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cryoFIT / cryo_fit2

cryo_fit2 source codes, test files, live at .../phenix-xxxx/modules
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no output pdb files #4

Open dhaselb opened 4 years ago

dhaselb commented 4 years ago

Hi,

I am trying to run cryofit2 on one of my maps. It seems it runs. But it ran already for 400 iteration but did not write a single pdb file yet. I am wondering how many iterations does it make? and doesn't it write intermediate files?

Best,

David

kimdn commented 4 years ago

Hello,

Unfortunately, cryo_fit2 is still being developed to optimize for best combinations of MD parameters.

I assume that your current cryo_fit2 is improving cc, that is the best possible case without looking at your log file, this is probably why your run is still running.

Hi Karissa,

Did Nick send subcontract to me yet? I saw at least one citation that actually used cryo_fit recently.

Thank you.

On Sun, Jun 14, 2020 at 12:10 AM dhaselb notifications@github.com wrote:

Hi,

I am trying to run cryofit2 on one of my maps. It seems it runs. But it ran already for 400 iteration but did not write a single pdb file yet. I am wondering how many iterations does it make? and doesn't it write intermediate files?

Best,

David

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dhaselb commented 4 years ago

it is indeed still improving cc and now running 10 days straight. is there anything I can do like lowering the threshold or so?

Best,

David

kimdn commented 4 years ago

If you increase map_weight_multiply as in https://phenix-online.org/documentation/tutorials/cryo_fit2_cmdline.html#options it will improve cc faster,

but too high map_weight_multiply may break secondary structure.

Later real_space_refine, rosetta refine (fastrelax), https://www.phenix-online.org/documentation/reference/model_idealization.html may recover "broken" secondary structure.

Unfortunately, this ideal balancing between map_weight_multiply and maintaining secondary structure needs further optimization either by phenix developer or by myself.

As of now, I'm not sure who can further fund for this optimization project.

The ideal balancing between "map_weight_multiply" and maintaining secondary structure is well optimized for real_space_refine.

On Wed, Jun 17, 2020 at 12:11 PM dhaselb notifications@github.com wrote:

it is indeed still improving cc and now running 10 days straight. is there anything I can do like lowering the threshold or so?

Best,

David

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