Re: [ccp4bb] Phenix refine distorting a sidechain despite correct density

[Pavel Afonine]

Hi Folmer,

I would choose to not do the real space refinement in phenix.refine during
> the last rounds of refinement of a model, when sidechain positions are
> essentially correct.
>

by design it is supposed to place and fit side chains as good as possible,
satisfying both map fit and geometry criteria (such as rotameric states and
NCIs). If it does not perform up to your expectations it is best to report
this to us and I will make sure the issue is taken care of immediately. I
wonder if you wouldn't mind explaining your choice and if possible argue it
with specific examples (preferable all done off mailing list as this gets
way too narrow and specific!). -Thanks!

Pavel



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Re: [ccp4bb] Phenix refine distorting a sidechain despite correct density

[Folmer Fredslund]

Dear Igor

There's a phenix bulletin board for question like this, which is where you
should post the question. ( I crosspost here)


I would choose to not do the real space refinement in phenix.refine during
the last rounds of refinement of a model, when sidechain positions are
essentially correct.


I hope this helps

Folmer



tor. 3. dec. 2020 05.48 skrev Igor Petrik :

> I am refining a 1.71A X-ray structure with phenix refine. I have
> everything modelled in - ~150 residues in the ASU and a heme - and my
> R-work/R-free is 0.17/0.22. But when I went to deposit it, PDB pointed out
> that two of my sidechains have distorted geometries. One is a His, and
> looking at it in Coot, I can clearly see the 2Fo-Fc density for the correct
> geometry, but the actual coordinates that phenix refine produce don't lie
> in that density; there are significant difference map peaks showing that
> the coordinates are in the wrong place. If I use real space refine in Coot
> to put the coordinates back into the correct density and refine it again in
> phenix, they get distorted again.
>
> What settings in phenix should I check to try to get it to properly refine
> the coordinates?
>
> Thanks,
> - Igor Petrik, PhD
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] Phenix refine distorting a sidechain despite correct density

[Nigel Moriarty]

Igor

There is a Phenix BB for your Phenix related questions. You can subscribe
here.

http://www.phenix-online.org/mailman/listinfo/phenixbb

In the meantime, please send the Phenix version and OS to myself and Pavel
privately and I'm sure we can help. We may also need the inputs (privately,
of course) so please forward them also, if possible.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : nwmoria...@lbl.gov
Fax   : 510-486-5909   Web  : CCI.LBL.gov


On Wed, Dec 2, 2020 at 8:48 PM Igor Petrik  wrote:

> I am refining a 1.71A X-ray structure with phenix refine. I have
> everything modelled in - ~150 residues in the ASU and a heme - and my
> R-work/R-free is 0.17/0.22. But when I went to deposit it, PDB pointed out
> that two of my sidechains have distorted geometries. One is a His, and
> looking at it in Coot, I can clearly see the 2Fo-Fc density for the correct
> geometry, but the actual coordinates that phenix refine produce don't lie
> in that density; there are significant difference map peaks showing that
> the coordinates are in the wrong place. If I use real space refine in Coot
> to put the coordinates back into the correct density and refine it again in
> phenix, they get distorted again.
>
> What settings in phenix should I check to try to get it to properly refine
> the coordinates?
>
> Thanks,
> - Igor Petrik, PhD
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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[ccp4bb] Phenix refine distorting a sidechain despite correct density

[Igor Petrik]

I am refining a 1.71A X-ray structure with phenix refine. I have everything
modelled in - ~150 residues in the ASU and a heme - and my R-work/R-free is
0.17/0.22. But when I went to deposit it, PDB pointed out that two of my
sidechains have distorted geometries. One is a His, and looking at it in
Coot, I can clearly see the 2Fo-Fc density for the correct geometry, but
the actual coordinates that phenix refine produce don't lie in that
density; there are significant difference map peaks showing that the
coordinates are in the wrong place. If I use real space refine in Coot to
put the coordinates back into the correct density and refine it again in
phenix, they get distorted again.

What settings in phenix should I check to try to get it to properly refine
the coordinates?

Thanks,
- Igor Petrik, PhD



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Re: [ccp4bb] Refmac not handling microheterogeneity?

[Ian Tickle]

Hi Keitaro

Perfect!

Thanks, that's great.

Cheers

-- Ian


On Wed, 2 Dec 2020 at 22:31, Keitaro Yamashita 
wrote:

> Dear Ian,
>
> For the moment in Refmac5 we need to use insertion codes to handle
> microheterogeneity. LINKR records are also needed in the header. So
> 7a5v.pdb should be changed like this:
>
> 954a955,957
> > LINKRTHR A 279 LYS A 279A
>  gap
> > LINKRC   VAL A 278 N   LYS A 279A
>  TRANS
> > LINKRC   THR A 279 N   ALA A 280
> TRANS
> 957c960
> < CRYST11.0001.0001.000  90.00  90.00  90.00 P 1
> ---
> > CRYST1  292.212  292.212  292.212  90.00  90.00  90.00 P 1
>
> 3332,3347c3335,3350
> < ATOM   2354  N  ATHR A 279 138.241 168.068 154.050  0.50 27.65
>  N
> < ATOM   2355  CA ATHR A 279 136.909 167.684 153.607  0.50 28.45
>  C
> < ATOM   2356  C  ATHR A 279 135.937 167.731 154.799  0.50 31.92
>  C
> < ATOM   2357  O  ATHR A 279 136.426 167.682 155.949  0.50 32.52
>  O
> < ATOM   2358  CB ATHR A 279 136.906 166.273 153.009  0.50 27.04
>  C
> < ATOM   2359  OG1ATHR A 279 137.119 165.333 154.066  0.50 28.59
>  O
> < ATOM   2360  CG2ATHR A 279 137.957 166.077 151.931  0.50 27.69
>  C
> < ATOM   2361  N  BLYS A 279 138.238 168.081 154.020  0.50 32.20
>  N
> < ATOM   2362  CA BLYS A 279 136.870 167.701 153.585  0.50 36.51
>  C
> < ATOM   2363  C  BLYS A 279 135.930 167.793 154.787  0.50 38.18
>  C
> < ATOM   2364  O  BLYS A 279 136.377 168.014 155.910  0.50 42.23
>  O
> < ATOM   2365  CB BLYS A 279 136.887 166.298 152.984  0.50 40.70
>  C
> < ATOM   2366  CG BLYS A 279 137.909 166.091 151.872  0.50 46.05
>  C
> < ATOM   2367  CD BLYS A 279 138.177 164.645 151.591  0.50 50.67
>  C
> < ATOM   2368  CE BLYS A 279 139.166 164.047 152.568  0.50 59.69
>  C
> < ATOM   2369  NZ BLYS A 279 140.515 163.892 151.967  0.50 59.05
>  N
> ---
> > ATOM   2354  N   THR A 279 138.241 168.068 154.050  0.50 27.65
>  N
> > ATOM   2355  CA  THR A 279 136.909 167.684 153.607  0.50 28.45
>  C
> > ATOM   2356  C   THR A 279 135.937 167.731 154.799  0.50 31.92
>  C
> > ATOM   2357  O   THR A 279 136.426 167.682 155.949  0.50 32.52
>  O
> > ATOM   2358  CB  THR A 279 136.906 166.273 153.009  0.50 27.04
>  C
> > ATOM   2359  OG1 THR A 279 137.119 165.333 154.066  0.50 28.59
>  O
> > ATOM   2360  CG2 THR A 279 137.957 166.077 151.931  0.50 27.69
>  C
> > ATOM   2361  N   LYS A 279A138.238 168.081 154.020  0.50 32.20
>  N
> > ATOM   2362  CA  LYS A 279A136.870 167.701 153.585  0.50 36.51
>  C
> > ATOM   2363  C   LYS A 279A135.930 167.793 154.787  0.50 38.18
>  C
> > ATOM   2364  O   LYS A 279A136.377 168.014 155.910  0.50 42.23
>  O
> > ATOM   2365  CB  LYS A 279A136.887 166.298 152.984  0.50 40.70
>  C
> > ATOM   2366  CG  LYS A 279A137.909 166.091 151.872  0.50 46.05
>  C
> > ATOM   2367  CD  LYS A 279A138.177 164.645 151.591  0.50 50.67
>  C
> > ATOM   2368  CE  LYS A 279A139.166 164.047 152.568  0.50 59.69
>  C
> > ATOM   2369  NZ  LYS A 279A140.515 163.892 151.967  0.50 59.05
>  N
>
> We deposited the PDB file that could be handled by Refmac5, but
> insertion code was replaced with alt loc code in the annotation
> process.
>
> Please also note that the NCS constraint function with evaluation of
> nonbonded interactions etc will be available in the next update.
>
> Best regards,
> Keitaro
>
> On 2020/12/02 21:41, Ian Tickle wrote:
> >
> > Sorry Eleanor, same problem in 'interleaved' order (except for 2 extra
> atoms in LYS).
> >
> > Strangely the error message is now repeated 91 times, even though there
> are only 16 atoms (7+9) in the 2 residues: previously I only got the
> message once !
> >
> > Guess I must have imagined that it worked - it's called 'expectation
> bias' !
> >
> > Thanks anyway.
> >
> > -- Ian
> >
> >
> > On Wed, 2 Dec 2020 at 18:34, Eleanor Dodson <
> 176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk  176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk>> wrote:
> >
> > Only a hunch but this works:
> >
> > ATOM 1036 OD1AASN A 172 -7.722 13.371 -18.195 0.50 5.12 O
> >
> > ATOM 1037 OD1BASN A 172 -7.152 14.800 -15.791 0.50 7.63 O
> >
> >
> > And here you have:ATOM 2354 N ATHR A 279 138.241 168.068 154.050
> 0.50 27.65 N
> >
> > ATOM 2355 CA ATHR A 279 136.909 167.684 153.607 0.50 28.45 C
> >
> > ATOM 2356 C ATHR A 279 135.937 167.731 154.799 0.50 31.92 C
> >
> > ATOM 2357 O ATHR A 279 136.426 167.682 155.949 0.50 32.52 O
> >
> > ATOM 2358 CB ATHR A 279 136.906 166.273 153.009 0.50 27.04 C
> >
> > ATOM 2359 OG1ATHR A 279 137.119 165.333 154.066 0.50 28.59 O
> >
> > ATOM 2360 CG2ATHR A 279 137.957 166.077 151.931 0.50 27.69 C
> >
> > ATOM 2361 N BLYS A 279 138.238 168.081 154.020 0.50 32.20 N
> >
> > ATOM 2362 CA BLYS A 279 

Re: [ccp4bb] Refmac not handling microheterogeneity?

[Keitaro Yamashita]

Dear Ian,

For the moment in Refmac5 we need to use insertion codes to handle
microheterogeneity. LINKR records are also needed in the header. So
7a5v.pdb should be changed like this:

954a955,957

LINKRTHR A 279 LYS A 279A   gap
LINKRC   VAL A 278 N   LYS A 279A   TRANS
LINKRC   THR A 279 N   ALA A 280TRANS

957c960
< CRYST11.0001.0001.000  90.00  90.00  90.00 P 1
---
CRYST1  292.212  292.212  292.212  90.00  90.00  90.00 P 1  

3332,3347c3335,3350
< ATOM   2354  N  ATHR A 279 138.241 168.068 154.050  0.50 27.65   N
< ATOM   2355  CA ATHR A 279 136.909 167.684 153.607  0.50 28.45   C
< ATOM   2356  C  ATHR A 279 135.937 167.731 154.799  0.50 31.92   C
< ATOM   2357  O  ATHR A 279 136.426 167.682 155.949  0.50 32.52   O
< ATOM   2358  CB ATHR A 279 136.906 166.273 153.009  0.50 27.04   C
< ATOM   2359  OG1ATHR A 279 137.119 165.333 154.066  0.50 28.59   O
< ATOM   2360  CG2ATHR A 279 137.957 166.077 151.931  0.50 27.69   C
< ATOM   2361  N  BLYS A 279 138.238 168.081 154.020  0.50 32.20   N
< ATOM   2362  CA BLYS A 279 136.870 167.701 153.585  0.50 36.51   C
< ATOM   2363  C  BLYS A 279 135.930 167.793 154.787  0.50 38.18   C
< ATOM   2364  O  BLYS A 279 136.377 168.014 155.910  0.50 42.23   O
< ATOM   2365  CB BLYS A 279 136.887 166.298 152.984  0.50 40.70   C
< ATOM   2366  CG BLYS A 279 137.909 166.091 151.872  0.50 46.05   C
< ATOM   2367  CD BLYS A 279 138.177 164.645 151.591  0.50 50.67   C
< ATOM   2368  CE BLYS A 279 139.166 164.047 152.568  0.50 59.69   C
< ATOM   2369  NZ BLYS A 279 140.515 163.892 151.967  0.50 59.05   N
---
ATOM   2354  N   THR A 279 138.241 168.068 154.050  0.50 27.65   N  
ATOM   2355  CA  THR A 279 136.909 167.684 153.607  0.50 28.45   C  
ATOM   2356  C   THR A 279 135.937 167.731 154.799  0.50 31.92   C  
ATOM   2357  O   THR A 279 136.426 167.682 155.949  0.50 32.52   O  
ATOM   2358  CB  THR A 279 136.906 166.273 153.009  0.50 27.04   C  
ATOM   2359  OG1 THR A 279 137.119 165.333 154.066  0.50 28.59   O  
ATOM   2360  CG2 THR A 279 137.957 166.077 151.931  0.50 27.69   C  
ATOM   2361  N   LYS A 279A138.238 168.081 154.020  0.50 32.20   N  
ATOM   2362  CA  LYS A 279A136.870 167.701 153.585  0.50 36.51   C  
ATOM   2363  C   LYS A 279A135.930 167.793 154.787  0.50 38.18   C  
ATOM   2364  O   LYS A 279A136.377 168.014 155.910  0.50 42.23   O  
ATOM   2365  CB  LYS A 279A136.887 166.298 152.984  0.50 40.70   C  
ATOM   2366  CG  LYS A 279A137.909 166.091 151.872  0.50 46.05   C  
ATOM   2367  CD  LYS A 279A138.177 164.645 151.591  0.50 50.67   C  
ATOM   2368  CE  LYS A 279A139.166 164.047 152.568  0.50 59.69   C  
ATOM   2369  NZ  LYS A 279A140.515 163.892 151.967  0.50 59.05   N  


We deposited the PDB file that could be handled by Refmac5, but
insertion code was replaced with alt loc code in the annotation
process.

Please also note that the NCS constraint function with evaluation of
nonbonded interactions etc will be available in the next update.

Best regards,
Keitaro

On 2020/12/02 21:41, Ian Tickle wrote:


Sorry Eleanor, same problem in 'interleaved' order (except for 2 extra atoms in 
LYS).

Strangely the error message is now repeated 91 times, even though there are 
only 16 atoms (7+9) in the 2 residues: previously I only got the message once !

Guess I must have imagined that it worked - it's called 'expectation bias' !

Thanks anyway.

-- Ian


On Wed, 2 Dec 2020 at 18:34, Eleanor Dodson 
<176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk 
> wrote:

Only a hunch but this works:

ATOM 1036 OD1AASN A 172 -7.722 13.371 -18.195 0.50 5.12 O

ATOM 1037 OD1BASN A 172 -7.152 14.800 -15.791 0.50 7.63 O


And here you have:ATOM 2354 N ATHR A 279 138.241 168.068 154.050 0.50 27.65 
N

ATOM 2355 CA ATHR A 279 136.909 167.684 153.607 0.50 28.45 C

ATOM 2356 C ATHR A 279 135.937 167.731 154.799 0.50 31.92 C

ATOM 2357 O ATHR A 279 136.426 167.682 155.949 0.50 32.52 O

ATOM 2358 CB ATHR A 279 136.906 166.273 153.009 0.50 27.04 C

ATOM 2359 OG1ATHR A 279 137.119 165.333 154.066 0.50 28.59 O

ATOM 2360 CG2ATHR A 279 137.957 166.077 151.931 0.50 27.69 C

ATOM 2361 N BLYS A 279 138.238 168.081 154.020 0.50 32.20 N

ATOM 2362 CA BLYS A 279 136.870 167.701 153.585 0.50 36.51 C

ATOM 2363 C BLYS A 279 135.930 167.793 154.787 0.50 38.18 C

ATOM 2364 O BLYS A 279 136.377 168.014 155.910 0.50 42.23 O

ATOM 2365 CB BLYS A 279 136.887 166.298 

Re: [ccp4bb] Refmac not handling microheterogeneity?

[Ian Tickle]

Sorry Eleanor, same problem in 'interleaved' order (except for 2 extra
atoms in LYS).

Strangely the error message is now repeated 91 times, even though there are
only 16 atoms (7+9) in the 2 residues: previously I only got the message
once !

Guess I must have imagined that it worked - it's called 'expectation bias' !

Thanks anyway.

-- Ian


On Wed, 2 Dec 2020 at 18:34, Eleanor Dodson <
176a9d5ebad7-dmarc-requ...@jiscmail.ac.uk> wrote:

> Only a hunch but this works:
>
> ATOM 1036 OD1AASN A 172 -7.722 13.371 -18.195 0.50 5.12 O
>
> ATOM 1037 OD1BASN A 172 -7.152 14.800 -15.791 0.50 7.63 O
>
>
> And here you have:ATOM 2354 N ATHR A 279 138.241 168.068 154.050 0.50
> 27.65 N
>
> ATOM 2355 CA ATHR A 279 136.909 167.684 153.607 0.50 28.45 C
>
> ATOM 2356 C ATHR A 279 135.937 167.731 154.799 0.50 31.92 C
>
> ATOM 2357 O ATHR A 279 136.426 167.682 155.949 0.50 32.52 O
>
> ATOM 2358 CB ATHR A 279 136.906 166.273 153.009 0.50 27.04 C
>
> ATOM 2359 OG1ATHR A 279 137.119 165.333 154.066 0.50 28.59 O
>
> ATOM 2360 CG2ATHR A 279 137.957 166.077 151.931 0.50 27.69 C
>
> ATOM 2361 N BLYS A 279 138.238 168.081 154.020 0.50 32.20 N
>
> ATOM 2362 CA BLYS A 279 136.870 167.701 153.585 0.50 36.51 C
>
> ATOM 2363 C BLYS A 279 135.930 167.793 154.787 0.50 38.18 C
>
> ATOM 2364 O BLYS A 279 136.377 168.014 155.910 0.50 42.23 O
>
> ATOM 2365 CB BLYS A 279 136.887 166.298 152.984 0.50 40.70 C
>
> ATOM 2366 CG BLYS A 279 137.909 166.091 151.872 0.50 46.05 C
>
> ATOM 2367 CD BLYS A 279 138.177 164.645 151.591 0.50 50.67 C
>
> ATOM 2368 CE BLYS A 279 139.166 164.047 152.568 0.50 59.69 C
>
> ATOM 2369 NZ BLYS A 279 140.515 163.892 151.967 0.50 59.05 N
>
>
>
>
> In case 1 OD1 A is immediately followed bu OD1B
>
>
> In second case - all As listed then all Bs
>
>
> Eleanor
>
>
>
>
> On Wed, 2 Dec 2020 at 14:34, Robbie Joosten 
> wrote:
>
>> Hi Ian,
>>
>> AFAIK there is no clean solution for this and I imagine this problem goes
>> very deep into the internal representation of the model in REFMAC. That
>> said, 1 in 6 missing PDB-REDO entries is caused by this problem, so a
>> solution would be very welcome.
>>
>> Cheers,
>> Robbie
>>
>> > -Original Message-
>> > From: CCP4 bulletin board  On Behalf Of Ian
>> > Tickle
>> > Sent: Wednesday, December 2, 2020 15:02
>> > To: CCP4BB@JISCMAIL.AC.UK
>> > Subject: [ccp4bb] Refmac not handling microheterogeneity?
>> >
>> >
>> > Dear All
>> >
>> > I just downloaded a PDB file (7A5V) from the EBI server, tried to run
>> Refmac
>> > on it and got the error:
>> >
>> > ERROR: in chain A residue: 279 different residues have the same number
>> > There is an error in the input coordinate file
>> >
>> > At least one the chains has 2 residues with the same number ===> Error:
>> > Problem with coordinate file
>> >
>> >
>> > and indeed residue A279 has:
>> >
>> > ATOM   2354  N  ATHR A 279 138.241 168.068 154.050  0.50 27.65
>>  N
>> >
>> > and
>> > ATOM   2361  N  BLYS A 279 138.238 168.081 154.020  0.50 32.20
>>  N
>> > and the same for all the other atoms in the residues.
>> >
>> > Searching the CCP4BB archives for "microheterogeneity" I see that this
>> has
>> > been discussed before and apparently it should "just work" if there are
>> alt
>> > atom indicators (check) and occupancies add up to <= 1 (check).  I must
>> say I
>> > also was of the impression that it "just worked" so I'm a bit confused
>> now
>> > why it doesn't.
>> >
>> > Version info:
>> > DISTRIB_DESCRIPTION="Ubuntu 20.04.1 LTS"
>> > ### CCP4 7.1.008: Refmac  version 5.8.0267 : 24/08/20##
>> >
>> > Is there some other hack I need to do to get it to work?
>> >
>> > Cheers
>> >
>> > -- Ian
>> >
>> >
>> >
>> >
>> > 
>> >
>> >
>> > To unsubscribe from the CCP4BB list, click the following link:
>> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
>>
>> 
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>>
>> This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a
>> mailing list hosted by www.jiscmail.ac.uk, terms & conditions are
>> available at https://www.jiscmail.ac.uk/policyandsecurity/
>>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] Refmac not handling microheterogeneity?

[Eleanor Dodson]

Only a hunch but this works:

ATOM 1036 OD1AASN A 172 -7.722 13.371 -18.195 0.50 5.12 O

ATOM 1037 OD1BASN A 172 -7.152 14.800 -15.791 0.50 7.63 O


And here you have:ATOM 2354 N ATHR A 279 138.241 168.068 154.050 0.50 27.65
N

ATOM 2355 CA ATHR A 279 136.909 167.684 153.607 0.50 28.45 C

ATOM 2356 C ATHR A 279 135.937 167.731 154.799 0.50 31.92 C

ATOM 2357 O ATHR A 279 136.426 167.682 155.949 0.50 32.52 O

ATOM 2358 CB ATHR A 279 136.906 166.273 153.009 0.50 27.04 C

ATOM 2359 OG1ATHR A 279 137.119 165.333 154.066 0.50 28.59 O

ATOM 2360 CG2ATHR A 279 137.957 166.077 151.931 0.50 27.69 C

ATOM 2361 N BLYS A 279 138.238 168.081 154.020 0.50 32.20 N

ATOM 2362 CA BLYS A 279 136.870 167.701 153.585 0.50 36.51 C

ATOM 2363 C BLYS A 279 135.930 167.793 154.787 0.50 38.18 C

ATOM 2364 O BLYS A 279 136.377 168.014 155.910 0.50 42.23 O

ATOM 2365 CB BLYS A 279 136.887 166.298 152.984 0.50 40.70 C

ATOM 2366 CG BLYS A 279 137.909 166.091 151.872 0.50 46.05 C

ATOM 2367 CD BLYS A 279 138.177 164.645 151.591 0.50 50.67 C

ATOM 2368 CE BLYS A 279 139.166 164.047 152.568 0.50 59.69 C

ATOM 2369 NZ BLYS A 279 140.515 163.892 151.967 0.50 59.05 N




In case 1 OD1 A is immediately followed bu OD1B


In second case - all As listed then all Bs


Eleanor




On Wed, 2 Dec 2020 at 14:34, Robbie Joosten 
wrote:

> Hi Ian,
>
> AFAIK there is no clean solution for this and I imagine this problem goes
> very deep into the internal representation of the model in REFMAC. That
> said, 1 in 6 missing PDB-REDO entries is caused by this problem, so a
> solution would be very welcome.
>
> Cheers,
> Robbie
>
> > -Original Message-
> > From: CCP4 bulletin board  On Behalf Of Ian
> > Tickle
> > Sent: Wednesday, December 2, 2020 15:02
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: [ccp4bb] Refmac not handling microheterogeneity?
> >
> >
> > Dear All
> >
> > I just downloaded a PDB file (7A5V) from the EBI server, tried to run
> Refmac
> > on it and got the error:
> >
> > ERROR: in chain A residue: 279 different residues have the same number
> > There is an error in the input coordinate file
> >
> > At least one the chains has 2 residues with the same number ===> Error:
> > Problem with coordinate file
> >
> >
> > and indeed residue A279 has:
> >
> > ATOM   2354  N  ATHR A 279 138.241 168.068 154.050  0.50 27.65
>  N
> >
> > and
> > ATOM   2361  N  BLYS A 279 138.238 168.081 154.020  0.50 32.20
>  N
> > and the same for all the other atoms in the residues.
> >
> > Searching the CCP4BB archives for "microheterogeneity" I see that this
> has
> > been discussed before and apparently it should "just work" if there are
> alt
> > atom indicators (check) and occupancies add up to <= 1 (check).  I must
> say I
> > also was of the impression that it "just worked" so I'm a bit confused
> now
> > why it doesn't.
> >
> > Version info:
> > DISTRIB_DESCRIPTION="Ubuntu 20.04.1 LTS"
> > ### CCP4 7.1.008: Refmac  version 5.8.0267 : 24/08/20##
> >
> > Is there some other hack I need to do to get it to work?
> >
> > Cheers
> >
> > -- Ian
> >
> >
> >
> >
> > 
> >
> >
> > To unsubscribe from the CCP4BB list, click the following link:
> > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>
>
> 
>
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Re: [ccp4bb] Refmac not handling microheterogeneity?

[Robbie Joosten]

Hi Ian,

AFAIK there is no clean solution for this and I imagine this problem goes very 
deep into the internal representation of the model in REFMAC. That said, 1 in 6 
missing PDB-REDO entries is caused by this problem, so a solution would be very 
welcome.

Cheers,
Robbie

> -Original Message-
> From: CCP4 bulletin board  On Behalf Of Ian
> Tickle
> Sent: Wednesday, December 2, 2020 15:02
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: [ccp4bb] Refmac not handling microheterogeneity?
> 
> 
> Dear All
> 
> I just downloaded a PDB file (7A5V) from the EBI server, tried to run Refmac
> on it and got the error:
> 
> ERROR: in chain A residue: 279 different residues have the same number
> There is an error in the input coordinate file
> 
> At least one the chains has 2 residues with the same number ===> Error:
> Problem with coordinate file
> 
> 
> and indeed residue A279 has:
> 
> ATOM   2354  N  ATHR A 279 138.241 168.068 154.050  0.50 27.65   N
> 
> and
> ATOM   2361  N  BLYS A 279 138.238 168.081 154.020  0.50 32.20   N
> and the same for all the other atoms in the residues.
> 
> Searching the CCP4BB archives for "microheterogeneity" I see that this has
> been discussed before and apparently it should "just work" if there are alt
> atom indicators (check) and occupancies add up to <= 1 (check).  I must say I
> also was of the impression that it "just worked" so I'm a bit confused now
> why it doesn't.
> 
> Version info:
> DISTRIB_DESCRIPTION="Ubuntu 20.04.1 LTS"
> ### CCP4 7.1.008: Refmac  version 5.8.0267 : 24/08/20##
> 
> Is there some other hack I need to do to get it to work?
> 
> Cheers
> 
> -- Ian
> 
> 
> 
> 
> 
> 
> 
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1




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[ccp4bb] Refmac not handling microheterogeneity?

[Ian Tickle]

Dear All

I just downloaded a PDB file (7A5V) from the EBI server, tried to run
Refmac on it and got the error:

ERROR: in chain A residue: 279 different residues have the same number
There is an error in the input coordinate file
At least one the chains has 2 residues with the same number
===> Error: Problem with coordinate file

and indeed residue A279 has:

ATOM   2354  N  ATHR A 279 138.241 168.068 154.050  0.50 27.65
 N
and
ATOM   2361  N  BLYS A 279 138.238 168.081 154.020  0.50 32.20
 N
and the same for all the other atoms in the residues.

Searching the CCP4BB archives for "microheterogeneity" I see that this has
been discussed before and apparently it should "just work" if there are alt
atom indicators (check) and occupancies add up to <= 1 (check).  I must say
I also was of the impression that it "just worked" so I'm a bit confused
now why it doesn't.

Version info:
DISTRIB_DESCRIPTION="Ubuntu 20.04.1 LTS"
### CCP4 7.1.008: Refmac  version 5.8.0267 : 24/08/20##

Is there some other hack I need to do to get it to work?

Cheers

-- Ian



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[ccp4bb] Registration for CCP4 Virtual Study Weekend 2021 is now live

[McIntyre, Karen (STFC,RAL,SC)]

The CCP4 study weekend is going online for 2021! We would like to welcome you 
to join us for this year's meeting which will run from 5th-8th January. The 
theme this year is:

Integrating Structural Biology

We have invited a diverse group of speakers to give insights into different 
methodological approaches that can enrich structural understanding of chemistry 
and biology beyond our crystal structures. Talks include several subjects on 
structural bioinformatics, time resolved and dynamics studies, in cell 
measurements, biophysical approaches to quantify macromolecular interactions, 
and many other novel and established integrative approaches.

See details of the programme and registration here:

https://ccp4sw2021.meeting-mojo.com/

Regards

Karen McIntyre
CCP4 Project Administrator
Science and Technology Facilities Council
RCaH 1.22
Rutherford Appleton Laboratory
Harwell Campus
Didcot
OX11 0FA

karen.mcint...@stfc.ac.uk
01235 44 5790


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