Re: [ccp4bb] modelling MET (methionine) and SME (met-sulfoxide)

[Abhishek Anan]

Dear all,

Thanks for the suggestions. It is synthetic peptide so the residue
identity is unambiguous.

I am not clear on how to model both MET and SME in coot, do a real
space refinement and then save the file for refinement in phenix. I
tried alternate conformation and then mutating one of them but that
didn't work as both conformations were mutated. What I also just
noticed is that the refinement of structure with just SME results in
positive densities around all side chain carbons even with the SME.cif
loaded into phenix. What could be wrong here?

best wishes,
Abhishek





On 4/26/20, Paul Emsley  wrote:
>
> On 26/04/2020 16:21, Abhishek Anan wrote:
>> Dear all,
>>
>> I have a peptide crystal structure at 0.97 Å that contains two surface
>> exposed Methionine. The CE atoms of both MET have a suspiciously high
>> b-factor >40 and a positive density. In addition, the sulfur atom SD
>> has a large negative density (b-factor ~23).
>>
>> I initially suspected that the MET may have oxidized to MET-sulfoxide
>> and tried to model only the MET-sulfoxide. This again resulted in
>> negative density.
>>
>> I think that the peptides might be partly oxidized which brings me to
>> my question. Is there a way to model both MET and MET-sulfoxide into
>> the density much like alternate conformation with options to refine
>> their respective occupancies.
>
>
> Yes. This is called micro-heterogeneity
>
> And is documented here:
>
> https://www.wwpdb.org/documentation/procedure
>
> That should "just work" if you then give the model to refmac.
>
> FWIW, Coot is, AFAIR, not 100% happy with such models.
>
> Paul.
>
>
>



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[ccp4bb] modelling MET (methionine) and SME (met-sulfoxide)

[Abhishek Anan]

Dear all,

I have a peptide crystal structure at 0.97 Å that contains two surface
exposed Methionine. The CE atoms of both MET have a suspiciously high
b-factor >40 and a positive density. In addition, the sulfur atom SD
has a large negative density (b-factor ~23).

I initially suspected that the MET may have oxidized to MET-sulfoxide
and tried to model only the MET-sulfoxide. This again resulted in
negative density.

I think that the peptides might be partly oxidized which brings me to
my question. Is there a way to model both MET and MET-sulfoxide into
the density much like alternate conformation with options to refine
their respective occupancies.

best wishes,
Abhishek



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Re: [ccp4bb] CCP4BB vs COVID19

[Abhishek Anan]

Dear all,

Not directly related to the discussion but does anyone know of a
antiretroviral protease inhibitor that is a peptide? I am new to the
topic and read that peptides suffer from bioavailability issues. Are
there any workarounds?

best,
Abhishek


On 3/21/20, Rigden, Dan  wrote:
> Hi James
>
>
> 5o32I is not a homolog of ORF8 - the BLAST e-value is insignificant. In
> fact, rather than the EGF-like fold of 5o32I, ORF8 has an Ig-like fold
> similar to ORF7 (for which there is a structure; 1xak).
>
>
> https://toolkit.tuebingen.mpg.de/jobs/2717885_1
>
>
> I must say I got quite excited seeing that until I noticed this pre-print
> which tells the whole story very nicely, including that key position 84
>
>
> https://www.biorxiv.org/content/10.1101/2020.03.04.977736v1
>
>
> Best wishes
>
> Dan
>
> 
> From: CCP4 bulletin board  on behalf of Patrick Shaw
> Stewart 
> Sent: 21 March 2020 15:41:17
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] CCP4BB vs COVID19
>
>
> James, this isn't conventional structural biology, but may be of interest,
> and I haven't been able get any mainstream virologists to think about it.
>
> The protein sequences are obviously of interest, but so are the RNA
> sequences at both ends of the Covid genome, which have conserved secondary
> structure.  A few years ago a paper came out suggesting that wild-type
> influenza has multiple "RNA thermometers", which may play an important role
> in the tropism of influenza.  Similar mechanisms may exist in other
> respiratory viruses, including Covid.
>
> My take on this, and the relevant papers, are below.
>
> Good luck to everyone and stay well,
>
> Patrick
>
>
> https://oldwivesandvirologists.blog/Covid-19-and-the-trade-off-model-of-selection/
>
> My paper in Medical Hypotheses
> http://douglas.co.uk/f_ftp1/ShawStewart_final_1-s2.pdf
>
> Narberhaus, Franz, Torsten Waldminghaus, and Saheli Chowdhury. "RNA
> thermometers." FEMS microbiology reviews 30.1 (2006): 3-16.
>
> Chursov, Andrey, et al. "Specific temperature-induced perturbations of
> secondary mRNA structures are associated with the cold-adapted
> temperature-sensitive phenotype of influenza A virus." RNA biology 9.10
> (2012): 1266-1274.
>
> Yang, Dong, and Julian L. Leibowitz. "The structure and functions of
> coronavirus genomic 3′ and 5′ ends." Virus research 206 (2015): 120-133.
>
>
>
> On Fri, Mar 20, 2020 at 10:59 PM James Holton
> mailto:jmhol...@lbl.gov>> wrote:
> You might think that as a structural biologist you won't be able to do
> much about COVID-19 anytime soon, but that is not true.  Yes, real-world
> therapeutics and vaccines take time, but we have already seen just how
> fast we can get started.  There are 21 PDBs already and some even have
> bound ligands.  Good job Frank et al. BTW!  And my personal thanks to
> all of you out there who are already hard at work on this.
>
> I believe this forum is an ideal place to share information and ideas on
> the structural biology of SARS-CoV-2 as we move forward. It's a big
> virus, but there are not that many proteins in it.  If all of us
> independently do the same bioinformatics and literature searches and end
> up trying exactly the same thing in every lab all over the world, then
> that would be more than unfortunate.  To that end, I am personally
> interested on ORF8 for reasons I will go into below.  Has anyone tried
> to solve it yet?  What happened?  Didn't express? Bad diffraction?
> What?  Do tell.
>
> Some of us, as you may have heard, are stuck at home, our beamlines and
> labs dark while we shelter-in-place.  That doesn't mean our hands are
> tied.  We are still allowed to think. The fraction of the human race
> that has a snowball's chance in Hades of figuring out this bug is very
> very small.  Structure may be your main skill set, but you are still a
> biologist.  Do you know how to run a PCR machine?  Do you know how to
> pipette?  You might think that anybody can do it, but that is really not
> the case. Ever trained a new student on sterile technique?  How many
> days did that take?  Now remember that your student was no dummy and
> already studying biology.  Everyone reading this will make an excellent
> volenteer at the very least.  I'm not saying this to belittle the
> average human, only to say that we scientists, moving in the circles we
> do, often forget that we have uncommon capabilities.
>
> For example, I also believe we can be useful in assay development. The
> void left by the dearth and delay of test results has been filled with
> fear, and that is a big problem.  The tests, as defined, are
> straightforward, but also extremely regimented like any good laboratory
> protocol should be.  The US CDC's instructions for academic labs are here:
> https://www.cdc.gov/coronavirus/2019-nCoV/lab/index.html
> My question is: how can this test be made faster, using more commonplace
> supplies, in high-throughput mode and still valid?  Not just for
> clinical 

Re: [ccp4bb] IMCBio International PhD Program Call 2019

[Abhishek Anan]

On 3/19/19, Albert Weixlbaumer  wrote:
> Hi everyone,
>
> This is a friendly reminder to draw your attention to a call for the
> International PhD program of the Integrative Molecular and Cellular Biology
> (IMCBio) graduate school at the University of Strasbourg, France:
> http://imcbio-phdprogram.unistra.fr
>
> The IMCBio graduate school builds on the strong research developed in four
> different institutes. This includes the IGBMC, which is a European Instruct
> center and thus houses state-of-the-art facilities for structural biology
> (NMR, X-ray crystallography, SAXS, and latest instrumentation for Cryo-EM).
>
> Structural biology at the IGBMC has a long tradition and focus on large
> macromolecular machines involved in gene expression (transcription and
> translation machineries), Chromatin organization, stability, and epigenetics
> (epigenetic regulators, topoisomerases, retroviral integrases, histone
> chaperones and deacetylases, methyltransferases), viral oncoproteins, motor
> proteins, and nuclear receptors.
> Strasbourg is a cosmopolitan city in the heart of Europe. The IGBMC is a
> vibrant and highly international institute (over 45 nationalities, working
> language is English) with about 250 PhD students:
> http://igbmc.fr/igbmc/vie_etudiante/
>
> Registration for the PhD program needs to be done until March 22nd, the
> deadline to complete the application is March 29th, 2019
>
> Please forward this to any interested candidate.
>
> Thanks,
> Albert
>
> 
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] Cys Lys bond?

[Abhishek Anan]

Hi,

Sulfilimine bond was identified in collagen IV using mass spec and NMR.

https://www.ncbi.nlm.nih.gov/pubmed/19729652

Best,
Abhishek

On 4/18/18, Jonathan Davies  wrote:
> Dear All,
>
>
> Thanks for all of the responses so far..
>
>
> Mark - I don't think it's caused by radiation damage, although this is
> certainly a concern. Using only a small subset of images from the start of
> data collection still gives fairly clear density with no positive or
> negative peaks around the cys and lys.
>
>
> Christian - I haven't used jligand before but that was nice and simple.. I
> think a simple link record may suffice here though.
>
>
> Matthew - Definitely a weird bond, potentially the cys was oxidised first
> and the beam caused more weirdness, I really have no idea! Having said that,
> I don't think this is the cause (see above).
>
>
> David - Thanks for the paper!
>
> Focco - Thanks for the publication!
>
>
> Paul - I tried the "Make link via Acedrg" route but had some issues (my
> model exploded).. I'll send you the details off list later! Cheers!
>
>
> Jonathan
>
>
>
> 
> From: Jonathan Davies
> Sent: 17 April 2018 18:03
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Cys Lys bond?
>
>
> Dear CCP4BB,
>
> I've recently solved a structure to 1.15 Angstrom which has extremely clear
> density for what appears to be a lysine covalently bound to a cysteine
> (S-N). The distance between the cys-S and lys-N is 1.8 A. I thought
> initially that there may be a methyl group between the two (based on this
> paper http://doi.org/10.1002/pro.2958) but there definitely isn't enough
> space.
>
> Some more info:
> The protein was purified from recombinant E. coli expression, standard
> buffers (Tris, NaCl).
> Crystallisation condition contains sodium acetate and PEG.
> The residues in question are not part of an active-site.
>
> I have two questions:
>
> Has anyone seen a cys that is involved in a sulfanamide bond with a lys?
>
> How would one go about modeling this bond in a way that doesn't upset coot,
> refmac or PDB validation?
>
> Thanks in advance!
> Jonathan
>

Re: [ccp4bb] AW: Re: [ccp4bb] Removing a ter line present in the middle of the chain

[Abhishek Anan]

I had a similar issue with refmac inserting TER card after some but
not all HETATM. It was inserting them before TYC (amidated tyrosine)
but not before norleucine or some of the other non-natural amino acids
I had. It might have something to do with the cif file and not
something particular to HETATM. Just a thought!

Abhishek

On 11/7/17, herman.schreu...@sanofi.com <herman.schreu...@sanofi.com> wrote:
> My feeling is that all non-standard amino acids should be labeled HETATM and
> that the overzealous introduction of TER cards by Refmac is the bad thing,
> but I might be mistaken…
> Herman
>
> Von: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] Im Auftrag von
> Eleanor Dodson
> Gesendet: Dienstag, 7. November 2017 13:28
> An: CCP4BB@JISCMAIL.AC.UK
> Betreff: [EXTERNAL] Re: [ccp4bb] Removing a ter line present in the middle
> of the chain
>
> Well - I just edited the HETATM to ATOM  and the TER went away..
> Something (Refmac? Coot?? mystery?) was labelling all atoms in MSE residues
> as HETATM and that was a BAD THING..
> Eleanor
>
>
> On 7 November 2017 at 08:05, Abhishek Anan
> <rendezvous.a...@gmail.com<mailto:rendezvous.a...@gmail.com>> wrote:
> Are you LINK records properly defined? You might want to check them. I
> had a similar issue and updating links fixed it.
>
> Best
> Abhishek
>
> On 11/7/17, Eleanor Dodson
> <eleanor.dod...@york.ac.uk<mailto:eleanor.dod...@york.ac.uk>> wrote:
>> No - it is not.
>>
>> I have seen similar problems.
>> Your atom records arent labelled as HETATM are they?
>>
>> That triggers strange behavior.
>> Eleanor
>>
>>
>> On 7 November 2017 at 07:13, Abhishek Anan
>> <rendezvous.a...@gmail.com<mailto:rendezvous.a...@gmail.com>>
>> wrote:
>>
>>> Are you adding the cif file of the unnatural amino acid on LIB in path
>>> in refmac.
>>>
>>> Best,
>>> Abhishek
>>>
>>>
>>>
>>> On 11/7/17, Rashi Aggarwal
>>> <agg.rash...@gmail.com<mailto:agg.rash...@gmail.com>> wrote:
>>> > Dear all,
>>> >
>>> > I have an unnatural amino acid in my structure which I could
>>> > successfully
>>> > add in coot. The amino acid is taking the right bonds when viewed with
>>> > coot. However, the pdb file has a ter line just above the residue.
>>> >
>>> > If I remove this line and submit the pdb to refmac it again adds the
>>> > ter
>>> > line, I can still remove it and go ahead with validation but is it the
>>> > right thing to do?
>>> >
>>> > Thanks
>>> >
>>> > Best,
>>> > Rashi
>>> >
>>>
>>
>
>

Re: [ccp4bb] Removing a ter line present in the middle of the chain

[Abhishek Anan]

Are you LINK records properly defined? You might want to check them. I
had a similar issue and updating links fixed it.

Best
Abhishek

On 11/7/17, Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote:
> No - it is not.
>
> I have seen similar problems.
> Your atom records arent labelled as HETATM are they?
>
> That triggers strange behavior.
> Eleanor
>
>
> On 7 November 2017 at 07:13, Abhishek Anan <rendezvous.a...@gmail.com>
> wrote:
>
>> Are you adding the cif file of the unnatural amino acid on LIB in path
>> in refmac.
>>
>> Best,
>> Abhishek
>>
>>
>>
>> On 11/7/17, Rashi Aggarwal <agg.rash...@gmail.com> wrote:
>> > Dear all,
>> >
>> > I have an unnatural amino acid in my structure which I could
>> > successfully
>> > add in coot. The amino acid is taking the right bonds when viewed with
>> > coot. However, the pdb file has a ter line just above the residue.
>> >
>> > If I remove this line and submit the pdb to refmac it again adds the
>> > ter
>> > line, I can still remove it and go ahead with validation but is it the
>> > right thing to do?
>> >
>> > Thanks
>> >
>> > Best,
>> > Rashi
>> >
>>
>

Re: [ccp4bb] Removing a ter line present in the middle of the chain

[Abhishek Anan]

Are you adding the cif file of the unnatural amino acid on LIB in path
in refmac.

Best,
Abhishek



On 11/7/17, Rashi Aggarwal  wrote:
> Dear all,
>
> I have an unnatural amino acid in my structure which I could successfully
> add in coot. The amino acid is taking the right bonds when viewed with
> coot. However, the pdb file has a ter line just above the residue.
>
> If I remove this line and submit the pdb to refmac it again adds the ter
> line, I can still remove it and go ahead with validation but is it the
> right thing to do?
>
> Thanks
>
> Best,
> Rashi
>

Re: [ccp4bb] Regarding Patents

[Abhishek Anan]

I second Gert's thoughts

Best,
Abhishek

On Sat, Nov 4, 2017 at 10:21 AM, Gert Vriend 
wrote:

> A related question. If you have a crystal structure and found a novel
>> ligand binding site that can be used to regulate protein activity, could
>> you patent such "binding site"? If not, how to make the best use of such
>> findings?
>>
>
> I would say that the best one can do with important novel
> data/information/knowledge/insights is to publish it so the world can
> benefit from it.
>
> Gert
>

Re: [ccp4bb] another unknown density problem

[Abhishek Anan]

Dear all,

My apology for the confusion!! I did mean the map radius is "truncated" at
5A. Poor choice of words :(

Any thoughts on what this density could be are still welcome.

Best regards,
Abhishek

On Fri, Nov 3, 2017 at 9:21 PM, Joern Krausze <j.krau...@tu-braunschweig.de>
wrote:

> Dear all,
>
> I think Abhishek means that the picture shows 5 A map radius.
>
> Best
> Joern
>
> On 3. Nov 2017, at 18:42, Pavel Afonine <pafon...@gmail.com> wrote:
>
> If by "it was truncated at 5A for clarity" you really mean you truncated
> all low-resolution data from 5A and lower then I am not surprised you see
> funny densities all over or don't see density where it is expected. Why?
> Consult a textbook for the answer.
>
> All the best,
> Pavel
>
> On Fri, Nov 3, 2017 at 3:10 AM, Abhishek Anan <rendezvous.a...@gmail.com>
> wrote:
>
>> Dear Prof Schreuder
>>
>> Here are another couple of perspectives from coot. The density is too far
>> and isolated from the peptide chain to be an alternate conformation or
>> conformational change. The density of the peptide chain does not look good
>> because it was truncated at 5A for clarity.
>>
>> Best regards
>> Abhishek
>>
>> On Fri, Nov 3, 2017 at 9:33 AM, <herman.schreu...@sanofi.com> wrote:
>>
>>> Dear Abhishek,
>>>
>>>
>>>
>>> To me, it looks like an alternative conformation of the peptide chain or
>>> maybe even a conformational change with respect to the starting model. The
>>> peptide chain does not look too well defined, despite high resolution
>>> electron density.
>>>
>>>
>>>
>>> Best,
>>>
>>> Herman
>>>
>>>
>>>
>>> *Von:* CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] *Im Auftrag
>>> von *Abhishek Anan
>>> *Gesendet:* Freitag, 3. November 2017 09:26
>>> *An:* CCP4BB@JISCMAIL.AC.UK
>>> *Betreff:* [EXTERNAL] [ccp4bb] another unknown density problem
>>>
>>>
>>>
>>> Hi all,
>>>
>>> I have an "unknown" density in the map. I have tried to fit it to PEG
>>> but it doesn't fit very well. I was wondering if there are other
>>> PEG-related or other molecules I could try.
>>>
>>> The crystal grew in TRIS-HCl and PEG MME 2K.
>>>
>>> Thank you
>>>
>>> Abhishek
>>>
>>
>>
>
>

Re: [ccp4bb] coot shelxl problem

[Abhishek Anan]

Dear all,

A simple work around is to add HOH in coot, copy their coordinates into the
*.ins fil and refine shelxl from the command line. I have done it a few
time and it seems to refine fine.

Best regards,

Abhishek

On Thu, Nov 2, 2017 at 5:40 PM,  wrote:

> > I am using 0.8.8 that comes with ccp4 on a Mac 10.10.5. I will give it a
> > go with the pre-release.
>
>
> As far as I understand, stand-alone binaries for 10.6 - 10.10 are no
> longer supported for coot pre-release.
>
> I'd rather that that was not the case, but peanuts and monkeys, hey-ho.
>
> Paul.
>
>
>
>

Re: [ccp4bb] coot shelxl problem

[Abhishek Anan]

I am using 0.8.8 that comes with ccp4 on a Mac 10.10.5. I will give it a go
with the pre-release.

Best
Abhishek



On Thu, Nov 2, 2017 at 3:47 PM, Paul Emsley <pems...@mrc-lmb.cam.ac.uk>
wrote:

> On 02/11/2017 09:34, Abhishek Anan wrote:
>
>> Dear all,
>>
>> I am trying to shelxl module from within coot after adding a few waters
>> but get the following error. Is there a work around?
>>
>>   ** INPUT INSTRUCTION HH1A   2  -1.5879950... IS LONGER THAN 79
>> CHARACTERS **
>>
>> I would appreciate any help.
>>
>>
> You don't say which version of Coot you are using or from where you
> acquired it.  As a general rule for Coot issues, I'd try out the latest
> pre-release.
>
> Paul.
>
>

[ccp4bb] coot shelxl problem

[Abhishek Anan]

Dear all,

I am trying to shelxl module from within coot after adding a few waters but
get the following error. Is there a work around?

 ** INPUT INSTRUCTION HH1A   2  -1.5879950... IS LONGER THAN 79 CHARACTERS
**

I would appreciate any help.

Thanks
abhishek

[ccp4bb] mtz2hkl for shelx

[Abhishek Anan]

Dear all,

I am trying to convert mtz file processed using DIALS to hkl format for
input into shelxL but I get the following warning about missing
reflections.

$ mtz2hkl  aj83.mtz

*** WARNING *** WARNING *** WARNING *** WARNING *** WARNING
**
* 1268 reflections were flagged missing based on
checking*
* Data-, Sigma-, AND Rfree-column. This is greater than 1% of the
total*
* Reflections. Please check your hkl-file contains all the data from
the*
* mtz-file. One reason might be unflagged Rfree-columns, e.g. if you
copied  *
* the Rfree-column from a file at lower
resolution.*
* The simplest remedy is to run the ccp4 program FREERFLAG with the*
* Keyword 'COMPLETE FREE=RFree_Flag
*
*** WARNING *** WARNING *** WARNING *** WARNING *** WARNING
**

mtz2hkl write data: 30228 lines written
 ** SUMMARY:
Data:  column  13, label: "IMEAN"
Sigma: column  14, label: "SIGIMEAN"
Rfree: column   3, label: "FreeR_flag"
Format: HKLF 4
Spacegroup: P 1 21 1
Cells present in mtz-file:
29.3205 26.6201 64.4701  90 92.26 90
29.3205 26.6201 64.4701  90 92.26 90
30228 reflections written to file "aj83.hkl"
1499 Reflections with FreeR_flag = 0 marked as test set (-1)


I tried FREERFLAG suggestion but to no avail. How do I fix this?

Thank you,
Abhishek

[ccp4bb] exclude water from anisotropic refinement in PDB_REDO

[Abhishek Anan]

Hi all,

Is there a way to exclude water from anisotropic refinement in PDB_REDO?

Best regards,

Abhishek

Re: [ccp4bb] AW: [ccp4bb] C-terminal amide

[Abhishek Anan]

 _chem_link_angle.atom_2_comp_id
>> _chem_link_angle.atom_id_2
>> _chem_link_angle.atom_3_comp_id
>> _chem_link_angle.atom_id_3
>> _chem_link_angle.value_angle
>> _chem_link_angle.value_angle_esd
>> PHE-NH2  1 O   1 C   2 N   122.0001.600
>> PHE-NH2  1 CA  1 C   2 N   118.2002.000
>> loop_
>> _chem_link_plane.link_id
>> _chem_link_plane.plane_id
>> _chem_link_plane.atom_comp_id
>> _chem_link_plane.atom_id
>> _chem_link_plane.dist_esd
>> PHE-NH2plane11 CA0.020
>> PHE-NH2plane11 C 0.020
>> PHE-NH2plane11 O 0.020
>> PHE-NH2plane12 N 0.020
>> # --
>>
>> -
>> > On Oct 12, 2017, at 2:53 PM, Abhishek Anan <rendezvous.a...@gmail.com>
>> wrote:
>> >
>> > Dear all,
>> >
>> > I am trying to solve the structure of a peptide with C-terminal amide.
>> In order to add the amide group to the c-terminal TYR, I substituted TYR
>> with TYC (tyrosinamide) and created a link between the preceding GLY and
>> TYC. When refined in refmac, the pdb inserts a TER card between GLY and
>> TYC
>> and no covalent bond is created between them. How do I fix this? I have
>> also tried to add NH2 pointer atom to TYR in coot and create a link
>> between
>> them but in vain. I also imported the NH2.cif file into coot and tried to
>> make a link but of no use. I also tried to import NH2.cif into Jligand so
>> I
>> could get a link record but it refuses to open the NH2.cif file.
>> >
>> > I would greatly appreciate any help!
>> >
>> > Best regards,
>> > Abhishek
>>
>

[ccp4bb] C-terminal amide

[Abhishek Anan]

Dear all,

I am trying to solve the structure of a peptide with C-terminal amide. In
order to add the amide group to the c-terminal TYR, I substituted TYR with
TYC (tyrosinamide) and created a link between the preceding GLY and TYC.
When refined in refmac, the pdb inserts a TER card between GLY and TYC and
no covalent bond is created between them. How do I fix this? I have also
tried to add NH2 pointer atom to TYR in coot and create a link between them
but in vain. I also imported the NH2.cif file into coot and tried to make a
link but of no use. I also tried to import NH2.cif into Jligand so I could
get a link record but it refuses to open the NH2.cif file.

I would greatly appreciate any help!

Best regards,
Abhishek

[ccp4bb] refmac mixed anisotropic refinement

[Abhishek Anan]

Dear all,

How does one exclude water from anisotropic refinement in refmac5.8 under
ccp4-7.0

Here is the relevant section from the com file,

refi -
type REST -
resi MLKF -
meth CGMAT -
bref MIXED anisou residues from 100 A to 200 A

This does not work and the logfile has the following warning,

Data line---

 refi type REST resi MLKF meth CGMAT bref MIXED anisou RESID

 UES 100 A to 200 A

 Unknown subkeyword of REFI

 ? ANIS ?

 Wrong residual option

 Unknown subkeyword of REFI

 ? A?

 Unknown subkeyword of REFI

 ? TO   ?

 Unknown subkeyword of REFI

 ? 200  ?

 Unknown subkeyword of REFI

 ? A?

Is there any other way of defining the residue range or excluding only water?

Thank you for your help,

Abhishek