Option Include non-water HETATM in Modeller Comparative
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@cnb.csic.es
Hi Marta, Thanks for reporting this problem. I have opened a ticket for the issue: #3814 (HETATM not passed through to Modeller when requested) <https://www.rbvi.ucsf.edu/trac/ChimeraX/ticket/3814>. 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@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@cnb.csic.es
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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/mo...> 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/mu...> 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@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@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@cnb.csic.es
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thank you very much Elaine. Best, MARTA Quoting Elaine Meng <meng@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/mo...>
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/mu...>
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@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@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@cnb.csic.es
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
-- 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@cnb.csic.es
participants (3)
-
Elaine Meng -
Eric Pettersen -
Marta Martinez