In theory (!) those should work.  If they import ok into Analysis (modulo this letter3Code issue) then when you do a save it should create an xml file (not sure off the top of my head if it would save that into your project directory or in the release directory).  So if the letter3Code is missing you could then edit that xml file.

Wayne

> On 30 Mar 2015, at 15:00, Almeida, Teresa <[log in to unmask]> wrote:
> 
> I've tried mol2 and pdb. And in both I've used the three letter code I wanted, SME (see an example bellow). Never tried to import as xml because this is the way I was told to it in previous email sent by you on the 27th of February 2014. Can I do it using these formats?
> 
>     1  CAB       -17.750   -30.680    31.470   C.3       1 SME       0.076
>     2  HAC       -17.320   -31.393    32.173   H         1 SME      -0.007
>     3  HAD       -17.995   -29.705    31.892   H         1 SME      -0.006
>     4  CAA       -19.010   -31.240    30.840   C.3       1 SME       0.076
>     5  HAA       -19.730   -30.449    30.630   H         1 SME      -0.007
>     6  HAB       -19.375   -32.045    31.478   H         1 SME      -0.007
>     7  CAE       -18.490   -31.860    29.560   C.3       1 SME       0.076
> 
> 
> Kind regards
> Teresa Almeida
> 
> PhD student
> Department of Chemistry/Institute of Integrative Biology
> University of Liverpool
> Liverpool
> L69 7ZD
> United Kingdom
> 
> ________________________________________
> From: CcpNmr software mailing list [[log in to unmask]] on behalf of Wayne Boucher [[log in to unmask]]
> Sent: 30 March 2015 13:49
> To: [log in to unmask]
> Subject: Re: small molecule  - ARIA/CCPN error
> 
> You have an xml file?  If so, you should add the code3Letter to that (in the file).  Here is the relevant line in ATP and your xml file is presumably missing the code3Letter attribute:
> 
> <CHEM.NonStdChemComp _ID="_1" ccpCode="Atp" code3Letter="ATP" createdBy="ccpnRef" guid="msd_ccpnRef_2007-12-11-10-14-47_00001" isModifiable="true" molType="other" name="ADENOSINE-5'-TRIPHOSPHATE">
> 
> I think when you use the “Import XML File” it then copies the file into the project chemComp data base (in ccpnmr/ccpnmr2.*/data/ccp/molecule/ChemComp) so you can edit that file directly and it should pick it up when you next start up Analysis.
> 
> (Assuming I am understanding what you are doing!)
> 
> Wayne
> 
>> On 30 Mar 2015, at 13:36, Almeida, Teresa <[log in to unmask]> wrote:
>> 
>> Forgot the attachment.
>> 
>> Kind regards
>> Teresa Almeida
>> 
>> PhD student
>> Department of Chemistry/Institute of Integrative Biology
>> University of Liverpool
>> Liverpool
>> L69 7ZD
>> United Kingdom
>> 
>> ________________________________________
>> From: CcpNmr software mailing list [[log in to unmask]] on behalf of Almeida, Teresa [[log in to unmask]]
>> Sent: 30 March 2015 13:35
>> To: [log in to unmask]
>> Subject: Re: small molecule  - ARIA/CCPN error
>> 
>> Hi,
>> 
>> Thanks, Brian. I modified atomnames.xml and got a bit further in the calculations. Now the peaks are assigned by aria complains about the missing residue name. I think my main issue here is  that I don't have a 3 letter code in CCPN for this molecule (please see attached). I've tried different ways to import molecules but I can never set the 3 letter code for my molecule.
>> 
>> Does anyone have a clue on this?
>> 
>> Kind regards
>> Teresa Almeida
>> 
>> PhD student
>> Department of Chemistry/Institute of Integrative Biology
>> University of Liverpool
>> Liverpool
>> L69 7ZD
>> United Kingdom
>> 
>> ________________________________________
>> From: CcpNmr software mailing list [[log in to unmask]] on behalf of Brian Smith [[log in to unmask]]
>> Sent: 30 March 2015 09:57
>> To: [log in to unmask]
>> Subject: Re: small molecule  - ARIA/CCPN error
>> 
>> I'm pretty sure that ARIA without some modification will not calculate structures including your small molecule. Below lists the changes I had to make for adding oleic acid to a structure calculation. I ran these calculations using restraint lists generated in analysis (direct, not exported as .tbl) rather than getting ARIA to make the assignments.
>> 
>> One further note: When generating the starting coordinates, ARIA uses a multiple of the residue number as the x coordinate to produce an initial linear structure. If your small molecule has a residue number significantly different from your protein residues, it will end up a long way away, and the minimization may fail to bring them together.
>> 
>> ---
>> Adding oleic acid ligand to structure calcs with aria 2.3.1
>> 
>> First copy and modify topallhdg5.3.pro and topallhdg5.3.pro to include topology and parameter definitions for ligand and ligand specific atoms, angles, dihedrals, impropers (and nonbonded if you need to - good luck!) etc. If there's an existing PDB entry then XPLO2D is a help for starting and testing the parameter and topology work. ACPYPE should be good for this also.
>> 
>> For the residue linking to work nicely, it seems best to leave the method on Automatic. Copy and modify ions.link to include something like
>> 
>> link  DUMM head - OLA tail + OLA end
>> first DUMM           tail + OLA end
>> last  DUMM head - OLA           end
>> 
>> once you have run aria -s <project.xml> copy your modified ions.link to run1/cns/toppar overwriting the default copy. Note that you will have to repeat this copying each time you set up the project. This method is also not very elegant because it uses an undefined patch that generates errors in generate.out
>> 
>> %PATCH-ERR: patch DUMM not found in topology file
>> %PATCH-ERR: patch DUMM not found in topology file
>> 
>> Add a definition of the new molecule in ARIA's atomnames.xml file - you'll find this at $ARIA2/src/py/data/atomnames.xml and there should be no problem with editing the copy in the ARIA installation directory (so long as you have write permission). In fact, as this file is not copied to the working directory, you have to do it this way. For oleate something like the following seems to work
>> 
>> <residue residue_type="NONBASE" iupac_name="OLA" cns_name="OLA" dyana_name="OLA">
>>   <atom iupac_name="C1" cns_name="C1" dyana_name="C1"/>
>>   <atom iupac_name="C2" cns_name="C2" dyana_name="C2"/>
>>   <atom iupac_name="C3" cns_name="C3" dyana_name="C3"/>
>>   <atom iupac_name="C4" cns_name="C4" dyana_name="C4"/>
>>   <atom iupac_name="C5" cns_name="C5" dyana_name="C5"/>
>>   <atom iupac_name="C6" cns_name="C6" dyana_name="C6"/>
>>   <atom iupac_name="C7" cns_name="C7" dyana_name="C7"/>
>>   <atom iupac_name="C8" cns_name="C8" dyana_name="C8"/>
>>   <atom iupac_name="C9" cns_name="C9" dyana_name="C9"/>
>>   <atom iupac_name="C10" cns_name="C10" dyana_name="C10"/>
>>   <atom iupac_name="C11" cns_name="C11" dyana_name="C11"/>
>>   <atom iupac_name="C12" cns_name="C12" dyana_name="C12"/>
>>   <atom iupac_name="C13" cns_name="C13" dyana_name="C13"/>
>>   <atom iupac_name="C14" cns_name="C14" dyana_name="C14"/>
>>   <atom iupac_name="C15" cns_name="C15" dyana_name="C15"/>
>>   <atom iupac_name="C16" cns_name="C16" dyana_name="C16"/>
>>   <atom iupac_name="C17" cns_name="C17" dyana_name="C17"/>
>>   <atom iupac_name="C18" cns_name="C18" dyana_name="C18"/>
>>   <atom iupac_name="H1" cns_name="H1" dyana_name="H1"/>
>>   <atom iupac_name="H21" cns_name="H21" dyana_name="H21"/>
>>   <atom iupac_name="H22" cns_name="H22" dyana_name="H22"/>
>>   <atom iupac_name="H31" cns_name="H31" dyana_name="H31"/>
>>   <atom iupac_name="H32" cns_name="H32" dyana_name="H32"/>
>>   <atom iupac_name="H41" cns_name="H41" dyana_name="H41"/>
>>   <atom iupac_name="H42" cns_name="H42" dyana_name="H42"/>
>>   <atom iupac_name="H51" cns_name="H51" dyana_name="H51"/>
>>   <atom iupac_name="H52" cns_name="H52" dyana_name="H52"/>
>>   <atom iupac_name="H61" cns_name="H61" dyana_name="H61"/>
>>   <atom iupac_name="H62" cns_name="H62" dyana_name="H62"/>
>>   <atom iupac_name="H71" cns_name="H71" dyana_name="H71"/>
>>   <atom iupac_name="H72" cns_name="H72" dyana_name="H72"/>
>>   <atom iupac_name="H81" cns_name="H81" dyana_name="H81"/>
>>   <atom iupac_name="H82" cns_name="H82" dyana_name="H82"/>
>>   <atom iupac_name="H9" cns_name="H9" dyana_name="H9"/>
>>   <atom iupac_name="H10" cns_name="H10" dyana_name="H10"/>
>>   <atom iupac_name="H111" cns_name="H111" dyana_name="H111"/>
>>   <atom iupac_name="H112" cns_name="H112" dyana_name="H112"/>
>>   <atom iupac_name="H121" cns_name="H121" dyana_name="H121"/>
>>   <atom iupac_name="H122" cns_name="H122" dyana_name="H122"/>
>>   <atom iupac_name="H131" cns_name="H131" dyana_name="H131"/>
>>   <atom iupac_name="H132" cns_name="H132" dyana_name="H132"/>
>>   <atom iupac_name="H141" cns_name="H141" dyana_name="H141"/>
>>   <atom iupac_name="H142" cns_name="H142" dyana_name="H142"/>
>>   <atom iupac_name="H151" cns_name="H151" dyana_name="H151"/>
>>   <atom iupac_name="H152" cns_name="H152" dyana_name="H152"/>
>>   <atom iupac_name="H161" cns_name="H161" dyana_name="H161"/>
>>   <atom iupac_name="H162" cns_name="H162" dyana_name="H162"/>
>>   <atom iupac_name="H171" cns_name="H172" dyana_name="H172"/>
>>   <atom iupac_name="H172" cns_name="H172" dyana_name="H172"/>
>>   <atom iupac_name="H181" cns_name="H181" dyana_name="H181"/>
>>   <atom iupac_name="H182" cns_name="H182" dyana_name="H182"/>
>>   <atom iupac_name="H183" cns_name="H183" dyana_name="H183"/>
>>   <atom iupac_name="O1" cns_name="O1" dyana_name="O1"/>
>>   <atom iupac_name="O2" cns_name="O2" dyana_name="O2"/>
>> </residue>
>> 
>> 
>> Dr. Brian O. Smith --------------------------- Brian Smith at glasgow ac uk
>> Institute of Molecular, Cell and Systems Biology & School of Life Sciences,
>>         College of Medical, Veterinary & Life Sciences,
>> Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
>> Tel: 0141 330 5167/6459/3089
>> ----------------------------------------------------------------------
>> The University of Glasgow, charity number SC004401
>> 
>> ________________________________________
>> From: CcpNmr software mailing list [[log in to unmask]] on behalf of Barsukov, Igor [[log in to unmask]]
>> Sent: 28 March 2015 14:43
>> To: [log in to unmask]
>> Subject: Re: small molecule  - ARIA/CCPN error
>> 
>> Hello,
>> 
>> This non-standard molecule is classified as "other" and lacks code3Letter that is used to for the residue name when generating Aria chains from CCPN project. This explains the missing residue name in the PDB file. Is there a way to set code3Letter for non-standard molecules in the project? Or should a different attribute be used for small molecules when generating the chain?
>> 
>> And a related question, would missing code3Letter create a problem when extracting peaks and shift lists from the CCPN project and converting them to Aria format? This is the second error message below.
>> 
>> Thanks
>> Igor
>> 
>> Dr. Igor Barsukov
>> University of Liverpool,
>> Institute of Integrative Biology,
>> Biosciences Building,
>> Crown Street,
>> Liverpool L69 7ZB
>> Tel: +44 151 795 4307
>> 
>> 
>> ________________________________________
>> From: CcpNmr software mailing list [[log in to unmask]] on behalf of Almeida, Teresa [[log in to unmask]]
>> Sent: 27 March 2015 17:16
>> To: [log in to unmask]
>> Subject: small molecule  - ARIA/CCPN error
>> 
>> Hi,
>> 
>> I have a complex between a protein and a small molecule that I would like to use for a structure calculation in ARIA.
>> 
>> The problem is if I try it straight from CCPN into ARIA, the PDB in the directory run1/cns/data/sequence doesn't have  residue name for the small molecule - file attached. I made sure the molecule name in CCPN is a three letter code as a residue would have (in case this was the problem).
>> 
>> The traceback is
>> 
>> ------------------------------------------------
>> Traceback (most recent call last):
>> File "/usr/local/prog/aria_cns/aria2.3/aria2.py", line 903, in <module>
>>   verbose_level, use_condor=condor)
>> File "/usr/local/prog/aria_cns/aria2.3/aria2.py", line 813, in run_aria
>>   project.go(use_condor)
>> File "/usr/local/prog/aria_cns/aria2.3/src/py/aria/Project.py", line 1573, in go
>>   first_iteration = self.finalize()
>> File "/usr/local/prog/aria_cns/aria2.3/src/py/aria/Project.py", line 1558, in finalize
>>   protocol.finalize_engine(self.getMolecule())
>> File "/usr/local/prog/aria_cns/aria2.3/src/py/aria/Protocol.py", line 1525, in finalize_engine
>>   engine.prepare(self.getSettings(), molecule)
>> File "/usr/local/prog/aria_cns/aria2.3/src/py/aria/cns.py", line 1958, in prepare
>>   self.generate_template_pdb(protocol_settings, replace)
>> File "/usr/local/prog/aria_cns/aria2.3/src/py/aria/cns.py", line 1910, in generate_template_pdb
>>   self.error(IOError, s)
>> File "/usr/local/prog/aria_cns/aria2.3/src/py/aria/ariabase.py", line 211, in error
>>   raise exception, msg
>> IOError: USER ERROR <aria.cns.CNS> File "/usr/local/prog/aria_cns/aria2.3/src/py/aria/cns.py", line 1958 in prepare
>> Creation of template PDB-file was not successful.
>> 
>> -----------------------------------------------
>> 
>> If I create the this PDB file myself I get, the following error:
>> 
>> ---------------------------------------------------------------------
>> WARNING [Project]: More than 90% of the cross peaks could not be assigned. This
>>                  might be due to interchanged frequency dimensions or
>>                  undersized frequency windows. Please check your setup.
>> --------------------------------------------------------------------
>> It doesn't seem to recognize any of the assigned peaks belonging to my small molecule.
>> 
>> The only way I managed to get my calculations to work is by creating pdb file manually and convert all the restraints in .tbl files and not using any spectra at all. It doesn't work if I use restraints from CCPN.
>> 
>> Is there an easier way of doing it, where I could use ARIA to extract information of the small molecule from CCPN as one would usually do for proteins?
>> 
>> Thanks in advance.
>> 
>> Kind regards
>> Teresa Almeida
>> 
>> PhD student
>> Department of Chemistry/Institute of Integrative Biology
>> University of Liverpool
>> Liverpool
>> L69 7ZD
>> United Kingdom
>> <prtscrn.png>