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

[Elaine Meng]

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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