How to pairfit with a certain part of multiple structures in a pse file in pymol using command lines

Question

[anndybud]

Hi all,

I am trying to align certain sequences from multiple pdb structures in pymol with command lines using the script in the link. So far, when I use the following command lines:

align_all target=ProteinA, mobile_selection=(resn 40-50+100-125), target_selection=(resn 40-50+100-125), cutoff=2, cycles=5, cgo_object=0, method=align.

I got an error as follows:

ExecutiveAlign: mobile selection must derive from one object only.

Could anyone give me any suggestions on how to modify the command lines to enable the execution? Thank you very much!

Bests,

Yaohui

Google Drive Link

[Ram]

Hi,

Please do not post code on Google Drive. Please use a GitHub Gist (or paste the code here directly). See here: A: How to Use Biostars Part-3: Formatting Text and Using GitHub Gists to learn how.

Also, please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

[anndybud]

Hi, Got it! Sorry about that. Thank you very much for reminding me!

[Ram]

The Google Drive link still exists. Can you please just copy-paste the code here?

Answer 1

[anndybud]

Finally, we tried the following commands to finish the above task in pymol command line:

 fair_fit ProteinA///40-50+100-125/CA, ProteinB///40-50+100-125/CA 
 fair_fit ProteinC///40-50+100-125/CA, ProteinB///40-50+100-125/CA 
...
fair_fit ProteinZ///40-50+100-125/CA, ProteinB///40-50+100-125/CA

Answer 2

[Mensur Dlakic]

Everything is spelled out in the error message:

ExecutiveAlign: mobile selection must derive from one object only.

Are you trying to move only residues 40-50 and separately residues 100-125? How can one do that without moving residues in between (51-99)? I suggest you try (resn 40-125). The error message is telling you that your selection must be a single object, which makes sense because you can move only one object at a time.

There are lots of PyMol tutorials explaining selection, and I think you will save yourself lots of time and frustration by reading through them. Unless this has changed in recent years, PyMol has a very simplistic structural alignment algorithm, and it seems like its command-line structure and error messages are not intuitive enough for you. It may help you to align proteins externally.

[anndybud]

Hi Dlakic, Thank you very much for your suggestions! It makes sense to me. However, I don't understand that if there is only two structures in the pse file, the following command works: pair_fit ProteinA///40-50+100-125/CA, ProteinB///40-50+100-125/CA. I can align the two pdb structures in the pse file in that way. Now I am trying to align multiple structures to ProteinA specifically targeted on residues 40-50 and 100-125 in the similar way. Principally, there should be a way to figure out that execution. Do you have any ideas how to fix that issue? Thank you very much!