[chimerax-users] Option Include non-water HETATM in Modeller Comparative

[Marta Martinez]

Thank you very much Elaine.

Best,
MARTA


Quoting Elaine Meng <meng at cgl.ucsf.edu>:

> Hi Marta,
> If you are modeling a monomer and you need to do this immediately,  
> you could use Chimera.  The process is similar except that in  
> Chimera, the sequence-window menu "Structure... Modeller (homology)"  
> is how you show the modeling dialog.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/modeller.html#comparative>
>
> In Chimera, there is at least one thing that may be less convenient:  
> you cannot show the modeling dialog if you only have a single  
> sequence instead of a multiple alignment.  So, if you were only  
> opening the single sequence of the target in ChimeraX, in Chimera  
> there would be an extra step:  using sequence-window menu Edit...  
> Add Sequence, choose the "from structure" tab and add the sequence  
> of the template so that it will be an alignment of 2 sequences.   
> Then you can show the modeling dialog, etc.
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#mavmenu-edit>
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>> On Oct 9, 2020, at 11:41 AM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>>
>> Hi Marta,
>> 	Thanks for reporting this problem.  I have opened a ticket for the  
>> issue: #3814 (HETATM not passed through to Modeller when  
>> requested).  Hopefully we will have it fixed in the next day or two.
>>
>> --Eric
>>
>> 	Eric Pettersen
>> 	UCSF Computer Graphics Lab
>>
>>> On Oct 9, 2020, at 10:45 AM, Marta Martinez <mmmtnez at cnb.csic.es> wrote:
>>>
>>>
>>> Hi all,
>>>
>>> I am running a very simple example in Modeller Comparative (a  
>>> small alignment including the template structure and the target  
>>> sequence to model). Since the template harbors a HEME group, I  
>>> decided to select the Advanced option "Include non-water molecules  
>>> HETATM residues from template". However, no one of the retrieved  
>>> models contains the HEME group. Does anyone know what could be  
>>> happening?
>>>
>>>
>>> Thanks in advance: MARTA
>>> --
>>> Marta Martinez Gonzalez
>>>
>>> Biocomputing Unit (Lab B13)
>>> National Center for Biotechnology-CSIC
>>> Darwin, 3. Campus de la Universidad Autonoma de Madrid
>>> 28049 Madrid. Spain
>>> Tel:+34 915854510 Fax:+34 913720112
>>> E-mail: mmmtnez at cnb.csic.es
>>>
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-- 
Marta Martinez Gonzalez

Biocomputing Unit (Lab B13)
National Center for Biotechnology-CSIC
Darwin, 3. Campus de la Universidad Autonoma de Madrid
28049 Madrid. Spain
Tel:+34 915854510 Fax:+34 913720112
E-mail: mmmtnez at cnb.csic.es