Command line syntax questions
Hi
I am trying to write an alias and am curious if I can do the following using command line (in order to include them in the alias):
1. Separate chains that belong to the same model – can I change the model # on a single chain from an existing model? For example, I built a DNA duplex, selected one chain (sel :.A) and tried to change the model # (combine sel model 8 close true) but the new model also includes chain B. 2. Change residue number of a residue in a chain. I combined a small molecule to a DNA chain between residues 18 and 19, but after combining, the molecule’s residue number remains 1. I would like to change it to 19 or 18. 3. Following point #2, I also want to assign the new molecule the same chain ID – A. In the pdb file, the chain ID is blank for the newly inserted molecule.
Thank you for your help. I also want to mention that the Chimera user discussion portal has been very helpful otherwise!
Best,
-- Divita Mathur Postdoctoral Research Fellow Center for Bio/Molecular Science and Engineering Naval Research Laboratory Washington DC 20375 (202) 767-0687 (Office) divita.mathur.ctr.in@nrl.navy.mil
Hi Divita, Answers interleaved below...
On May 30, 2018, at 10:53 AM, Divita Mathur, Contractor Code 6910, FN divita.mathur.ctr.in@nrl.navy.mil wrote:
Hi I am trying to write an alias and am curious if I can do the following using command line (in order to include them in the alias): • Separate chains that belong to the same model – can I change the model # on a single chain from an existing model? For example, I built a DNA duplex, selected one chain (sel :.A) and tried to change the model # (combine sel model 8 close true) but the new model also includes chain B.
Yes, as mentioned in the “combine” documentation, http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/combine.html “Although a narrower atom-spec may be supplied, the entire model(s) containing the specified atoms will be included in a new model”
Ways to do it: (A) if you want multiple models with different parts of the same initial model, use “split”: http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/split.html
It will make model #0 into model #0.1, #0.2, etc. Even though they have the same main number, you can specify or otherwise deal with them independently like other models. Then if you want to renumber and/or change chain ID, you can use commands “resrenumber” and “changechains”: http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/resrenumber.html http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/changechains.html
(B) simply delete the rest of the structure, e.g. command “delete ~sel” (delete NOT selected) or “delete ~:.a” (delete NOT chain A), command “delete solvent” etc. to get rid of what you don’t want. Then you can change chain ID and residue numbering as above.
• Change residue number of a residue in a chain. I combined a small molecule to a DNA chain between residues 18 and 19, but after combining, the molecule’s residue number remains 1. I would like to change it to 19 or 18.
• Following point #2, I also want to assign the new molecule the same chain ID – A. In the pdb file, the chain ID is blank for the newly inserted molecule.
Sorry, you can’t use “resrenumber” and “changechains” to assign some atoms the same residue number and chain ID as another residue that is already in the model. The easiest way by far is to text-edit the PDB file (using your favorite text-editor outside of Chimera), but of course that can’t be done in your alias.
It sounds like you wanted that molecule to be bonded to something in the DNA. There is a “bond” command, but you would need to specify the two atoms to bond. http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/bond.html
Thank you for your help. I also want to mention that the Chimera user discussion portal has been very helpful otherwise!
You’re welcome, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
Hi Elaine
Thank you for your response. I am using the bond function to bind a molecule to DNA. But the bond function is not changing the residue number of the new molecule (which has a residue number 1), which is causing issues (as there is base #1 in the DNA). So far I am editing the pdb file as a text document like you said, but I was just wondering if there was another way.
Thank you, again! The Split function is working for me!
Hi Divita, I believe you just have to text-edit the PDB file to change the residue number if other atoms already have that same residue number. As you said, “bond” only adds the bond without changing any numbering. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 31, 2018, at 8:42 AM, Divita Mathur, Contractor Code 6910, FN divita.mathur.ctr.in@nrl.navy.mil wrote:
Hi Elaine
Thank you for your response. I am using the bond function to bind a molecule to DNA. But the bond function is not changing the residue number of the new molecule (which has a residue number 1), which is causing issues (as there is base #1 in the DNA). So far I am editing the pdb file as a text document like you said, but I was just wondering if there was another way.
Thank you, again! The Split function is working for me!
Hi all,As mentioned you can use pdb Editor to change the residue numbers.
Sent from Yahoo Mail on Android
On Thu, May 31, 2018 at 9:03 PM, Elaine Mengmeng@cgl.ucsf.edu wrote: Hi Divita, I believe you just have to text-edit the PDB file to change the residue number if other atoms already have that same residue number. As you said, “bond” only adds the bond without changing any numbering. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On May 31, 2018, at 8:42 AM, Divita Mathur, Contractor Code 6910, FN divita.mathur.ctr.in@nrl.navy.mil wrote:
Hi Elaine
Thank you for your response. I am using the bond function to bind a molecule to DNA. But the bond function is not changing the residue number of the new molecule (which has a residue number 1), which is causing issues (as there is base #1 in the DNA). So far I am editing the pdb file as a text document like you said, but I was just wondering if there was another way.
Thank you, again! The Split function is working for me!
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Elaine (and other Chimera users)
I figured that if I have to text-edit eventually, I might as well text edit the molecule in the beginning (assign a random 'X' chainID), then before binding it to the DNA I changechains X A ('A' matches the chainID of the DNA); resrenumber 19 #1 (residue 19 is the desired residue number for the molecule after binding to DNA and #1 is the molecule model #) then I go ahead and combine. Here's the code:
changechains #1:.X A; resrenumber 19 #1; sel #1@P, #0.1:18@O3’; combine sel refSpec #0.1:18 newchainids false close true;
This saves me the hassle of opening the pdb in text file to change the residue number of the molecule.
Hi Divita, You are welcome to try it, but I don’t think that approach will work. That is, it will not let you combine without renumbering or changing chain ID when both input models already have the same residue number with same chain ID. I believe I even tried that yesterday to confirm it didn’t work. Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 1, 2018, at 10:47 AM, Divita Mathur, Contractor Code 6910, FN divita.mathur.ctr.in@nrl.navy.mil wrote:
Hi Elaine (and other Chimera users)
I figured that if I have to text-edit eventually, I might as well text edit the molecule in the beginning (assign a random 'X' chainID), then before binding it to the DNA I changechains X A ('A' matches the chainID of the DNA); resrenumber 19 #1 (residue 19 is the desired residue number for the molecule after binding to DNA and #1 is the molecule model #) then I go ahead and combine. Here's the code:
changechains #1:.X A; resrenumber 19 #1; sel #1@P, #0.1:18@O3’; combine sel refSpec #0.1:18 newchainids false close true;
This saves me the hassle of opening the pdb in text file to change the residue number of the molecule.
Hi Elaine
I will give it a shot (with same residue number). Though I tried the code I sent in the last email and it worked - however, the residue number was different but chain IDs were the same. Now, the molecule is inserted between bases 18 and 20 as residue #19 (I ended up building the DNA with an unnecessary extra base which I deleted to make room for the molecule). Now, the two input models have same chain ID but different residue numbers. I can work with that!
Like you said, perhaps identical residue numbers AND chain ID would not work.
Thank you for this discussion!
participants (3)
-
Divita Mathur, Contractor Code 6910, FN -
Elaine Meng -
Nabil Abid