Dear Elaine,   thanx! I understand (more or less)... But what if the region I consider includes parts of more symmetry-related subunits? Do I have to make a pdb file including all atoms of the virus then make my selection and save the pdb with the coordinates contributed by adjacent subunits? If so, what would be the best and easiest way of doing so? best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas@meduniwien.ac.at ------------------------------------------------------------------------ On 27.11.2023 18:37, Elaine Meng wrote:

Hi Dieter, The message says literally what you need to include in the name. You can't just give a single name because you are writing out multiple files. For example, if you give a name that includes "$number":

blahblah$number

you would get filenames that include the model number, something like:

blahblah0.1.pdb blahblah0.2.pdb

...and so on.

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Nov 27, 2023, at 9:26 AM, Dieter Blaas via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Hi,

I selected several residues in an icosahedral viral capsid and want to save the corresponding pdb. However, whatever name I try to give this selection I receive the error "You must provide a file name that contains either $name or $number, which will be changed to the model name or model number (respectively) in the final saved file name". Can you please give me an example of a valid name! The viral subunits are 6sk5.pdb1 (#0.1), 6sk5.pdb1 (#0.2), and so on. I have no clue what I should call this selection for it being accepted.

Thanks a lot, Dieter

Dear Elaine,     thank you very much! Saving as a single model did the job! best, Dieter ------------------------------------------------------------------------ Dieter Blaas, Max Perutz Laboratories Medical University of Vienna, Inst. Med. Biochem., Vienna Biocenter (VBC), Dr. Bohr Gasse 9/3, A-1030 Vienna, Austria, Tel: 0043 1 4277 61630, Mobile: 0043 699 1942 1659 e-mail: dieter.blaas@meduniwien.ac.at ------------------------------------------------------------------------ On 27.11.2023 20:30, Elaine Meng wrote:

Hi Dieter,

First thing to consider is whether the subunits are all really loaded as atomic models, or just surfaces. Make sure they are all loaded as atomic models (i.e. it is possible to display atoms) if you want to save their atom coordinates. See "sym" option "surfaces false" to build multimer as full atomic models. <https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html#surfaces>

Second thing to consider is whether these subunits are open as separate models (#0.1,#0.2, ...) vs. a single model. If they are open as separate models, do you want to save the atoms as separate models or a single combined model?

If you want to save as separate models, you can choose (in the PDB-saving dialog) either to save multiple files, or a single multi-model PDB file.

If you want to save the atoms from multiple models as a single model, you would have to combine the subunits into a single model before you save. This can be done with the "copy/combine" option in the Model Panel or the "copy" command. See this previous post for details:

<https://mail.cgl.ucsf.edu/mailman/archives/list/chimera-users@cgl.ucsf.edu/message/XU5LEV6BUV3X5EXJZBZOTLXAC4URXWOH/>

...then save your new combined model.

I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

...

On Nov 27, 2023, at 11:13 AM, Dieter Blaas via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:

Dear Elaine,

thanx! I understand (more or less)... But what if the region I consider includes parts of more symmetry-related subunits? Do I have to make a pdb file including all atoms of the virus then make my selection and save the pdb with the coordinates contributed by adjacent subunits? If so, what would be the best and easiest way of doing so?

best, Dieter