Hello, I hope you all are well and had a lovely holiday. I have a couple questions. I was able to measure the inner volumes through the directions Tom had given me a couple months ago: open 1lp3 open alphafold prediction matchmaker #2 to #1 sym #2 symmetry #1 copies true molmap #3 12 volume #4 level 0.07 choose "blob", right click to color it surface splitbycolor #4.1 view position #5 sameAs #4 hide #4,5.1 model measure volume #5.2 For some reason, on one of my AAVs it is giving me a different volume that is not accurate. The AAV3B inner volumes seems correct since the sequence for VP4 is shorter, therefore has more space in the inside: AAV3B VP3 only: 2.348 X 10^6 AAV3B VP4 only: 2.488 x 10^6 However, the AAV8 is showing the opposite with VP4 having less space compared to VP3, and the sequences are very similar between AAV3B and AAV8. I am hoping you may know why? or was curious if this may be a bug? And how can I fix it to reflect the data given to me? AAV8 VP3: 2.558 x 10^6 AAV8 VP4: 2.478 x 10^6 I also attached an MSA to help show that the sequences are very similar length wise, so they should come out to be close in inner volume measurements. Last question, I am still learning but is there a way to use the Chimera and ChimeraX through a command prompt with the computer or is the command line the only thing available? I thought maybe I could try to see where the error is coming from using a prompt, but I do not know how to access this. Thank you, and I hope to hear from you soon. Thank you, Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega@bison.howard.edu 520-203-1883
Hi Heather, If there were a bug causing a calculation error, you would not get a value, and there would be an error message in the Log. So even if you did run commands directly from the system prompt, I don't think that would give you any more information than you have already. Stepping back, it sounds like you are expecting a much greater level of precision than this type of calculation can give. Because ChimeraX cannot calculate the volume of a cavity surrounded by surface in which there are holes, it requires first making a density map and then adjusting the density map threshold to make a surface that does not have holes. It is not giving the exact precise volume value that would be given if you calculated a detailed molecular surface and then (in some way we don't have in ChimeraX) blocked off any small openings to the exterior. Secondarily, I don't think you can predict a priori a bigger or smaller volume based solely on sequence length of the capsid protein. Maybe it is a characteristic of this specific system (family of viruses) that I don't know, since I'm not an expert about it... but in general, it would depend on loop conformations, sidechain types and how they pack, etc. For example, a longer sequence could just have an extra domain or loop that sits on the outside without affecting the interior volume. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 10, 2022, at 9:45 AM, Noriega, Heather via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, I hope you all are well and had a lovely holiday. I have a couple questions. I was able to measure the inner volumes through the directions Tom had given me a couple months ago:
open 1lp3 open alphafold prediction matchmaker #2 to #1 sym #2 symmetry #1 copies true molmap #3 12 volume #4 level 0.07 choose "blob", right click to color it surface splitbycolor #4.1 view position #5 sameAs #4 hide #4,5.1 model measure volume #5.2
For some reason, on one of my AAVs it is giving me a different volume that is not accurate. The AAV3B inner volumes seems correct since the sequence for VP4 is shorter, therefore has more space in the inside:
AAV3B VP3 only: 2.348 X 10^6 AAV3B VP4 only: 2.488 x 10^6
However, the AAV8 is showing the opposite with VP4 having less space compared to VP3, and the sequences are very similar between AAV3B and AAV8. I am hoping you may know why? or was curious if this may be a bug? And how can I fix it to reflect the data given to me?
AAV8 VP3: 2.558 x 10^6 AAV8 VP4: 2.478 x 10^6
I also attached an MSA to help show that the sequences are very similar length wise, so they should come out to be close in inner volume measurements.
Last question, I am still learning but is there a way to use the Chimera and ChimeraX through a command prompt with the computer or is the command line the only thing available? I thought maybe I could try to see where the error is coming from using a prompt, but I do not know how to access this.
Thank you, and I hope to hear from you soon.
Thank you,
Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega@bison.howard.edu 520-203-1883 <AAV3B VP3.pdb><AAV8_VP3.pdb><AAV8_VP4.pdb><AAV3BVP4_best_model.pdb><AAV3B_AAV8_MSA.afasta>
Maybe you can try to find alternative ways of measuring the volume (other programs/web servers), then see if they corroborate the estimates from ChimeraX. E.g. see suggestions in earlier posts, Uppsala software factory: Flood + VOIDOO <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-November/002868.html> 3V web server <https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-November/002871.html> I also like Castp but have only used it on pockets in monomers. I don't know if it can be used for something like a virus capsid... <http://sts.bioe.uic.edu/castp/calculation.html> Elaine
On Jan 10, 2022, at 11:07 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Heather, If there were a bug causing a calculation error, you would not get a value, and there would be an error message in the Log. So even if you did run commands directly from the system prompt, I don't think that would give you any more information than you have already.
Stepping back, it sounds like you are expecting a much greater level of precision than this type of calculation can give. Because ChimeraX cannot calculate the volume of a cavity surrounded by surface in which there are holes, it requires first making a density map and then adjusting the density map threshold to make a surface that does not have holes. It is not giving the exact precise volume value that would be given if you calculated a detailed molecular surface and then (in some way we don't have in ChimeraX) blocked off any small openings to the exterior.
Secondarily, I don't think you can predict a priori a bigger or smaller volume based solely on sequence length of the capsid protein. Maybe it is a characteristic of this specific system (family of viruses) that I don't know, since I'm not an expert about it... but in general, it would depend on loop conformations, sidechain types and how they pack, etc. For example, a longer sequence could just have an extra domain or loop that sits on the outside without affecting the interior volume.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 10, 2022, at 9:45 AM, Noriega, Heather via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hello, I hope you all are well and had a lovely holiday. I have a couple questions. I was able to measure the inner volumes through the directions Tom had given me a couple months ago:
open 1lp3 open alphafold prediction matchmaker #2 to #1 sym #2 symmetry #1 copies true molmap #3 12 volume #4 level 0.07 choose "blob", right click to color it surface splitbycolor #4.1 view position #5 sameAs #4 hide #4,5.1 model measure volume #5.2
For some reason, on one of my AAVs it is giving me a different volume that is not accurate. The AAV3B inner volumes seems correct since the sequence for VP4 is shorter, therefore has more space in the inside:
AAV3B VP3 only: 2.348 X 10^6 AAV3B VP4 only: 2.488 x 10^6
However, the AAV8 is showing the opposite with VP4 having less space compared to VP3, and the sequences are very similar between AAV3B and AAV8. I am hoping you may know why? or was curious if this may be a bug? And how can I fix it to reflect the data given to me?
AAV8 VP3: 2.558 x 10^6 AAV8 VP4: 2.478 x 10^6
I also attached an MSA to help show that the sequences are very similar length wise, so they should come out to be close in inner volume measurements.
Last question, I am still learning but is there a way to use the Chimera and ChimeraX through a command prompt with the computer or is the command line the only thing available? I thought maybe I could try to see where the error is coming from using a prompt, but I do not know how to access this.
Thank you, and I hope to hear from you soon.
Thank you,
Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega@bison.howard.edu 520-203-1883 <AAV3B VP3.pdb><AAV8_VP3.pdb><AAV8_VP4.pdb><AAV3BVP4_best_model.pdb><AAV3B_AAV8_MSA.afasta>
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Ok, thank you. I will look into it and discuss with my advisor. I appreciate it. Thank you, Heather Noriega PhD-Pharmaceutical Science student College of Pharmacy Howard University heather.noriega@bison.howard.edu 520-203-1883 On Mon, Jan 10, 2022, 2:26 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Maybe you can try to find alternative ways of measuring the volume (other programs/web servers), then see if they corroborate the estimates from ChimeraX.
E.g. see suggestions in earlier posts,
Uppsala software factory: Flood + VOIDOO < https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-November/002868.html
3V web server < https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-November/002871.html
I also like Castp but have only used it on pockets in monomers. I don't know if it can be used for something like a virus capsid... <http://sts.bioe.uic.edu/castp/calculation.html>
Elaine
On Jan 10, 2022, at 11:07 AM, Elaine Meng via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hi Heather, If there were a bug causing a calculation error, you would not get a value, and there would be an error message in the Log. So even if you did run commands directly from the system prompt, I don't think that would give you any more information than you have already.
Stepping back, it sounds like you are expecting a much greater level of precision than this type of calculation can give. Because ChimeraX cannot calculate the volume of a cavity surrounded by surface in which there are holes, it requires first making a density map and then adjusting the density map threshold to make a surface that does not have holes. It is not giving the exact precise volume value that would be given if you calculated a detailed molecular surface and then (in some way we don't have in ChimeraX) blocked off any small openings to the exterior.
Secondarily, I don't think you can predict a priori a bigger or smaller volume based solely on sequence length of the capsid protein. Maybe it is a characteristic of this specific system (family of viruses) that I don't know, since I'm not an expert about it... but in general, it would depend on loop conformations, sidechain types and how they pack, etc. For example, a longer sequence could just have an extra domain or loop that sits on the outside without affecting the interior volume.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 10, 2022, at 9:45 AM, Noriega, Heather via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:
Hello, I hope you all are well and had a lovely holiday. I have a couple questions. I was able to measure the inner volumes through the directions Tom had given me a couple months ago:
open 1lp3 open alphafold prediction matchmaker #2 to #1 sym #2 symmetry #1 copies true molmap #3 12 volume #4 level 0.07 choose "blob", right click to color it surface splitbycolor #4.1 view position #5 sameAs #4 hide #4,5.1 model measure volume #5.2
For some reason, on one of my AAVs it is giving me a different volume that is not accurate. The AAV3B inner volumes seems correct since the sequence for VP4 is shorter, therefore has more space in the inside:
AAV3B VP3 only: 2.348 X 10^6 AAV3B VP4 only: 2.488 x 10^6
However, the AAV8 is showing the opposite with VP4 having less space compared to VP3, and the sequences are very similar between AAV3B and AAV8. I am hoping you may know why? or was curious if this may be a bug? And how can I fix it to reflect the data given to me?
AAV8 VP3: 2.558 x 10^6 AAV8 VP4: 2.478 x 10^6
I also attached an MSA to help show that the sequences are very similar length wise, so they should come out to be close in inner volume measurements.
Last question, I am still learning but is there a way to use the Chimera and ChimeraX through a command prompt with the computer or is the command line the only thing available? I thought maybe I could try to see where the error is coming from using a prompt, but I do not know how to access this.
Thank you, and I hope to hear from you soon.
Thank you,
Heather Noriega PhD-Pharmaceutical Science student Howard University heather.noriega@bison.howard.edu 520-203-1883 <AAV3B VP3.pdb><AAV8_VP3.pdb><AAV8_VP4.pdb><AAV3BVP4_best_model.pdb><AAV3B_AAV8_MSA.afasta>
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participants (2)
-
Elaine Meng -
Noriega, Heather