Reading and saving large files in chimera
Hi Chimera developers and users,
I have faced a problem with chain IDs and secondary structure while working on a large file. As I am refining my model in Phenix and visualizing in Chimera, I need to go back and forth between these two software and that creates a problem. To replicate my problem, here I have taken an example from PDB so that you get the idea. If I take model bearing PDB id 5IRE and apply "phenix.pdb.biomt_reconstruction" I can generate the complete virus icosahedral structure from the asymmetric unit. But when I open this complete virus structure in Chimera and save it back again the chain IDs get changed. Is there any work around to maintain the original chain IDs and therefore maintain the secondary structure definitions in the file header, after opening and thereafter saving using Chimera?
Best regards,
Tofayel
NTU Singapore
Hi Tofayel, Not being a phenix user, I may need more specifics, like:
- are you getting a single PDB file of the whole capsid from applying the biomt in phenix, and opening that single PDB file in Chimera? - does that file have more than one chain with the same ID, or chain IDs with multiple characters? - is the chain ID different as soon as you read the structure in to Chimera, or is it only different when you write to an output file? - are you saving as Chimera session or writing a single PDB file?
I know the capsid in your example has many chains, so I can only guess that in the file from phenix, there are either duplicate chain IDs or chain IDs with more characters than Chimera or PDB format allow.
One idea is to try using ChimeraX instead. It can write mmCIF format. However, with my limited understanding of what is happening (sorry), I don’t know if that would solve your problem. Best regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 26, 2018, at 4:03 AM, #TOFAYEL AHMED# TOFAYEL001@e.ntu.edu.sg wrote:
Hi Chimera developers and users,
I have faced a problem with chain IDs and secondary structure while working on a large file. As I am refining my model in Phenix and visualizing in Chimera, I need to go back and forth between these two software and that creates a problem. To replicate my problem, here I have taken an example from PDB so that you get the idea. If I take model bearing PDB id 5IRE and apply "phenix.pdb.biomt_reconstruction" I can generate the complete virus icosahedral structure from the asymmetric unit. But when I open this complete virus structure in Chimera and save it back again the chain IDs get changed. Is there any work around to maintain the original chain IDs and therefore maintain the secondary structure definitions in the file header, after opening and thereafter saving using Chimera?
Best regards, Tofayel NTU Singapore
Hi Elaine,
Thanks for getting back to me so promptly. Please find below the google drive link for the files. I am describing what I have in the folder: I have downloaded the model 5IRE from PDB website (filename:5ire.pdb) and applied phenix to operate on the transformation matrix (BIOMT record in REMARK 350) to generate the icosahedral complete virus (filename:5ire_BIOMT_expanded.pdb). Now, phenix has used two letter IDs for the chains and these chain IDs get changed when I open 5ire_BIOMT_expanded.pdb in Chimera1.12. I have then resaved the file again using Chimera1.12 and this file is named as chimera-saved.pdb.
This is just an example case and it closely matches my problem. In real scenario, I need to use fit in map option in chimera and move the coordinates, so there is no way I can avoid "opening my model in chimera and resave them in new position".
Kindly suggest after going through the files !
Link: https://drive.google.com/drive/folders/1p8-QxEDjlszAbQ3M-f9MREo2gCHgIOWQ?usp...
Best regards,
Tofayel
________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: Tuesday, March 27, 2018 1:04:22 AM To: #TOFAYEL AHMED# Cc: UCSF Chimera Mailing List Subject: Re: [Chimera-users] Reading and saving large files in chimera
Hi Tofayel, Not being a phenix user, I may need more specifics, like:
- are you getting a single PDB file of the whole capsid from applying the biomt in phenix, and opening that single PDB file in Chimera? - does that file have more than one chain with the same ID, or chain IDs with multiple characters? - is the chain ID different as soon as you read the structure in to Chimera, or is it only different when you write to an output file? - are you saving as Chimera session or writing a single PDB file?
I know the capsid in your example has many chains, so I can only guess that in the file from phenix, there are either duplicate chain IDs or chain IDs with more characters than Chimera or PDB format allow.
One idea is to try using ChimeraX instead. It can write mmCIF format. However, with my limited understanding of what is happening (sorry), I don’t know if that would solve your problem. Best regards, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 26, 2018, at 4:03 AM, #TOFAYEL AHMED# TOFAYEL001@e.ntu.edu.sg wrote:
Hi Chimera developers and users,
I have faced a problem with chain IDs and secondary structure while working on a large file. As I am refining my model in Phenix and visualizing in Chimera, I need to go back and forth between these two software and that creates a problem. To replicate my problem, here I have taken an example from PDB so that you get the idea. If I take model bearing PDB id 5IRE and apply "phenix.pdb.biomt_reconstruction" I can generate the complete virus icosahedral structure from the asymmetric unit. But when I open this complete virus structure in Chimera and save it back again the chain IDs get changed. Is there any work around to maintain the original chain IDs and therefore maintain the secondary structure definitions in the file header, after opening and thereafter saving using Chimera?
Best regards, Tofayel NTU Singapore
Hi, Tofayel.
Elaine is indisposed for a few days, so I'm looking into this problem.
Unfortunately, from what I can tell, it is a problem with the PDB format itself.The official standard (https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#...) only allows for three-character residue names in columns 18-20 and one-character chain identifiers in column 22. It looks like Phenix, seeing that column 21 is unused, is allowing two-character chain identifiers in columns 21-22. Chimera (and ChimeraX), on the other hand, seeing that column 21 is unused, is allowing four-character residue names. So the string "ASPA1" is interpreted by Phenix as residue "ASP" in chain "A1", but by Chimera as residue "ASPA" in chain "1". (Doubly unfortunate, the one-character chain identifier limit is built into the Chimera data structures so we cannot simply change the PDB parser to support two-character chains.)
As Elaine suggested earlier, your best bet is probably using mmCIF format instead of PDB. mmCIF is not column-based and is explicitly designed to handle very large structures. Phenix version 1.8.2 and later support mmCIF as does ChimeraX. I would not recommend Chimera for large mmCIF files as it requires excessive memory resources and is very slow to boot. (ChimeraX can open 5ire_BIOMT_expanded.pdb in under a minute and renders a beautiful [tooting our own horn :-)] image with ambient occlusion.)
Conrad
On 3/26/2018 10:08 PM, #TOFAYEL AHMED# wrote:
Hi Elaine,
Thanks for getting back to me so promptly. Please find below the google drive link for the files. I am describing what I have in the folder: I have downloaded the model 5IRE from PDB website (filename:5ire.pdb) and applied phenix to operate on the transformation matrix (BIOMT record in REMARK 350) to generate the icosahedral complete virus (filename:5ire_BIOMT_expanded.pdb). Now, phenix has used two letter IDs for the chains and these chain IDs get changed when I open 5ire_BIOMT_expanded.pdb in Chimera1.12. I have then resaved the file again using Chimera1.12 and this file is named as chimera-saved.pdb.
This is just an example case and it closely matches my problem. In real scenario, I need to use fit in map option in chimera and move the coordinates, so there is no way I can avoid "opening my model in chimera and resave them in new position".
Kindly suggest after going through the files !
Link: https://drive.google.com/drive/folders/1p8-QxEDjlszAbQ3M-f9MREo2gCHgIOWQ?usp...
Best regards,
Tofayel
*From:* Elaine Meng meng@cgl.ucsf.edu *Sent:* Tuesday, March 27, 2018 1:04:22 AM *To:* #TOFAYEL AHMED# *Cc:* UCSF Chimera Mailing List *Subject:* Re: [Chimera-users] Reading and saving large files in chimera Hi Tofayel, Not being a phenix user, I may need more specifics, like:
- are you getting a single PDB file of the whole capsid from applying
the biomt in phenix, and opening that single PDB file in Chimera?
- does that file have more than one chain with the same ID, or chain IDs
with multiple characters?
- is the chain ID different as soon as you read the structure in to
Chimera, or is it only different when you write to an output file?
- are you saving as Chimera session or writing a single PDB file?
I know the capsid in your example has many chains, so I can only guess that in the file from phenix, there are either duplicate chain IDs or chain IDs with more characters than Chimera or PDB format allow.
One idea is to try using ChimeraX instead. It can write mmCIF format. However, with my limited understanding of what is happening (sorry), I don’t know if that would solve your problem. Best regards, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 26, 2018, at 4:03 AM, #TOFAYEL AHMED# TOFAYEL001@e.ntu.edu.sg wrote:
Hi Chimera developers and users,
I have faced a problem with chain IDs and secondary structure while working on a large file. As I am refining my model in Phenix and visualizing in Chimera, I need to go back and forth between these two software and that creates a problem. To replicate my problem, here I have taken an example from PDB so that you get the
idea. If I take model bearing PDB id 5IRE and apply "phenix.pdb.biomt_reconstruction" I can generate the complete virus icosahedral structure from the asymmetric unit. But when I open this complete virus structure in Chimera and save it back again the chain IDs get changed. Is there any work around to maintain the original chain IDs and therefore maintain the secondary structure definitions in the file header, after opening and thereafter saving using Chimera?
Best regards, Tofayel NTU Singapore
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Also, just FYI, if you open the regular 5ire mmCIF entry (i.e. asymmetric unit) in ChimeraX, it will show a table of possible assemblies (as listed in the mmCIF file). The first entry in the table is the complete icosahedral virus assembly. If you click on that link in the table it will show the complete assembly.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Mar 27, 2018, at 12:46 PM, Conrad Huang conrad@cgl.ucsf.edu wrote:
Hi, Tofayel.
Elaine is indisposed for a few days, so I'm looking into this problem.
Unfortunately, from what I can tell, it is a problem with the PDB format itself.The official standard (https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#...) only allows for three-character residue names in columns 18-20 and one-character chain identifiers in column 22. It looks like Phenix, seeing that column 21 is unused, is allowing two-character chain identifiers in columns 21-22. Chimera (and ChimeraX), on the other hand, seeing that column 21 is unused, is allowing four-character residue names. So the string "ASPA1" is interpreted by Phenix as residue "ASP" in chain "A1", but by Chimera as residue "ASPA" in chain "1". (Doubly unfortunate, the one-character chain identifier limit is built into the Chimera data structures so we cannot simply change the PDB parser to support two-character chains.)
As Elaine suggested earlier, your best bet is probably using mmCIF format instead of PDB. mmCIF is not column-based and is explicitly designed to handle very large structures. Phenix version 1.8.2 and later support mmCIF as does ChimeraX. I would not recommend Chimera for large mmCIF files as it requires excessive memory resources and is very slow to boot. (ChimeraX can open 5ire_BIOMT_expanded.pdb in under a minute and renders a beautiful [tooting our own horn :-)] image with ambient occlusion.)
Conrad
On 3/26/2018 10:08 PM, #TOFAYEL AHMED# wrote:
Hi Elaine, Thanks for getting back to me so promptly. Please find below the google drive link for the files. I am describing what I have in the folder: I have downloaded the model 5IRE from PDB website (filename:5ire.pdb) and applied phenix to operate on the transformation matrix (BIOMT record in REMARK 350) to generate the icosahedral complete virus (filename:5ire_BIOMT_expanded.pdb). Now, phenix has used two letter IDs for the chains and these chain IDs get changed when I open 5ire_BIOMT_expanded.pdb in Chimera1.12. I have then resaved the file again using Chimera1.12 and this file is named as chimera-saved.pdb. This is just an example case and it closely matches my problem. In real scenario, I need to use fit in map option in chimera and move the coordinates, so there is no way I can avoid "opening my model in chimera and resave them in new position". Kindly suggest after going through the files ! Link: https://drive.google.com/drive/folders/1p8-QxEDjlszAbQ3M-f9MREo2gCHgIOWQ?usp... Best regards, Tofayel
*From:* Elaine Meng meng@cgl.ucsf.edu *Sent:* Tuesday, March 27, 2018 1:04:22 AM *To:* #TOFAYEL AHMED# *Cc:* UCSF Chimera Mailing List *Subject:* Re: [Chimera-users] Reading and saving large files in chimera Hi Tofayel, Not being a phenix user, I may need more specifics, like:
- are you getting a single PDB file of the whole capsid from applying the biomt in phenix, and opening that single PDB file in Chimera?
- does that file have more than one chain with the same ID, or chain IDs with multiple characters?
- is the chain ID different as soon as you read the structure in to Chimera, or is it only different when you write to an output file?
- are you saving as Chimera session or writing a single PDB file?
I know the capsid in your example has many chains, so I can only guess that in the file from phenix, there are either duplicate chain IDs or chain IDs with more characters than Chimera or PDB format allow. One idea is to try using ChimeraX instead. It can write mmCIF format. However, with my limited understanding of what is happening (sorry), I don’t know if that would solve your problem. Best regards, Elaine
Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Mar 26, 2018, at 4:03 AM, #TOFAYEL AHMED# TOFAYEL001@e.ntu.edu.sg wrote: Hi Chimera developers and users, I have faced a problem with chain IDs and secondary structure while working on a large file. As I am refining my model in Phenix and visualizing in Chimera, I need to go back and forth between these two software and that creates a problem. To replicate my problem, here I have taken an example from PDB so that you get the
idea. If I take model bearing PDB id 5IRE and apply "phenix.pdb.biomt_reconstruction" I can generate the complete virus icosahedral structure from the asymmetric unit. But when I open this complete virus structure in Chimera and save it back again the chain IDs get changed. Is there any work around to maintain the original chain IDs and therefore maintain the secondary structure definitions in the file header, after opening and thereafter saving using Chimera?
Best regards, Tofayel NTU Singapore
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Using the links in the Log table adds the copies as graphical clones. To get the all-atom copies (which can be colored independently etc.), you’d need to use a similar “sym” command (as using the links echoes in the Log) but with the option “copies true”.
http://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#copies
(Pardon my terseness… arm injury, difficult to type.)
Elaine
On Mar 27, 2018, at 1:14 PM, Eric Pettersen pett@cgl.ucsf.edu wrote:
Also, just FYI, if you open the regular 5ire mmCIF entry (i.e. asymmetric unit) in ChimeraX, it will show a table of possible assemblies (as listed in the mmCIF file). The first entry in the table is the complete icosahedral virus assembly. If you click on that link in the table it will show the complete assembly.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
Hi Conrad, Eric and Elaine,
Thanks so much for your valuable inputs. I will try to give ChimeraX a shot. From the ChimeraX download page, it looks like installation is difficult in CentOS. I am running CentOS 6.6 with gcc 4.4.7 in my workstation. Any upfront suggestion from your side before I try to install? Sorry, I am not a very techie person !
Best regards, Tofayel
________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: Wednesday, March 28, 2018 4:26:04 AM To: #TOFAYEL AHMED# Cc: Chimera User Help Subject: Re: [Chimera-users] Reading and saving large files in chimera
Using the links in the Log table adds the copies as graphical clones. To get the all-atom copies (which can be colored independently etc.), you’d need to use a similar “sym” command (as using the links echoes in the Log) but with the option “copies true”.
http://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#copies
(Pardon my terseness… arm injury, difficult to type.)
Elaine
On Mar 27, 2018, at 1:14 PM, Eric Pettersen pett@cgl.ucsf.edu wrote:
Also, just FYI, if you open the regular 5ire mmCIF entry (i.e. asymmetric unit) in ChimeraX, it will show a table of possible assemblies (as listed in the mmCIF file). The first entry in the table is the complete icosahedral virus assembly. If you click on that link in the table it will show the complete assembly.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
This link has some info on installing gcc 4.9 on CentOS 6: https://gist.github.com/WisdomFusion/a60285c8f7cd9faf06ef8c9244133219 https://gist.github.com/WisdomFusion/a60285c8f7cd9faf06ef8c9244133219
—Eric
Eric Pettersen UCSF Computer Graphics Lab
On Mar 27, 2018, at 9:04 PM, #TOFAYEL AHMED# TOFAYEL001@e.ntu.edu.sg wrote:
Hi Conrad, Eric and Elaine,
Thanks so much for your valuable inputs. I will try to give ChimeraX a shot. From the ChimeraX download page, it looks like installation is difficult in CentOS. I am running CentOS 6.6 with gcc 4.4.7 in my workstation. Any upfront suggestion from your side before I try to install? Sorry, I am not a very techie person !
Best regards, Tofayel
From: Elaine Meng meng@cgl.ucsf.edu Sent: Wednesday, March 28, 2018 4:26:04 AM To: #TOFAYEL AHMED# Cc: Chimera User Help Subject: Re: [Chimera-users] Reading and saving large files in chimera
Using the links in the Log table adds the copies as graphical clones. To get the all-atom copies (which can be colored independently etc.), you’d need to use a similar “sym” command (as using the links echoes in the Log) but with the option “copies true”.
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#copies http://rbvi.ucsf.edu/chimerax/docs/user/commands/sym.html#copies>
(Pardon my terseness… arm injury, difficult to type.)
Elaine
On Mar 27, 2018, at 1:14 PM, Eric Pettersen pett@cgl.ucsf.edu wrote:
Also, just FYI, if you open the regular 5ire mmCIF entry (i.e. asymmetric unit) in ChimeraX, it will show a table of possible assemblies (as listed in the mmCIF file). The first entry in the table is the complete icosahedral virus assembly. If you click on that link in the table it will show the complete assembly.
—Eric
Eric Pettersen UCSF Computer Graphics Lab
participants (4)
-
#TOFAYEL AHMED# -
Conrad Huang -
Elaine Meng -
Eric Pettersen