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Hello, I've bumped into a contig error when doing partial diffusion of a PDB composed of chains 'A' and 'B'
When I want to keep fixed chain A but diffuse some residues in chain B by using this cont…
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# The problem
I encoutered some problems when trying to load PDB files that do not have bonds information and more than one chain identifier, such as
```
REMARK original generated coordinate pdb…
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Hi! Nice library, has a lot of potential.
Is there a way to renumber residues?
Renumbering atoms seems trivial (just assign a range to the atom_number), however renumbering residues would probab…
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In mol*, you can click on a residue to generate a detailed view of the atomic interactions surrounding the target residue, including hydrogen bonding interactions. Is there a (easy?) way to achieve th…
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Dear Dr. Mulligan,
I have a question about the script NDM1i_1_design.xml. In the script the pdb 4EXS_Dcys_Lpro.pdb is loaded, where the dipeptide DCys- LPro has residues numbers 301 and 302 respect…
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Hi,
Thank you for all the previous help.
I am having issues with the ExtendModel function. It seems like my selections for the backbone and calphas are correct, but I am continuously getting the…
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Hello, we have used NineTails on a direct RNA run of k562 samples that contains sequins, in which we mapped the SEQUINS only. We would expect all SEQUINS to have only A tails, but we get non-A residue…
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has anyone been able to get --flex or flexible residues in the receptor to work? Or are they interested?
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Hi,
I was simulating a crop/pasture sequence of Lucerne - Lucerne - Lucerne - Lucerne - Canola - Wheat - Barley - Faba Beans - Canola - DP Wheat - Barley. I used SCRUM to account for Faba Beans. My…
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This bug exists for both NHCH3Cap and COCH3 cap.
When PRO is the "socket" residue of the free terminal residue, there will not be a "H" atom to align the conjugation plane.
Can be fixed by aligning …