From meng at cgl.ucsf.edu  Thu Jun  1 11:09:27 2017
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 1 Jun 2017 11:09:27 -0700
Subject: [Chimera-users] surfaces
In-Reply-To: <004801d2da58$e4700710$ad501530$@umn.edu>
References: <009e01d2d468$6c88d600$459a8200$@umn.edu>
 <DFF6748C-3F4D-4985-AA7A-FEE2DCE5ABBC@cgl.ucsf.edu>
 <000a01d2d9f8$4a6697c0$df33c740$@umn.edu>
 <8FC1F0C9-D351-4C9B-BCB2-B831102AC7EE@cgl.ucsf.edu>
 <004801d2da58$e4700710$ad501530$@umn.edu>
Message-ID: <2A0F47B2-F35E-480D-9544-A8ED455D2A52@cgl.ucsf.edu>

Not that I know of, sorry.

Elaine

> On May 31, 2017, at 2:57 PM, P. Buscemi <busce004 at umn.edu> wrote:
> 
> Thanks Elaine for all your help.
> 
> One small question.  Is there a way to stop a simulation without terminating the program as occurs by using  the command "stop" ?   You know,  in the rare event, things are not quite right.
> 
> Paul
> 




From chiendarret at gmail.com  Mon Jun  5 00:15:38 2017
From: chiendarret at gmail.com (Francesco Pietra)
Date: Mon, 5 Jun 2017 09:15:38 +0200
Subject: [Chimera-users] failure to add-H to quaternary C
Message-ID: <CAEv0nmv3J-ofC+jWg9iHkdce8EhAXU+8s5ynS9NNjOnVRufaoA@mail.gmail.com>

pdbqt from autodock-vina -> pdb with chimera -> addH with chimera.

Chimera fails (systematically) to add one H to a quaternary carbon of the
diterpenoid.

avogadro (which does not understand pdbqt) does the addH job correctly from
chimera-savedpdb.

Should Eric be interested, I could send (privately) the file

best regards

francesco pietra
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From meng at cgl.ucsf.edu  Mon Jun  5 09:46:35 2017
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 5 Jun 2017 09:46:35 -0700
Subject: [Chimera-users] failure to add-H to quaternary C
In-Reply-To: <CAEv0nmv3J-ofC+jWg9iHkdce8EhAXU+8s5ynS9NNjOnVRufaoA@mail.gmail.com>
References: <CAEv0nmv3J-ofC+jWg9iHkdce8EhAXU+8s5ynS9NNjOnVRufaoA@mail.gmail.com>
Message-ID: <CDAFCE56-62F5-496F-88C0-B70CDCAB881A@cgl.ucsf.edu>

HI Francesco,
It is probably that the automatic atom-type identification does not assign the type that you wanted, maybe because it is difficult to tell from the atomic coordinates.  Atom types are listed here:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/idatm.html>

The workaround is simply to change the atom type to sp3 carbon right before adding hydrogens.  In your case, in the model from the pdbqt file, select just the carbon whose type you want to change (Ctrl-click) and then use command

setattr a idatmType C3 sel

Or, instead of ?sel? to specify the selected atom(s), you can specify by name, for example if it was atom C12 in residue DTP:

setattr a idatmType C3 :DTP at C12

You can label to show atom type.  Example commands to label the selected atoms:

labelopt info idatmType
label sel

The labels will not change automatically, so if you showed these labels before changing the type, you have to show labels again (using command or menu) to show the new type.
I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jun 5, 2017, at 12:15 AM, Francesco Pietra <chiendarret at gmail.com> wrote:
> 
> pdbqt from autodock-vina -> pdb with chimera -> addH with chimera.
> 
> Chimera fails (systematically) to add one H to a quaternary carbon of the diterpenoid.
> 
> avogadro (which does not understand pdbqt) does the addH job correctly from chimera-savedpdb.
> 
> Should Eric be interested, I could send (privately) the file
> 
> best regards
> 
> francesco pietra




From meng at cgl.ucsf.edu  Mon Jun  5 09:55:25 2017
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 5 Jun 2017 09:55:25 -0700
Subject: [Chimera-users] Chimera how to question
In-Reply-To: <CAPAU3wcUrc=3CMchErbHcm3c-Fg5AqH+TMfWNc4Mqu8wCez-JQ@mail.gmail.com>
References: <CAPAU3wcUrc=3CMchErbHcm3c-Fg5AqH+TMfWNc4Mqu8wCez-JQ@mail.gmail.com>
Message-ID: <BC58474B-E586-4FCD-8908-465EDD410D0B@cgl.ucsf.edu>



> On Jun 5, 2017, at 5:59 AM, Egor Tchesnokov <tchesnok at ualberta.ca> wrote:
> 
> Hello,
> Is there a way to delete a set of residues in the beginning of the sequence, so these residues disappear from the sequence in the pdb file? 
> I am working on the structure-base alignment and the exogneous residues in the protein sequence (eg. affinity-tag) interfere with the nubmering of the endigenous residues.
> Thank you
> Egor

Hi Egor,
Of course you can delete atoms.  You can select them and then use menu: Actions? Atoms/Bonds? delete, or you can use the ?delete? command ...either with selection (delete sel) or with some other kind of specification of what you wanted to delete, e.g.

delete :1-20.A

...to delete residues 1-20 of chain A.  
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/delete.html>

Maybe in your case it would be easiest to use the sequence window (Favories? Sequence) to select the set of residues you want to delete by dragging a box around them, and then using the menu or command.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/delete.html>

However, this will not change any sequence numbering.  Chimera just uses the numbers that are in the input file.  Sometimes but not always, affinity-tag residues are given negative residue numbers in the input file.  If you want to renumber residues, see menu: Tools.. Structure Editing? Renumber Residues, or the command ?resrenumber?:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/renumber.html>
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/resrenumber.html>

Chimera questions should be sent to chimera-users at cgl.ucsf.edu (CC?d here) to ensure that they will be answered.
I hope this helps,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco





From tchesnok at ualberta.ca  Mon Jun  5 10:09:29 2017
From: tchesnok at ualberta.ca (Egor Tchesnokov)
Date: Mon, 5 Jun 2017 11:09:29 -0600
Subject: [Chimera-users] Chimera how to question
In-Reply-To: <BC58474B-E586-4FCD-8908-465EDD410D0B@cgl.ucsf.edu>
References: <CAPAU3wcUrc=3CMchErbHcm3c-Fg5AqH+TMfWNc4Mqu8wCez-JQ@mail.gmail.com>
 <BC58474B-E586-4FCD-8908-465EDD410D0B@cgl.ucsf.edu>
Message-ID: <CAPAU3wc5k4d6ARrYtdO3j0OS4RVs4VYhKRUp6Xtc32Jca9PxOg@mail.gmail.com>

Thank you so much for the suggestions. I will try them.

In the meantime what worked for now is generating an alignment from
superposition, saving it as .fasta, then opening .fasta file in text editor
and deleting the extra residues by replacing them with dots. Now this
alignment can be used in Espript for example, and numbering is as desired.

Best
Egor

On Mon, Jun 5, 2017 at 10:55 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

>
>
> > On Jun 5, 2017, at 5:59 AM, Egor Tchesnokov <tchesnok at ualberta.ca>
> wrote:
> >
> > Hello,
> > Is there a way to delete a set of residues in the beginning of the
> sequence, so these residues disappear from the sequence in the pdb file?
> > I am working on the structure-base alignment and the exogneous residues
> in the protein sequence (eg. affinity-tag) interfere with the nubmering of
> the endigenous residues.
> > Thank you
> > Egor
>
> Hi Egor,
> Of course you can delete atoms.  You can select them and then use menu:
> Actions? Atoms/Bonds? delete, or you can use the ?delete? command ...either
> with selection (delete sel) or with some other kind of specification of
> what you wanted to delete, e.g.
>
> delete :1-20.A
>
> ...to delete residues 1-20 of chain A.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/delete.html>
>
> Maybe in your case it would be easiest to use the sequence window
> (Favories? Sequence) to select the set of residues you want to delete by
> dragging a box around them, and then using the menu or command.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/delete.html>
>
> However, this will not change any sequence numbering.  Chimera just uses
> the numbers that are in the input file.  Sometimes but not always,
> affinity-tag residues are given negative residue numbers in the input
> file.  If you want to renumber residues, see menu: Tools.. Structure
> Editing? Renumber Residues, or the command ?resrenumber?:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/editing/
> renumber.html>
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/resrenumber.html>
>
> Chimera questions should be sent to chimera-users at cgl.ucsf.edu (CC?d
> here) to ensure that they will be answered.
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>
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From heirtzlerchempro at gmail.com  Mon Jun  5 11:04:06 2017
From: heirtzlerchempro at gmail.com (Fenton Heirtzler)
Date: Mon, 5 Jun 2017 11:04:06 -0700
Subject: [Chimera-users] extracting real numerical values for steric energies
Message-ID: <CAAdrprojKbH76LWdiA5YQgU7ycHoCQ_ZgzQS=24jZtNRCEG6wA@mail.gmail.com>

Hello,
I'm using Chimera to optimize the structures of several small-molecule
transition metal complexes. The goal is to compare the steric energies of
different diastereomers.

I
?'ve searched the local documentation on version 1.11.2 (Macintosh) for the
term "Minimize structure" but found nothing which actually described the
meaning,number format,  reference points and units which are produced by
the "Minimize Structure" command and appear in the "Reply log".

For example, the potential energy values which are returned can be either <
0 or > 0 (!!)

If a minimization is occurring, then the force field will describe those
parameters - but the preceding values make no sense.

Some advice and instruction would be appreciated.

Thanks


*Dr. Fenton Heirtzler*
-------------------------------
Phone: +1-301-312-5145
LinkedIn <http://www.linkedin.com/in/fentonhorgchem/>
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From tulimukhopadhyay2015 at gmail.com  Mon Jun  5 15:27:09 2017
From: tulimukhopadhyay2015 at gmail.com (Tuli Mukhopadhyay)
Date: Mon, 5 Jun 2017 18:27:09 -0400
Subject: [Chimera-users] Chimera files to be read in Pymol?
Message-ID: <CABVwtEFULizXe_oDNS6i2ShBf+SmLxvjm3gQZgG61Zrs3saVsA@mail.gmail.com>

Hello,
Is there a (simple) way to read Chimera session in Pymol or vice versa?
Tuli?

-- 
--
Tuli Mukhopadhyay
Department of Biology
Indiana University
Simon Hall MSBI, Room 220C
212 S. Hawthorne Drive
Bloomington, IN 47405-7003

Phone 812.856.3686
Fax 812.856.5710

sumukhop at indiana.edu  |  Tuli Lab Webpage
<http://www.bio.indiana.edu/~tulilab/>  |  @TuliLab
<https://twitter.com/TuliLab>
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From meng at cgl.ucsf.edu  Mon Jun  5 16:01:16 2017
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 5 Jun 2017 16:01:16 -0700
Subject: [Chimera-users] Chimera files to be read in Pymol?
In-Reply-To: <CABVwtEFULizXe_oDNS6i2ShBf+SmLxvjm3gQZgG61Zrs3saVsA@mail.gmail.com>
References: <CABVwtEFULizXe_oDNS6i2ShBf+SmLxvjm3gQZgG61Zrs3saVsA@mail.gmail.com>
Message-ID: <351289E0-A31A-4B2E-80C8-BC87535B73D6@cgl.ucsf.edu>

Hello Tuli,
Sorry, I don?t know of any converter between Chimera sessions and Pymol sessions.
Best,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jun 5, 2017, at 3:27 PM, Tuli Mukhopadhyay <tulimukhopadhyay2015 at gmail.com> wrote:
> 
> Hello,
> Is there a (simple) way to read Chimera session in Pymol or vice versa?
> Tuli?
> 




From meng at cgl.ucsf.edu  Mon Jun  5 16:25:08 2017
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 5 Jun 2017 16:25:08 -0700
Subject: [Chimera-users] extracting real numerical values for steric
 energies
In-Reply-To: <CAAdrprojKbH76LWdiA5YQgU7ycHoCQ_ZgzQS=24jZtNRCEG6wA@mail.gmail.com>
References: <CAAdrprojKbH76LWdiA5YQgU7ycHoCQ_ZgzQS=24jZtNRCEG6wA@mail.gmail.com>
Message-ID: <CFD65178-FEA7-49A9-BC53-4A8EFBD01EF8@cgl.ucsf.edu>

Hello Dr. Fenton Heirtzler,
I agree it can be difficult to find specifics amongst a lot of text.  I don?t know if this is what you meant, but from the ?Minimize Structure? page:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html>

"Energies (kJ/mol) are reported in the Reply Log. **Step numbers reported by MMTK are 2 greater than the actual numbers of minimization steps performed. The additional ?steps? are not minimization steps but operations required to obtain gradient values and updated coordinates.**?

As I understand it there is no energy decomposition available directly from MMTK to Chimera, and thus only the total energy is reported.  Total energies may be positive or negative depending on whether the positive interactions outweigh the negative interactions and conformational strain.  As there is no decomposition, there is no way to tell how much of the total is from the strain vs. nonbonded interactions, or electrostatic vs. VDW interactions.

That said, my understanding is that simple molecular mechanics with atoms as nonpolarizable point charges is unlikely to provide an accurate representation of transition metal complexes, and Antechamber parametrization was not developed to handle such cases.  This reply from several years ago somewhat addresses this issue, although the URL within it is no longer valid:
<http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-June/001665.html>

In short, you may need to use some other program to accurately model these situations.  I hope this clarifies the situation,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco



> On Jun 5, 2017, at 11:04 AM, Fenton Heirtzler <heirtzlerchempro at gmail.com> wrote:
> 
> Hello,
> I'm using Chimera to optimize the structures of several small-molecule transition metal complexes. The goal is to compare the steric energies of different diastereomers. 
> 
> I?'ve searched the local documentation on version 1.11.2 (Macintosh) for the term "Minimize structure" but found nothing which actually described the meaning,number format,  reference points and units which are produced by the "Minimize Structure" command and appear in the "Reply log".
> 
> For example, the potential energy values which are returned can be either < 0 or > 0 (!!)
> 
> If a minimization is occurring, then the force field will describe those parameters - but the preceding values make no sense.
> 
> Some advice and instruction would be appreciated.
> 
> Thanks
> Dr. Fenton Heirtzler




From 519198561 at 163.com  Mon Jun  5 20:06:17 2017
From: 519198561 at 163.com (=?GBK?B?s8LB+Mfg?=)
Date: Tue, 6 Jun 2017 11:06:17 +0800 (CST)
Subject: [Chimera-users] measure surface area
Message-ID: <52190fb8.431a.15c7b5e02bb.Coremail.519198561@163.com>

Hi!
i want measure several selected residues surface area and volume,  but in the reply log, it always give the total surface area and volume of the protein,   
how can i get only the selected residues surface area? because this residues make a cavity , which may binding substrate.   in addition,  the castP server 
can't give me the pocket i wanted, because it give a bigger pocket than i wanted.
thanks in advance?
liuqing chen





--

Liuqing Chen

School of Life Science & Biotechnology
Minhang Campus
Shanghai Jiao Tong University 

No. 800 Dongchuan Road
Shanghai 200240
P.R. China
Tel: +86 21 34207247
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From heirtzlerchempro at gmail.com  Mon Jun  5 17:24:39 2017
From: heirtzlerchempro at gmail.com (Fenton Heirtzler)
Date: Mon, 5 Jun 2017 17:24:39 -0700
Subject: [Chimera-users] extracting real numerical values for steric
	energies
In-Reply-To: <CFD65178-FEA7-49A9-BC53-4A8EFBD01EF8@cgl.ucsf.edu>
References: <CAAdrprojKbH76LWdiA5YQgU7ycHoCQ_ZgzQS=24jZtNRCEG6wA@mail.gmail.com>
 <CFD65178-FEA7-49A9-BC53-4A8EFBD01EF8@cgl.ucsf.edu>
Message-ID: <CAAdrpros4xzZ5BF2hh3cBNZbnHU2FuP5i1Gy8nWjuZAE-4KUkQ@mail.gmail.com>

Hello Dr. Meng,

Thanks for your explanations on this. Yes, of course Chimera really isn't
even intended to handle the sort of molecules of interest.

The transition metal complexes have organic ligands with asymmetric centers
attached. The idea was to compare the ligand steric interactions while
considering the point chirality about the central tetrahedral copper(I)
center. Not so much molecular orbitals or electronics.

As an organic chemist, I'm more accustomed to seeing energies having
positive values, i.e. stability increases as energy drops. Since Chimera
optimizes according to energies becoming increasingly negative, then it
looks like you're using the opposite scale. For example, for -20 vs -14
kJ/mol , -20 is more stable than -14.

Thanks again and have a nice evening.

Fenton

*Dr. Fenton Heirtzler*
-------------------------------
Phone: +1-301-312-5145
LinkedIn <http://www.linkedin.com/in/fentonhorgchem/>

On Mon, Jun 5, 2017 at 4:25 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hello Dr. Fenton Heirtzler,
> I agree it can be difficult to find specifics amongst a lot of text.  I
> don?t know if this is what you meant, but from the ?Minimize Structure?
> page:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/
> minimize.html>
>
> "Energies (kJ/mol) are reported in the Reply Log. **Step numbers reported
> by MMTK are 2 greater than the actual numbers of minimization steps
> performed. The additional ?steps? are not minimization steps but operations
> required to obtain gradient values and updated coordinates.**?
>
> As I understand it there is no energy decomposition available directly
> from MMTK to Chimera, and thus only the total energy is reported.  Total
> energies may be positive or negative depending on whether the positive
> interactions outweigh the negative interactions and conformational strain.
> As there is no decomposition, there is no way to tell how much of the total
> is from the strain vs. nonbonded interactions, or electrostatic vs. VDW
> interactions.
>
> That said, my understanding is that simple molecular mechanics with atoms
> as nonpolarizable point charges is unlikely to provide an accurate
> representation of transition metal complexes, and Antechamber
> parametrization was not developed to handle such cases.  This reply from
> several years ago somewhat addresses this issue, although the URL within it
> is no longer valid:
> <http://www.cgl.ucsf.edu/pipermail/chimera-users/2007-June/001665.html>
>
> In short, you may need to use some other program to accurately model these
> situations.  I hope this clarifies the situation,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>
> > On Jun 5, 2017, at 11:04 AM, Fenton Heirtzler <
> heirtzlerchempro at gmail.com> wrote:
> >
> > Hello,
> > I'm using Chimera to optimize the structures of several small-molecule
> transition metal complexes. The goal is to compare the steric energies of
> different diastereomers.
> >
> > I?'ve searched the local documentation on version 1.11.2 (Macintosh) for
> the term "Minimize structure" but found nothing which actually described
> the meaning,number format,  reference points and units which are produced
> by the "Minimize Structure" command and appear in the "Reply log".
> >
> > For example, the potential energy values which are returned can be
> either < 0 or > 0 (!!)
> >
> > If a minimization is occurring, then the force field will describe those
> parameters - but the preceding values make no sense.
> >
> > Some advice and instruction would be appreciated.
> >
> > Thanks
> > Dr. Fenton Heirtzler
>
>
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From meng at cgl.ucsf.edu  Tue Jun  6 09:35:00 2017
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 6 Jun 2017 09:35:00 -0700
Subject: [Chimera-users] measure surface area
In-Reply-To: <52190fb8.431a.15c7b5e02bb.Coremail.519198561@163.com>
References: <52190fb8.431a.15c7b5e02bb.Coremail.519198561@163.com>
Message-ID: <4D4C859A-4A81-40DB-BBC4-92D109B0AF33@cgl.ucsf.edu>

Hi Liuqing Chen!
After you show a surface, each residue has a surface area value. If you have selected a group of residues, you can add up their values to get the total for just those residues.   You can also write out a list of the value for each residue.

First, you have to show a surface to calculate the residue areas.  Then each residue has two values, for attributes named areaSES (solvent-excluded surface, which is the one that Chimera displays) and areaSAS (solvent-accessible surface, not shown by Chimera even though the values are calculated). 
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/representation.html#surfaces>

Next, select the set of residues for which you want to get a total.  This is probably the hard part. You could select in many ways, by Shift-Ctrl-click, or by residue number and chain with the ?select? command, by dragging a box in the Sequence window, etc.  
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/selection.html>

Then use the Attribute Calculator tool (menu: Tools? Structure Analysis? Attribute Calculator) to calculate a new attribute of ?molecules? (because you want only one total for the structure) with Formula:  sum(residue.areaSAS)

?or areaSES intead of areaSAS if that?s the one you want.  To use just the selected residues, make sure to turn on the option ?Restrict formula domain to current selection, if any?.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calculator.html>

Or, to just write a list of the individual residue areas, menu: Tools? Structure Analysis? Render by Attribute, and in the resulting dialog, use File? Save Attributes and choose the level (residues) and attribute name (e.g. areaSAS) that you want.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/render/render.html>

Chimera does not have a special pocket-volume calculation like CASTp.  It can only calculate the volume of a pocket that is a completely enclosed bubble of surface, but not ones with an opening (see Tools? Volume Data? Measure and Color Blobs).
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/pickblobs/pickblobs.html>

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


> On Jun 5, 2017, at 8:06 PM, ??? <519198561 at 163.com> wrote:
> 
> Hi!
> i want measure several selected residues surface area and volume,  but in the reply log, it always give the total surface area and volume of the protein,   
> how can i get only the selected residues surface area? because this residues make a cavity , which may binding substrate.   in addition,  the castP server 
> can't give me the pocket i wanted, because it give a bigger pocket than i wanted.
> thanks in advance?
> liuqing chen




From catrajen at umail.iu.edu  Tue Jun  6 13:22:32 2017
From: catrajen at umail.iu.edu (Catherine Jenifer Rajam Rajendran)
Date: Tue, 6 Jun 2017 16:22:32 -0400
Subject: [Chimera-users] Axis Of Symmetry
Message-ID: <CAEJvEi3+YWJk5_f3F2ohHHuSxCZC+F_iwsbr5VmP8PbuU=D-+A@mail.gmail.com>

Hi Eric,

I am trying to find Axis of Symmetry in Dimers. I executed mm command, and then tried to execute measure rotation #0 #1 command. It throws me an error:



I am using chimera version 1.11.2. Can you please help me with this?

Thanks,
Catherine
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From meng at cgl.ucsf.edu  Tue Jun  6 13:33:42 2017
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 6 Jun 2017 13:33:42 -0700
Subject: [Chimera-users] Axis Of Symmetry
In-Reply-To: <CAEJvEi3+YWJk5_f3F2ohHHuSxCZC+F_iwsbr5VmP8PbuU=D-+A@mail.gmail.com>
References: <CAEJvEi3+YWJk5_f3F2ohHHuSxCZC+F_iwsbr5VmP8PbuU=D-+A@mail.gmail.com>
Message-ID: <8EB7A2D7-C94E-4284-94A7-DC0842B9FF90@cgl.ucsf.edu>

Hi Catherine,
(Cc?ing chimera-users at cgl.ucsf.edu which is the recommended address for Chimera questions)

As the message suggests, your models #0 and #1 are not rotated from each other. I?m guessing that you opened the same dimer structure twice and then matched it to itself.  For example, if your structure contains chains A and B, it sounds like A was matched to A and B to B, so there was no rotation (zero degrees).  You have to make sure that the matching is A to B and B to A.  To do this with the ?mm? command, for example, you would have to specify the chains AND use the ?pair ss? option.

There is a specific example of commands for structure 5hvp in this previous post. 
<http://plato.cgl.ucsf.edu/pipermail/chimera-users/2017-April/013290.html>

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



> On Jun 6, 2017, at 1:22 PM, Catherine Jenifer Rajam Rajendran <catrajen at umail.iu.edu> wrote:
> 
> Hi Eric,
> I am trying to find Axis of Symmetry in Dimers. I executed mm command, and then tried to execute measure rotation #0 #1 command. It throws me an error:
> 
> <image.png>
> 
> I am using chimera version 1.11.2. Can you please help me with this?
> Thanks,
> Catherine




From catrajen at umail.iu.edu  Tue Jun  6 13:38:16 2017
From: catrajen at umail.iu.edu (Catherine Jenifer Rajam Rajendran)
Date: Tue, 6 Jun 2017 16:38:16 -0400
Subject: [Chimera-users] Axis Of Symmetry
In-Reply-To: <8EB7A2D7-C94E-4284-94A7-DC0842B9FF90@cgl.ucsf.edu>
References: <CAEJvEi3+YWJk5_f3F2ohHHuSxCZC+F_iwsbr5VmP8PbuU=D-+A@mail.gmail.com>
 <8EB7A2D7-C94E-4284-94A7-DC0842B9FF90@cgl.ucsf.edu>
Message-ID: <CAEJvEi03wPgc2juLwm-x2KdwEEWERx03wySh0J7+EcMH8xg3fQ@mail.gmail.com>

Hi Elaine,

I was missing pair ss in the mm command. Now its working! Thank you so much.

- Catherine

On Tue, Jun 6, 2017 at 4:33 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Catherine,
> (Cc?ing chimera-users at cgl.ucsf.edu which is the recommended address for
> Chimera questions)
>
> As the message suggests, your models #0 and #1 are not rotated from each
> other. I?m guessing that you opened the same dimer structure twice and then
> matched it to itself.  For example, if your structure contains chains A and
> B, it sounds like A was matched to A and B to B, so there was no rotation
> (zero degrees).  You have to make sure that the matching is A to B and B to
> A.  To do this with the ?mm? command, for example, you would have to
> specify the chains AND use the ?pair ss? option.
>
> There is a specific example of commands for structure 5hvp in this
> previous post.
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2017-April/013290.html>
>
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>
> > On Jun 6, 2017, at 1:22 PM, Catherine Jenifer Rajam Rajendran <
> catrajen at umail.iu.edu> wrote:
> >
> > Hi Eric,
> > I am trying to find Axis of Symmetry in Dimers. I executed mm command,
> and then tried to execute measure rotation #0 #1 command. It throws me an
> error:
> >
> > <image.png>
> >
> > I am using chimera version 1.11.2. Can you please help me with this?
> > Thanks,
> > Catherine
>
>
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From pbuscemi at q.com  Tue Jun  6 17:42:23 2017
From: pbuscemi at q.com (P. Buscemi Ph.D.)
Date: Tue, 6 Jun 2017 19:42:23 -0500
Subject: [Chimera-users] model recordings
Message-ID: <005f01d2df26$ee461f90$cad25eb0$@q.com>

 
 
Dear Users groups.
 
I've been struggling  with this issue for some weeks.  I will describe the
problem and then as what information I should supply to help me solve the
issue.
 
It's a prototype adsorption experiment. Water onto polyethylene oxide.  Each
component, when run individually in a simulation will complete in a normal
fashion with a good recorded video. All simulations were run with live
presentation.   However when the two models are run together, the story is
different.
 
The sequence below represents 1) the two loaded files ( water and PEO)  2)
the PEO selected for later constraint  ( control drag)  3) moving the water
into positon.  At this state the " live"  simulation aappears normal.  The
peo does not move, and the water more or less jiggles into position on the
PEO.  However, in running the movie,  molecules of the PEO are disrupted (4)
and occupy the space in fragments  originally occupied by the water
molecules when it was first loaded.  The same phenomenon occurs with a PE
surface and with models of EtOH.  
 
The temperature is set to 0->100K,  Hydrogents added Gasteiger charge
calculation, 0 charge total, no periodic box.  Again, I do not expect any
suggestions ( although none would be refused !) only to ask the proper
channels and information needed to approach the issue.
 
Regards
Paul Buscemi
 
 
 

cid:image002.jpg at 01D2DED8.C01C06501
cid:image001.jpg at 01D2DED8.C01C06502

cid:image002.jpg at 01D2DED8.64FCD8803
cid:image003.jpg at 01D2DED8.64FCD8804
 
 
 
 
    
 
 
 
 
 
 
 
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From nikolaosbismpikos at gmail.com  Wed Jun  7 09:42:36 2017
From: nikolaosbismpikos at gmail.com (Nikolaos Bismpikos)
Date: Wed, 7 Jun 2017 18:42:36 +0200
Subject: [Chimera-users] PDB file opens from chimera GUI but not from python
	script ( )
Message-ID: <CAMGDjVsdMdJixdRrk9sZXc5R9RTROECyBBVt_5T9jKweFnk6wA@mail.gmail.com>

Hello, I am having a problem with trying to open a .pdb file using a python
script.

The file opens and the protein structure is displayed properly when I open
the file using the Chimera GUI. However, when I try to run the code from a
python script, using the demo script for looping through .pdb files I get
the following error:

----------------------------------------------------------------------

File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/re.py", line
251, in _compile
    raise error, v # invalid expression

----------------------------------------------------------------------
This is the code I am trying to run:
----------------------------------------------------------------------

import sys
import os
from chimera import runCommand as rc # use 'rc' as shorthand for runCommand
from chimera import replyobj # for emitting status messages

# change to folder with data files
os.chdir("/home/nick/Python/pdb")
print >> sys.stdout, retval

# gather the names of .pdb files in the folder
file_names = [fn for fn in os.listdir(".") if fn.endswith(".pdb")]

# loop through the files, opening, processing, and closing each in turn
for fn in file_names:
    replyobj.status("Processing " + fn) # show what file we're working on
    rc("open " + fn)
    replyobj.status("Opened " + fn) # show what file we're working on
    rc("align ligand ~ligand") # put ligand in front of remainder of
molecule
    rc("focus ligand") # center/zoom ligand
    rc("surf") # surface receptor
    rc("preset apply publication 1") # make everything look nice
    rc("surftransp 15") # make the surface a little bit see-through
    # save image to a file that ends in .png rather than .pdb
    png_name = fn[:-3] + "png"
    rc("copy file " + png_name + " supersample 3")
    rc("close all")

----------------------------------------------------------------------

The error in more detail, including the traceback from the terminal is the
following:

----------------------------------------------------------------------

Processing prediction[NoEnergy-K:0-BS:0.00]-21(20.310186).pdb

Traceback (most recent call last):
  File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimeraInit.py", line
683, in init
    chimera.openModels.open(a, prefixableType=1)
  File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/__init__.py",
line 1929, in open
    models = func(filename, *args, **kw)
  File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/__init__.py",
line 1299, in _openPython
    loadFunc(sandboxName, fileName, f)
  File "test1.py", line 23, in <module>
    rc("open " + fn)
  File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/__init__.py",
line 2747, in runCommand
    makeCommand(*args, **kw)
  File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/Midas/midas_text.py",
line 69, in makeCommand
    f(c, args)
  File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/Midas/midas_text.py",
line 1552, in doOpen
    paths = testPath(text, wildcarding)
  File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/Midas/midas_text.py",
line 1538, in testPath
    return glob(expanded)
  File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/glob.py",
line 27, in glob
    return list(iglob(pathname))
  File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/glob.py",
line 49, in iglob
    for name in glob1(os.curdir, basename):
  File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/glob.py",
line 83, in glob1
    return fnmatch.filter(names, pattern)
  File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/fnmatch.py",
line 56, in filter
    _cache[pat] = re_pat = re.compile(res)
  File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/re.py", line
194, in compile
    return _compile(pattern, flags)
  File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/re.py", line
251, in _compile
    raise error, v # invalid expression
error: bad character range

Error while processing test1.py:
error: bad character range

  File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/re.py", line
251, in _compile
    raise error, v # invalid expression

See reply log for Python traceback.


----------------------------------------------------------------------
The error obviously appears at the 2nd line of the for loop (  rc("open " +
fn) )

Any tips on why this might happen? I am using Ubuntu 14.04 LTS and the
Chimera version I installed is chimera-1.11.2-linux_x86_64.bin
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From meng at cgl.ucsf.edu  Wed Jun  7 10:02:48 2017
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 7 Jun 2017 10:02:48 -0700
Subject: [Chimera-users] model recordings
In-Reply-To: <005f01d2df26$ee461f90$cad25eb0$@q.com>
References: <005f01d2df26$ee461f90$cad25eb0$@q.com>
Message-ID: <D710BE54-1018-4DCC-BB97-15080410C1A4@cgl.ucsf.edu>

Dear Paul,
You may be stretching the program far beyond what it was intended to do.  You might want to ask on CCL.net what might be a more appropriate program to simulate your system.

I assume you are still using the Molecular Dynamics Simulation tool to actually calculate the trajectory, and then using the MD Movie tool to view and record it as a movie file.  Your description is very confusing because it melds these two separate things into one.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>

The first tool (simulation) requires specifying which model to use.  One idea is that the water and the PE surface may be two different models, which isn?t handled by the tool.  Another idea is that the hand-positioning generated a few overlapping atoms which gives  extremely large forces that can make molecules explode.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco




> On Jun 6, 2017, at 5:42 PM, P. Buscemi Ph.D. <pbuscemi at q.com> wrote:
> 
>  
>  
> Dear Users groups.
>  
> I?ve been struggling  with this issue for some weeks.  I will describe the problem and then as what information I should supply to help me solve the issue.
>  
> It?s a prototype adsorption experiment. Water onto polyethylene oxide.  Each component, when run individually in a simulation will complete in a normal fashion with a good recorded video. All simulations were run with live presentation.   However when the two models are run together, the story is different.
>  
> The sequence below represents 1) the two loaded files ( water and PEO)  2) the PEO selected for later constraint  ( control drag)  3) moving the water into positon.  At this state the ? live?  simulation aappears normal.  The peo does not move, and the water more or less jiggles into position on the PEO.  However, in running the movie,  molecules of the PEO are disrupted (4)  and occupy the space in fragments  originally occupied by the water molecules when it was first loaded.  The same phenomenon occurs with a PE surface and with models of EtOH.  
>  
> The temperature is set to 0->100K,  Hydrogents added Gasteiger charge calculation, 0 charge total, no periodic box.  Again, I do not expect any suggestions ( although none would be refused !) only to ask the proper channels and information needed to approach the issue.
>  
> Regards
> Paul Buscemi
>  
>  
>  
> <image001.jpg>1
> <image002.jpg>2
> <image003.jpg>3
> <image004.jpg>4
>  
>  
>  
>  
>     
>  
>  
>  
>  
>  
>  
>  
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users




From pett at cgl.ucsf.edu  Wed Jun  7 10:19:42 2017
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Wed, 7 Jun 2017 10:19:42 -0700
Subject: [Chimera-users] PDB file opens from chimera GUI but not from
 python script ( )
In-Reply-To: <CAMGDjVsdMdJixdRrk9sZXc5R9RTROECyBBVt_5T9jKweFnk6wA@mail.gmail.com>
References: <CAMGDjVsdMdJixdRrk9sZXc5R9RTROECyBBVt_5T9jKweFnk6wA@mail.gmail.com>
Message-ID: <3D4A2B6C-2439-4082-A9C6-62593211F18B@cgl.ucsf.edu>

It looks like some of your file names have non-alphanumeric characters in them, which is causing the ?wildcard matching? of file names to throw an error.  In the script, instead of:

	rc(?open ? + fn)

try:

	rc(?open nowildcard ? + fn)

If that still doesn?t work, try:

	rc(?open ?? + fn + ???)

(i.e. single quote just before the double quote that ends the first string, and single quote between two double quotes in the second string).

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Jun 7, 2017, at 9:42 AM, Nikolaos Bismpikos <nikolaosbismpikos at gmail.com> wrote:
> 
> Hello, I am having a problem with trying to open a .pdb file using a python script.
> 
> The file opens and the protein structure is displayed properly when I open the file using the Chimera GUI. However, when I try to run the code from a python script, using the demo script for looping through .pdb files I get the following error:
> 
> ----------------------------------------------------------------------
> 
> File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/re.py", line 251, in _compile
>     raise error, v # invalid expression
> 
> ----------------------------------------------------------------------
> This is the code I am trying to run:
> ----------------------------------------------------------------------
> 
> import sys
> import os
> from chimera import runCommand as rc # use 'rc' as shorthand for runCommand
> from chimera import replyobj # for emitting status messages
> 
> # change to folder with data files
> os.chdir("/home/nick/Python/pdb")
> print >> sys.stdout, retval
> 
> # gather the names of .pdb files in the folder
> file_names = [fn for fn in os.listdir(".") if fn.endswith(".pdb")]
> 
> # loop through the files, opening, processing, and closing each in turn
> for fn in file_names:
>     replyobj.status("Processing " + fn) # show what file we're working on
>     rc("open " + fn)
>     replyobj.status("Opened " + fn) # show what file we're working on
>     rc("align ligand ~ligand") # put ligand in front of remainder of molecule
>     rc("focus ligand") # center/zoom ligand
>     rc("surf") # surface receptor
>     rc("preset apply publication 1") # make everything look nice
>     rc("surftransp 15") # make the surface a little bit see-through
>     # save image to a file that ends in .png rather than .pdb
>     png_name = fn[:-3] + "png"
>     rc("copy file " + png_name + " supersample 3")
>     rc("close all")
> 
> ----------------------------------------------------------------------
> 
> The error in more detail, including the traceback from the terminal is the following:
> 
> ----------------------------------------------------------------------
> 
> Processing prediction[NoEnergy-K:0-BS:0.00]-21(20.310186).pdb
> 
> Traceback (most recent call last):
>   File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimeraInit.py", line 683, in init
>     chimera.openModels.open(a, prefixableType=1)
>   File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/__init__.py", line 1929, in open
>     models = func(filename, *args, **kw)
>   File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/__init__.py", line 1299, in _openPython
>     loadFunc(sandboxName, fileName, f)
>   File "test1.py", line 23, in <module>
>     rc("open " + fn)
>   File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/__init__.py", line 2747, in runCommand
>     makeCommand(*args, **kw)
>   File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/Midas/midas_text.py", line 69, in makeCommand
>     f(c, args)
>   File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/Midas/midas_text.py", line 1552, in doOpen
>     paths = testPath(text, wildcarding)
>   File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/Midas/midas_text.py", line 1538, in testPath
>     return glob(expanded)
>   File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/glob.py", line 27, in glob
>     return list(iglob(pathname))
>   File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/glob.py", line 49, in iglob
>     for name in glob1(os.curdir, basename):
>   File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/glob.py", line 83, in glob1
>     return fnmatch.filter(names, pattern)
>   File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/fnmatch.py", line 56, in filter
>     _cache[pat] = re_pat = re.compile(res)
>   File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/re.py", line 194, in compile
>     return _compile(pattern, flags)
>   File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/re.py", line 251, in _compile
>     raise error, v # invalid expression
> error: bad character range
> 
> Error while processing test1.py:
> error: bad character range
> 
>   File "/home/nick/.local/UCSF-Chimera64-1.11.2/lib/python2.7/re.py", line 251, in _compile
>     raise error, v # invalid expression
> 
> See reply log for Python traceback.
> 
> 
> ----------------------------------------------------------------------
> The error obviously appears at the 2nd line of the for loop (  rc("open " + fn) ) 
> 
> Any tips on why this might happen? I am using Ubuntu 14.04 LTS and the Chimera version I installed is chimera-1.11.2-linux_x86_64.bin
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From pbuscemi at q.com  Wed Jun  7 11:23:48 2017
From: pbuscemi at q.com (pbuscemi)
Date: Wed, 7 Jun 2017 13:23:48 -0500
Subject: [Chimera-users] model recordings
In-Reply-To: <D710BE54-1018-4DCC-BB97-15080410C1A4@cgl.ucsf.edu>
References: <005f01d2df26$ee461f90$cad25eb0$@q.com>
 <D710BE54-1018-4DCC-BB97-15080410C1A4@cgl.ucsf.edu>
Message-ID: <00ab01d2dfbb$355b4ce0$a011e6a0$@q.com>

Thanks Elaine,

Your assumptions were correct..and I apologize for the poor description.

  If I were to open the two files as two models - surface and water - and select only water to run the simulation ( only water is active ) would the water  know the surface was present ?

Paul

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Wednesday, June 07, 2017 12:03 PM
To: P. Buscemi Ph.D.
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] model recordings

Dear Paul,
You may be stretching the program far beyond what it was intended to do.  You might want to ask on CCL.net what might be a more appropriate program to simulate your system.

I assume you are still using the Molecular Dynamics Simulation tool to actually calculate the trajectory, and then using the MD Movie tool to view and record it as a movie file.  Your description is very confusing because it melds these two separate things into one.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>

The first tool (simulation) requires specifying which model to use.  One idea is that the water and the PE surface may be two different models, which isn?t handled by the tool.  Another idea is that the hand-positioning generated a few overlapping atoms which gives  extremely large forces that can make molecules explode.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco




> On Jun 6, 2017, at 5:42 PM, P. Buscemi Ph.D. <pbuscemi at q.com> wrote:
> 
>  
>  
> Dear Users groups.
>  
> I?ve been struggling  with this issue for some weeks.  I will describe the problem and then as what information I should supply to help me solve the issue.
>  
> It?s a prototype adsorption experiment. Water onto polyethylene oxide.  Each component, when run individually in a simulation will complete in a normal fashion with a good recorded video. All simulations were run with live presentation.   However when the two models are run together, the story is different.
>  
> The sequence below represents 1) the two loaded files ( water and PEO)  2) the PEO selected for later constraint  ( control drag)  3) moving the water into positon.  At this state the ? live?  simulation aappears normal.  The peo does not move, and the water more or less jiggles into position on the PEO.  However, in running the movie,  molecules of the PEO are disrupted (4)  and occupy the space in fragments  originally occupied by the water molecules when it was first loaded.  The same phenomenon occurs with a PE surface and with models of EtOH.  
>  
> The temperature is set to 0->100K,  Hydrogents added Gasteiger charge calculation, 0 charge total, no periodic box.  Again, I do not expect any suggestions ( although none would be refused !) only to ask the proper channels and information needed to approach the issue.
>  
> Regards
> Paul Buscemi
>  
>  
>  
> <image001.jpg>1
> <image002.jpg>2
> <image003.jpg>3
> <image004.jpg>4
>  
>  
>  
>  
>     
>  
>  
>  
>  
>  
>  
>  
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu Manage 
> subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users




From meng at cgl.ucsf.edu  Wed Jun  7 12:37:49 2017
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 7 Jun 2017 12:37:49 -0700
Subject: [Chimera-users] model recordings
In-Reply-To: <00ab01d2dfbb$355b4ce0$a011e6a0$@q.com>
References: <005f01d2df26$ee461f90$cad25eb0$@q.com>
 <D710BE54-1018-4DCC-BB97-15080410C1A4@cgl.ucsf.edu>
 <00ab01d2dfbb$355b4ce0$a011e6a0$@q.com>
Message-ID: <731ECCAE-36C8-430A-8D26-CA136F3A6C35@cgl.ucsf.edu>

Hi Paul,
>From the manual page for Molecular Dynamics Simulation:

"Select model: The model of interest should be chosen by clicking to highlight its name in the list of models. All of the atoms for simulation should be included in this model; any other models will be ignored.?

You can see that page by clicking the Help button on the tool dialog, or view the copy on our website:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html>

Elaine

> On Jun 7, 2017, at 11:23 AM, pbuscemi <pbuscemi at q.com> wrote:
> 
> Thanks Elaine,
> 
> Your assumptions were correct..and I apologize for the poor description.
> 
>  If I were to open the two files as two models - surface and water - and select only water to run the simulation ( only water is active ) would the water  know the surface was present ?
> 
> Paul




From pbuscemi at q.com  Thu Jun  8 12:37:58 2017
From: pbuscemi at q.com (P. Buscemi Ph.D.)
Date: Thu, 8 Jun 2017 14:37:58 -0500
Subject: [Chimera-users] model recordings
In-Reply-To: <D710BE54-1018-4DCC-BB97-15080410C1A4@cgl.ucsf.edu>
References: <005f01d2df26$ee461f90$cad25eb0$@q.com>
 <D710BE54-1018-4DCC-BB97-15080410C1A4@cgl.ucsf.edu>
Message-ID: <001e01d2e08e$bc37ff50$34a7fdf0$@q.com>

Elaine,

I found that placing all the components into one file helps tremendously.  The video shows a droplet of water forming on PE along with adsorption  of PVP.  None of the disruption, seen sing separate files, was noted in several trials.

 I think Chimera is up to the task.

Paul

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Wednesday, June 07, 2017 12:03 PM
To: P. Buscemi Ph.D.
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] model recordings

Dear Paul,
You may be stretching the program far beyond what it was intended to do.  You might want to ask on CCL.net what might be a more appropriate program to simulate your system.

I assume you are still using the Molecular Dynamics Simulation tool to actually calculate the trajectory, and then using the MD Movie tool to view and record it as a movie file.  Your description is very confusing because it melds these two separate things into one.
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>

The first tool (simulation) requires specifying which model to use.  One idea is that the water and the PE surface may be two different models, which isn?t handled by the tool.  Another idea is that the hand-positioning generated a few overlapping atoms which gives  extremely large forces that can make molecules explode.
I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco



>  
>  
>  
>  
>  
>  
>  
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu Manage 
> subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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From meng at cgl.ucsf.edu  Fri Jun  9 12:18:46 2017
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 9 Jun 2017 12:18:46 -0700
Subject: [Chimera-users] Axis Of Symmetry
In-Reply-To: <CAEJvEi2fJP31MBDzeh+h31j4YKiFL_JVbq4UVjMKyqGo7QAFNA@mail.gmail.com>
References: <CAEJvEi3+YWJk5_f3F2ohHHuSxCZC+F_iwsbr5VmP8PbuU=D-+A@mail.gmail.com>
 <8EB7A2D7-C94E-4284-94A7-DC0842B9FF90@cgl.ucsf.edu>
 <CAEJvEi2fJP31MBDzeh+h31j4YKiFL_JVbq4UVjMKyqGo7QAFNA@mail.gmail.com>
Message-ID: <DA179028-675E-4EC8-82EB-E1CDC11B5065@cgl.ucsf.edu>

Hi Catherine,
Please send Chimera questions to chimera-users at cgl.ucsf (CC?d here) to ensure a response.

This "measure rotation? command does not use any atoms, it merely reports how a model is currently rotated and translated relative to the another model.  The rotating/translating is done by the matching command before that measurement.  From our previous emails I see you were using the ?matchmaker?  command (same as ?mmaker?) which, as described in the manual, uses only CA atoms:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html>

If you want to use other atoms in the fitting, you have to instead use the ?match? command with the specific atoms given in the command.  See the manual:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/matchmaker.html>

See also the page on ?Superimposing Structures?
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/superposition.html>

and for a specific example, the ?Matching? section in the Glycoside Hydrolases tutorial:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/frameimages.html>

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


> On Jun 9, 2017, at 12:02 PM, Catherine Jenifer Rajam Rajendran <catrajen at umail.iu.edu> wrote:
> 
> Hi Elaine,
> 
> Can you tell me how Axis is configured? after using the command measure rotation, it gives me the reply log with information like axis, axis point, rotation angle etc., But I want to know specifically if Axis is calculated by just using the CA atoms of the chains or All atoms? Is there a way to find axis only using CA/All atoms.
> 
> Thanks,
> Catherine
> 
> On Tue, Jun 6, 2017 at 4:33 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> Hi Catherine,
> (Cc?ing chimera-users at cgl.ucsf.edu which is the recommended address for Chimera questions)
> 
> As the message suggests, your models #0 and #1 are not rotated from each other. I?m guessing that you opened the same dimer structure twice and then matched it to itself.  For example, if your structure contains chains A and B, it sounds like A was matched to A and B to B, so there was no rotation (zero degrees).  You have to make sure that the matching is A to B and B to A.  To do this with the ?mm? command, for example, you would have to specify the chains AND use the ?pair ss? option.
> 
> There is a specific example of commands for structure 5hvp in this previous post.
> <http://plato.cgl.ucsf.edu/pipermail/chimera-users/2017-April/013290.html>
> 
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
> 
> > On Jun 6, 2017, at 1:22 PM, Catherine Jenifer Rajam Rajendran <catrajen at umail.iu.edu> wrote:
> >
> > Hi Eric,
> > I am trying to find Axis of Symmetry in Dimers. I executed mm command, and then tried to execute measure rotation #0 #1 command. It throws me an error:
> >
> > <image.png>
> >
> > I am using chimera version 1.11.2. Can you please help me with this?
> > Thanks,
> > Catherine
> 
> 




From shabnam.nadjafi at gmail.com  Sun Jun 11 02:08:38 2017
From: shabnam.nadjafi at gmail.com (Shabnam Nadjafi)
Date: Sun, 11 Jun 2017 13:38:38 +0430
Subject: [Chimera-users] Question about Chimera
Message-ID: <CAAeZFmp1s8UuCv7WzX-YREOoL18dk_R-cBn7Ph1THE98YVoE=A@mail.gmail.com>

Dear Manager

I have a question about "Chimera".
Is " "Chimera" free ? Can this program be used without license and complete
freely?

Thanks,
Sincerely Yours,

Shabnam Nadjafi
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From visvaldaskairys at gmail.com  Mon Jun 12 01:57:26 2017
From: visvaldaskairys at gmail.com (Visvaldas Kairys)
Date: Mon, 12 Jun 2017 11:57:26 +0300
Subject: [Chimera-users] DockPrep sometimes fails with altPos
Message-ID: <80DB3DBF-EBA9-4E21-A565-E6281B668115@gmail.com>

Dear Chimera users and developers,

I?d like to point out I often have a minor inconvenience when dealing with high resolution Xray structures when trying to add hydrogens
via DockPrep. 

If two consecutive residues have both alternative postions A and B, Chimera in the process of hydrogen addition often gets confused 
and puts ?TER? between the
residues, also reporting non-integer charges in the log. I think what is happening, the program picks ?A? variant for one residue and ?B? for the consecutive residue, and apparently this causes bond detection algorithm to ignore the bond between the residues (due to length I guess).
I resolve this by manually editing out one of the AltPos (say, ?B?) out of the PDB file for the offending residues, 
but I guess the program should be able to do it automatically.

A PDB example where this happens is 2r3i (or 2r3r).

Best regards,

Vis





From meng at cgl.ucsf.edu  Mon Jun 12 09:41:17 2017
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 12 Jun 2017 09:41:17 -0700
Subject: [Chimera-users] Question about Chimera
In-Reply-To: <CAAeZFmp1s8UuCv7WzX-YREOoL18dk_R-cBn7Ph1THE98YVoE=A@mail.gmail.com>
References: <CAAeZFmp1s8UuCv7WzX-YREOoL18dk_R-cBn7Ph1THE98YVoE=A@mail.gmail.com>
Message-ID: <287A146A-6ADA-4FA3-B1CC-E8ABB1E7A687@cgl.ucsf.edu>

Dear Shabnam Nadjafi,

The complete information is on the Chimera website, see ?licensing? here:
<http://www.rbvi.ucsf.edu/chimera/docs/licensing.html>

In summary:

Chimera is free for noncommercial use, but you will need to agree to the license that is automatically shown when you download the program.

To get Chimera for commercial use, you should contact chimera at cgl.ucsf.edu about the cost and terms.

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

> On Jun 11, 2017, at 2:08 AM, Shabnam Nadjafi <shabnam.nadjafi at gmail.com> wrote:
> 
> Dear Manager
> I have a question about "Chimera".  
> Is " "Chimera" free ? Can this program be used without license and complete freely?
> Thanks, 
> Sincerely Yours,
> Shabnam Nadjafi




From pochapsk at brandeis.edu  Mon Jun 12 10:35:01 2017
From: pochapsk at brandeis.edu (Thomas Pochapsky)
Date: Mon, 12 Jun 2017 13:35:01 -0400
Subject: [Chimera-users] sphere transparency
Message-ID: <1d6a3c8d-f546-be5a-4361-f2e990667187@brandeis.edu>

Is there any command corresponding to surft (surface transparency) that 
will modulate the visibility of a sphere representation of a ligand?  I 
want to change it in the course of a morph between substrate-bound and 
substrate free forms of the same enzyme.  I will probably have other 
questions, but this seems like a good place to start...

Thanks,
Tom Pochapsky



From meng at cgl.ucsf.edu  Mon Jun 12 10:50:09 2017
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 12 Jun 2017 10:50:09 -0700
Subject: [Chimera-users] sphere transparency
In-Reply-To: <1d6a3c8d-f546-be5a-4361-f2e990667187@brandeis.edu>
References: <1d6a3c8d-f546-be5a-4361-f2e990667187@brandeis.edu>
Message-ID: <C47BF3F7-B735-4812-9338-58E748F3C288@cgl.ucsf.edu>

Hi Tom,
The broader command is simply ?transparency? ? it applies to not only surfaces, but also atomic representations, ribbons, etc. (whichever you specify) and there is a ?frames? option for fading in/out over a specified number of frames.  So for example with this ligand in 2gbp, the last command would fade it from the initial 0% to 100% transparent over 100 frames:

open 2gbp
show :bgc
repr sphere :bgc
transp 100,a :bgc  frames 100

? in this case ?ligand? could be used instead of ?:bgc? but I showed a more general case of specifying by residue name, since ?ligand? doesn?t always get what you want.  The ?,a? means to affect atomic representations, not surfaces, ribbons, etc.  See the manpage:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/transparency.html>

The ?surftransparency? manpage (e.g. shown with command ?help surftransparency? refers to this ?transparency? command which essentially replaces it, although surftransparency still works too.   See also the movie-related commands list, including ?coordset? to play through your morph.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands>

There is also a list of all commands, of course?
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>

? and you can also use "Help? Search Documentation? in the menu to search for specific terms like ?transparency"

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

> On Jun 12, 2017, at 10:35 AM, Thomas Pochapsky <pochapsk at brandeis.edu> wrote:
> 
> Is there any command corresponding to surft (surface transparency) that will modulate the visibility of a sphere representation of a ligand?  I want to change it in the course of a morph between substrate-bound and substrate free forms of the same enzyme.  I will probably have other questions, but this seems like a good place to start...
> Thanks,
> Tom Pochapsky




From pochapsk at brandeis.edu  Mon Jun 12 13:12:05 2017
From: pochapsk at brandeis.edu (Thomas Pochapsky)
Date: Mon, 12 Jun 2017 16:12:05 -0400
Subject: [Chimera-users] sphere transparency
In-Reply-To: <C47BF3F7-B735-4812-9338-58E748F3C288@cgl.ucsf.edu>
References: <1d6a3c8d-f546-be5a-4361-f2e990667187@brandeis.edu>
 <C47BF3F7-B735-4812-9338-58E748F3C288@cgl.ucsf.edu>
Message-ID: <f5f737c9-48f5-1484-606e-a73bb2d9c106@brandeis.edu>

Thanks, Elaine,

This works independently (just applying through the per-frame script in 
the movie viewer), but I am trying to integrate it with the morph that I 
generated (120 frames); right now it keeps flashing the structure of the 
ligand as it appears to fade back and forth on each frame of the morph 
(at least that is what it looks like to me).

Here are the script commands I have tried, again in the per-frame 
scripting window accessed from the movie viewer:

transp 100,a #4:MIV1
transp 0,a #4:MIV frames 60
transp 100,a #4:MIV frames 121

Ideally, the substrate-bound form is reached at frame 60 of the morph, 
by the time it reaches 121 it has gone back to the substrate-free form.  
So I would like to have the substrate fade in by frame 60, and back out 
again by 121.

And while we are at it, how would I go about selecting side chains that 
interact with the substrate on the morph model?   If I use *ligand 
zr<5*, Chimera decides that the heme is the ligand, not the :MIV.

Thanks in advance.  Sorry, I am brand-new to this, I just found out that 
PyMOL can't do all the things I need...

Tom Pochapsky


On 6/12/17 1:50 PM, Elaine Meng wrote:
> Hi Tom,
> The broader command is simply ?transparency? ? it applies to not only surfaces, but also atomic representations, ribbons, etc. (whichever you specify) and there is a ?frames? option for fading in/out over a specified number of frames.  So for example with this ligand in 2gbp, the last command would fade it from the initial 0% to 100% transparent over 100 frames:
>
> open 2gbp
> show :bgc
> repr sphere :bgc
> transp 100,a :bgc  frames 100
>
> ? in this case ?ligand? could be used instead of ?:bgc? but I showed a more general case of specifying by residue name, since ?ligand? doesn?t always get what you want.  The ?,a? means to affect atomic representations, not surfaces, ribbons, etc.  See the manpage:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/transparency.html>
>
> The ?surftransparency? manpage (e.g. shown with command ?help surftransparency? refers to this ?transparency? command which essentially replaces it, although surftransparency still works too.   See also the movie-related commands list, including ?coordset? to play through your morph.
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands>
>
> There is also a list of all commands, of course?
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>
>
> ? and you can also use "Help? Search Documentation? in the menu to search for specific terms like ?transparency"
>
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>> On Jun 12, 2017, at 10:35 AM, Thomas Pochapsky <pochapsk at brandeis.edu> wrote:
>>
>> Is there any command corresponding to surft (surface transparency) that will modulate the visibility of a sphere representation of a ligand?  I want to change it in the course of a morph between substrate-bound and substrate free forms of the same enzyme.  I will probably have other questions, but this seems like a good place to start...
>> Thanks,
>> Tom Pochapsky

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From meng at cgl.ucsf.edu  Mon Jun 12 13:48:23 2017
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 12 Jun 2017 13:48:23 -0700
Subject: [Chimera-users] sphere transparency
In-Reply-To: <f5f737c9-48f5-1484-606e-a73bb2d9c106@brandeis.edu>
References: <1d6a3c8d-f546-be5a-4361-f2e990667187@brandeis.edu>
 <C47BF3F7-B735-4812-9338-58E748F3C288@cgl.ucsf.edu>
 <f5f737c9-48f5-1484-606e-a73bb2d9c106@brandeis.edu>
Message-ID: <76B80CA1-289C-49A4-9540-6CA7F7E6C694@cgl.ucsf.edu>

Hi Tom,
Ah, you don?t want this fading to execute at EACH frame of the morph, considering that the fade itself is a multi-frame process...?frames 60? means it changes the transparency to the target value over 60 frames. So it cannot be done within a per-frame script in the playback tool (MD Movie).  Instead you would need to generate the morph (I?d recommend saving a session with the morph already calculated) and then in that session or after restoring the session, executing a script that plays the morph trajectory with the ?coordset" command and simultaneously fades the ligand.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/coordset.html>

E.g. if your  morph trajectory with 121 frames is model #5 and the model with your ligand (residue name MIV) is model #4, the script would contain something like the following to play the first 60 frames before starting the ligand fade:

trans 100,a #4:miv
coordset #5 1,60; trans 0,a #4:miv frames 60; wait 60
coordset #5 61,121; trans 100,a #4:miv frames 60; wait 60

There are some other example scripts with morph playback in the Animations gallery, see ?kinase morph? at the top and ?ball-and-socket motion? about halfway down the page:
<http://www.rbvi.ucsf.edu/chimera/animations/animations.html>
<http://www.rbvi.ucsf.edu/chimera/animations/animations.html#trmovie>

For your zone question, instead of using the word ?ligand? you?d simply use the residue-name specifier instead, 
 :miv zr<5

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


> On Jun 12, 2017, at 1:12 PM, Thomas Pochapsky <pochapsk at brandeis.edu> wrote:
> 
> Thanks, Elaine,
> 
> This works independently (just applying through the per-frame script in the movie viewer), but I am trying to integrate it with the morph that I generated (120 frames); right now it keeps flashing the structure of the ligand as it appears to fade back and forth on each frame of the morph (at least that is what it looks like to me). 
> Here are the script commands I have tried, again in the per-frame scripting window accessed from the movie viewer:
> 
> transp 100,a #4:MIV1
> transp 0,a #4:MIV frames 60 
> transp 100,a #4:MIV frames 121 
> Ideally, the substrate-bound form is reached at frame 60 of the morph, by the time it reaches 121 it has gone back to the substrate-free form.  So I would like to have the substrate fade in by frame 60, and back out again by 121.
> 
> And while we are at it, how would I go about selecting side chains that interact with the substrate on the morph model?   If I use  ligand zr<5, Chimera decides that the heme is the ligand, not the :MIV.
> 
> Thanks in advance.  Sorry, I am brand-new to this, I just found out that PyMOL can't do all the things I need...
> 
> Tom Pochapsky
> 
> On 6/12/17 1:50 PM, Elaine Meng wrote:
>> Hi Tom,
>> The broader command is simply ?transparency? ? it applies to not only surfaces, but also atomic representations, ribbons, etc. (whichever you specify) and there is a ?frames? option for fading in/out over a specified number of frames.  So for example with this ligand in 2gbp, the last command would fade it from the initial 0% to 100% transparent over 100 frames:
>> 
>> open 2gbp
>> show :bgc
>> repr sphere :bgc
>> transp 100,a :bgc  frames 100
>> 
>> ? in this case ?ligand? could be used instead of ?:bgc? but I showed a more general case of specifying by residue name, since ?ligand? doesn?t always get what you want.  The ?,a? means to affect atomic representations, not surfaces, ribbons, etc.  See the manpage:
>> 
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/transparency.html>
>> 
>> 
>> The ?surftransparency? manpage (e.g. shown with command ?help surftransparency? refers to this ?transparency? command which essentially replaces it, although surftransparency still works too.   See also the movie-related commands list, including ?coordset? to play through your morph.
>> 
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/movies.html#moviecommands>
>> 
>> 
>> There is also a list of all commands, of course?
>> 
>> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/framecommand.html>
>> 
>> 
>> ? and you can also use "Help? Search Documentation? in the menu to search for specific terms like ?transparency"
>> 
>> I hope this helps,
>> Elaine
>> ----------
>> Elaine C. Meng, Ph.D. 
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>> 
>>> On Jun 12, 2017, at 10:35 AM, Thomas Pochapsky <pochapsk at brandeis.edu>
>>>  wrote:
>>> 
>>> Is there any command corresponding to surft (surface transparency) that will modulate the visibility of a sphere representation of a ligand?  I want to change it in the course of a morph between substrate-bound and substrate free forms of the same enzyme.  I will probably have other questions, but this seems like a good place to start...
>>> Thanks,
>>> Tom Pochapsky
>>> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users




From meng at cgl.ucsf.edu  Mon Jun 12 14:38:13 2017
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 12 Jun 2017 14:38:13 -0700
Subject: [Chimera-users] sphere transparency
In-Reply-To: <76B80CA1-289C-49A4-9540-6CA7F7E6C694@cgl.ucsf.edu>
References: <1d6a3c8d-f546-be5a-4361-f2e990667187@brandeis.edu>
 <C47BF3F7-B735-4812-9338-58E748F3C288@cgl.ucsf.edu>
 <f5f737c9-48f5-1484-606e-a73bb2d9c106@brandeis.edu>
 <76B80CA1-289C-49A4-9540-6CA7F7E6C694@cgl.ucsf.edu>
Message-ID: <A1923F4D-12D1-48A5-A9A1-890663AAB8CB@cgl.ucsf.edu>


> On Jun 12, 2017, at 1:48 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> So it cannot be done within a per-frame script in the playback tool (MD Movie). 

Correction:
It turns out that ?cannot? was a little too strong? I?d forgotten that there is a mechanism in per-frame scripts to only execute a command at a particular trajectory frame, by prefixing it with #N:.  I had an example morph (2fw0 -> 2gbp -> 2fw0) 121 frames where the middle structure has bound BGC, and in that case I could use this per-frame script

#1:trans 0,a :bgc frames 60
#61:trans 100,a :bgc frames 60

However, the other method with ?coordset? in a script may still be superior for  at least two reasons:
 
(1) If you use the per-frame script method above, you also have to move the MD Movie slider to the far right to ensure a 1-to-1 relationship between trajectory frames and image update frames.  If you have the slider somewhat to the left there will be more than one image update frame per trajectory frame and the fade-in and fade-out over 60 frames will occupy a smaller fraction of the trajectory.  Yes, you could increase the transparency command frames number from 60 to something bigger, but hard to tell exactly how much bigger to make it.

(2) The ?coordset? command method has more control.  You could choose to insert a pause between the two stages of the morph, for example to linger on the bound state for a while before starting the fade-out and morph to unbound state:

trans 100,a :miv
coordset #5 1,60; trans 0,a :miv frames 60; wait 60
wait 20
coordset #5 61,121; trans 100,a :miv frames 60; wait 60

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






From yoland.savriama at helsinki.fi  Mon Jun 12 09:18:46 2017
From: yoland.savriama at helsinki.fi (Savriama, Yoland F)
Date: Mon, 12 Jun 2017 16:18:46 +0000
Subject: [Chimera-users] Files generated by UCSF Chimera as .MRC format do
 not open with AMIRA 5.3.3
Message-ID: <HE1PR0701MB225099446A60A9C88F7D7E6CE1CD0@HE1PR0701MB2250.eurprd07.prod.outlook.com>


Greetings,

I am a researcher working at the University of Helsinki (Finland) and I have used the software UCSF Chimera to process 3D CT-Scans data. I saved the process files as a single .MRC file. When I tried to open it with Amira 5.3.3 it displays the following error message:

"No valid licence found for extension Amira Microscopy Option 5.3 Please contact us". The console also says "Access denied for 'readMRCFileStack'"

I thought that Amira could read these standard .MRC files? Could it be there was an issue during the file export with Chimera?

Best wishes,
Yoland Savriama, PhD
P/O Jernvall
Institute of Biotechnology
P.O. Box 56 (Viikinkaari 5)
FIN-00014 FINLAND
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From meng at cgl.ucsf.edu  Mon Jun 12 16:26:11 2017
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 12 Jun 2017 16:26:11 -0700
Subject: [Chimera-users] Files generated by UCSF Chimera as .MRC format
 do not open with AMIRA 5.3.3
In-Reply-To: <HE1PR0701MB225099446A60A9C88F7D7E6CE1CD0@HE1PR0701MB2250.eurprd07.prod.outlook.com>
References: <HE1PR0701MB225099446A60A9C88F7D7E6CE1CD0@HE1PR0701MB2250.eurprd07.prod.outlook.com>
Message-ID: <C5910D47-DB2F-4322-8549-EA51B3A97ACA@cgl.ucsf.edu>

Hi Yolanda,
I?m not aware of anything special about the MRC files from Chimera.  It sounds like you simply don?t have a license to use the part of Amira that reads/handles MRC files, in which case you would need to contact the Amira folks about getting such a license.  Can you open any MRC files in Amira, like from sources other than Chimera?
Best,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jun 12, 2017, at 9:18 AM, Savriama, Yoland F <yoland.savriama at helsinki.fi> wrote:
> 
> Greetings,
>  
> I am a researcher working at the University of Helsinki (Finland) and I have used the software UCSF Chimera to process 3D CT-Scans data. I saved the process files as a single .MRC file. When I tried to open it with Amira 5.3.3 it displays the following error message:
>  
> "No valid licence found for extension Amira Microscopy Option 5.3 Please contact us". The console also says "Access denied for 'readMRCFileStack'"
>  
> I thought that Amira could read these standard .MRC files? Could it be there was an issue during the file export with Chimera?
>  
> Best wishes,
> Yoland Savriama, PhD
> P/O Jernvall
> Institute of Biotechnology
> P.O. Box 56 (Viikinkaari 5)
> FIN-00014 FINLAND




From yoland.savriama at helsinki.fi  Tue Jun 13 01:35:20 2017
From: yoland.savriama at helsinki.fi (Savriama, Yoland F)
Date: Tue, 13 Jun 2017 08:35:20 +0000
Subject: [Chimera-users] Files generated by UCSF Chimera as .MRC format
 do not open with AMIRA 5.3.3
In-Reply-To: <C5910D47-DB2F-4322-8549-EA51B3A97ACA@cgl.ucsf.edu>
References: <HE1PR0701MB225099446A60A9C88F7D7E6CE1CD0@HE1PR0701MB2250.eurprd07.prod.outlook.com>,
 <C5910D47-DB2F-4322-8549-EA51B3A97ACA@cgl.ucsf.edu>
Message-ID: <HE1PR0701MB22507801D43D3857B4E412C8E1C20@HE1PR0701MB2250.eurprd07.prod.outlook.com>


Hi Elaine,


Thank you very much for your prompt reply!


I guess you are right although Amira suggests different file formats to open a given file including .MRC, this is why I found it strange Amira could not open it. Meanwhile I contacted Amira and I am in touch with them to solve this issue. Yes, I can open this .MRC file via Fiji, but I experience issues when I save it as a .tiff or .raw file and I tried to open it with Amira again. Amira only recognises 1 slice. It would be nice to have a save as .tiff stack or image sequence from Chimera.


Also, could you tell me how one enters the voxel size and other information when one imports a file, please?


Another thing I was curious about is whether or not it is possible to specify memory allocation to process volume rendering for instance. I found Chimera very slow and it often displays errors while using the volume eraser and volume rendering at a number of 2, even if I process the volume at 16 it is still really slow.


Here are the specs of my machine: Desktop computer with Windows 7 Intel Xeon CPU X5550 @ 2.67 GHz 2.66 Ghz (2 processors) 48 Gigs of Ram 64 bit OS

Graphic Card: Nvidia GeForce GTX 680 Total available graphics : 7934Mb and dedicated video memory: 4096 MB GDDR 5

I can easily open and process a 10 gbs file and even 20 gbs with Amira without having it to crash or running too slow.

I think Chimera is a really nice software and I am using it since I was particularly interested in this volume eraser tool.

Best,
Yoland



________________________________
From: Elaine Meng <meng at cgl.ucsf.edu>
Sent: Tuesday, June 13, 2017 2:26:11 AM
To: Savriama, Yoland F
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Files generated by UCSF Chimera as .MRC format do not open with AMIRA 5.3.3

Hi Yolanda,
I?m not aware of anything special about the MRC files from Chimera.  It sounds like you simply don?t have a license to use the part of Amira that reads/handles MRC files, in which case you would need to contact the Amira folks about getting such a license.  Can you open any MRC files in Amira, like from sources other than Chimera?
Best,
Elaine
----------
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco


> On Jun 12, 2017, at 9:18 AM, Savriama, Yoland F <yoland.savriama at helsinki.fi> wrote:
>
> Greetings,
>
> I am a researcher working at the University of Helsinki (Finland) and I have used the software UCSF Chimera to process 3D CT-Scans data. I saved the process files as a single .MRC file. When I tried to open it with Amira 5.3.3 it displays the following error message:
>
> "No valid licence found for extension Amira Microscopy Option 5.3 Please contact us". The console also says "Access denied for 'readMRCFileStack'"
>
> I thought that Amira could read these standard .MRC files? Could it be there was an issue during the file export with Chimera?
>
> Best wishes,
> Yoland Savriama, PhD
> P/O Jernvall
> Institute of Biotechnology
> P.O. Box 56 (Viikinkaari 5)
> FIN-00014 FINLAND

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From matthias.vorlaender at embl.de  Tue Jun 13 04:21:52 2017
From: matthias.vorlaender at embl.de (=?utf-8?B?TWF0dGhpYXMgVm9ybMOkbmRlcg==?=)
Date: Tue, 13 Jun 2017 11:21:52 +0000
Subject: [Chimera-users] Helix represented as sheet, dispite best efforts
Message-ID: <1c79aa7bd1ce848db6b070ed86301700@webmail.embl.de>

Hi everyone,

for some reason, chimera displays one helix in a structure as a messed up beta sheet. I am attaching the PDB file and an image (same structure as backbone and ribbon representation). I have tried adding HELIX records manually, ksdssp or the setattr command, but the result is always the same. I would be very grateful for suggestions what could be causing this problem, as I will have to remake all my figures in pymol otherwise (which displays the helix correctly). 

Many thanks
Matthias Vorl?nder
PhD student
EMBL Heidelberg - M?ller Lab
Meyerhofstra?e 1, 69126 Heidelberg
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From meng at cgl.ucsf.edu  Tue Jun 13 10:10:18 2017
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 13 Jun 2017 10:10:18 -0700
Subject: [Chimera-users] Helix represented as sheet, dispite best efforts
In-Reply-To: <1c79aa7bd1ce848db6b070ed86301700@webmail.embl.de>
References: <1c79aa7bd1ce848db6b070ed86301700@webmail.embl.de>
Message-ID: <1F313F1C-DA90-4F78-835C-52ECDFD2E364@cgl.ucsf.edu>

Hi Matthias,
The problem is not helix vs. sheet (it is definitely assigned as helix, for example try command ?select helix?), but instead how the ribbon is calculated for that helix.  I don?t know the precise problem nor have I been able to identify a workaround, so I?ll submit it as bug report.  If I come up with anything, will let you know.

In the meanwhile, I note that our newer program ChimeraX uses different methods to calculate the ribbon and does not have a problem with this structure - image attached.  You can get ChimeraX prerelease daily builds; it has some features Chimera does not, but it?s not a replacement (overall functionality-wise) for Chimera yet, so it all depends on what you want to do.  You could certainly use both programs.
<http://www.rbvi.ucsf.edu/chimerax/index.html>

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


> On Jun 13, 2017, at 4:21 AM, Matthias Vorl?nder <matthias.vorlaender at embl.de> wrote:
> 
> Hi everyone,
> for some reason, chimera displays one helix in a structure as a messed up beta sheet. I am attaching the PDB file and an image (same structure as backbone and ribbon representation). I have tried adding HELIX records manually, ksdssp or the setattr command, but the result is always the same. I would be very grateful for suggestions what could be causing this problem, as I will have to remake all my figures in pymol otherwise (which displays the helix correctly). 
> Many thanks
> Matthias Vorl?nder

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From meng at cgl.ucsf.edu  Tue Jun 13 10:17:03 2017
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 13 Jun 2017 10:17:03 -0700
Subject: [Chimera-users] Files generated by UCSF Chimera as .MRC format
 do not open with AMIRA 5.3.3
In-Reply-To: <HE1PR0701MB22507801D43D3857B4E412C8E1C20@HE1PR0701MB2250.eurprd07.prod.outlook.com>
References: <HE1PR0701MB225099446A60A9C88F7D7E6CE1CD0@HE1PR0701MB2250.eurprd07.prod.outlook.com>
 <C5910D47-DB2F-4322-8549-EA51B3A97ACA@cgl.ucsf.edu>
 <HE1PR0701MB22507801D43D3857B4E412C8E1C20@HE1PR0701MB2250.eurprd07.prod.outlook.com>
Message-ID: <1C5BAAE7-F023-46FA-873D-C21223700478@cgl.ucsf.edu>

Hi Yoland,
(sorry for getting your name wrong before!)

Maybe others can comment on the rest, but I'll address this point:

> On Jun 13, 2017, at 1:35 AM, Savriama, Yoland F <yoland.savriama at helsinki.fi> wrote:
> 
> Also, could you tell me how one enters the voxel size and other information when one imports a file, please?
> 

In the Volume Viewer menu, choose Features? Coordinates.  Then there will be entry fields where you can change voxel size etc.:

<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/volumeviewer.html#coordinates>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/volumeviewer/framevolumeviewer.html>

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






From meng at cgl.ucsf.edu  Tue Jun 13 10:22:46 2017
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 13 Jun 2017 10:22:46 -0700
Subject: [Chimera-users] Helix represented as sheet, dispite best efforts
In-Reply-To: <1F313F1C-DA90-4F78-835C-52ECDFD2E364@cgl.ucsf.edu>
References: <1c79aa7bd1ce848db6b070ed86301700@webmail.embl.de>
 <1F313F1C-DA90-4F78-835C-52ECDFD2E364@cgl.ucsf.edu>
Message-ID: <6C7B2586-8A38-434C-A984-80524AF7D824@cgl.ucsf.edu>

Oh, I see it is a left-handed helix, and (apparently) the Chimera ribbon calculation does not handle such helices well.  Before my previous reply I?d checked the chirality of the amino acids but had forgotten to examine the handedness of the helix.

I do not know if this is something that will be fixed in Chimera since we are concentrating more on ChimeraX now, but I will still report the bug.
Best,
Elaine

> On Jun 13, 2017, at 10:10 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Matthias,
> The problem is not helix vs. sheet (it is definitely assigned as helix, for example try command ?select helix?), but instead how the ribbon is calculated for that helix.  I don?t know the precise problem nor have I been able to identify a workaround, so I?ll submit it as bug report.  If I come up with anything, will let you know.
> 
> In the meanwhile, I note that our newer program ChimeraX uses different methods to calculate the ribbon and does not have a problem with this structure - image attached.  You can get ChimeraX prerelease daily builds; it has some features Chimera does not, but it?s not a replacement (overall functionality-wise) for Chimera yet, so it all depends on what you want to do.  You could certainly use both programs.
> <http://www.rbvi.ucsf.edu/chimerax/index.html>
> 
> Best,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> <grab.png>
> 
>> On Jun 13, 2017, at 4:21 AM, Matthias Vorl?nder <matthias.vorlaender at embl.de> wrote:
>> 
>> Hi everyone,
>> for some reason, chimera displays one helix in a structure as a messed up beta sheet. I am attaching the PDB file and an image (same structure as backbone and ribbon representation). I have tried adding HELIX records manually, ksdssp or the setattr command, but the result is always the same. I would be very grateful for suggestions what could be causing this problem, as I will have to remake all my figures in pymol otherwise (which displays the helix correctly). 
>> Many thanks
>> Matthias Vorl?nder
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users




From goddard at sonic.net  Tue Jun 13 11:10:04 2017
From: goddard at sonic.net (Tom Goddard)
Date: Tue, 13 Jun 2017 11:10:04 -0700
Subject: [Chimera-users] Files generated by UCSF Chimera as .MRC format
 do not open with AMIRA 5.3.3
In-Reply-To: <HE1PR0701MB22507801D43D3857B4E412C8E1C20@HE1PR0701MB2250.eurprd07.prod.outlook.com>
References: <HE1PR0701MB225099446A60A9C88F7D7E6CE1CD0@HE1PR0701MB2250.eurprd07.prod.outlook.com>
 <C5910D47-DB2F-4322-8549-EA51B3A97ACA@cgl.ucsf.edu>
 <HE1PR0701MB22507801D43D3857B4E412C8E1C20@HE1PR0701MB2250.eurprd07.prod.outlook.com>
Message-ID: <F278F865-E393-4AB0-968F-5CDA72171E7A@sonic.net>

If you get errors or crashes you should report a bug (Chimera will often ask after an error if you want to report it, or use menu Help / Report a Bug?) ? describe exactly what you were doing before the error.  There is a volume data cache size ? see the Chimera volume command documentation to learn how to use it.  I don?t know if that will speed up your operation because you did not explain exactly what operations are slow.  With a 10 or 20 Gb map everything is likely to be slow.

	Tom


> On Jun 13, 2017, at 1:35 AM, Savriama, Yoland F <yoland.savriama at helsinki.fi> wrote:
> 
> 
> Hi Elaine,
> 
> Thank you very much for your prompt reply! 
> 
> I guess you are right although Amira suggests different file formats to open a given file including .MRC, this is why I found it strange Amira could not open it. Meanwhile I contacted Amira and I am in touch with them to solve this issue. Yes, I can open this .MRC file via Fiji, but I experience issues when I save it as a .tiff or .raw file and I tried to open it with Amira again. Amira only recognises 1 slice. It would be nice to have a save as .tiff stack or image sequence from Chimera.
> 
> Also, could you tell me how one enters the voxel size and other information when one imports a file, please?
> 
> Another thing I was curious about is whether or not it is possible to specify memory allocation to process volume rendering for instance. I found Chimera very slow and it often displays errors while using the volume eraser and volume rendering at a number of 2, even if I process the volume at 16 it is still really slow.
> 
> Here are the specs of my machine: Desktop computer with Windows 7 Intel Xeon CPU X5550 @ 2.67 GHz 2.66 Ghz (2 processors) 48 Gigs of Ram 64 bit OS
> Graphic Card: Nvidia GeForce GTX 680 Total available graphics : 7934Mb and dedicated video memory: 4096 MB GDDR 5
> 
> I can easily open and process a 10 gbs file and even 20 gbs with Amira without having it to crash or running too slow.
> 
> I think Chimera is a really nice software and I am using it since I was particularly interested in this volume eraser tool.
> 
> Best,
> Yoland
> 
> 
> 
> From: Elaine Meng <meng at cgl.ucsf.edu <mailto:meng at cgl.ucsf.edu>>
> Sent: Tuesday, June 13, 2017 2:26:11 AM
> To: Savriama, Yoland F
> Cc: chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu>
> Subject: Re: [Chimera-users] Files generated by UCSF Chimera as .MRC format do not open with AMIRA 5.3.3
>  
> Hi Yolanda,
> I?m not aware of anything special about the MRC files from Chimera.  It sounds like you simply don?t have a license to use the part of Amira that reads/handles MRC files, in which case you would need to contact the Amira folks about getting such a license.  Can you open any MRC files in Amira, like from sources other than Chimera?
> Best,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
> > On Jun 12, 2017, at 9:18 AM, Savriama, Yoland F <yoland.savriama at helsinki.fi <mailto:yoland.savriama at helsinki.fi>> wrote:
> > 
> > Greetings,
> >  
> > I am a researcher working at the University of Helsinki (Finland) and I have used the software UCSF Chimera to process 3D CT-Scans data. I saved the process files as a single .MRC file. When I tried to open it with Amira 5.3.3 it displays the following error message:
> >  
> > "No valid licence found for extension Amira Microscopy Option 5.3 Please contact us". The console also says "Access denied for 'readMRCFileStack'"
> >  
> > I thought that Amira could read these standard .MRC files? Could it be there was an issue during the file export with Chimera?
> >  
> > Best wishes,
> > Yoland Savriama, PhD
> > P/O Jernvall
> > Institute of Biotechnology
> > P.O. Box 56 (Viikinkaari 5)
> > FIN-00014 FINLAND
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
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From pett at cgl.ucsf.edu  Tue Jun 13 15:49:24 2017
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Tue, 13 Jun 2017 15:49:24 -0700
Subject: [Chimera-users] DockPrep sometimes fails with altPos
In-Reply-To: <80DB3DBF-EBA9-4E21-A565-E6281B668115@gmail.com>
References: <80DB3DBF-EBA9-4E21-A565-E6281B668115@gmail.com>
Message-ID: <C3C0E7BE-5425-4AC7-B65D-F477660AA782@cgl.ucsf.edu>

Yes, the altlocs are chosen on a per-residue basis, which can lead to inconsistencies when different altlocs are chosen for connected residues (the cross-residue bond(s) gets deleted and hydrogens get added to the now-valence-available atoms).  I will work to fix this when I have time and will report back here when I do.  In the interim, you may want to simply delete non-A altlocs before running DockPrep.  Assuming there are no more than three altlocs per atom then this command will do that:

	del @.b @.c

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Jun 12, 2017, at 1:57 AM, Visvaldas Kairys <visvaldaskairys at gmail.com> wrote:
> 
> Dear Chimera users and developers,
> 
> I?d like to point out I often have a minor inconvenience when dealing with high resolution Xray structures when trying to add hydrogens
> via DockPrep. 
> 
> If two consecutive residues have both alternative postions A and B, Chimera in the process of hydrogen addition often gets confused 
> and puts ?TER? between the
> residues, also reporting non-integer charges in the log. I think what is happening, the program picks ?A? variant for one residue and ?B? for the consecutive residue, and apparently this causes bond detection algorithm to ignore the bond between the residues (due to length I guess).
> I resolve this by manually editing out one of the AltPos (say, ?B?) out of the PDB file for the offending residues, 
> but I guess the program should be able to do it automatically.
> 
> A PDB example where this happens is 2r3i (or 2r3r).
> 
> Best regards,
> 
> Vis
> 
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 

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From eddimpri at biophys.mpg.de  Wed Jun 14 03:06:54 2017
From: eddimpri at biophys.mpg.de (Edoardo D'Imprima)
Date: Wed, 14 Jun 2017 12:06:54 +0200
Subject: [Chimera-users] region bounds for pdb
Message-ID: <F47EC4E7-6E2A-4ABC-AFDD-697892EB33AD@biophys.mpg.de>

Dear Chimera users,

I find very handy the function ?Region bounds? to cut the EM maps in order to better visualise some part of the volume. I was wondering if there is an equivalent for PDBs. 

Many thanks in advance,

Edoardo
---------------------------------------------------
Edoardo D'Imprima
PhD Student
Max Planck Institute of Biophysics
Structural Biology Department
Max-von-Laue Stra?e 3
60438 Frankfurt am Main
Germany

Tel: +49 (0) 69 6303 3015






From meng at cgl.ucsf.edu  Wed Jun 14 10:32:10 2017
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 14 Jun 2017 10:32:10 -0700
Subject: [Chimera-users] Generate the tranfromation or bio matrix from
 the docking complex using Chimera
In-Reply-To: <BLUPR0501MB1732F3F72B5D636368FDE507D5C30@BLUPR0501MB1732.namprd05.prod.outlook.com>
References: <BLUPR0501MB1732F3F72B5D636368FDE507D5C30@BLUPR0501MB1732.namprd05.prod.outlook.com>
Message-ID: <A68480D0-4632-4A32-871F-EE3F4D8EA67E@cgl.ucsf.edu>


> On Jun 14, 2017, at 9:35 AM, Elumalai Pavadai <epavadai at fiu.edu> wrote:
> 
> Dear Meng,
> 
> I have a cylindrical symmetry protein complex modeled with the protein-protein docking.  Since the docking complex is very big in terms of size and number of atoms, I would like to generate the transformation matrix from it. Using the  matrix , I can be able to generate the complex with Chimera. So, my question is that how to generate the transformation matrix from the protein complex with Chimera?
> 
> Thank you, and I look forward to hearing from you. 
> 
> Kind regards,
> Elumalai

Dear Elumalai,

I?m CC-ing chimera-users at cgl.ucsf.edu ? it is the recommended address for Chimera questions, to ensure you get a response and allowing others to make suggestions.

I?m guessing that you mean your large complex is several copies of the same protein, arranged in some symmetrical way, and instead you would like to have a file with only one copy but also the matrices describing the whole thing.  If you had such a file, you could open it in Chimera and then generate the whole thing from the matrices.

However, Chimera does not have the tools to go in the opposite direction, to figure out all the matrices from the whole complex.  So if I understood your problem correctly, you would need to find some other program to do this.  I haven?t done it myself, so I don?t know what you could use. If your protein-protein docking program created this symmetrical structure, maybe it can output the needed matrices.

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




From meng at cgl.ucsf.edu  Wed Jun 14 11:30:25 2017
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 14 Jun 2017 11:30:25 -0700
Subject: [Chimera-users] region bounds for pdb
In-Reply-To: <F47EC4E7-6E2A-4ABC-AFDD-697892EB33AD@biophys.mpg.de>
References: <F47EC4E7-6E2A-4ABC-AFDD-697892EB33AD@biophys.mpg.de>
Message-ID: <51149837-0434-4D7F-9979-04632B97EAB7@cgl.ucsf.edu>

Dear Eduardo,
It isn?t exactly the same for atomic structures, but consider these approaches:

(1) You can specify exactly which atoms, residues, etc. to display using selections and the  Actions menu, or directly using commands.  If there is some central area of interest, the atom specification can include a zone operator.  For example, to show only residues within 4.5 Angstroms of residue HEM in chain A of 4hhb:

open 4hhb
~displayhttp://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html
display :hem.a z<4.5
~ribbon
ribbon :hem.a z<4.5

See atom specifications, zones:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>

(2) clipping.  You can adjust front-back clipping in the Side View or with commands, and per-model clipping (affects individual models, can be at any angle) with Per-Model Clipping or with commands. See this page and links within:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/clipping.html>

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

> On Jun 14, 2017, at 3:06 AM, Edoardo D'Imprima <eddimpri at biophys.mpg.de> wrote:
> 
> Dear Chimera users,
> I find very handy the function ?Region bounds? to cut the EM maps in order to better visualise some part of the volume. I was wondering if there is an equivalent for PDBs. 
> Many thanks in advance,
> Edoardo




From goddard at sonic.net  Wed Jun 14 12:19:58 2017
From: goddard at sonic.net (Tom Goddard)
Date: Wed, 14 Jun 2017 12:19:58 -0700
Subject: [Chimera-users] region bounds for pdb
In-Reply-To: <51149837-0434-4D7F-9979-04632B97EAB7@cgl.ucsf.edu>
References: <F47EC4E7-6E2A-4ABC-AFDD-697892EB33AD@biophys.mpg.de>
 <51149837-0434-4D7F-9979-04632B97EAB7@cgl.ucsf.edu>
Message-ID: <071DC72F-1B03-49EA-9885-08889320A7AB@sonic.net>

One more way to show just a slab of an atomic structure is to drag select (mouse ctrl-drag) a region ? this selects all the atoms in the green rectangle you drag out.  Then you can invert the selection (menu Selection / Invert) and hide the atoms not in the box (menu Actions / Atoms / hide).

	Tom

> On Jun 14, 2017, at 11:30 AM, Elaine Meng  wrote:
> 
> Dear Eduardo,
> It isn?t exactly the same for atomic structures, but consider these approaches:
> 
> (1) You can specify exactly which atoms, residues, etc. to display using selections and the  Actions menu, or directly using commands.  If there is some central area of interest, the atom specification can include a zone operator.  For example, to show only residues within 4.5 Angstroms of residue HEM in chain A of 4hhb:
> 
> open 4hhb
> ~displayhttp://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html
> display :hem.a z<4.5
> ~ribbon
> ribbon :hem.a z<4.5
> 
> See atom specifications, zones:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>
> 
> (2) clipping.  You can adjust front-back clipping in the Side View or with commands, and per-model clipping (affects individual models, can be at any angle) with Per-Model Clipping or with commands. See this page and links within:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/clipping.html>
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
>> On Jun 14, 2017, at 3:06 AM, Edoardo D'Imprima <eddimpri at biophys.mpg.de> wrote:
>> 
>> Dear Chimera users,
>> I find very handy the function ?Region bounds? to cut the EM maps in order to better visualise some part of the volume. I was wondering if there is an equivalent for PDBs. 
>> Many thanks in advance,
>> Edoardo
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 




From goddard at sonic.net  Wed Jun 14 12:26:14 2017
From: goddard at sonic.net (Tom Goddard)
Date: Wed, 14 Jun 2017 12:26:14 -0700
Subject: [Chimera-users] Generate the tranfromation or bio matrix from
 the docking complex using Chimera
In-Reply-To: <A68480D0-4632-4A32-871F-EE3F4D8EA67E@cgl.ucsf.edu>
References: <BLUPR0501MB1732F3F72B5D636368FDE507D5C30@BLUPR0501MB1732.namprd05.prod.outlook.com>
 <A68480D0-4632-4A32-871F-EE3F4D8EA67E@cgl.ucsf.edu>
Message-ID: <8E1D3D92-830B-493A-91E5-2E60BABD43D7@sonic.net>

Hi Elumalai,

  You can get the symmetry operations out of Chimera.   Open your complex twice, models #0 and #1.  Suppose chains A and B are the same protein and you want the transformation to get from A to B.  First align the first copy chain A to the second copy chain B:

	matchmaker #2:.B  #1:.A

Then measure the motion

	measure rotation #1 #2

The 3 by 4 matrix (rotation in first 3 columns, translation in 4th column) is output to the reply log.  Also a rotation axis and angle is output.  You can use the matrix and add in a text editor REMARK 350 BIOMT matrices to the PDB file containing just chain A to place it using the matrix.  Take a look at an example PDB file to see the format (e.g. 2bbv).  Or you can use the Chimera sym command with the rotation axis and angle to create copies of chain A in Chimera.

	Tom



> On Jun 14, 2017, at 10:32 AM, Elaine Meng wrote:
> 
> 
>> On Jun 14, 2017, at 9:35 AM, Elumalai Pavadai <epavadai at fiu.edu> wrote:
>> 
>> Dear Meng,
>> 
>> I have a cylindrical symmetry protein complex modeled with the protein-protein docking.  Since the docking complex is very big in terms of size and number of atoms, I would like to generate the transformation matrix from it. Using the  matrix , I can be able to generate the complex with Chimera. So, my question is that how to generate the transformation matrix from the protein complex with Chimera?
>> 
>> Thank you, and I look forward to hearing from you. 
>> 
>> Kind regards,
>> Elumalai
> 
> Dear Elumalai,
> 
> I?m CC-ing chimera-users at cgl.ucsf.edu ? it is the recommended address for Chimera questions, to ensure you get a response and allowing others to make suggestions.
> 
> I?m guessing that you mean your large complex is several copies of the same protein, arranged in some symmetrical way, and instead you would like to have a file with only one copy but also the matrices describing the whole thing.  If you had such a file, you could open it in Chimera and then generate the whole thing from the matrices.
> 
> However, Chimera does not have the tools to go in the opposite direction, to figure out all the matrices from the whole complex.  So if I understood your problem correctly, you would need to find some other program to do this.  I haven?t done it myself, so I don?t know what you could use. If your protein-protein docking program created this symmetrical structure, maybe it can output the needed matrices.
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 




From aoliver2 at hotmail.com  Wed Jun 14 05:38:20 2017
From: aoliver2 at hotmail.com (Andrew Oliver, II)
Date: Wed, 14 Jun 2017 12:38:20 +0000
Subject: [Chimera-users] Smooth "Rocking" Loop Movie
Message-ID: <DM5PR2201MB14663963422BBBECDFB3FAA597C30@DM5PR2201MB1466.namprd22.prod.outlook.com>

Dear Chimera,


I am trying to create a "rocking" movie of a molecule that will continuously loop. I am using the command:


movie record; rock y 10 68; wait; rock y -10 68; wait; movie stop; movie encode


However, when I do this, there is always a slight pause at the end of the movie, before it starts the next loop -- which means it doesn't loop smoothly.


Is there a way to create the movie so that there will be no pause before each successive loop?


Many thanks,

Andrew Oliver
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From meng at cgl.ucsf.edu  Wed Jun 14 14:00:00 2017
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Wed, 14 Jun 2017 14:00:00 -0700
Subject: [Chimera-users] Smooth "Rocking" Loop Movie
In-Reply-To: <DM5PR2201MB14663963422BBBECDFB3FAA597C30@DM5PR2201MB1466.namprd22.prod.outlook.com>
References: <DM5PR2201MB14663963422BBBECDFB3FAA597C30@DM5PR2201MB1466.namprd22.prod.outlook.com>
Message-ID: <58777ADB-F4A5-4F71-9A0A-AE96E36592DD@cgl.ucsf.edu>

Hi Andrew,
I don?t know how you are looping, but if I use View? Loop in Quicktime Player, I don?t see any pause in the movie created with command script:

movie record
rock y 10 68;wait
rock y -10 68; wait
movie stop
movie encode ~/Desktop/test.mov

? also your commands are a little weird because rock will already change direction, so you get an identical movie by running a full cycle of rocking, e.g.:

movie record
rock y 10 136;wait
movie stop
movie encode ~/Desktop/test2.mov

If you are using some other method of looping, maybe it is repeating the end frames.  I don?t know if this ?View? Loop? display in Quicktime Player goes from the 136th to the first or assumes they are the same and goes to the second instead.
Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jun 14, 2017, at 5:38 AM, Andrew Oliver, II <aoliver2 at hotmail.com> wrote:
> 
> Dear Chimera,
> I am trying to create a "rocking" movie of a molecule that will continuously loop. I am using the command:
> 
> movie record; rock y 10 68; wait;
>  rock y -10 68; wait; movie stop; movie encode
> 
> However, when I do this, there is always a slight pause at the end of the movie, before it starts the next loop -- which means it doesn't loop smoothly.
> 
> Is there a way to create the movie so that there will be no pause before each successive loop?
> 
> Many thanks,
> Andrew Oliver




From goddard at sonic.net  Wed Jun 14 18:00:06 2017
From: goddard at sonic.net (Tom Goddard)
Date: Wed, 14 Jun 2017 18:00:06 -0700
Subject: [Chimera-users] Generate the tranfromation or bio matrix from
 the docking complex using Chimera
In-Reply-To: <8E1D3D92-830B-493A-91E5-2E60BABD43D7@sonic.net>
References: <BLUPR0501MB1732F3F72B5D636368FDE507D5C30@BLUPR0501MB1732.namprd05.prod.outlook.com>
 <A68480D0-4632-4A32-871F-EE3F4D8EA67E@cgl.ucsf.edu>
 <8E1D3D92-830B-493A-91E5-2E60BABD43D7@sonic.net>
Message-ID: <F8D79766-5CB5-453D-BB91-EAB1909158FD@sonic.net>

One more trick to help get BIOMT matrices into a PDB file to place multiple copies of a chain.  If you figure out the symmetry parameters, e.g. symmetry axis direction, axis point for say C6 symmetry, then use the Chimera ?sym? command to create the copies from a single chain, you can use the ?biomtSet true? option with the sym command and it will include the BIOMT matrices in a PDB file written from Chimera (menu File / Save PDB?).

	https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html <https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/sym.html>

  Tom

> On Jun 14, 2017, at 12:26 PM, Tom Goddard <goddard at sonic.net> wrote:
> 
> Hi Elumalai,
> 
>  You can get the symmetry operations out of Chimera.   Open your complex twice, models #0 and #1.  Suppose chains A and B are the same protein and you want the transformation to get from A to B.  First align the first copy chain A to the second copy chain B:
> 
> 	matchmaker #2:.B  #1:.A
> 
> Then measure the motion
> 
> 	measure rotation #1 #2
> 
> The 3 by 4 matrix (rotation in first 3 columns, translation in 4th column) is output to the reply log.  Also a rotation axis and angle is output.  You can use the matrix and add in a text editor REMARK 350 BIOMT matrices to the PDB file containing just chain A to place it using the matrix.  Take a look at an example PDB file to see the format (e.g. 2bbv).  Or you can use the Chimera sym command with the rotation axis and angle to create copies of chain A in Chimera.
> 
> 	Tom
> 
> 
> 
>> On Jun 14, 2017, at 10:32 AM, Elaine Meng wrote:
>> 
>> 
>>> On Jun 14, 2017, at 9:35 AM, Elumalai Pavadai <epavadai at fiu.edu> wrote:
>>> 
>>> Dear Meng,
>>> 
>>> I have a cylindrical symmetry protein complex modeled with the protein-protein docking.  Since the docking complex is very big in terms of size and number of atoms, I would like to generate the transformation matrix from it. Using the  matrix , I can be able to generate the complex with Chimera. So, my question is that how to generate the transformation matrix from the protein complex with Chimera?
>>> 
>>> Thank you, and I look forward to hearing from you. 
>>> 
>>> Kind regards,
>>> Elumalai
>> 
>> Dear Elumalai,
>> 
>> I?m CC-ing chimera-users at cgl.ucsf.edu ? it is the recommended address for Chimera questions, to ensure you get a response and allowing others to make suggestions.
>> 
>> I?m guessing that you mean your large complex is several copies of the same protein, arranged in some symmetrical way, and instead you would like to have a file with only one copy but also the matrices describing the whole thing.  If you had such a file, you could open it in Chimera and then generate the whole thing from the matrices.
>> 
>> However, Chimera does not have the tools to go in the opposite direction, to figure out all the matrices from the whole complex.  So if I understood your problem correctly, you would need to find some other program to do this.  I haven?t done it myself, so I don?t know what you could use. If your protein-protein docking program created this symmetrical structure, maybe it can output the needed matrices.
>> 
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.                       
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>> 
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
>> 
> 

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From hypowergravity at gmail.com  Wed Jun 14 21:30:20 2017
From: hypowergravity at gmail.com (sriram raghavan)
Date: Thu, 15 Jun 2017 10:00:20 +0530
Subject: [Chimera-users] structureViz Path problem
Message-ID: <CABp6A+K_5pPVUM1FbRLjJNiY6S+U1C-vRHfAKPwdZdroy2OoqQ@mail.gmail.com>

Dear Sir,
I find it difficult to troubleshoot the path setting problem, which I am
facing while operating with the structureViz plugin. Please kindly help me
in installing the app.
I have set UCSF chimera path as below but still i am not able to save the
setting if default setting is the problem.[image: Inline image 1]

I get the following error.
[image: Inline image 2]
With Regards

S.Sriram
Ph.D. Research Scholar
CAS in Crystallography and Biophysics
University Of Madras
Mail:hypowergravity at gmail.com
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From meng at cgl.ucsf.edu  Thu Jun 15 11:43:20 2017
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 15 Jun 2017 11:43:20 -0700
Subject: [Chimera-users] structureViz Path problem
In-Reply-To: <CABp6A+K_5pPVUM1FbRLjJNiY6S+U1C-vRHfAKPwdZdroy2OoqQ@mail.gmail.com>
References: <CABp6A+K_5pPVUM1FbRLjJNiY6S+U1C-vRHfAKPwdZdroy2OoqQ@mail.gmail.com>
Message-ID: <22D0C031-4F41-401B-B3F3-E9583F4A6397@cgl.ucsf.edu>

Dear S.Sriram,
I don?t use Windows, but one idea is that maybe you need to add chimera.exe at the end. E.g. instead of what you had:

C:\Program Files\Chimera 1.11.2\bin

? maybe should be:

C:\Program Files\Chimera 1.11.2\bin\chimera.exe

(as per the Chimera startup information  
http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/startup.html )

Other ideas are to make sure that is the correct installation location and name, e.g. it might be ?Chimera? instead of ?Chimera 1.11.2?

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


> On Jun 14, 2017, at 9:30 PM, sriram raghavan <hypowergravity at gmail.com> wrote:
> 
> Dear Sir,
> I find it difficult to troubleshoot the path setting problem, which I am facing while operating with the structureViz plugin. Please kindly help me in installing the app.
> I have set UCSF chimera path as below but still i am not able to save the setting if default setting is the problem.<image.png>
> 
> I get the following error.
> <image.png>
> With Regards
> 
> S.Sriram




From scooter at cgl.ucsf.edu  Thu Jun 15 12:43:42 2017
From: scooter at cgl.ucsf.edu (Scooter Morris)
Date: Thu, 15 Jun 2017 12:43:42 -0700
Subject: [Chimera-users] structureViz Path problem
In-Reply-To: <CABp6A+K_5pPVUM1FbRLjJNiY6S+U1C-vRHfAKPwdZdroy2OoqQ@mail.gmail.com>
References: <CABp6A+K_5pPVUM1FbRLjJNiY6S+U1C-vRHfAKPwdZdroy2OoqQ@mail.gmail.com>
Message-ID: <303882d8-b23f-b982-bc25-2763b570a3a3@cgl.ucsf.edu>

Greetings,
     The path needs to include the actual binary.  So, in your case, it 
should be C:\Program Files\Chimera 1.11.2\bin\chimera.exe

-- scooter

On 06/14/2017 09:30 PM, sriram raghavan wrote:
> Dear Sir,
> I find it difficult to troubleshoot the path setting problem, which I 
> am facing while operating with the structureViz plugin. Please kindly 
> help me in installing the app.
> I have set UCSF chimera path as below but still i am not able to save 
> the setting if default setting is the problem.Inline image 1
>
> I get the following error.
> Inline image 2
> With Regards
>
> S.Sriram
> Ph.D. Research Scholar
> CAS in Crystallography and Biophysics
> University Of Madras
> Mail:hypowergravity at gmail.com <mailto:hypowergravity at gmail.com>
>
>
>
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users


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From hypowergravity at gmail.com  Fri Jun 16 01:59:17 2017
From: hypowergravity at gmail.com (sriram raghavan)
Date: Fri, 16 Jun 2017 14:29:17 +0530
Subject: [Chimera-users] structureViz Path problem
In-Reply-To: <22D0C031-4F41-401B-B3F3-E9583F4A6397@cgl.ucsf.edu>
References: <CABp6A+K_5pPVUM1FbRLjJNiY6S+U1C-vRHfAKPwdZdroy2OoqQ@mail.gmail.com>
 <22D0C031-4F41-401B-B3F3-E9583F4A6397@cgl.ucsf.edu>
Message-ID: <CABp6A+KQcvnLppZUf04RixTFMqTrHPgR3XtKMfSe-QUS0x6EnA@mail.gmail.com>

thank you for the mail the solution works.

With Regards

S.Sriram
Ph.D. Research Scholar
CAS in Crystallography and Biophysics
University Of Madras
Mail:hypowergravity at gmail.com


On Fri, Jun 16, 2017 at 12:13 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Dear S.Sriram,
> I don?t use Windows, but one idea is that maybe you need to add
> chimera.exe at the end. E.g. instead of what you had:
>
> C:\Program Files\Chimera 1.11.2\bin
>
> ? maybe should be:
>
> C:\Program Files\Chimera 1.11.2\bin\chimera.exe
>
> (as per the Chimera startup information
> http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/startup.html )
>
> Other ideas are to make sure that is the correct installation location and
> name, e.g. it might be ?Chimera? instead of ?Chimera 1.11.2?
>
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
> > On Jun 14, 2017, at 9:30 PM, sriram raghavan <hypowergravity at gmail.com>
> wrote:
> >
> > Dear Sir,
> > I find it difficult to troubleshoot the path setting problem, which I am
> facing while operating with the structureViz plugin. Please kindly help me
> in installing the app.
> > I have set UCSF chimera path as below but still i am not able to save
> the setting if default setting is the problem.<image.png>
> >
> > I get the following error.
> > <image.png>
> > With Regards
> >
> > S.Sriram
>
>
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From meng at cgl.ucsf.edu  Fri Jun 16 12:41:31 2017
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 16 Jun 2017 12:41:31 -0700
Subject: [Chimera-users] Run procedure
In-Reply-To: <005f01d2e6d3$36997400$a3cc5c00$@q.com>
References: <005f01d2e6d3$36997400$a3cc5c00$@q.com>
Message-ID: <7D81F8B6-398E-4C8A-9F22-0700F203EB7D@cgl.ucsf.edu>

Hi Paul,
(1) please send questions to the chimera-users address, CC?d here.  Questions sent just to me may fall through the cracks.

(2) all I know about the Molecular Dynamics Simulation tool, I have written in its documentation.  You can see it by clicking the Help button on the dialog or viewing the copy at our website:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html>

See the sentence containing ?clicking Run? about 1/3 of the way down and the last sentence in the page starting with "After the completion of any MD run??

I am guessing that you chose the recording option in the MD Movie dialog.  If you are not sure which data it is showing, Quit from the MD Movie dialog. Then from the Tools menu, restart MD Movie and specify the specific MMTK input (trajectory) file that you want, like we discussed earlier.  Although I said earlier that if you gave the same output name for both equilibration and production, the production might overwrite the equilibration, I?m no longer sure about whether it overwrites or just gets added to the end.  However, you should be able to tell by the number of frames in the output trajectory.

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




> On Jun 16, 2017, at 12:03 PM, pbuscemi <pbuscemi at q.com> wrote:
> 
> Elaine,
> 
> In doing a simulation, does it matter which screen is used to select "RUN"  ie,  minimize, equilibrium,production, or other.
> 
> i.e  If I select equlibrium,  is production also run ?  When a movie is recorded,  is it from equilibrium or production portion ?
> 
> thanks 
> Paul
> 
> 




From pbuscemi at q.com  Fri Jun 16 15:14:19 2017
From: pbuscemi at q.com (paul buscemi)
Date: Fri, 16 Jun 2017 17:14:19 -0500
Subject: [Chimera-users] Run procedure
In-Reply-To: <7D81F8B6-398E-4C8A-9F22-0700F203EB7D@cgl.ucsf.edu>
References: <005f01d2e6d3$36997400$a3cc5c00$@q.com>
 <7D81F8B6-398E-4C8A-9F22-0700F203EB7D@cgl.ucsf.edu>
Message-ID: <4A9E18AF-546B-4229-96BC-838E9007B6F5@q.com>

thanks Elaine,  I promise t be more compliant ! 
> On Jun 16, 2017, at 2:41 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:
> 
> Hi Paul,
> (1) please send questions to the chimera-users address, CC?d here.  Questions sent just to me may fall through the cracks.
> 
> (2) all I know about the Molecular Dynamics Simulation tool, I have written in its documentation.  You can see it by clicking the Help button on the dialog or viewing the copy at our website:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html>
> 
> See the sentence containing ?clicking Run? about 1/3 of the way down and the last sentence in the page starting with "After the completion of any MD run??
> 
> I am guessing that you chose the recording option in the MD Movie dialog.  If you are not sure which data it is showing, Quit from the MD Movie dialog. Then from the Tools menu, restart MD Movie and specify the specific MMTK input (trajectory) file that you want, like we discussed earlier.  Although I said earlier that if you gave the same output name for both equilibration and production, the production might overwrite the equilibration, I?m no longer sure about whether it overwrites or just gets added to the end.  However, you should be able to tell by the number of frames in the output trajectory.
> 
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
> 
> 
>> On Jun 16, 2017, at 12:03 PM, pbuscemi <pbuscemi at q.com> wrote:
>> 
>> Elaine,
>> 
>> In doing a simulation, does it matter which screen is used to select "RUN"  ie,  minimize, equilibrium,production, or other.
>> 
>> i.e  If I select equlibrium,  is production also run ?  When a movie is recorded,  is it from equilibrium or production portion ?
>> 
>> thanks 
>> Paul
>> 
>> 
> 




From shabnam.nadjafi at gmail.com  Fri Jun 16 22:17:08 2017
From: shabnam.nadjafi at gmail.com (Shabnam Nadjafi)
Date: Sat, 17 Jun 2017 09:47:08 +0430
Subject: [Chimera-users] Question about Chimera
In-Reply-To: <287A146A-6ADA-4FA3-B1CC-E8ABB1E7A687@cgl.ucsf.edu>
References: <CAAeZFmp1s8UuCv7WzX-YREOoL18dk_R-cBn7Ph1THE98YVoE=A@mail.gmail.com>
 <287A146A-6ADA-4FA3-B1CC-E8ABB1E7A687@cgl.ucsf.edu>
Message-ID: <CAAeZFmr-JHeKHQ0GzEAYHYt7esPA5EqS_x5Gmk8sJ9ck-1H-8g@mail.gmail.com>

Dear Elaine C. Meng

I thank you for your attention and reply.

Regards,

Shabnam Ndadjafi

On Mon, Jun 12, 2017 at 9:11 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Dear Shabnam Nadjafi,
>
> The complete information is on the Chimera website, see ?licensing? here:
> <http://www.rbvi.ucsf.edu/chimera/docs/licensing.html>
>
> In summary:
>
> Chimera is free for noncommercial use, but you will need to agree to the
> license that is automatically shown when you download the program.
>
> To get Chimera for commercial use, you should contact chimera at cgl.ucsf.edu
> about the cost and terms.
>
> Regards,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> > On Jun 11, 2017, at 2:08 AM, Shabnam Nadjafi <shabnam.nadjafi at gmail.com>
> wrote:
> >
> > Dear Manager
> > I have a question about "Chimera".
> > Is " "Chimera" free ? Can this program be used without license and
> complete freely?
> > Thanks,
> > Sincerely Yours,
> > Shabnam Nadjafi
>
>
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From pbuscemi at q.com  Sat Jun 17 11:44:53 2017
From: pbuscemi at q.com (paul buscemi)
Date: Sat, 17 Jun 2017 13:44:53 -0500
Subject: [Chimera-users] alter to periodic box
Message-ID: <6FA489C6-BE5E-4C12-BB65-7886C895E246@q.com>



I was experimenting with mixed solvents and found that if you create a box around a molecule say 10A on a side,  then de-select "remove solvent" and then create a second box, say 2A on a side,  that second box forms around the first.  You can then constrain the second box which will for the most part retain the first and the parent molecule during a simulation.  This allows visualization of the live trajectory as well.  I used MON around water and he process is faster to create than selecting the six outside surfaces of a solvent box.

Paul


From J.R.J.Healey at warwick.ac.uk  Mon Jun 19 04:49:19 2017
From: J.R.J.Healey at warwick.ac.uk (Healey, Joe)
Date: Mon, 19 Jun 2017 11:49:19 +0000
Subject: [Chimera-users] Installing Chimera and ChimeraX on a CentOS box
	without root
Message-ID: <AM4PR01MB1458E2327AB184DBE72B648BD4C40@AM4PR01MB1458.eurprd01.prod.exchangelabs.com>

Hi Chimera team,


I need to install chimera and chimeraX on a server with a GPU which I now have access to assist in visualising larger structures, but I don't have any root privileges.



After the first pass installing both, Chimera 1.11 gives me this warning/error when attempting to run:


"OpenGL misconfiguration detected. /usr/lib/libGL.so.1 differs from /usr/X11R6/lib/libGL.so.1"


And when I close this dialogue box, I get this:


"Error of failed request:  BadValue (integer parameter out of range for operation)

  Major opcode of failed request:  149 (GLX)
  Minor opcode of failed request:  3 (X_GLXCreateContext)
  Value in failed request:  0x0
  Serial number of failed request:  717
  Current serial number in output stream:  718
libxcb: WARNING! Program tries to lock an already locked connection,
        which indicates a programming error.
        There will be no further warnings about this issue."


-----------


And when running ChimeraX for the first time, I get this:


"

ChimeraX: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by ChimeraX)
ChimeraX: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /cold/chem/msrnbi/bin/chimerax/bin/../lib/libpython3.6m.so.1.0)
ChimeraX: /lib64/libc.so.6: version `GLIBC_2.17' not found (required by /cold/chem/msrnbi/bin/chimerax/bin/../lib/libpython3.6m.so.1.0)
"


Evidently I need 2 different versions of GLIBC for ChimeraX, but assuming I can install these concurrently without root access, how would I go about telling ChimeraX where to look for the libraries?



Any advice/documentation you have to get the programs working would be much appreciated.


Joe Healey


M.Sc. B.Sc. (Hons) MSRB
PhD Student
MOAC CDT, Senate House
University of Warwick
Coventry
CV47AL
Mob: +44 (0) 7536 042620  |  Email: J.R.J.Healey at warwick.ac.uk

Jointly working in:
Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/> (WMS Microbiology and Infection Unit)
and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry)

Twitter: @JRJHealey<https://twitter.com/JRJHealey>  |  Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738
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From goddard at sonic.net  Mon Jun 19 10:38:49 2017
From: goddard at sonic.net (Tom Goddard)
Date: Mon, 19 Jun 2017 10:38:49 -0700
Subject: [Chimera-users] Installing Chimera and ChimeraX on a CentOS box
 without root
In-Reply-To: <AM4PR01MB1458E2327AB184DBE72B648BD4C40@AM4PR01MB1458.eurprd01.prod.exchangelabs.com>
References: <AM4PR01MB1458E2327AB184DBE72B648BD4C40@AM4PR01MB1458.eurprd01.prod.exchangelabs.com>
Message-ID: <C5289677-832D-4431-B04D-FC1440A0813D@sonic.net>

Hi Joe,

  Chimera and ChimeraX are best run on your laptop and desktop.  Trying to get it to run on a Linux server with remote display is asking for failure.  But if you still want to pursue that here is what your errors mean.  The first error starting Chimera 1.11 means that there inconsistent versions of OpenGL on the server ? two different OpenGL libraries.  Only a system administrator can fix this, usually by installing a new graphics driver which will hopefully remove any old ones it finds.  For ChimeraX, as it says on our download page "It does not run on RHEL/CentOS 7 as is??  and on our download it suggests speculative and difficult steps if you are not accustomed to installing software on Linux.  By far the best option is to find a machine capable of running Chimera/ChimeraX rather than trying to prod a totally unsuitable machine into running them.

	Tom


> On Jun 19, 2017, at 4:49 AM, Healey, Joe <J.R.J.Healey at warwick.ac.uk> wrote:
> 
> Hi Chimera team,
> 
> I need to install chimera and chimeraX on a server with a GPU which I now have access to assist in visualising larger structures, but I don't have any root privileges.
> 
> 
> After the first pass installing both, Chimera 1.11 gives me this warning/error when attempting to run:
> 
> "OpenGL misconfiguration detected. /usr/lib/libGL.so.1 differs from /usr/X11R6/lib/libGL.so.1"
> 
> And when I close this dialogue box, I get this:
> 
> "Error of failed request:  BadValue (integer parameter out of range for operation)
>   Major opcode of failed request:  149 (GLX)
>   Minor opcode of failed request:  3 (X_GLXCreateContext)
>   Value in failed request:  0x0
>   Serial number of failed request:  717
>   Current serial number in output stream:  718
> libxcb: WARNING! Program tries to lock an already locked connection,
>         which indicates a programming error.
>         There will be no further warnings about this issue."
> 
> -----------
> 
> And when running ChimeraX for the first time, I get this:
> 
> "
> ChimeraX: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by ChimeraX)
> ChimeraX: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /cold/chem/msrnbi/bin/chimerax/bin/../lib/libpython3.6m.so.1.0)
> ChimeraX: /lib64/libc.so.6: version `GLIBC_2.17' not found (required by /cold/chem/msrnbi/bin/chimerax/bin/../lib/libpython3.6m.so.1.0)
> "
> 
> Evidently I need 2 different versions of GLIBC for ChimeraX, but assuming I can install these concurrently without root access, how would I go about telling ChimeraX where to look for the libraries?
> 
> 
> Any advice/documentation you have to get the programs working would be much appreciated.
> 
> Joe Healey
> 
>                                        
> M.Sc. B.Sc. (Hons) MSRB
> PhD Student
> MOAC CDT, Senate House
> University of Warwick
> Coventry
> CV47AL
> Mob: +44 (0) 7536 042620  |  Email: J.R.J.Healey at warwick.ac.uk <mailto:J.R.J.Healey at warwick.ac.uk>
> 
> Jointly working in:
> Waterfield Lab <http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/> (WMS Microbiology and Infection Unit)
> and the Gibson Lab <http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry)
> 
> Twitter: @JRJHealey <https://twitter.com/JRJHealey>  |  Website: MOAC Page <http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738 <http://orcid.org/0000-0002-9569-6738>_______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
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From aomdahl at gmail.com  Mon Jun 19 14:00:55 2017
From: aomdahl at gmail.com (Ashton Omdahl)
Date: Mon, 19 Jun 2017 17:00:55 -0400
Subject: [Chimera-users] Selecting only protein surfaces programmatically
Message-ID: <59483b88.043aed0a.b0399.af82@mx.google.com>

Chimera friends-
I am creating a python script to take the sum of the distance from every atom in a given zone around selected residues to the surface of the protein. As part of this, I would also like to calculate the minimum distance to the surface of any given atom (based on the current surface rolling ball radius algorithm). However, I have been unable to find a command to select only the surface of a protein that works consistently across interfaces. What commands could I do this with both programmatically (in python) and in the GUI command line?
Thanks!
Ashton

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From J.R.J.Healey at warwick.ac.uk  Tue Jun 20 00:30:02 2017
From: J.R.J.Healey at warwick.ac.uk (Healey, Joe)
Date: Tue, 20 Jun 2017 07:30:02 +0000
Subject: [Chimera-users] Installing Chimera and ChimeraX on a CentOS box
 without root
In-Reply-To: <C5289677-832D-4431-B04D-FC1440A0813D@sonic.net>
References: <AM4PR01MB1458E2327AB184DBE72B648BD4C40@AM4PR01MB1458.eurprd01.prod.exchangelabs.com>,
 <C5289677-832D-4431-B04D-FC1440A0813D@sonic.net>
Message-ID: <AM4PR01MB14582B79D3C7603FF117AD15D4C50@AM4PR01MB1458.eurprd01.prod.exchangelabs.com>

Hi Tom,


Ah ok, I understand, thanks for the reply. I didn't realise it was going to be quite so complicated!


My mac can't really handle the structures I'm trying to model, as it only has integrated graphics. But, perhaps I can use this to convince the Uni to buy me a more capable machine! ;)


Thanks again,


Joe



Joe Healey


M.Sc. B.Sc. (Hons) MSRB
PhD Student
MOAC CDT, Senate House
University of Warwick
Coventry
CV47AL
Mob: +44 (0) 7536 042620  |  Email: J.R.J.Healey at warwick.ac.uk

Jointly working in:
Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/> (WMS Microbiology and Infection Unit)
and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry)

Twitter: @JRJHealey<https://twitter.com/JRJHealey>  |  Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738
________________________________
From: Tom Goddard <goddard at sonic.net>
Sent: 19 June 2017 18:38:49
To: Healey, Joe
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Installing Chimera and ChimeraX on a CentOS box without root

Hi Joe,

  Chimera and ChimeraX are best run on your laptop and desktop.  Trying to get it to run on a Linux server with remote display is asking for failure.  But if you still want to pursue that here is what your errors mean.  The first error starting Chimera 1.11 means that there inconsistent versions of OpenGL on the server ? two different OpenGL libraries.  Only a system administrator can fix this, usually by installing a new graphics driver which will hopefully remove any old ones it finds.  For ChimeraX, as it says on our download page "It does not run on RHEL/CentOS 7 as is??  and on our download it suggests speculative and difficult steps if you are not accustomed to installing software on Linux.  By far the best option is to find a machine capable of running Chimera/ChimeraX rather than trying to prod a totally unsuitable machine into running them.

Tom


On Jun 19, 2017, at 4:49 AM, Healey, Joe <J.R.J.Healey at warwick.ac.uk<mailto:J.R.J.Healey at warwick.ac.uk>> wrote:

Hi Chimera team,

I need to install chimera and chimeraX on a server with a GPU which I now have access to assist in visualising larger structures, but I don't have any root privileges.


After the first pass installing both, Chimera 1.11 gives me this warning/error when attempting to run:

"OpenGL misconfiguration detected. /usr/lib/libGL.so.1 differs from /usr/X11R6/lib/libGL.so.1"

And when I close this dialogue box, I get this:

"Error of failed request:  BadValue (integer parameter out of range for operation)
  Major opcode of failed request:  149 (GLX)
  Minor opcode of failed request:  3 (X_GLXCreateContext)
  Value in failed request:  0x0
  Serial number of failed request:  717
  Current serial number in output stream:  718
libxcb: WARNING! Program tries to lock an already locked connection,
        which indicates a programming error.
        There will be no further warnings about this issue."

-----------

And when running ChimeraX for the first time, I get this:

"
ChimeraX: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by ChimeraX)
ChimeraX: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /cold/chem/msrnbi/bin/chimerax/bin/../lib/libpython3.6m.so.1.0)
ChimeraX: /lib64/libc.so.6: version `GLIBC_2.17' not found (required by /cold/chem/msrnbi/bin/chimerax/bin/../lib/libpython3.6m.so.1.0)
"


Evidently I need 2 different versions of GLIBC for ChimeraX, but assuming I can install these concurrently without root access, how would I go about telling ChimeraX where to look for the libraries?



Any advice/documentation you have to get the programs working would be much appreciated.


Joe Healey


M.Sc. B.Sc. (Hons) MSRB
PhD Student
MOAC CDT, Senate House
University of Warwick
Coventry
CV47AL
Mob: +44 (0) 7536 042620  |  Email: J.R.J.Healey at warwick.ac.uk<mailto:J.R.J.Healey at warwick.ac.uk>

Jointly working in:
Waterfield Lab<http://www2.warwick.ac.uk/fac/med/research/tsm/microinfect/staff/waterfieldlab/> (WMS Microbiology and Infection Unit)
and the Gibson Lab<http://www2.warwick.ac.uk/fac/sci/chemistry/research/gibson/gibsongroup/> (Warwick Chemistry)

Twitter: @JRJHealey<https://twitter.com/JRJHealey>  |  Website: MOAC Page<http://www2.warwick.ac.uk/fac/sci/moac/people/students/2013/joseph_healey> | ORCID: orcid.org/0000-0002-9569-6738<http://orcid.org/0000-0002-9569-6738>
_______________________________________________
Chimera-users mailing list: Chimera-users at cgl.ucsf.edu<mailto:Chimera-users at cgl.ucsf.edu>
Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From sarah.azzam at kustar.ac.ae  Tue Jun 20 04:04:56 2017
From: sarah.azzam at kustar.ac.ae (Sarah Qassem Azzam)
Date: Tue, 20 Jun 2017 11:04:56 +0000
Subject: [Chimera-users] Please Help Me: Vina Tool Error  in Chimera:
Message-ID: <07939DA3F9D0F449B178D45488CE8EC802791D61DC@KU-SH-MBX02.kustar.ac.ae>

Dear Chimera help desk,

Hope this email finds you well.
I am facing a problem with Vina Tool in Chimera, while running molecular docking.
I got the following error message:
"\Program Files\The Scripps Research Institute\vina.exe"' is not recognized as an internal or external command, operable program or batch file.
----
Application stdout
-----
[no output]

I did install Vina, and I am trying to run it in Chimera using 'Local' option for executable location.
Can you please advise on how to solve this issue?
Your time is highly appreciated.

Kind regards,
Sarah Azzam
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From meng at cgl.ucsf.edu  Tue Jun 20 09:09:27 2017
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 20 Jun 2017 09:09:27 -0700
Subject: [Chimera-users] Please Help Me: Vina Tool Error  in Chimera:
In-Reply-To: <07939DA3F9D0F449B178D45488CE8EC802791D61DC@KU-SH-MBX02.kustar.ac.ae>
References: <07939DA3F9D0F449B178D45488CE8EC802791D61DC@KU-SH-MBX02.kustar.ac.ae>
Message-ID: <6F23B4D7-EF42-47E8-8DF2-08E98E996F9F@cgl.ucsf.edu>

Dear Sarah Azzam,
As far as I can tell, this isn?t really a Chimera question but a question of where you installed the vina executable, whether you correctly specified the location, and whether the file is really executable.  It is impossible for me to tell any of these things, because they are specific to your own computer.

I don?t use Windows myself, but doesn?t the location have to start with something like C: or D: ? for example, ?C:\Program Files\[?]? That?s my guess as to the most likely problem. Secondly, even if you give the location correctly, maybe you have to make the file executable, but that should be described in the installation instructions for Autodock Vina.

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


> On Jun 20, 2017, at 4:04 AM, Sarah Qassem Azzam <sarah.azzam at kustar.ac.ae> wrote:
> 
> Dear Chimera help desk,
>  
> Hope this email finds you well.
> I am facing a problem with Vina Tool in Chimera, while running molecular docking.
> I got the following error message:
> "\Program Files\The Scripps Research Institute\vina.exe"' is not recognized as an internal or external command, operable program or batch file.
> ----
> Application stdout
> -----
> [no output]
>  
> I did install Vina, and I am trying to run it in Chimera using ?Local? option for executable location.
> Can you please advise on how to solve this issue?
> Your time is highly appreciated.
>  
> Kind regards,
> Sarah Azzam




From meng at cgl.ucsf.edu  Tue Jun 20 09:23:25 2017
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Tue, 20 Jun 2017 09:23:25 -0700
Subject: [Chimera-users] Selecting only protein surfaces programmatically
In-Reply-To: <59483b88.043aed0a.b0399.af82@mx.google.com>
References: <59483b88.043aed0a.b0399.af82@mx.google.com>
Message-ID: <D53BC0CD-7638-42DF-9DA6-0DEE3C5EF957@cgl.ucsf.edu>

Hi Ashton,
The ?measure distance? command gives the shortest distance between one set of atoms and/or surface pieces and another set of atoms or surface pieces. However, this may not help you because you can?t specify only using the surface of a specific atom; the entire molecular surface is one piece and can only be specified as a whole.  You might be able to use some of the code from that command?s implementation, however.
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/measure.html#distance>

Further, as you have discovered, Chimera is limited in ways you can specify surface models or surface pieces: only as a model number or as a selection, as described at the bottom of this page:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/atom_spec.html#othermodels>

Here is a tricky command to select models that are not atomic models (select models and not atoms):

sel # &~ @

I can?t advise on python details, but I believe that everything that can be run as a Chimera command can be python-ified by the general mechanism described here:
<http://www.rbvi.ucsf.edu/chimera/docs/ProgrammersGuide/basicPrimer.html>

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

> On Jun 19, 2017, at 2:00 PM, Ashton Omdahl <aomdahl at gmail.com> wrote:
> 
> Chimera friends-
> I am creating a python script to take the sum of the distance from every atom in a given zone around selected residues to the surface of the protein. As part of this, I would also like to calculate the minimum distance to the surface of any given atom (based on the current surface rolling ball radius algorithm). However, I have been unable to find a command to select only the surface of a protein that works consistently across interfaces. What commands could I do this with both programmatically (in python) and in the GUI command line?
> Thanks!
> Ashton
>  



From sarah.azzam at kustar.ac.ae  Tue Jun 20 13:12:54 2017
From: sarah.azzam at kustar.ac.ae (Sarah Qassem Azzam)
Date: Tue, 20 Jun 2017 20:12:54 +0000
Subject: [Chimera-users] Please Help Me: Vina Tool Error  in Chimera:
In-Reply-To: <6F23B4D7-EF42-47E8-8DF2-08E98E996F9F@cgl.ucsf.edu>
References: <07939DA3F9D0F449B178D45488CE8EC802791D61DC@KU-SH-MBX02.kustar.ac.ae>
 <6F23B4D7-EF42-47E8-8DF2-08E98E996F9F@cgl.ucsf.edu>
Message-ID: <07939DA3F9D0F449B178D45488CE8EC802791D6384@KU-SH-MBX02.kustar.ac.ae>

Dear Dr. Meng,

Thank you for your kind email and reply.
I did ensure that I specify the location of the vina executable correctly, and yes you are right the error that pops-up in chimera does start with C:\Program Files ...............
I did consult with our institutions IT specialist about ensuring that Vina is executable and she did confirm that; yet, we were unable to detect the source of this error.
I was kindly hoping that Chimera Help Desk may have encountered a request regarding this error from other users, and you may possibly have some recommendations to help with this matter.

Your help is highly appreciated.
Kind regards,
Sarah Azzam

-----Original Message-----
From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
Sent: Tuesday, June 20, 2017 8:09 PM
To: Sarah Qassem Azzam <sarah.azzam at kustar.ac.ae>
Cc: chimera-users at cgl.ucsf.edu
Subject: Re: [Chimera-users] Please Help Me: Vina Tool Error in Chimera:

Dear Sarah Azzam,
As far as I can tell, this isn?t really a Chimera question but a question of where you installed the vina executable, whether you correctly specified the location, and whether the file is really executable.  It is impossible for me to tell any of these things, because they are specific to your own computer.

I don?t use Windows myself, but doesn?t the location have to start with something like C: or D: ? for example, ?C:\Program Files\[?]? That?s my guess as to the most likely problem. Secondly, even if you give the location correctly, maybe you have to make the file executable, but that should be described in the installation instructions for Autodock Vina.

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


> On Jun 20, 2017, at 4:04 AM, Sarah Qassem Azzam <sarah.azzam at kustar.ac.ae> wrote:
> 
> Dear Chimera help desk,
>  
> Hope this email finds you well.
> I am facing a problem with Vina Tool in Chimera, while running molecular docking.
> I got the following error message:
> "\Program Files\The Scripps Research Institute\vina.exe"' is not recognized as an internal or external command, operable program or batch file.
> ----
> Application stdout
> -----
> [no output]
>  
> I did install Vina, and I am trying to run it in Chimera using ?Local? option for executable location.
> Can you please advise on how to solve this issue?
> Your time is highly appreciated.
>  
> Kind regards,
> Sarah Azzam




From pett at cgl.ucsf.edu  Thu Jun 22 11:05:04 2017
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Thu, 22 Jun 2017 11:05:04 -0700
Subject: [Chimera-users] Please Help Me: Vina Tool Error  in Chimera:
In-Reply-To: <07939DA3F9D0F449B178D45488CE8EC802791D6384@KU-SH-MBX02.kustar.ac.ae>
References: <07939DA3F9D0F449B178D45488CE8EC802791D61DC@KU-SH-MBX02.kustar.ac.ae>
 <6F23B4D7-EF42-47E8-8DF2-08E98E996F9F@cgl.ucsf.edu>
 <07939DA3F9D0F449B178D45488CE8EC802791D6384@KU-SH-MBX02.kustar.ac.ae>
Message-ID: <54139BC7-C572-4320-A8FF-BE86DE992119@cgl.ucsf.edu>

Really, other than meticulously check that the file and folders exist exactly as you typed them, and that there were no typos, we don?t have any further suggestions.  Sorry.

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Jun 20, 2017, at 1:12 PM, Sarah Qassem Azzam <sarah.azzam at kustar.ac.ae> wrote:
> 
> Dear Dr. Meng,
> 
> Thank you for your kind email and reply.
> I did ensure that I specify the location of the vina executable correctly, and yes you are right the error that pops-up in chimera does start with C:\Program Files ...............
> I did consult with our institutions IT specialist about ensuring that Vina is executable and she did confirm that; yet, we were unable to detect the source of this error.
> I was kindly hoping that Chimera Help Desk may have encountered a request regarding this error from other users, and you may possibly have some recommendations to help with this matter.
> 
> Your help is highly appreciated.
> Kind regards,
> Sarah Azzam
> 
> -----Original Message-----
> From: Elaine Meng [mailto:meng at cgl.ucsf.edu] 
> Sent: Tuesday, June 20, 2017 8:09 PM
> To: Sarah Qassem Azzam <sarah.azzam at kustar.ac.ae>
> Cc: chimera-users at cgl.ucsf.edu
> Subject: Re: [Chimera-users] Please Help Me: Vina Tool Error in Chimera:
> 
> Dear Sarah Azzam,
> As far as I can tell, this isn?t really a Chimera question but a question of where you installed the vina executable, whether you correctly specified the location, and whether the file is really executable.  It is impossible for me to tell any of these things, because they are specific to your own computer.
> 
> I don?t use Windows myself, but doesn?t the location have to start with something like C: or D: ? for example, ?C:\Program Files\[?]? That?s my guess as to the most likely problem. Secondly, even if you give the location correctly, maybe you have to make the file executable, but that should be described in the installation instructions for Autodock Vina.
> 
> I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
>> On Jun 20, 2017, at 4:04 AM, Sarah Qassem Azzam <sarah.azzam at kustar.ac.ae> wrote:
>> 
>> Dear Chimera help desk,
>> 
>> Hope this email finds you well.
>> I am facing a problem with Vina Tool in Chimera, while running molecular docking.
>> I got the following error message:
>> "\Program Files\The Scripps Research Institute\vina.exe"' is not recognized as an internal or external command, operable program or batch file.
>> ----
>> Application stdout
>> -----
>> [no output]
>> 
>> I did install Vina, and I am trying to run it in Chimera using ?Local? option for executable location.
>> Can you please advise on how to solve this issue?
>> Your time is highly appreciated.
>> 
>> Kind regards,
>> Sarah Azzam
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 

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From lawrence at chemistry.montana.edu  Thu Jun 22 11:42:15 2017
From: lawrence at chemistry.montana.edu (Martin Lawrence)
Date: Thu, 22 Jun 2017 12:42:15 -0600
Subject: [Chimera-users] Measuring Distances in the Reciprocal Space
	Transform
Message-ID: <CAKvkAjUgQOJUTtAx8Fg4vYzxUP4Ct4YVe8efT1ZT10-yTkbV1Q@mail.gmail.com>

Dear Chimera Users,

I would like to measure the reciprocal space distance between features in
the fourier transform of my map.   Can anyone give me a hint as to the
easiest way to do this?

Thanks,
Martin

Martin Lawrence
Department of Chemistry and Biochemistry
Montana State University
Bozeman, MT 59717
USA
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From goddard at sonic.net  Thu Jun 22 18:09:45 2017
From: goddard at sonic.net (Tom Goddard)
Date: Thu, 22 Jun 2017 18:09:45 -0700
Subject: [Chimera-users] Measuring Distances in the Reciprocal Space
 Transform
In-Reply-To: <CAKvkAjUgQOJUTtAx8Fg4vYzxUP4Ct4YVe8efT1ZT10-yTkbV1Q@mail.gmail.com>
References: <CAKvkAjUgQOJUTtAx8Fg4vYzxUP4Ct4YVe8efT1ZT10-yTkbV1Q@mail.gmail.com>
Message-ID: <3BFC3255-9D9D-403D-AFA1-32683A159A01@sonic.net>

Place markers between on the Fourier space map features with Volume Tracer and measure the distance between those markers (which are just like atoms) using the Distances tool (menu Tools / Structure Comparison) or distances command.

	Tom

> On Jun 22, 2017, at 11:42 AM, Martin Lawrence <lawrence at chemistry.montana.edu> wrote:
> 
> Dear Chimera Users,
> 
> I would like to measure the reciprocal space distance between features in the fourier transform of my map.   Can anyone give me a hint as to the easiest way to do this?
> 
> Thanks,
> Martin
> 
> Martin Lawrence
> Department of Chemistry and Biochemistry
> Montana State University
> Bozeman, MT 59717
> USA
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users




From kylelmorris at berkeley.edu  Thu Jun 22 18:21:06 2017
From: kylelmorris at berkeley.edu (Kyle Morris)
Date: Thu, 22 Jun 2017 18:21:06 -0700
Subject: [Chimera-users] strand inside and edge color
Message-ID: <737BEC64-59E7-4F1D-A9B0-0D00E434214A@berkeley.edu>

Dear Chimera dev,

Sorry if I missed this in the documentation and online?

Is it possible to make the inside and side edges of strands a color independent of the models coloring? Akin to using ribinsidecolor white to color the inside of helices white, I would like to color the inside and side edges of strands white.

Thanks for your help as always!

Best wishes,
Kyle


From meng at cgl.ucsf.edu  Fri Jun 23 09:29:09 2017
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Fri, 23 Jun 2017 09:29:09 -0700
Subject: [Chimera-users] strand inside and edge color
In-Reply-To: <737BEC64-59E7-4F1D-A9B0-0D00E434214A@berkeley.edu>
References: <737BEC64-59E7-4F1D-A9B0-0D00E434214A@berkeley.edu>
Message-ID: <D531478B-BE0C-4C45-B2E8-A24C17FB70F6@cgl.ucsf.edu>

Hi Kyle,
Sorry, there isn?t any option to color the edges of strand ribbons differently.  A secondary issue is that if you are thinking of the broader sides of the strand representation, inside vs. outside is not clearly defined.  Even if it were, however, there isn?t an option to color any sides of strand or coil ribbons differently from others? there is only the inside color for helices.

Now, you might be able to do something very fudgy by opening the structure twice and changing the strand ribbon scaling (in Ribbon Style Editor, in Tools under Depiction) of one copy to have slightly broader but thinner strands, and in a different color than the first copy. However, I haven?t tried it myself and it might look very bad. This also would not get at coloring the broad sides differently, only the edges of ribbons with a rectangular cross-section.

Ribbon Style Editor, see ?scalings?
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html>

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


> On Jun 22, 2017, at 6:21 PM, Kyle Morris <kylelmorris at berkeley.edu> wrote:
> 
> Dear Chimera dev,
> Sorry if I missed this in the documentation and online?
> 
> Is it possible to make the inside and side edges of strands a color independent of the models coloring? Akin to using ribinsidecolor white to color the inside of helices white, I would like to color the inside and side edges of strands white.
> 
> Thanks for your help as always!
> Best wishes,
> Kyle




From matthewd at bcm.edu  Fri Jun 23 08:53:12 2017
From: matthewd at bcm.edu (Dougherty, Matthew T)
Date: Fri, 23 Jun 2017 15:53:12 +0000
Subject: [Chimera-users] suggestion: data mode
Message-ID: <DM5PR06MB35159C3DF44D27FAD816E942DED80@DM5PR06MB3515.namprd06.prod.outlook.com>

would be helpful to display data mode (byte, float, etc) on the volume viewer panel, approximately in the same location as origin index, voxel size, etc.


For mrc files I can dump the header and pick thru it, for other formats the method is not so clear.


Matthew Dougherty
National Center for Macromolecular Imaging
Baylor College of Medicine
=================================================
=================================================
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From goddard at sonic.net  Fri Jun 23 10:01:56 2017
From: goddard at sonic.net (Tom Goddard)
Date: Fri, 23 Jun 2017 10:01:56 -0700
Subject: [Chimera-users] suggestion: data mode
In-Reply-To: <DM5PR06MB35159C3DF44D27FAD816E942DED80@DM5PR06MB3515.namprd06.prod.outlook.com>
References: <DM5PR06MB35159C3DF44D27FAD816E942DED80@DM5PR06MB3515.namprd06.prod.outlook.com>
Message-ID: <45B3C773-2D63-4F05-888F-973D74D44E77@sonic.net>

Hi Matt,

  The density map value type (int8, uint8, float, int16, ...) is shown in a popup balloon if you hover the mouse over the word "Range" (range of data values) in the volume viewer window beneath the histogram.  I know this is impossible to discover (without reading documentation), but I felt that information was not important enough to take up precious space in the volume viewer window.

	Tom

> On Jun 23, 2017, at 8:53 AM, Dougherty, Matthew T <matthewd at bcm.edu> wrote:
> 
> would be helpful to display data mode (byte, float, etc) on the volume viewer panel, approximately in the same location as origin index, voxel size, etc. 
> 
> For mrc files I can dump the header and pick thru it, for other formats the method is not so clear.
> 
> Matthew Dougherty
> National Center for Macromolecular Imaging
> Baylor College of Medicine
> =================================================
> =================================================
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
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From kylelmorris at berkeley.edu  Fri Jun 23 15:04:59 2017
From: kylelmorris at berkeley.edu (Kyle Morris)
Date: Fri, 23 Jun 2017 15:04:59 -0700
Subject: [Chimera-users] strand inside and edge color
In-Reply-To: <D531478B-BE0C-4C45-B2E8-A24C17FB70F6@cgl.ucsf.edu>
References: <737BEC64-59E7-4F1D-A9B0-0D00E434214A@berkeley.edu>
 <D531478B-BE0C-4C45-B2E8-A24C17FB70F6@cgl.ucsf.edu>
Message-ID: <062BEE27-A23F-489F-BCDD-C3A5386714BF@berkeley.edu>

Hi Elaine,

OK thanks! It is pretty specific but I saw a figure apparently from PyMol like this and rather liked it. Just to clarify, what I was trying to describe is as in the attached. Just hacked in photoshop on a couple of the central strands to illustrate. 

Not essential, but maybe chimeraX will be able to do this :)

Thanks,
Kyle

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> On 23 Jun 2017, at 09:29, Elaine Meng <meng at cgl.ucsf.EDU> wrote:
> 
> Hi Kyle,
> Sorry, there isn?t any option to color the edges of strand ribbons differently.  A secondary issue is that if you are thinking of the broader sides of the strand representation, inside vs. outside is not clearly defined.  Even if it were, however, there isn?t an option to color any sides of strand or coil ribbons differently from others? there is only the inside color for helices.
> 
> Now, you might be able to do something very fudgy by opening the structure twice and changing the strand ribbon scaling (in Ribbon Style Editor, in Tools under Depiction) of one copy to have slightly broader but thinner strands, and in a different color than the first copy. However, I haven?t tried it myself and it might look very bad. This also would not get at coloring the broad sides differently, only the edges of ribbons with a rectangular cross-section.
> 
> Ribbon Style Editor, see ?scalings?
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/ribbonstyle/ribbonstyle.html>
> 
> Best,
> Elaine 
> -----
> Elaine C. Meng, Ph.D.                       
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
>> On Jun 22, 2017, at 6:21 PM, Kyle Morris <kylelmorris at berkeley.edu> wrote:
>> 
>> Dear Chimera dev,
>> Sorry if I missed this in the documentation and online?
>> 
>> Is it possible to make the inside and side edges of strands a color independent of the models coloring? Akin to using ribinsidecolor white to color the inside of helices white, I would like to color the inside and side edges of strands white.
>> 
>> Thanks for your help as always!
>> Best wishes,
>> Kyle
> 


From pett at cgl.ucsf.edu  Fri Jun 23 17:22:07 2017
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Fri, 23 Jun 2017 17:22:07 -0700
Subject: [Chimera-users] DockPrep sometimes fails with altPos
In-Reply-To: <C3C0E7BE-5425-4AC7-B65D-F477660AA782@cgl.ucsf.edu>
References: <80DB3DBF-EBA9-4E21-A565-E6281B668115@gmail.com>
 <C3C0E7BE-5425-4AC7-B65D-F477660AA782@cgl.ucsf.edu>
Message-ID: <55027E76-4EC5-4ED4-9F51-B94E5F78BC57@cgl.ucsf.edu>

Okay, I have fixed this behavior.  Available in the next daily build.

?Eric

> On Jun 13, 2017, at 3:49 PM, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> 
> Yes, the altlocs are chosen on a per-residue basis, which can lead to inconsistencies when different altlocs are chosen for connected residues (the cross-residue bond(s) gets deleted and hydrogens get added to the now-valence-available atoms).  I will work to fix this when I have time and will report back here when I do.  In the interim, you may want to simply delete non-A altlocs before running DockPrep.  Assuming there are no more than three altlocs per atom then this command will do that:
> 
> 	del @.b @.c
> 
> ?Eric
> 
> 	Eric Pettersen
> 	UCSF Computer Graphics Lab
> 
> 
>> On Jun 12, 2017, at 1:57 AM, Visvaldas Kairys <visvaldaskairys at gmail.com <mailto:visvaldaskairys at gmail.com>> wrote:
>> 
>> Dear Chimera users and developers,
>> 
>> I?d like to point out I often have a minor inconvenience when dealing with high resolution Xray structures when trying to add hydrogens
>> via DockPrep. 
>> 
>> If two consecutive residues have both alternative postions A and B, Chimera in the process of hydrogen addition often gets confused 
>> and puts ?TER? between the
>> residues, also reporting non-integer charges in the log. I think what is happening, the program picks ?A? variant for one residue and ?B? for the consecutive residue, and apparently this causes bond detection algorithm to ignore the bond between the residues (due to length I guess).
>> I resolve this by manually editing out one of the AltPos (say, ?B?) out of the PDB file for the offending residues, 
>> but I guess the program should be able to do it automatically.
>> 
>> A PDB example where this happens is 2r3i (or 2r3r).
>> 
>> Best regards,
>> 
>> Vis
>> 
>> 
>> 
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
>> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From fabio2.pereira at usp.br  Fri Jun 23 18:31:11 2017
From: fabio2.pereira at usp.br (=?UTF-8?Q?F=C3=A1bio_Pereira?=)
Date: Fri, 23 Jun 2017 22:31:11 -0300
Subject: [Chimera-users] Chimera to Excel
Message-ID: <CALC_WiNm2G6XiY_81vGdQ-x6Q-wob1pRbevU6Y32FpDXFUR1ag@mail.gmail.com>

Good Afternoon,


I would like to know if i can to export informations opened in View Dock to
Microsoft Excel. If this is possible, how can i do ?


great!
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From meng at cgl.ucsf.edu  Sat Jun 24 09:07:27 2017
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Sat, 24 Jun 2017 09:07:27 -0700
Subject: [Chimera-users] Chimera to Excel
In-Reply-To: <CALC_WiNm2G6XiY_81vGdQ-x6Q-wob1pRbevU6Y32FpDXFUR1ag@mail.gmail.com>
References: <CALC_WiNm2G6XiY_81vGdQ-x6Q-wob1pRbevU6Y32FpDXFUR1ag@mail.gmail.com>
Message-ID: <79C33FA5-9693-4054-9DEB-82BF75245276@cgl.ucsf.edu>

Hi F?bio,

Sorry, there is no option to export to Excel.

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

> On Jun 23, 2017, at 6:31 PM, F?bio Pereira <fabio2.pereira at usp.br> wrote:
> 
> Good Afternoon,
> I would like to know if i can to export informations opened in View Dock to Microsoft Excel. If this is possible, how can i do ?
> great!




From nikolaosbismpikos at gmail.com  Mon Jun 26 11:31:48 2017
From: nikolaosbismpikos at gmail.com (Nikolaos Bismpikos)
Date: Mon, 26 Jun 2017 20:31:48 +0200
Subject: [Chimera-users] Trying to change dihedrals: ValueError: bond is
	part of a cycle
Message-ID: <CAMGDjVt39vXXCv4Tf4Kmp4m-qgc07CDrEhwOcP=HFVr4zepdmw@mail.gmail.com>

Hey, my goal is to change the dihedrals of an already existing pdb template
in order to find low-energy protein conformations.

The issue I have here is that for some residues the dihedrals phi and psi
cannot be changed. That's the error I get:

Traceback (most recent call last):
  File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimeraInit.py", line
683, in init
    chimera.openModels.open(a, prefixableType=1)
  File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/__init__.py",
line 1929, in open
    models = func(filename, *args, **kw)
  File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/__init__.py",
line 1299, in _openPython
    loadFunc(sandboxName, fileName, f)
  File "predictor.py", line 40, in <module>
    es.main_loop();
  File "/home/nick/Python/pdb/AbstractOptimizer.py", line 97, in main_loop
    self.fs, self.evals, self.terminate =
self.eval_pop(self.eval_func,self.pop,self.evals,self.eval_budget,self.extra_par)
  File "/home/nick/Python/pdb/eval_energy.py", line 20, in eval_energy
    allR[j].phi = pop[i,j];
  File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/phipsi.py",
line 98, in setPhi
    _setAngle(bond, phi, getPhi(res, missingIsError=True), "phi",
anchorSide)
  File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/phipsi.py",
line 147, in _setAngle
    br = BondRot(bond)
ValueError: bond is part of a cycle


Is there a way to determine beforehand which bonds are part of circle and
hence which residues' dihedral information cannot be changed?

Thank you in advanced for your time,

Nikolaos Bismpikos
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From pett at cgl.ucsf.edu  Mon Jun 26 11:55:03 2017
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Mon, 26 Jun 2017 11:55:03 -0700
Subject: [Chimera-users] Trying to change dihedrals: ValueError: bond is
 part of a cycle
In-Reply-To: <CAMGDjVt39vXXCv4Tf4Kmp4m-qgc07CDrEhwOcP=HFVr4zepdmw@mail.gmail.com>
References: <CAMGDjVt39vXXCv4Tf4Kmp4m-qgc07CDrEhwOcP=HFVr4zepdmw@mail.gmail.com>
Message-ID: <59569E7A-EAC9-4CFC-A841-D832651B1EFE@cgl.ucsf.edu>

Hi Nikolaos,
	Chimera doesn?t store that information, so there?s no direct way to find out.  Obviously, you could loop through your residues beforehand and do ?r.phi = r.phi? and catch ValueError to mark the residues involved in cycles.
	The other option is to edit phipsi.py in /home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera and in the setPhi and setPsi functions add ValueError to the list of errors that it ignores.

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On Jun 26, 2017, at 11:31 AM, Nikolaos Bismpikos <nikolaosbismpikos at gmail.com> wrote:
> 
> Hey, my goal is to change the dihedrals of an already existing pdb template in order to find low-energy protein conformations.
> 
> The issue I have here is that for some residues the dihedrals phi and psi cannot be changed. That's the error I get:
> 
> Traceback (most recent call last):
>   File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimeraInit.py", line 683, in init
>     chimera.openModels.open(a, prefixableType=1)
>   File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/__init__.py", line 1929, in open
>     models = func(filename, *args, **kw)
>   File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/__init__.py", line 1299, in _openPython
>     loadFunc(sandboxName, fileName, f)
>   File "predictor.py", line 40, in <module>
>     es.main_loop();
>   File "/home/nick/Python/pdb/AbstractOptimizer.py", line 97, in main_loop
>     self.fs, self.evals, self.terminate = self.eval_pop(self.eval_func,self.pop,self.evals,self.eval_budget,self.extra_par)
>   File "/home/nick/Python/pdb/eval_energy.py", line 20, in eval_energy
>     allR[j].phi = pop[i,j];
>   File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/phipsi.py", line 98, in setPhi
>     _setAngle(bond, phi, getPhi(res, missingIsError=True), "phi", anchorSide)
>   File "/home/nick/.local/UCSF-Chimera64-1.11.2/share/chimera/phipsi.py", line 147, in _setAngle
>     br = BondRot(bond)
> ValueError: bond is part of a cycle
> 
> 
> Is there a way to determine beforehand which bonds are part of circle and hence which residues' dihedral information cannot be changed?
> 
> Thank you in advanced for your time,
> 
> Nikolaos Bismpikos
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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From bikwuagwu at u.northwestern.edu  Mon Jun 26 08:52:42 2017
From: bikwuagwu at u.northwestern.edu (Bon Ikwuagwu)
Date: Mon, 26 Jun 2017 10:52:42 -0500
Subject: [Chimera-users] Difference between Chimera and ChimeraX
Message-ID: <CAKhTURgGaJh3=BdtRMEop8cNyBsHsT9_9_2C-Bw8bVePkhyXGA@mail.gmail.com>

Hello,

I'm a first year graduate student and I am wondering what the differences
are between Chimera and ChimeraX? I want to use the tools that are present
in Chimera, but I don't know if those tools are also present in ChimeraX.
Any feedback would be helpful.

Best,

Bon Ikwuagwu
-- 
Bon Ikwuagwu
PhD Student, Chemical and Biological Engineering
Northwestern University
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From robert.waugh94 at gmail.com  Mon Jun 26 13:04:50 2017
From: robert.waugh94 at gmail.com (Robert Waugh)
Date: Mon, 26 Jun 2017 21:04:50 +0100
Subject: [Chimera-users] Libfftw3.so.3
Message-ID: <CAPi+-Ae5cyeCEJNf+fQPaDv8xZLKuNZSqd_0wR7Navr11ywrAQ@mail.gmail.com>

Hello,

I am a Masters Student from Kingston University, I am currently using
Chimera as part of a Bioinformatics Project. For this project, I have
decided to use IMP to integrate the data I have to make a coarse grained
model. Unfortunately, upon using MultiFit I receive the error which I have
posted below which states that I cannot open the shared object file
libfftw3.so.3. I was wondering if it would be possible if you were to make
this file available so that I can complete my Multifit Modelling.

https://pastebin.com/kkRW6X3U

Thank you,
It would be much appreciated,
Robert Waugh
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From mheller at cdrd.ca  Mon Jun 26 13:45:16 2017
From: mheller at cdrd.ca (Markus Heller)
Date: Mon, 26 Jun 2017 20:45:16 +0000
Subject: [Chimera-users] Difference between Chimera and ChimeraX
In-Reply-To: <CAKhTURgGaJh3=BdtRMEop8cNyBsHsT9_9_2C-Bw8bVePkhyXGA@mail.gmail.com>
References: <CAKhTURgGaJh3=BdtRMEop8cNyBsHsT9_9_2C-Bw8bVePkhyXGA@mail.gmail.com>
Message-ID: <1BBC8C44802DFA4FBF69CC371B45149B1D851022@MERCURY.cdrd.ca>

Advantages compared to Chimera: https://www.cgl.ucsf.edu/chimerax/docs/user/advantages.html
See ?Missing Features? here: http://www.rbvi.ucsf.edu/chimerax/download.html


From: Chimera-users [mailto:chimera-users-bounces at cgl.ucsf.edu] On Behalf Of Bon Ikwuagwu
Sent: Monday, June 26, 2017 8:53 AM
To: chimera-users at cgl.ucsf.edu
Subject: [Chimera-users] Difference between Chimera and ChimeraX


Hello,

I'm a first year graduate student and I am wondering what the differences are between Chimera and ChimeraX? I want to use the tools that are present in Chimera, but I don't know if those tools are also present in ChimeraX. Any feedback would be helpful.

Best,

Bon Ikwuagwu
--
Bon Ikwuagwu
PhD Student, Chemical and Biological Engineering
Northwestern University
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From meng at cgl.ucsf.edu  Mon Jun 26 14:40:03 2017
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Mon, 26 Jun 2017 14:40:03 -0700
Subject: [Chimera-users] Difference between Chimera and ChimeraX
In-Reply-To: <1BBC8C44802DFA4FBF69CC371B45149B1D851022@MERCURY.cdrd.ca>
References: <CAKhTURgGaJh3=BdtRMEop8cNyBsHsT9_9_2C-Bw8bVePkhyXGA@mail.gmail.com>
 <1BBC8C44802DFA4FBF69CC371B45149B1D851022@MERCURY.cdrd.ca>
Message-ID: <9538BBAB-69CC-491C-824D-7B4D4F350D64@cgl.ucsf.edu>

Thanks Markus, I was going to say exactly the same, at least for those who wanted a short summary.

If anybody wants a little more detail, I recommend scanning through just the top index of the ChimeraX User Guide and seeing if your features of interest are listed:
http://www.rbvi.ucsf.edu/chimerax/docs/user/index.html

Of course, you can certainly use both programs.
Best,
Elaine
----------
Elaine C. Meng, Ph.D. 
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Jun 26, 2017, at 1:45 PM, Markus Heller <mheller at cdrd.ca> wrote:
> 
> Advantages compared to Chimera: https://www.cgl.ucsf.edu/chimerax/docs/user/advantages.html
> See ?Missing Features? here: http://www.rbvi.ucsf.edu/chimerax/download.html
> 
> From: Chimera-users [mailto:chimera-users-bounces at cgl.ucsf.edu] On Behalf Of Bon Ikwuagwu
> Sent: Monday, June 26, 2017 8:53 AM
> To: chimera-users at cgl.ucsf.edu
> Subject: [Chimera-users] Difference between Chimera and ChimeraX
>  
> Hello, 
> I'm a first year graduate student and I am wondering what the differences are between Chimera and ChimeraX? I want to use the tools that are present in Chimera, but I don't know if those tools are also present in ChimeraX. Any feedback would be helpful. 
> Best, 
> Bon Ikwuagwu




From berenger at bioreg.kyushu-u.ac.jp  Mon Jun 26 16:18:11 2017
From: berenger at bioreg.kyushu-u.ac.jp (Francois BERENGER)
Date: Tue, 27 Jun 2017 08:18:11 +0900
Subject: [Chimera-users] Difference between Chimera and ChimeraX
In-Reply-To: <1BBC8C44802DFA4FBF69CC371B45149B1D851022@MERCURY.cdrd.ca>
References: <CAKhTURgGaJh3=BdtRMEop8cNyBsHsT9_9_2C-Bw8bVePkhyXGA@mail.gmail.com>
 <1BBC8C44802DFA4FBF69CC371B45149B1D851022@MERCURY.cdrd.ca>
Message-ID: <6b8ba122-5a82-605d-f940-200006cf5b08@bioreg.kyushu-u.ac.jp>

On 06/27/2017 05:45 AM, Markus Heller wrote:
> Advantages compared to Chimera: 
> https://www.cgl.ucsf.edu/chimerax/docs/user/advantages.html

Hello,

In advantages: "Fast and robust solvent-excluded surfaces".
What is the algorithm used to compute those?

Regards,
F.

> See ?Missing Features? here: http://www.rbvi.ucsf.edu/chimerax/download.html
> 
> *From:*Chimera-users [mailto:chimera-users-bounces at cgl.ucsf.edu] *On 
> Behalf Of *Bon Ikwuagwu
> *Sent:* Monday, June 26, 2017 8:53 AM
> *To:* chimera-users at cgl.ucsf.edu
> *Subject:* [Chimera-users] Difference between Chimera and ChimeraX
> 
> 
> Hello,
> 
> I'm a first year graduate student and I am wondering what the 
> differences are between Chimera and ChimeraX? I want to use the tools 
> that are present in Chimera, but I don't know if those tools are also 
> present in ChimeraX. Any feedback would be helpful.
> 
> Best,
> 
> Bon Ikwuagwu
> -- 
> 
> Bon Ikwuagwu
> 
> PhD Student, Chemical and Biological Engineering
> 
> Northwestern University
> 
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 


From goddard at sonic.net  Mon Jun 26 16:58:50 2017
From: goddard at sonic.net (Tom Goddard)
Date: Mon, 26 Jun 2017 16:58:50 -0700
Subject: [Chimera-users] Difference between Chimera and ChimeraX
In-Reply-To: <6b8ba122-5a82-605d-f940-200006cf5b08@bioreg.kyushu-u.ac.jp>
References: <CAKhTURgGaJh3=BdtRMEop8cNyBsHsT9_9_2C-Bw8bVePkhyXGA@mail.gmail.com>
 <1BBC8C44802DFA4FBF69CC371B45149B1D851022@MERCURY.cdrd.ca>
 <6b8ba122-5a82-605d-f940-200006cf5b08@bioreg.kyushu-u.ac.jp>
Message-ID: <86E15F50-4E54-4CDA-AE4D-E62010702A68@sonic.net>

Hi Francois,

  We wrote the ChimeraX solvent excluded surface code a few years ago using a distance grid-based calculation (by default using a grid spacing of 0.5 Angstroms).  It is about the same speed as the Chimera surface calculation (MSMS from Michel Sanner) but the appearance is a bit smoother, and it works 100% reliably even on 100,000 or million atom structures.  We also added separate code that does an analytic calculation of solvent accessible surface area.

	Tom


> On Jun 26, 2017, at 4:18 PM, Francois BERENGER <berenger at bioreg.kyushu-u.ac.jp> wrote:
> 
> On 06/27/2017 05:45 AM, Markus Heller wrote:
>> Advantages compared to Chimera: https://www.cgl.ucsf.edu/chimerax/docs/user/advantages.html
> 
> Hello,
> 
> In advantages: "Fast and robust solvent-excluded surfaces".
> What is the algorithm used to compute those?
> 
> Regards,
> F.
> 
>> See ?Missing Features? here: http://www.rbvi.ucsf.edu/chimerax/download.html
>> *From:*Chimera-users [mailto:chimera-users-bounces at cgl.ucsf.edu] *On Behalf Of *Bon Ikwuagwu
>> *Sent:* Monday, June 26, 2017 8:53 AM
>> *To:* chimera-users at cgl.ucsf.edu
>> *Subject:* [Chimera-users] Difference between Chimera and ChimeraX
>> Hello,
>> I'm a first year graduate student and I am wondering what the differences are between Chimera and ChimeraX? I want to use the tools that are present in Chimera, but I don't know if those tools are also present in ChimeraX. Any feedback would be helpful.
>> Best,
>> Bon Ikwuagwu
>> -- 
>> Bon Ikwuagwu
>> PhD Student, Chemical and Biological Engineering
>> Northwestern University
>> _______________________________________________
>> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
> 




From pett at cgl.ucsf.edu  Wed Jun 28 13:08:21 2017
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Wed, 28 Jun 2017 13:08:21 -0700
Subject: [Chimera-users] Fwd: pdb-l:  EMBL-EBI user survey
References: <alpine.LRH.2.20.1706271230090.1413@struktbio205.bmc.uu.se>
Message-ID: <CA0AC8A6-2D93-4CB7-A412-8F9B9C0D4A49@cgl.ucsf.edu>



> Begin forwarded message:
> 
> From: Gerard DVD Kleywegt <gerard at xray.bmc.uu.se>
> Subject: pdb-l: EMBL-EBI user survey
> Date: June 27, 2017 at 3:30:30 AM PDT
> To: pdb-l at ucsd.edu
> Cc: Gerard Kleywegt <gerard at xray.bmc.uu.se>, "Gerard Kleywegt \(EBI account\)" <gerard at ebi.ac.uk>
> 
> Dear colleagues,
> 
> EMBL-EBI (http://www.ebi.ac.uk/) is running a worldwide survey to understand 
> usage of its resources (there are several dozen, including UniProt, Ensembl, 
> ChEMBL, EuropePMC, PDBe, EMDB/EMPIAR and many more). We would like to ask you 
> to forward this request within your department, company or institution. We are 
> interested in responses from a wide range of scientists, in particular those 
> who do not think of themselves as bioinformaticians. The results are extremely 
> valuable to EBI in helping us to understand our users, and our users' needs.
> 
> Here is the link to the survey: 
> https://www.surveymonkey.co.uk/r/2017_EBI_survey
> 
> Many thanks!
> 
> --Gerard
> 
> ---
> Gerard J. Kleywegt, EMBL-EBI, Hinxton, UK
> Head of Molecular and  Cellular Structure
> gerard at ebi.ac.uk pdbe.org emdb-empiar.org
> PA: Pauline Haslam   pdbe_admin at ebi.ac.uk
> 
> TO UNSUBSCRIBE OR CHANGE YOUR SUBSCRIPTION OPTIONS, please see
> https://lists.sdsc.edu/mailman/listinfo/pdb-l . 

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From catrajen at umail.iu.edu  Thu Jun 29 14:14:58 2017
From: catrajen at umail.iu.edu (Catherine Jenifer Rajam Rajendran)
Date: Thu, 29 Jun 2017 17:14:58 -0400
Subject: [Chimera-users] Define Plane
Message-ID: <CAEJvEi3=nQzEaZt6uV2OF_N_s=TKpo-k5sOSitfA8d_05FkQkg@mail.gmail.com>

Hi,

I am trying to understand how the plane is defined in chimera. Can you
please help me with that?

"Define a plane for the specified
<https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>
atoms.
Eigenvectors/values are calculated from the atomic coordinates after
subtracting the position of their non-mass-weighted centroid. The plane is
anchored at the centroid and aligned with the first two eigenvectors (the
third eigenvector is normal to the plane)."

Define a plane for the specified
<https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/frameatom_spec.html>
 atoms.
- specified atoms, i use 'sel protein'

Eigenvectors/values are calculated from the atomic coordinates
- atomic coordinates, so x,y,z coordinates of all atoms. (Can you please
explain a bit more like how and what you read from PDB file to define
plane).

after subtracting the position of their non-mass-weighted centroid
- how is non-mass-weighted centroid is calculated

The plane is anchored at the centroid
- which centroid is this? Is the protein moved to the origin(0,0,0)
position?


Thanks,
Catherine
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From meng at cgl.ucsf.edu  Thu Jun 29 16:23:04 2017
From: meng at cgl.ucsf.edu (Elaine Meng)
Date: Thu, 29 Jun 2017 16:23:04 -0700
Subject: [Chimera-users] Define Plane
In-Reply-To: <CAEJvEi3=nQzEaZt6uV2OF_N_s=TKpo-k5sOSitfA8d_05FkQkg@mail.gmail.com>
References: <CAEJvEi3=nQzEaZt6uV2OF_N_s=TKpo-k5sOSitfA8d_05FkQkg@mail.gmail.com>
Message-ID: <91FE08BE-4E5C-4A3F-AD59-832E209701C0@cgl.ucsf.edu>



> On Jun 29, 2017, at 2:14 PM, Catherine Jenifer Rajam Rajendran <catrajen at umail.iu.edu> wrote:
> 
> Hi,
> 
Hi Catherine,

> I am trying to understand how the plane is defined in chimera. Can you please help me with that?
> 
> "Define a plane for the specified atoms. Eigenvectors/values are calculated from the atomic coordinates after subtracting the position of their non-mass-weighted centroid. The plane is anchored at the centroid and aligned with the first two eigenvectors (the third eigenvector is normal to the plane)."
> 
> Define a plane for the specified atoms.
> - specified atoms, i use 'sel protein?

OK, so if using the graphical tool (Axes/Planes/Centroids) it uses the selected atoms, meaning all the protein atoms if you had used ?sel protein.?  If using the ?define? command, you can just specify ?protein? directly in the command to use all the protein atoms, without making a selection.
> 
> Eigenvectors/values are calculated from the atomic coordinates
> - atomic coordinates, so x,y,z coordinates of all atoms. (Can you please explain a bit more like how and what you read from PDB file to define plane).

For the atoms you specified, there are ATOM lines in the PDB file with X,Y,Z coordinates.  Each atom is a point in 3D (X,Y,Z).

> 
> after subtracting the position of their non-mass-weighted centroid
> - how is non-mass-weighted centroid is calculated

It is the centroid of the points (atomic positions), not sure how else to say it.  The average position of all the atomic points is the centroid.  Non-mass-weighted just means all the atomic points are treated equally, instead of heavier atoms being treated as more important than lighter atoms.
> 
> The plane is anchored at the centroid
> - which centroid is this? Is the protein moved to the origin(0,0,0) position?
> 
The centroid is the same centroid as in your previous question. Nothing is moved.
> 
> Thanks,
> Catherine

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






From catrajen at umail.iu.edu  Fri Jun 30 10:09:04 2017
From: catrajen at umail.iu.edu (Catherine Jenifer Rajam Rajendran)
Date: Fri, 30 Jun 2017 13:09:04 -0400
Subject: [Chimera-users] Define Plane
In-Reply-To: <91FE08BE-4E5C-4A3F-AD59-832E209701C0@cgl.ucsf.edu>
References: <CAEJvEi3=nQzEaZt6uV2OF_N_s=TKpo-k5sOSitfA8d_05FkQkg@mail.gmail.com>
 <91FE08BE-4E5C-4A3F-AD59-832E209701C0@cgl.ucsf.edu>
Message-ID: <CAEJvEi2fN_7-bMdJqUXzT5x8ZM5W_WbTMXD2bRDhpz-ce=dARg@mail.gmail.com>

Hi Elaine,

Thank you for helping me understand it. Can you give me more details about
how PDB file is decomposed to find the plane and normal. Like, how the
eigenvectors are calculated from the atomic coordinates.

Thanks,
Catherine

On Thu, Jun 29, 2017 at 7:23 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

>
>
> > On Jun 29, 2017, at 2:14 PM, Catherine Jenifer Rajam Rajendran <
> catrajen at umail.iu.edu> wrote:
> >
> > Hi,
> >
> Hi Catherine,
>
> > I am trying to understand how the plane is defined in chimera. Can you
> please help me with that?
> >
> > "Define a plane for the specified atoms. Eigenvectors/values are
> calculated from the atomic coordinates after subtracting the position of
> their non-mass-weighted centroid. The plane is anchored at the centroid and
> aligned with the first two eigenvectors (the third eigenvector is normal to
> the plane)."
> >
> > Define a plane for the specified atoms.
> > - specified atoms, i use 'sel protein?
>
> OK, so if using the graphical tool (Axes/Planes/Centroids) it uses the
> selected atoms, meaning all the protein atoms if you had used ?sel
> protein.?  If using the ?define? command, you can just specify ?protein?
> directly in the command to use all the protein atoms, without making a
> selection.
> >
> > Eigenvectors/values are calculated from the atomic coordinates
> > - atomic coordinates, so x,y,z coordinates of all atoms. (Can you please
> explain a bit more like how and what you read from PDB file to define
> plane).
>
> For the atoms you specified, there are ATOM lines in the PDB file with
> X,Y,Z coordinates.  Each atom is a point in 3D (X,Y,Z).
>
> >
> > after subtracting the position of their non-mass-weighted centroid
> > - how is non-mass-weighted centroid is calculated
>
> It is the centroid of the points (atomic positions), not sure how else to
> say it.  The average position of all the atomic points is the centroid.
> Non-mass-weighted just means all the atomic points are treated equally,
> instead of heavier atoms being treated as more important than lighter atoms.
> >
> > The plane is anchored at the centroid
> > - which centroid is this? Is the protein moved to the origin(0,0,0)
> position?
> >
> The centroid is the same centroid as in your previous question. Nothing is
> moved.
> >
> > Thanks,
> > Catherine
>
> You?re welcome.  I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
>
>
>
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From pett at cgl.ucsf.edu  Fri Jun 30 16:13:09 2017
From: pett at cgl.ucsf.edu (Eric Pettersen)
Date: Fri, 30 Jun 2017 16:13:09 -0700
Subject: [Chimera-users] Define Plane
In-Reply-To: <CAEJvEi2fN_7-bMdJqUXzT5x8ZM5W_WbTMXD2bRDhpz-ce=dARg@mail.gmail.com>
References: <CAEJvEi3=nQzEaZt6uV2OF_N_s=TKpo-k5sOSitfA8d_05FkQkg@mail.gmail.com>
 <91FE08BE-4E5C-4A3F-AD59-832E209701C0@cgl.ucsf.edu>
 <CAEJvEi2fN_7-bMdJqUXzT5x8ZM5W_WbTMXD2bRDhpz-ce=dARg@mail.gmail.com>
Message-ID: <2E71F60E-DDFB-4C9C-8C6D-1F416093BAEE@cgl.ucsf.edu>

Chimera simply calls numpy.linalg.svd (singular value decomposition) on an array of the xyz coordinate (after the centroid position has been subtracted from them).  The documentation for numpy.linalg.svd is here:

https://docs.scipy.org/doc/numpy/reference/generated/numpy.linalg.svd.html <https://docs.scipy.org/doc/numpy/reference/generated/numpy.linalg.svd.html>

It looks like it in turn calls LAPACK routine_gesdd, which is documented, in general, here:

https://software.intel.com/en-us/mkl-developer-reference-c-singular-value-decomposition-lapack-computational-routines?language=es <https://software.intel.com/en-us/mkl-developer-reference-c-singular-value-decomposition-lapack-computational-routines?language=es>

It?s an implementation of singular value decomposition, described in general terms here:

https://en.wikipedia.org/wiki/Singular_value_decomposition#Relation_to_eigenvalue_decomposition <https://en.wikipedia.org/wiki/Singular_value_decomposition#Relation_to_eigenvalue_decomposition>

The math is pretty complicated.

?Eric

	Eric Pettersen
	UCSF Computer Graphics Lab




> On Jun 30, 2017, at 10:09 AM, Catherine Jenifer Rajam Rajendran <catrajen at umail.iu.edu> wrote:
> 
> Hi Elaine,
> 
> Thank you for helping me understand it. Can you give me more details about how PDB file is decomposed to find the plane and normal. Like, how the eigenvectors are calculated from the atomic coordinates.
> 
> Thanks,
> Catherine
> 
> On Thu, Jun 29, 2017 at 7:23 PM, Elaine Meng <meng at cgl.ucsf.edu <mailto:meng at cgl.ucsf.edu>> wrote:
> 
> 
> > On Jun 29, 2017, at 2:14 PM, Catherine Jenifer Rajam Rajendran <catrajen at umail.iu.edu <mailto:catrajen at umail.iu.edu>> wrote:
> >
> > Hi,
> >
> Hi Catherine,
> 
> > I am trying to understand how the plane is defined in chimera. Can you please help me with that?
> >
> > "Define a plane for the specified atoms. Eigenvectors/values are calculated from the atomic coordinates after subtracting the position of their non-mass-weighted centroid. The plane is anchored at the centroid and aligned with the first two eigenvectors (the third eigenvector is normal to the plane)."
> >
> > Define a plane for the specified atoms.
> > - specified atoms, i use 'sel protein?
> 
> OK, so if using the graphical tool (Axes/Planes/Centroids) it uses the selected atoms, meaning all the protein atoms if you had used ?sel protein.?  If using the ?define? command, you can just specify ?protein? directly in the command to use all the protein atoms, without making a selection.
> >
> > Eigenvectors/values are calculated from the atomic coordinates
> > - atomic coordinates, so x,y,z coordinates of all atoms. (Can you please explain a bit more like how and what you read from PDB file to define plane).
> 
> For the atoms you specified, there are ATOM lines in the PDB file with X,Y,Z coordinates.  Each atom is a point in 3D (X,Y,Z).
> 
> >
> > after subtracting the position of their non-mass-weighted centroid
> > - how is non-mass-weighted centroid is calculated
> 
> It is the centroid of the points (atomic positions), not sure how else to say it.  The average position of all the atomic points is the centroid.  Non-mass-weighted just means all the atomic points are treated equally, instead of heavier atoms being treated as more important than lighter atoms.
> >
> > The plane is anchored at the centroid
> > - which centroid is this? Is the protein moved to the origin(0,0,0) position?
> >
> The centroid is the same centroid as in your previous question. Nothing is moved.
> >
> > Thanks,
> > Catherine
> 
> You?re welcome.  I hope this helps,
> Elaine
> ----------
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> 
> 
> 
> 
> _______________________________________________
> Chimera-users mailing list: Chimera-users at cgl.ucsf.edu
> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users

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