NE BARG A 1 28.377 67.657 47.707 0.50
> 42.06 A N
> ATOM 61 CZ BARG A 1 29.349 68.269 48.373 0.50
> 44.78 A C
> ATOM 62 NH1BARG A 1 30.572 67.836 48.373 0.50
> 45.37 A N
> ATOM 63 NH2BARG A 1 29.066 69.368 49.034 0.50
> 45.67 A N
> ATOM 64 C BARG A 1 25.822 63.636 48.638 0.50
> 30.37 A C
> ATOM 65 O BARG A 1 24.698 63.372 48.403 0.50
> 31.24 A O
>
>
>
> John Pascal, PhD
> Thomas Jefferson University
> Department of Biochemistry & Molecular Biology
> 233 South 10th Street, BLSB 804
> Philadelphia, Pennsylvania 19107
>
> ph 215.503.4596
> fx 215.923.2117

CCP4bb navigation

CCP4bb <-- 1999 <-- November 1999 <-- 30 November 1999
Previous message:
Subject: Bad geometry for alt. conformation refined in Refmac5
From: John Pascal John {- dot -} Pascal {- at -} JEFFERSON {- dot -} EDU
Date: 2009-11-25		Next message:
Subject: Re: Help request: Failed MR using the same molecule as model
From: Roger Rowlett rrowlett {- at -} COLGATE {- dot -} EDU
Date: 2009-11-25
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