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getting residue position over the 2d map #7
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Dear Yogesh, hello to you too, I think the command you are looking for is the following:
Here is an example of such a file:
Please also note that:
Hope I answered your question, let me know if you are facing any issue or have other related questions. |
hi nchenche actually i want to find differential regions in two hydrophobicity plots. so i will have to visually inspect the 2d plot and shortlist the residues which can differentiate two structures(for example two conformations of a protein). so i am doing exactly opposite. also during electrostatics run i am getting error |
Hi Yogesh, Ok I better understand your purpose now. So if you need to compare 2 maps (or more) quantitatively, you can do it with the file found in the
You will have to consider cells for which there is an associated svalue. Unfortunately we don't provide (yet) scripts to do such computations so you will have to build you own in-house tool with your favorite programmatic language. I understand that this is not a really simple solution but this is the only one I am able to provide right now :/ I am going to take a look and try to retrieve a version in which an interactive map could be visualized through a local server. You could for example hover over a cell and it will show you its associated property value and amino acid(s). But I can't guarantee i am gonna find it... |
APBS can be really tricky to install, that is one of the reason we also provide a docker image to prevent the user falling into cumbersome process installation. So I recommend using the docker image for this. For using the docker image of surfmap, you will have to install docker and that's all. Then, since you have already installed the surfmap package, you should be able to use the image by simply adding the
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hi again, i dont know why --docker option as you specified is not working. |
Hi again, I at least understand that you have correctly pulled the docker image. But I have absolutely no idea why If you are comfortable with docker command line, you can do without By the way, I think I get why you don't have any output files. You need to add
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hi nchenche. |
Hello Yogesh, The only thing I can tell is that surfmap has the
Besides that I can't really help. I would advise you though to analyse your binding site residues and their associated electrostatics value computed with surfmap and pymol in order to check if the fact that surfmap map display no major differences in the binding site region is totally inconsistent with what you would expect (in terms of residue composition for instance) |
Hello, in response to APBS issue in this topic, also raised here (1) If after install SURFMAP and APBS (from apt or any other source) we had something like: TypeError: expected str, bytes or os.PathLike object, not NoneType we took the latest APBS release 3.4.1 of pre-compiled binaries (https://github.com/Electrostatics/apbs/releases), downloaded, unpacked and placed its content into /home/USERNAME/apbs (folder after will contain "bin, include, lib and share" sub-folders) and then did path export (export APBS='/home/USERNAME/apbs') using terminal for current session or added this line into .bashrc using vim to open it for all sessions. (2) after we tried to run the standard command surfmap -pdb xyz.pdb -tomap electrostatics. If in this case we had an error like this: SURFACE MAPPING OF THE ELECTROSTATICS PROPERTY so we had to fix a pdb itself, since it may contain something that pdb2pqr/apbs cannot parcel (like doubling chains residues/rotamers). Also adding hydrogens in pymol/chimera and saving in another pdb may solve the problem. (3) if after we run a normal/fixed pdb file and we got something like this: SURFACE MAPPING OF THE ELECTROSTATICS PROPERTY so in this case we went to this file: /home/USERNAME/apbs/share/apbs/tools/manip/psize.py located to the line 173 and in this code fragment we added [i] in nsmall variable in a line 174: After we run everything successfully. Also during installation do not forget to install freesasa dependencies from here (https://freesasa.github.io/doxygen/md__Users_n642254_code_proteins_freesasa_README.html)
otherwise it may "unable to build wheels for freesasa". PS. In addition to the error If pdb file contains charged atoms SPECIFICALLY O1- you may get this error, so you need to clarify the protein structure. N1+pdb2pqr "eats" well. If the pdb file contains specific section prior atoms' coordinates you may get the same error and this section should be removed. |
I have a question regarding the comparison of multiple proteins, you mention that: '_if you need to compare 2 maps (or more) quantitatively, you can do it with the file found in the smoothed_matrices/ directory whose name is suffixed with smoothed_matrices.txt. This file contains all numeric data used to plot the projection: the coordinates of each cell, their associated property value and amino acid(s). ' . In the publication it says that to compare surfaces, proteins need to be structurally aligned prior to running surfmap. Do you have a recommended tool or method you use to align the structures where the output provides separate aligned pdb files? |
You can align protein directly in pymol cealign command.
…On Tue, 19 Mar, 2024, 3:15 pm JonathanLV123, ***@***.***> wrote:
I have a question regarding the comparison of multiple proteins, you
mention that: '_if you need to compare 2 maps (or more) quantitatively, you
can do it with the file found in the smoothed_matrices/ directory whose
name is suffixed with *smoothed_matrices.txt. This file contains all
numeric data used to plot the projection: the coordinates of each cell,
their associated property value and amino acid(s).* ' . In the
publication it says that to compare surfaces, proteins need to be
structurally aligned prior to running surfmap. Do you have a recommended
tool or method you use to align the structures where the output provides
separate aligned pdb files?
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Thank you for the quick response, that is very helpful! |
how can one mark the position or contribution of a particular residues or get the residues responsible for a surface property from surfmap 2d plot
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